{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:08:59Z","timestamp":1792782539907,"version":"4.5.0"},"reference-count":184,"publisher":"Springer Science and Business Media LLC","issue":"11","license":[{"start":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:00:00Z","timestamp":1792713600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T00:00:00Z","timestamp":1792713600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"funder":[{"name":"Department of Biotechnology, Government of India","award":["BT\/PR32853\/AGill\/103\/1159\/2019"],"award-info":[{"award-number":["BT\/PR32853\/AGill\/103\/1159\/2019"]}],"id":[{"id":"https:\/\/ror.org\/036h6g940","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Theor Appl Genet"],"published-print":{"date-parts":[[2026,11]]},"DOI":"10.1007\/s00122-026-05337-z","type":"journal-article","created":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T02:57:52Z","timestamp":1792724272000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Superior haplotypes for transforming crop breeding"],"prefix":"10.1007","volume":"139","author":[{"given":"Nandigam Vinay","family":"Kumar","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ajay","family":"Bogati","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Uma Maheshwar","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"A. Prasanna","family":"Rajesh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"T.","family":"Srinivas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ajay","family":"Kohli","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sanjay","family":"Kalia","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arvind","family":"Kumar","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pallavi","family":"Sinha","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1560-1648","authenticated-orcid":false,"given":"Vikas Kumar","family":"Singh","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,10,23]]},"reference":[{"issue":"8","key":"5337_CR1","doi-asserted-by":"publisher","first-page":"1612","DOI":"10.1111\/pbi.13087","volume":"17","author":"R Abbai","year":"2019","unstructured":"Abbai R, Singh VK, Nachimuthu VV, Sinha P, Selvaraj R, Vipparla AK, Singh AK, Singh UM, Varshney RK, Kumar A (2019) Haplotype analysis of key genes governing grain yield and quality traits across 3K RG panel reveals scope for the development of tailor-made rice with enhanced genetic gains. Plant Biotechnol J 17(8):1612\u20131622. https:\/\/doi.org\/10.1111\/pbi.13087","journal-title":"Plant Biotechnol J"},{"key":"5337_CR2","doi-asserted-by":"publisher","first-page":"190036","DOI":"10.3835\/plantgenome2019.05.0036","volume":"12","author":"A Abed","year":"2019","unstructured":"Abed A, Belzile F (2019) Comparing single-SNP, multi-SNP, and haplotype-based approaches in association studies for major traits in barley. Plant Genome 12:190036. https:\/\/doi.org\/10.3835\/plantgenome2019.05.0036","journal-title":"Plant Genome"},{"key":"5337_CR3","doi-asserted-by":"publisher","first-page":"1272326","DOI":"10.3389\/fpls.2024.1272326","volume":"15","author":"S Alam","year":"2024","unstructured":"Alam S, Sundaram KT, Singh UM, Srinivas Prasad M, Laha GS, Sinha P, Singh VK, Sinha P (2024) Superior haplotypes towards the development of blast and bacterial blight-resistant rice. Front Plant Sci 15:1272326. https:\/\/doi.org\/10.3389\/fpls.2024.1272326","journal-title":"Front Plant Sci"},{"key":"5337_CR4","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1007\/s00122-023-04352-8","volume":"136","author":"A Alemu","year":"2023","unstructured":"Alemu A, Batista L, Singh PK, Ceplitis A, Chawade A (2023) Haplotype-tagged SNPs improve genomic prediction accuracy for Fusarium head blight resistance and yield-related traits in wheat. Theor Appl Genet 136:92. https:\/\/doi.org\/10.1007\/s00122-023-04352-8","journal-title":"Theor Appl Genet"},{"key":"5337_CR5","doi-asserted-by":"publisher","first-page":"911775","DOI":"10.3389\/fpls.2022.911775","volume":"13","author":"A Anandan","year":"2022","unstructured":"Anandan A, Panda S, Sabarinathan S, Travis AJ, Norton GJ, Price AH (2022) Superior haplotypes for early root vigour traits in rice under dry direct-seeded low nitrogen condition through genome-wide association mapping. Front Plant Sci 13:911775. https:\/\/doi.org\/10.3389\/fpls.2022.911775","journal-title":"Front Plant Sci"},{"key":"5337_CR6","doi-asserted-by":"publisher","first-page":"336","DOI":"10.1086\/377106","volume":"73","author":"EC Anderson","year":"2003","unstructured":"Anderson EC, Novembre J (2003) Finding haplotype block boundaries by using the minimum-description-length principle. Am J Hum Genet 73:336\u2013354. https:\/\/doi.org\/10.1086\/377106","journal-title":"Am J Hum Genet"},{"key":"5337_CR7","doi-asserted-by":"publisher","first-page":"190010","DOI":"10.3835\/plantgenome2019.02.0010","volume":"12","author":"B Angira","year":"2019","unstructured":"Angira B, Addison CK, Cerioli T, Rebong DB, Wang DR, Pumplin N, Ham JH, Oard JH, Linscombe SD, Famoso AN (2019) Haplotype characterization of the sd1 semidwarf gene in United States rice. Plant Genome 12:190010. https:\/\/doi.org\/10.3835\/plantgenome2019.02.0010","journal-title":"Plant Genome"},{"key":"5337_CR201","doi-asserted-by":"publisher","unstructured":"Arojju SK, Barth S, Milbourne D, Conaghan P, Velmurugan J, Hodkinson TR, Byrne SL (2016) Markers associated with heading and aftermath heading in perennial ryegrass full-sib families. BMC Plant Biol 16:160. https:\/\/doi.org\/10.1186\/s12870-016-0844-y","DOI":"10.1186\/s12870-016-0844-y"},{"key":"5337_CR8","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1186\/s12284-021-00520-w","volume":"14","author":"S Bai","year":"2021","unstructured":"Bai S, Hong J, Li L, Su S, Li Z, Wang W, Zhang F, Liang W, Zhang D (2021) Dissection of the genetic basis of rice panicle architecture using a genome-wide association study. Rice 14:77. https:\/\/doi.org\/10.1186\/s12284-021-00520-w","journal-title":"Rice"},{"key":"5337_CR9","doi-asserted-by":"publisher","first-page":"7255","DOI":"10.1093\/jxb\/erac348","volume":"73","author":"R Barmukh","year":"2022","unstructured":"Barmukh R, Roorkiwal M, Dixit GP, Bajaj P, Kholova J, Smith MR, Chitikineni A, Bharadwaj C, Sreeman SM, Rathore A, Tripathi S, Yasin M, Vijayakumar AG, Rao Sagurthi S, Siddique KHM, Varshney RK (2022a) Characterization of \u2018QTL-hotspot\u2019 introgression lines reveals physiological mechanisms and candidate genes associated with drought adaptation in chickpea. J Exp Bot 73:7255\u20137272. https:\/\/doi.org\/10.1093\/jxb\/erac348","journal-title":"J Exp Bot"},{"key":"5337_CR10","doi-asserted-by":"publisher","first-page":"1701","DOI":"10.1111\/pbi.13840","volume":"20","author":"R Barmukh","year":"2022","unstructured":"Barmukh R, Roorkiwal M, Garg V, Khan AW, German L, Jaganathan D, Chitikineni A, Kholova J, Kudapa H, Sivasakthi K, Samineni S, Kale SM, Gaur PM, Sagurthi SR, Benitez-Alfonso Y, Varshney RK (2022b) Genetic variation in CaTIFY4b contributes to drought adaptation in chickpea. Plant Biotechnol J 20:1701\u20131715. https:\/\/doi.org\/10.1111\/pbi.13840","journal-title":"Plant Biotechnol J"},{"key":"5337_CR12","doi-asserted-by":"publisher","first-page":"1452","DOI":"10.1111\/pbi.12888","volume":"16","author":"WA Bekele","year":"2018","unstructured":"Bekele WA, Wight CP, Chao S, Howarth CJ, Tinker NA (2018) Haplotype-based genotyping-by-sequencing in oat genome research. Plant Biotechnol J 16:1452\u20131463. https:\/\/doi.org\/10.1111\/pbi.12888","journal-title":"Plant Biotechnol J"},{"key":"5337_CR13","doi-asserted-by":"publisher","first-page":"2407","DOI":"10.1007\/s00122-022-04120-0","volume":"135","author":"JA Bhat","year":"2022","unstructured":"Bhat JA, Karikari B, Adeboye KA, Ganie SA, Barmukh R, Hu D, Varshney RK, Yu D (2022) Identification of superior haplotypes in a diverse natural population for breeding desirable plant height in soybean. Theor Appl Genet 135:2407\u20132422. https:\/\/doi.org\/10.1007\/s00122-022-04120-0","journal-title":"Theor Appl Genet"},{"key":"5337_CR14","doi-asserted-by":"publisher","first-page":"1266","DOI":"10.1038\/s42003-021-02782-y","volume":"4","author":"JA Bhat","year":"2021","unstructured":"Bhat JA, Yu D, Bohra A, Ganie SA, Varshney RK (2021) Features and applications of haplotypes in crop breeding. Commun Biol 4:1266. https:\/\/doi.org\/10.1038\/s42003-021-02782-y","journal-title":"Commun Biol"},{"key":"5337_CR15","doi-asserted-by":"publisher","first-page":"1286","DOI":"10.3390\/agriculture13071286","volume":"13","author":"V Bhatt","year":"2023","unstructured":"Bhatt V, Muthusamy V, Chhabra R, Katral A, Ragi S, Rojaria V, Chand G, Sarma GR, Zunjare RU, Panda KK, Singh AK (2023) Molecular characterization and haplotype analysis of low phytic acid-1 (lpa1) gene governing accumulation of kernel phytic acid in subtropically-adapted Zea mays. Agriculture 13:1286. https:\/\/doi.org\/10.3390\/agriculture13071286","journal-title":"Agriculture"},{"key":"5337_CR16","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1007\/s00122-021-03967-z","volume":"135","author":"L Bouvet","year":"2022","unstructured":"Bouvet L, Percival-Alwyn L, Berry S, Fenwick P, Mantello CC, Sharma R, Holdgate S, Mackay IJ, Cockram J (2022) Wheat genetic loci conferring resistance to stripe rust in the face of genetically diverse races of the fungus Puccinia striiformis f. sp. tritici. Theor Appl Genet 135:301\u2013319. https:\/\/doi.org\/10.1007\/s00122-021-03967-z","journal-title":"Theor Appl Genet"},{"key":"5337_CR17","doi-asserted-by":"publisher","unstructured":"Bradbury PJ, Casstevens T, Jensen SE, Johnson LC, Miller ZR, Monier B, Romay MC, Song B, Buckler ES (2022) The practical haplotype graph, a platform for storing and using pangenomes for imputation. Bioinformatics 38:3698\u20133702. https:\/\/doi.org\/10.1093\/bioinformatics\/btac410sss","DOI":"10.1093\/bioinformatics\/btac410sss"},{"key":"5337_CR18","doi-asserted-by":"publisher","first-page":"1178624","DOI":"10.3389\/fpls.2023.1178624","volume":"14","author":"L Cao","year":"2023","unstructured":"Cao L, Li T, Geng S, Zhang Y, Pan Y, Zhang X, Wang F, Hao C (2023) TaSPL14-7A is a conserved regulator controlling plant architecture and yield traits in common wheat (Triticum aestivum L.). Front Plant Sci 14:1178624. https:\/\/doi.org\/10.3389\/fpls.2023.1178624","journal-title":"Front Plant Sci"},{"key":"5337_CR19","doi-asserted-by":"publisher","first-page":"1229827","DOI":"10.3389\/fpls.2023.1229827","volume":"14","author":"H Chen","year":"2023","unstructured":"Chen H, Zhang X, Xu S, Song C, Mao H (2023) TaSPL17s act redundantly with TaSPL14s to control spike development, and their elite haplotypes may improve wheat grain yield. Front Plant Sci 14:1229827. https:\/\/doi.org\/10.3389\/fpls.2023.1229827","journal-title":"Front Plant Sci"},{"key":"5337_CR20","doi-asserted-by":"publisher","first-page":"4804","DOI":"10.1038\/s41598-019-41217-x","volume":"9","author":"K Chen","year":"2019","unstructured":"Chen K, Zhang Q, Wang CC, Liu ZX, Jiang YJ, Zhai LY, Zheng TQ, Xu JL, Li ZK (2019) Genetic dissection of seedling vigour in a diverse panel from the 3,000 rice (Oryza sativa L.) genome project. Sci Rep 9:4804. https:\/\/doi.org\/10.1038\/s41598-019-41217-x","journal-title":"Sci Rep"},{"key":"5337_CR21","doi-asserted-by":"publisher","first-page":"1061490","DOI":"10.3389\/fpls.2022.1061490","volume":"13","author":"S Cloutier","year":"2023","unstructured":"Cloutier S, Reimer E, Khadka B, McCallum BD (2023) Variations in exons 11 and 12 of the multi-pest resistance wheat gene Lr34 are independently additive for leaf rust resistance. Front Plant Sci 13:1061490. https:\/\/doi.org\/10.3389\/fpls.2022.1061490","journal-title":"Front Plant Sci"},{"key":"5337_CR22","doi-asserted-by":"publisher","first-page":"e0171105","DOI":"10.1371\/journal.pone.0171105","volume":"12","author":"RI Contreras-Soto","year":"2017","unstructured":"Contreras-Soto RI, Mora F, de Oliveira MAR, Higashi W, Scapim CA, Schuster I (2017) A genome-wide association study for agronomic traits in soybean using SNP markers and SNP-based haplotype analysis. PLoS ONE 12:e0171105. https:\/\/doi.org\/10.1371\/journal.pone.0171105","journal-title":"PLoS ONE"},{"key":"5337_CR23","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1038\/ng1001-229","volume":"29","author":"MJ Daly","year":"2001","unstructured":"Daly MJ, Rioux JD, Schaffner SF, Hudson TJ, Lander ES (2001) High-resolution haplotype structure in the human genome. Nat Genet 29:229\u2013232. https:\/\/doi.org\/10.1038\/ng1001-229","journal-title":"Nat Genet"},{"key":"5337_CR202","doi-asserted-by":"publisher","unstructured":"Dipta B, Sood S, Mangal V, Bhardwaj V, Thakur AK, Kumar V, Singh B (2024) KASP: a high-throughput genotyping system and its applications in major crop plants for biotic and abiotic stress tolerance. Mol Biol Rep 51:508. https:\/\/doi.org\/10.1007\/s11033-024-09455-z","DOI":"10.1007\/s11033-024-09455-z"},{"key":"5337_CR24","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1038\/s41467-023-36271-z","volume":"14","author":"C Dong","year":"2023","unstructured":"Dong C, Zhang L, Zhang Q, Yang Y, Li D, Xie Z, Cui G, Chen Y, Wu L, Li Z, Liu G, Zhang X, Liu C, Chu J, Zhao G, Xia C, Jia J, Sun J, Kong X, Liu X (2023) Tiller Number1 encodes an ankyrin repeat protein that controls tillering in bread wheat. Nat Commun 14:836. https:\/\/doi.org\/10.1038\/s41467-023-36271-z","journal-title":"Nat Commun"},{"key":"5337_CR203","doi-asserted-by":"publisher","unstructured":"Ertiro BT, Ogugo V, Worku M, Das B, Olsen M, Labuschagne M, Semagn K (2015) Comparison of Kompetitive Allele Specific PCR (KASP) and genotyping by sequencing (GBS) for quality control analysis in maize. BMC Genomics 16:908. https:\/\/doi.org\/10.1186\/s12864-015-2180-2","DOI":"10.1186\/s12864-015-2180-2"},{"issue":"4","key":"5337_CR25","doi-asserted-by":"publisher","first-page":"921","DOI":"10.1111\/padr.12508","volume":"48","author":"WP Falcon","year":"2022","unstructured":"Falcon WP, Naylor RL, Shankar ND (2022) Rethinking global food demand for 2050. Popul Dev Rev 48(4):921\u2013957. https:\/\/doi.org\/10.1111\/padr.12508","journal-title":"Popul Dev Rev"},{"key":"5337_CR26","doi-asserted-by":"publisher","first-page":"1164","DOI":"10.1007\/s00122-006-0218-1","volume":"112","author":"C Fan","year":"2006","unstructured":"Fan C, Xing Y, Mao H, Lu T, Han B, Xu C, Li X, Zhang Q (2006) GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein. Theor Appl Genet 112:1164\u20131171. https:\/\/doi.org\/10.1007\/s00122-006-0218-1","journal-title":"Theor Appl Genet"},{"key":"5337_CR27","doi-asserted-by":"publisher","first-page":"891","DOI":"10.1016\/j.tig.2024.07.001","volume":"40","author":"MA Farooq","year":"2024","unstructured":"Farooq MA, Gao S, Hassan MA, Huang Z, Rasheed A, Hearne S, Prasanna B, Li X, Li H (2024) Artificial intelligence in plant breeding. Trends Genet 40:891\u2013908. https:\/\/doi.org\/10.1016\/j.tig.2024.07.001","journal-title":"Trends Genet"},{"key":"5337_CR28","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1186\/s12284-017-0174-1","volume":"10","author":"X Feng","year":"2017","unstructured":"Feng X, Wang C, Nan J, Zhang X, Wang R, Jiang G, Yuan Q, Lin S (2017) Updating the elite rice variety Oryza sativa Kongyu 131 by improving the Gn1a locus. Rice 10:35. https:\/\/doi.org\/10.1186\/s12284-017-0174-1","journal-title":"Rice"},{"key":"5337_CR29","doi-asserted-by":"publisher","unstructured":"Valdes Franco JA, Gage J, Johnson LC, Bradbury PJ, Buckler ES, Romay MC (2020) A maize practical haplotype graph leverages diverse NAM assemblies. bioRxiv (Cold Spring Harbor Laboratory). https:\/\/doi.org\/10.1101\/2020.08.31.268425","DOI":"10.1101\/2020.08.31.268425"},{"issue":"1","key":"5337_CR30","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1093\/aob\/mcn172","volume":"103","author":"T Fukao","year":"2009","unstructured":"Fukao T, Harris T, Bailey-Serres J (2009) Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice. Ann Bot 103(1):143\u2013150. https:\/\/doi.org\/10.1093\/aob\/mcn172","journal-title":"Ann Bot"},{"key":"5337_CR31","doi-asserted-by":"publisher","first-page":"2225","DOI":"10.1126\/science.1069424","volume":"296","author":"SB Gabriel","year":"2002","unstructured":"Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, Liu-Cordero SN, Rotimi C, Adeyemo A, Cooper R, Ward R, Lander ES, Daly MJ, Altshuler D (2002) The structure of haplotype blocks in the human genome. Science 296:2225\u20132229. https:\/\/doi.org\/10.1126\/science.1069424","journal-title":"Science"},{"issue":"7412","key":"5337_CR32","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1038\/nature11346","volume":"488","author":"R Gamuyao","year":"2012","unstructured":"Gamuyao R, Chin JH, Pariasca-Tanaka J, Pesaresi P, Catausan S, Dalid C, Slamet-Loedin I, Tecson-Mendoza EM, Wissuwa M, Heuer S (2012) The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency. Nature 488(7412):535\u2013539. https:\/\/doi.org\/10.1038\/nature11346","journal-title":"Nature"},{"key":"5337_CR204","doi-asserted-by":"publisher","unstructured":"Garg S (2021) Computational methods for chromosome-scale haplotype reconstruction. Genome Biol 22:101. https:\/\/doi.org\/10.1186\/s13059-021-02328-9","DOI":"10.1186\/s13059-021-02328-9"},{"issue":"1","key":"5337_CR33","doi-asserted-by":"publisher","first-page":"28","DOI":"10.1111\/pbr.12237","volume":"134","author":"I Gawenda","year":"2015","unstructured":"Gawenda I, Thorwarth P, G\u00fcnther T, Ordon F, Schmid KJ (2015) Genome-wide association studies in elite varieties of German winter barley using single-marker and haplotype-based methods. Plant Breed 134(1):28\u201339. https:\/\/doi.org\/10.1111\/pbr.12237","journal-title":"Plant Breed"},{"key":"5337_CR205","doi-asserted-by":"publisher","unstructured":"Grzybowski MW, Mural RV, Xu G, Turkus J, Yang J, Schnable JC (2023) A common resequencing-based genetic marker data set for global maize diversity. Plant J 113:1109\u20131121. https:\/\/doi.org\/10.1111\/tpj.16123","DOI":"10.1111\/tpj.16123"},{"key":"5337_CR206","doi-asserted-by":"publisher","unstructured":"Gu X, Pipatpongpinyo W, Zhang L, Zhou Y, Ye H, Feng J (2018) Two contrasting patterns and underlying genes for coadaptation of seed dormancy and flowering time in rice. Sci Rep 8:16813. https:\/\/doi.org\/10.1038\/s41598-018-34850-5","DOI":"10.1038\/s41598-018-34850-5"},{"issue":"5","key":"5337_CR34","doi-asserted-by":"publisher","first-page":"937","DOI":"10.1111\/tpj.12695","volume":"80","author":"R Guan","year":"2014","unstructured":"Guan R, Qu Y, Guo Y, Yu L, Liu Y, Jiang J, Chen J, Ren Y, Liu G, Tian L, Jin L, Liu Z, Hong H, Chang R, Gilliham M, Qiu L (2014) Salinity tolerance in soybean is modulated by natural variation in GmSALT3. Plant J 80(5):937\u2013950. https:\/\/doi.org\/10.1111\/tpj.12695","journal-title":"Plant J"},{"key":"5337_CR35","doi-asserted-by":"publisher","first-page":"223","DOI":"10.1186\/s12943-024-02140-6","volume":"23","author":"S-B Guo","year":"2024","unstructured":"Guo S-B, Meng Y, Lin L et al (2024) Artificial intelligence alphafold model for molecular biology and drug discovery: a machine-learning-driven informatics investigation. Mol Cancer 23:223. https:\/\/doi.org\/10.1186\/s12943-024-02140-6","journal-title":"Mol Cancer"},{"key":"5337_CR36","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1038\/ejhg.2010.161","volume":"19","author":"D Haig","year":"2011","unstructured":"Haig D (2011) Does heritability hide in epistasis between linked SNPs? Eur J Hum Genet 19:123. https:\/\/doi.org\/10.1038\/ejhg.2010.161","journal-title":"Eur J Hum Genet"},{"issue":"4","key":"5337_CR37","doi-asserted-by":"publisher","first-page":"e1007663","DOI":"10.1371\/journal.pcbi.1007663","volume":"16","author":"K Hamazaki","year":"2020","unstructured":"Hamazaki K, Iwata H (2020) RAINBOW: haplotype-based genome-wide association study using a novel SNP-set method. PLoS Comput Biol 16(4):e1007663. https:\/\/doi.org\/10.1371\/journal.pcbi.1007663","journal-title":"PLoS Comput Biol"},{"issue":"7258","key":"5337_CR38","doi-asserted-by":"publisher","first-page":"1026","DOI":"10.1038\/nature08258","volume":"460","author":"Y Hattori","year":"2009","unstructured":"Hattori Y, Nagai K, Furukawa S, Song XJ, Kawano R, Sakakibara H, Wu J, Matsumoto T, Yoshimura A, Kitano H, Matsuoka M, Mori H, Ashikari M (2009) The ethylene response factors SNORKEL1 and SNORKEL2 allow rice to adapt to deep water. Nature 460(7258):1026\u20131030. https:\/\/doi.org\/10.1038\/nature08258","journal-title":"Nature"},{"key":"5337_CR39","doi-asserted-by":"publisher","first-page":"1933","DOI":"10.1111\/pbi.13353","volume":"18","author":"Y He","year":"2020","unstructured":"He Y, Zhao J, Yang B, Sun S, Peng L, Wang Z (2020) Indole-3-acetate beta-glucosyltransferase OsIAGLU regulates seed vigour through mediating crosstalk between auxin and abscisic acid in Oryza sativa. Plant Biotechnol J 18:1933\u20131945. https:\/\/doi.org\/10.1111\/pbi.13353","journal-title":"Plant Biotechnol J"},{"key":"5337_CR40","doi-asserted-by":"publisher","first-page":"2475","DOI":"10.3390\/plants10112475","volume":"10","author":"M Helal","year":"2021","unstructured":"Helal M, Gill RA, Tang M, Yang L, Hu M, Yang L, Xie M, Zhao C, Cheng X, Zhang Y, Zhang X, Liu S (2021) SNP- and haplotype-based GWAS of flowering-related traits in Brassica napus. Plants 10:2475. https:\/\/doi.org\/10.3390\/plants10112475","journal-title":"Plants"},{"key":"5337_CR41","doi-asserted-by":"publisher","first-page":"834","DOI":"10.1038\/ng.3337","volume":"47","author":"B Hu","year":"2015","unstructured":"Hu B, Wang W, Ou S, Tang J, Li H, Che R, Zhang Z, Chai X, Wang H, Wang Y, Liang C, Liu L, Piao Z, Deng Q, Deng K, Xu C, Liang Y, Zhang L, Li L, Chu C (2015) Variation in NRT1.1B contributes to nitrate-use divergence between rice subspecies. Nat Genet 47:834\u2013838. https:\/\/doi.org\/10.1038\/ng.3337","journal-title":"Nat Genet"},{"key":"5337_CR42","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1002\/gepi.20242","volume":"31","author":"BE Huang","year":"2007","unstructured":"Huang BE, Amos CI, Lin DY (2007) Detecting haplotype effects in genome-wide association studies. Genet Epidemiol 31:803\u2013812. https:\/\/doi.org\/10.1002\/gepi.20242","journal-title":"Genet Epidemiol"},{"key":"5337_CR43","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1093\/genetics\/111.1.147","volume":"111","author":"RR Hudson","year":"1985","unstructured":"Hudson RR, Kaplan NL (1985) Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111:147\u2013164. https:\/\/doi.org\/10.1093\/genetics\/111.1.147","journal-title":"Genetics"},{"key":"5337_CR44","doi-asserted-by":"publisher","first-page":"909","DOI":"10.1111\/j.1469-8137.2010.03593.x","volume":"189","author":"PK Ingvarsson","year":"2011","unstructured":"Ingvarsson PK, Street NR (2011) Association genetics of complex traits in plants. New Phytol 189:909\u2013922. https:\/\/doi.org\/10.1111\/j.1469-8137.2010.03593.x","journal-title":"New Phytol"},{"key":"5337_CR45","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1016\/j.plantsci.2019.02.007","volume":"283","author":"HU Jan","year":"2019","unstructured":"Jan HU, Guan M, Yao M, Liu W, Wei D, Abbadi A, Zheng M, He X, Chen H, Guan C, Nichols RA (2019) Genome-wide haplotype analysis improves trait predictions in Brassica napus hybrids. Plant Sci 283:157\u2013164. https:\/\/doi.org\/10.1016\/j.plantsci.2019.02.007","journal-title":"Plant Sci"},{"issue":"1","key":"5337_CR46","doi-asserted-by":"publisher","first-page":"e20009","DOI":"10.1002\/tpg2.20009","volume":"13","author":"SE Jensen","year":"2020","unstructured":"Jensen SE, Charles JR, Muleta K, Bradbury PJ, Casstevens T, Deshpande SP, Gore MA, Gupta R, Ilut DC, Johnson L, Lozano R, Miller Z, Ramu P, Rathore A, Romay MC, Upadhyaya HD, Varshney RK, Morris GP, Pressoir G, Buckler ES, Ramstein GP (2020) A sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction. Plant Genome 13(1):e20009. https:\/\/doi.org\/10.1002\/tpg2.20009","journal-title":"Plant Genome"},{"issue":"1","key":"5337_CR47","doi-asserted-by":"publisher","first-page":"131","DOI":"10.1007\/s00122-014-2417-5","volume":"128","author":"Y Jiang","year":"2015","unstructured":"Jiang Y, Jiang Q, Hao C, Hou J, Wang L, Zhang H, Zhang S, Chen X, Zhang X (2015) A yield-associated gene TaCWI, in wheat: its function, selection and evolution in global breeding revealed by haplotype analysis. Theor Appl Genet 128(1):131\u2013143. https:\/\/doi.org\/10.1007\/s00122-014-2417-5","journal-title":"Theor Appl Genet"},{"issue":"3","key":"5337_CR48","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1038\/ng1001-233","volume":"29","author":"GCL Johnson","year":"2001","unstructured":"Johnson GCL, Esposito L, Barratt BJ, Smith AN, Heward J, Di Genova G, Ueda H, Cordell HJ, Eaves IA, Dudbridge F, Twells RCJ, Payne F, Hughes W, Nutland S, Stevens H, Carr P, Tuomilehto-Wolf E, Tuomilehto J, Gough SCL, Clayton DG, Todd JA (2001) Haplotype tagging for the identification of common disease genes. Nat Genet 29(3):233\u2013237. https:\/\/doi.org\/10.1038\/ng1001-233","journal-title":"Nat Genet"},{"key":"5337_CR49","doi-asserted-by":"publisher","first-page":"jkab390","DOI":"10.1093\/g3journal\/jkab390","volume":"12","author":"KW Jordan","year":"2021","unstructured":"Jordan KW, Bradbury PJ, Miller ZR, Nyine M, He F, Fraser M, Anderson J, Mason E, Katz A, Pearce S, Carter AH, Prather S, Pumphrey M, Chen J, Cook J, Liu S, Rudd JC, Wang Z, Chu C, Akhunov ED (2021) Development of the wheat practical haplotype graph database as a resource for genotyping data storage and genotype imputation. G3 Genes Genomes Genet 12:jkab390. https:\/\/doi.org\/10.1093\/g3journal\/jkab390","journal-title":"G3 Genes Genomes Genet"},{"key":"5337_CR50","doi-asserted-by":"publisher","first-page":"1827","DOI":"10.3389\/fpls.2018.01827","volume":"9","author":"SR Kim","year":"2018","unstructured":"Kim SR, Torollo G, Yoon MR, Kwak J, Lee CK, Prahalada GD, Choi IR, Yeo US, Jeong OY, Jena KK, Lee JS (2018) Loss-of-function alleles of Heading date 1 (Hd1) are associated with adaptation of temperate japonica rice plants to the tropical region. Front Plant Sci 9:1827. https:\/\/doi.org\/10.3389\/fpls.2018.01827","journal-title":"Front Plant Sci"},{"issue":"3","key":"5337_CR51","doi-asserted-by":"publisher","first-page":"663","DOI":"10.1007\/s00122-012-2009-1","volume":"126","author":"SG Krattinger","year":"2013","unstructured":"Krattinger SG, Jordan DR, Mace ES, Raghavan C, Luo MC, Keller B, Lagudah ES (2013) Recent emergence of the wheat Lr34 multi-pathogen resistance: insights from haplotype analysis in wheat, rice, sorghum, and Aegilops tauschii. Theor Appl Genet 126(3):663\u2013672. https:\/\/doi.org\/10.1007\/s00122-012-2009-1","journal-title":"Theor Appl Genet"},{"key":"5337_CR207","doi-asserted-by":"publisher","unstructured":"Ksouri N, S\u00e1nchez G, Forcada CFI, Contreras-Moreira B, Gogorcena Y (2025) A reproducible ddRAD-seq protocol reveals novel genomic association signatures for fruit-related traits in peach. Plant Methods 21:101. https:\/\/doi.org\/10.1186\/s13007-025-01415-3","DOI":"10.1186\/s13007-025-01415-3"},{"issue":"6403","key":"5337_CR52","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1126\/science.aat1577","volume":"361","author":"T Kuroha","year":"2018","unstructured":"Kuroha T, Nagai K, Gamuyao R, Wang DR, Furuta T, Nakamor M, Kitaoka T, Adachi K, Minami A, Mori Y, Mashiguchi K, Seto Y, Yamaguchi S, Kojima M, Sakakibara H, Wu J, Ebana K, Mitsuda N, Ohme-Takagi M, Yanagisawa S, Yamasaki M, Yokoyama R, Nishitani K, Mochizuki T, Tamiya G, McCouch SR, Ashikari M (2018) Ethylene-gibberellin signalling underlies adaptation of rice to periodic flooding. Science 361(6403):181\u2013186. https:\/\/doi.org\/10.1126\/science.aat1577","journal-title":"Science"},{"key":"5337_CR53","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1007\/s00122-025-04908-w","volume":"138","author":"X Lai","year":"2025","unstructured":"Lai X, Zhu Z, Zhang Y, Lu T, Qin J, Xu S (2025) The selection and application of tiller number QTLs in modern wheat breeding. Theor Appl Genet 138:124. https:\/\/doi.org\/10.1007\/s00122-025-04908-w","journal-title":"Theor Appl Genet"},{"key":"5337_CR54","doi-asserted-by":"publisher","first-page":"2190","DOI":"10.1093\/bioinformatics\/btm316","volume":"23","author":"JM Laramie","year":"2007","unstructured":"Laramie JM, Wilk JB, DeStefano AL, Myers RH (2007) HaploBuild: an algorithm to construct non-contiguous associated haplotypes in family based genetic studies. Bioinformatics 23:2190\u20132192. https:\/\/doi.org\/10.1093\/bioinformatics\/btm316","journal-title":"Bioinformatics"},{"key":"5337_CR55","doi-asserted-by":"publisher","first-page":"2504","DOI":"10.3390\/plants11192504","volume":"11","author":"L Li","year":"2022","unstructured":"Li L, Wu X, Chen J, Wang S, Wan Y, Ji H, Wen Y, Zhang J (2022) Genetic dissection of epistatic interactions contributing yield-related agronomic traits in rice using the compressed mixed model. Plants 11:2504. https:\/\/doi.org\/10.3390\/plants11192504","journal-title":"Plants"},{"key":"5337_CR56","doi-asserted-by":"publisher","first-page":"1540","DOI":"10.1038\/s41588-019-0503-y","volume":"51","author":"N Li","year":"2019","unstructured":"Li N, Lin B, Wang H, Li X, Yang F, Ding X, Yan J, Chu Z (2019) Natural variation in ZmFBL41 confers banded leaf and sheath blight resistance in maize. Nat Genet 51:1540\u20131548. https:\/\/doi.org\/10.1038\/s41588-019-0503-y","journal-title":"Nat Genet"},{"key":"5337_CR57","doi-asserted-by":"publisher","first-page":"449","DOI":"10.1111\/j.1469-8137.2010.03490.x","volume":"189","author":"XP Li","year":"2011","unstructured":"Li XP, Zhao XQ, He X, Zhao GY, Li B, Liu DC, Zhang AM, Zhang XY, Tong YP, Li ZS (2011a) Haplotype analysis of the genes encoding glutamine synthetase plastic isoforms and their association with nitrogen-use-and yield-related traits in Triticum aestivum. New Phytol 189:449\u2013458. https:\/\/doi.org\/10.1111\/j.1469-8137.2010.03490.x","journal-title":"New Phytol"},{"key":"5337_CR58","doi-asserted-by":"publisher","first-page":"1266","DOI":"10.1038\/ng.977","volume":"43","author":"Y Li","year":"2011","unstructured":"Li Y, Fan C, Xing Y, Jiang Y, Luo L, Sun L, Shao D, Xu C, Li X, Xiao J, He Y, Zhang Q (2011b) Natural variation in GS5 plays an important role in regulating grain size and yield in rice. Nat Genet 43:1266\u20131269. https:\/\/doi.org\/10.1038\/ng.977","journal-title":"Nat Genet"},{"key":"5337_CR59","doi-asserted-by":"publisher","first-page":"2587","DOI":"10.1007\/s00122-017-2978-1","volume":"130","author":"Y Li","year":"2017","unstructured":"Li Y, Tong L, Deng L, Liu Q, Xing Y, Wang C, Liu B, Yang X, Xu M (2017) Evaluation of ZmCCT haplotypes for genetic improvement of maize hybrids. Theor Appl Genet 130:2587\u20132600. https:\/\/doi.org\/10.1007\/s00122-017-2978-1","journal-title":"Theor Appl Genet"},{"key":"5337_CR60","doi-asserted-by":"publisher","first-page":"227","DOI":"10.1016\/j.cj.2019.09.012","volume":"8","author":"Z Li","year":"2020","unstructured":"Li Z, Liu X, Xu X, Liu J, Sang Z, Yu K, Yang Y, Dai W, Jin X, Xu Y (2020) Favorable haplotypes and associated genes for flowering time and photoperiod sensitivity identified by comparative selective signature analysis and GWAS in temperate and tropical maize. Crop J 8:227\u2013242. https:\/\/doi.org\/10.1016\/j.cj.2019.09.012","journal-title":"Crop J"},{"key":"5337_CR208","doi-asserted-by":"publisher","unstructured":"Li P, Li Z, Liu X, Zhang H, Zhang S, Liu F, et al (2023) Haplotype analysis and marker development of five salt-tolerant-related genes in rice (Oryza sativa L.). Front Plant Sci 14:1259462. https:\/\/doi.org\/10.3389\/fpls.2023.1259462","DOI":"10.3389\/fpls.2023.1259462"},{"key":"5337_CR61","doi-asserted-by":"publisher","first-page":"3129","DOI":"10.1534\/g3.119.400537","volume":"9","author":"F Lin","year":"2019","unstructured":"Lin F, Fan J, Rhee SY (2019) QTG-Finder: a machine-learning based algorithm to prioritize causal genes of quantitative trait loci in Arabidopsis and rice. G3 Genes Genomes Genet 9:3129\u20133138. https:\/\/doi.org\/10.1534\/g3.119.400537","journal-title":"G3 Genes Genomes Genet"},{"key":"5337_CR62","doi-asserted-by":"publisher","first-page":"1181","DOI":"10.1038\/ng1457","volume":"36","author":"S Lin","year":"2004","unstructured":"Lin S, Chakravarti A, Cutler DJ (2004) Exhaustive allelic transmission disequilibrium tests as a new approach to genome-wide association studies. Nat Genet 36:1181\u20131188. https:\/\/doi.org\/10.1038\/ng1457","journal-title":"Nat Genet"},{"key":"5337_CR63","doi-asserted-by":"publisher","first-page":"4115","DOI":"10.1534\/g3.119.400451","volume":"9","author":"F Liu","year":"2019","unstructured":"Liu F, Schmidt RH, Reif JC, Jiang Y (2019) Selecting closely-linked SNPs based on local epistatic effects for haplotype construction improves power of association mapping. G3 (Bethesda) 9:4115\u20134126. https:\/\/doi.org\/10.1534\/g3.119.400451","journal-title":"G3 (Bethesda)"},{"key":"5337_CR64","doi-asserted-by":"publisher","unstructured":"Liu Q, Ma H, Zhang Z, Hu Z, Wang X, Li R, Cai Y, Jiang Y (2024) GP-ML-DC: an ensemble machine learning-based genomic prediction approach with automated two-phase dimensionality reduction via divide-and-conquer techniques. bioRxiv. https:\/\/doi.org\/10.1101\/2024.12.26.630443","DOI":"10.1101\/2024.12.26.630443"},{"key":"5337_CR65","doi-asserted-by":"publisher","unstructured":"Liu R, Cheng H, Qin D, Xu L, Xu F, Xu Q, Peng Y, Ge S, Sun L, Dong G, Dong J (2025) Functional characterization and identification of superior haplotypes of barley HvGL7-2H (Hordeum vulgare L.) in grain features. J Integr Agric 24:4153\u20134167. https:\/\/doi.org\/10.1016\/j.jia.2024.03.025","DOI":"10.1016\/j.jia.2024.03.025"},{"key":"5337_CR209","doi-asserted-by":"publisher","unstructured":"Lopez-Cruz M, Beyene Y, Gowda M, Crossa J, P\u00e9rez-Rodr\u00edguez P, De Los Campos G (2021) Multi-generation genomic prediction of maize yield using parametric and non-parametric sparse selection indices. Heredity 127:423\u2013432. https:\/\/doi.org\/10.1038\/s41437-021-00474-1","DOI":"10.1038\/s41437-021-00474-1"},{"key":"5337_CR66","doi-asserted-by":"publisher","first-page":"658","DOI":"10.1111\/jipb.12797","volume":"61","author":"X Luo","year":"2019","unstructured":"Luo X, Wang B, Gao S, Zhang F, Terzaghi W, Dai M (2019) Genome-wide association study dissects the genetic bases of salt tolerance in maize seedlings. J Integr Plant Biol 61:658\u2013674. https:\/\/doi.org\/10.1111\/jipb.12797","journal-title":"J Integr Plant Biol"},{"key":"5337_CR67","doi-asserted-by":"publisher","first-page":"3305","DOI":"10.1007\/s00122-021-03897-w","volume":"134","author":"L Ma","year":"2021","unstructured":"Ma L, Zhang M, Chen J, Qing C, He S, Zou C, Yuan G, Yang C, Peng H, Pan G, L\u00fcbberstedt T, Shen Y (2021) GWAS and WGCNA uncover hub genes controlling salt tolerance in maize (Zea mays L.) seedlings. Theor Appl Genet 134:3305\u20133318. https:\/\/doi.org\/10.1007\/s00122-021-03897-w","journal-title":"Theor Appl Genet"},{"key":"5337_CR68","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1007\/s11032-016-0504-9","volume":"36","author":"Y Ma","year":"2016","unstructured":"Ma Y, Reif JC, Jiang Y, Wen Z, Wang D, Liu Z, Guo Y, Wei S, Wang S et al (2016) Potential of marker selection to increase prediction accuracy of genomic selection in soybean (Glycine max L.). Mol Breed 36:113. https:\/\/doi.org\/10.1007\/s11032-016-0504-9","journal-title":"Mol Breed"},{"key":"5337_CR69","doi-asserted-by":"publisher","first-page":"803","DOI":"10.1038\/s41588-018-0119-7","volume":"50","author":"Z Ma","year":"2018","unstructured":"Ma Z, He S, Wang X, Sun J, Zhang Y, Zhang G, Wu L, Li Z et al (2018) Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield. Nat Genet 50:803\u2013813. https:\/\/doi.org\/10.1038\/s41588-018-0119-7","journal-title":"Nat Genet"},{"key":"5337_CR70","doi-asserted-by":"publisher","first-page":"728398","DOI":"10.1155\/2012\/728398","volume":"2012","author":"J Mammadov","year":"2012","unstructured":"Mammadov J, Aggarwal R, Buyyarapu R, Kumpatla S (2012) SNP markers and their impact on plant breeding. Int J Plant Genomics 2012:728398. https:\/\/doi.org\/10.1155\/2012\/728398","journal-title":"Int J Plant Genomics"},{"key":"5337_CR71","doi-asserted-by":"publisher","first-page":"19579","DOI":"10.1073\/pnas.1014419107","volume":"107","author":"H Mao","year":"2010","unstructured":"Mao H, Sun S, Yao J, Wang C, Yu S, Xu C, Li X, Zhang Q (2010) Linking differential domain functions of the GS3 protein to natural variation of grain size in rice. Proc Natl Acad Sci USA 107:19579\u201319584. https:\/\/doi.org\/10.1073\/pnas.1014419107","journal-title":"Proc Natl Acad Sci USA"},{"key":"5337_CR210","doi-asserted-by":"publisher","unstructured":"Marand AP, Eveland AL, Kaufmann K, Springer NM (2023) Cis-regulatory elements in plant development, adaptation, and evolution. Annu Rev Plant Biol 74:111\u2013137. https:\/\/doi.org\/10.1146\/annurev-arplant-070122-030236","DOI":"10.1146\/annurev-arplant-070122-030236"},{"key":"5337_CR72","doi-asserted-by":"publisher","first-page":"198","DOI":"10.1016\/j.rsci.2017.01.002","volume":"24","author":"ASM Masuduzzaman","year":"2017","unstructured":"Masuduzzaman ASM, Haque MM, Shamsuddin AKM, Salam MA, Ali MA (2017) Haplotype diversity at Sub1 locus and allelic distribution among rice varieties of tide and flood-prone areas of South-East Asia. Rice Sci 24:198\u2013206. https:\/\/doi.org\/10.1016\/j.rsci.2017.01.002","journal-title":"Rice Sci"},{"key":"5337_CR73","doi-asserted-by":"publisher","first-page":"4954","DOI":"10.1038\/s41467-020-18683-3","volume":"11","author":"M Mayer","year":"2020","unstructured":"Mayer M, Holker AC, Gonzalez-Segovia E, Bauer E, Presterl T, Ouzunova M, Melchinger AE, Schon CC (2020) Discovery of beneficial haplotypes for complex traits in maize landraces. Nat Commun 11:4954. https:\/\/doi.org\/10.1038\/s41467-020-18683-3","journal-title":"Nat Commun"},{"key":"5337_CR211","doi-asserted-by":"publisher","unstructured":"Meena VK, Thribhuvan R, Dinkar V, Bhatt A, Pandey S, Abhinav et al (2025) Haplotype breeding: fast-track the crop improvements. Planta 261:51. https:\/\/doi.org\/10.1007\/s00425-025-04622-3","DOI":"10.1007\/s00425-025-04622-3"},{"key":"5337_CR74","doi-asserted-by":"publisher","first-page":"4227","DOI":"10.1016\/j.ygeno.2021.11.006","volume":"113","author":"G Menard","year":"2021","unstructured":"Menard G, Sandhu N, Anderson D, Catolos M, Hassall KL, Eastmond PJ, Kumar A, Kurup S (2021) Laboratory phenomics predicts field performance and identifies superior indica haplotypes for early seedling vigour in dry direct-seeded rice. Genomics 113:4227\u20134236. https:\/\/doi.org\/10.1016\/j.ygeno.2021.11.006","journal-title":"Genomics"},{"key":"5337_CR212","doi-asserted-by":"publisher","unstructured":"Merrick LF, Burke AB, Zhang Z, Carter AH (2022) Comparison of single-trait and multi-trait genome-wide association models and inclusion of correlated traits in the dissection of the genetic architecture of a complex trait in a breeding program. Front Plant Sci 12:772907. https:\/\/doi.org\/10.3389\/fpls.2021.772907","DOI":"10.3389\/fpls.2021.772907"},{"key":"5337_CR75","doi-asserted-by":"publisher","first-page":"2295","DOI":"10.1007\/s00299-016-2035-6","volume":"35","author":"S Mishra","year":"2016","unstructured":"Mishra S, Singh B, Misra P, Rai V, Singh NK (2016a) Haplotype distribution and association of candidate genes with salt tolerance in Indian wild rice germplasm. Plant Cell Rep 35:2295\u20132308. https:\/\/doi.org\/10.1007\/s00299-016-2035-6","journal-title":"Plant Cell Rep"},{"key":"5337_CR76","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s12284-016-0083-8","volume":"9","author":"S Mishra","year":"2016","unstructured":"Mishra S, Singh B, Panda K, Singh BP, Singh N, Misra P, Rai V, Singh NK (2016b) Association of SNP haplotypes of HKT family genes with salt tolerance in Indian wild rice germplasm. Rice 9:15. https:\/\/doi.org\/10.1186\/s12284-016-0083-8","journal-title":"Rice"},{"key":"5337_CR213","doi-asserted-by":"publisher","unstructured":"Mohanavel V, Yesudhas AS, Sharma A, Ramasamy A, Samy PMA, Subramanian M, Muthusamy R (2021) Haplotype and diversity analysis of indigenous rice for salinity tolerance in early-stage seedling using simple sequence repeat markers. Biotechnol Rep 31:e00666. https:\/\/doi.org\/10.1016\/j.btre.2021.e00666","DOI":"10.1016\/j.btre.2021.e00666"},{"key":"5337_CR77","doi-asserted-by":"publisher","first-page":"13853","DOI":"10.1038\/s41598-019-50331-9","volume":"9","author":"QH Muqaddasi","year":"2019","unstructured":"Muqaddasi QH, Brassac J, Koppolu R, Plieske J, Ganal MW, R\u00f6der MS (2019) TaAPO-A1, an ortholog of rice ABERRANT PANICLE ORGANIZATION 1, is associated with total spikelet number per spike in elite European hexaploid winter wheat (Triticum aestivum L.) varieties. Sci Rep 9:13853. https:\/\/doi.org\/10.1038\/s41598-019-50331-9","journal-title":"Sci Rep"},{"key":"5337_CR78","doi-asserted-by":"publisher","first-page":"e0170941","DOI":"10.1371\/journal.pone.0170941","volume":"12","author":"A N\u2019Diaye","year":"2017","unstructured":"N\u2019Diaye A, Haile JK, Cory AT, Clarke FR, Clarke JM, Knox RE, Pozniak CJ (2017) Single marker and haplotype-based association analysis of semolina and pasta color in elite durum wheat breeding lines using a high-density consensus map. PLoS ONE 12:e0170941. https:\/\/doi.org\/10.1371\/journal.pone.0170941","journal-title":"PLoS ONE"},{"key":"5337_CR79","doi-asserted-by":"publisher","first-page":"1800432","DOI":"10.3389\/fpls.2026.1800432","volume":"17","author":"YD Naik","year":"2026","unstructured":"Naik YD, Thudi M, Kamal N, Egan AN, Janga MR, Puppala N (2026) Pan-genomics of polyploid crops: from complexity to breeding. Front Plant Sci 17:1800432. https:\/\/doi.org\/10.3389\/fpls.2026.1800432","journal-title":"Front Plant Sci"},{"key":"5337_CR80","doi-asserted-by":"publisher","first-page":"509","DOI":"10.3389\/fpls.2017.00509","volume":"8","author":"K Neelam","year":"2017","unstructured":"Neelam K, Thakur S, Neha Y, Yadav IS, Kumar K, Dhaliwal SS, Singh K (2017) Novel alleles of Phosphorus-Starvation Tolerance 1 gene (PSTOL1) from Oryza rufipogon confer high phosphorus uptake efficiency. Front Plant Sci 8:509. https:\/\/doi.org\/10.3389\/fpls.2017.00509","journal-title":"Front Plant Sci"},{"key":"5337_CR214","doi-asserted-by":"publisher","unstructured":"Nisa WU, Sandhu S, Nair SK, Kaur H, Kumar A, Rashid Z, et al (2024) Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India. BMC Genomics 25:760. https:\/\/doi.org\/10.1186\/s12864-024-10655-x","DOI":"10.1186\/s12864-024-10655-x"},{"key":"5337_CR215","doi-asserted-by":"publisher","unstructured":"Niu F, Liu Z, Zhang F, Yuan S, Bai J, Liu Y et al (2023) Identification and validation of major-effect quantitative trait locus QMS-5B associated with male sterility in photo-thermo-sensitive genic male sterile wheat. Theor Appl Genet 136:257. https:\/\/doi.org\/10.1007\/s00122-023-04500-0","DOI":"10.1007\/s00122-023-04500-0"},{"key":"5337_CR82","doi-asserted-by":"publisher","first-page":"jkad174","DOI":"10.1093\/g3journal\/jkad174","volume":"13","author":"F Ntakirutimana","year":"2023","unstructured":"Ntakirutimana F, Tranchant-Dubreuil C, Cubry P, Chougule K, Zhang J, Wing RA, Adam H, Lorieux M, Jouannic S (2023) Genome-wide association analysis identifies natural allelic variants associated with panicle architecture variation in African rice, Oryza glaberrima Steud. G3 (Bethesda) 13:jkad174. https:\/\/doi.org\/10.1093\/g3journal\/jkad174","journal-title":"G3 (Bethesda)"},{"key":"5337_CR83","doi-asserted-by":"publisher","first-page":"253","DOI":"10.56093\/ijas.v88i2.79199","volume":"88","author":"NE Pandey","year":"2018","unstructured":"Pandey NE, Hossain F, Muthusamy VI, Vishwakarma AK, Zunjare RU (2018) Haplotypes of recessive opaque2 allele in exotic-and indigenous\u2013quality protein maize inbreds. Indian J Agric Sci 88:253\u2013259. https:\/\/doi.org\/10.56093\/ijas.v88i2.79199","journal-title":"Indian J Agric Sci"},{"key":"5337_CR84","doi-asserted-by":"publisher","first-page":"1387","DOI":"10.1007\/s00122-014-2306-y","volume":"127","author":"J Pariasca-Tanaka","year":"2014","unstructured":"Pariasca-Tanaka J, Chin JH, Drame KN, Dalid C, Heuer S, Wissuwa M (2015) A novel allele of the P-starvation tolerance gene OsPSTOL1 from African rice (Oryza glaberrima Steud) and its distribution in the genus Oryza. Theor Appl Genet 127:1387\u20131398. https:\/\/doi.org\/10.1007\/s00122-014-2306-y","journal-title":"Theor Appl Genet"},{"key":"5337_CR85","doi-asserted-by":"publisher","first-page":"1396","DOI":"10.1111\/pbi.13560","volume":"19","author":"EA Pasion","year":"2021","unstructured":"Pasion EA, Badoni S, Misra G, Anacleto R, Parween S, Kohli A, Sreenivasulu N (2021) OsTPR boosts the superior grains through increase in upper secondary rachis branches without incurring a grain quality penalty. Plant Biotechnol J 19:1396\u20131411. https:\/\/doi.org\/10.1111\/pbi.13560","journal-title":"Plant Biotechnol J"},{"key":"5337_CR86","doi-asserted-by":"publisher","first-page":"19199","DOI":"10.1038\/srep19199","volume":"6","author":"G Patil","year":"2016","unstructured":"Patil G, Do T, Vuong TD, Valliyodan B, Lee JD, Chaudhary J, Shannon JG, Nguyen HT (2016) Genomic-assisted haplotype analysis and the development of high-throughput SNP markers for salinity tolerance in soybean. Sci Rep 6:19199. https:\/\/doi.org\/10.1038\/srep19199","journal-title":"Sci Rep"},{"key":"5337_CR87","doi-asserted-by":"publisher","first-page":"1719","DOI":"10.1126\/science.1065573","volume":"294","author":"N Patil","year":"2001","unstructured":"Patil N, Berno AJ, Hinds DA, Barrett WA, Doshi JM, Hacker CR, Kautzer CR, Lee DH, Marjoribanks C, McDonough DP, Nguyen BTN, Norris MC, Sheehan JB, Shen N, Stern D, Stokowski RP, Thomas DJ, Trulson MO, Vyas KR, Frazer KA, Fodor SPA, Cox DR (2001) Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294:1719\u20131723. https:\/\/doi.org\/10.1126\/science.1065573","journal-title":"Science"},{"key":"5337_CR88","doi-asserted-by":"publisher","first-page":"485","DOI":"10.1111\/pbi.13731","volume":"20","author":"L Peng","year":"2022","unstructured":"Peng L, Sun S, Yang B, Zhao J, Li W, Huang Z, Li Z, He Y, Wang Z (2022) Genome-wide association study reveals that the cupin domain protein OsCDP3.10 regulates seed vigour in rice. Plant Biotechnol J 20:485\u2013498. https:\/\/doi.org\/10.1111\/pbi.13731","journal-title":"Plant Biotechnol J"},{"key":"5337_CR89","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1186\/1471-2229-13-32","volume":"13","author":"JD Platten","year":"2013","unstructured":"Platten JD, Egdane JA, Ismail AM (2013) Salinity tolerance, Na+ exclusion, and allele mining of HKT1;5 in Oryza sativa and O. glaberrima: many sources, many genes, one mechanism? BMC Plant Biol 13:32. https:\/\/doi.org\/10.1186\/1471-2229-13-32","journal-title":"BMC Plant Biol"},{"key":"5337_CR217","doi-asserted-by":"publisher","unstructured":"Pruthi R, Chaudhary C, Chapagain S, Abozaid MME, Rana P, Kondi RKR, et al (2024) Deciphering the genetic basis of salinity tolerance in a diverse panel of cultivated and wild soybean accessions by genome-wide association mapping. Theor Appl Genet 137:238. https:\/\/doi.org\/10.1007\/s00122-024-04752-4","DOI":"10.1007\/s00122-024-04752-4"},{"key":"5337_CR218","doi-asserted-by":"publisher","unstructured":"Pulipati S, Somasundaram S, Rana N, Kumaresan K, Shafi M, Civ\u00e1\u0148 P et al (2022) Diversity of sodium transporter HKT1;5 in genus Oryza. Rice Sci 29:31\u201346. https:\/\/doi.org\/10.1016\/j.rsci.2021.12.003","DOI":"10.1016\/j.rsci.2021.12.003"},{"key":"5337_CR90","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1016\/0092-8674(95)90288-0","volume":"80","author":"J Putterill","year":"1995","unstructured":"Putterill J, Robson F, Lee K, Simon R, Coupland G (1995) The CONSTANS gene of Arabidopsis promotes flowering and encodes a protein showing similarities to zinc finger transcription factors. Cell 80:847\u2013857. https:\/\/doi.org\/10.1016\/0092-8674(95)90288-0","journal-title":"Cell"},{"key":"5337_CR91","doi-asserted-by":"publisher","first-page":"4734","DOI":"10.1038\/s41467-025-60076-x","volume":"16","author":"G Qi","year":"2025","unstructured":"Qi G, Li Y, Zhang W, Han Z, Chen J, Zhang Z, Xuan L, Chen R, Fang L, Hu Y et al (2025) Reveal genomic insights into cotton domestication and improvement using gene level functional haplotype-based GWAS. Nat Commun 16:4734. https:\/\/doi.org\/10.1038\/s41467-025-60076-x","journal-title":"Nat Commun"},{"key":"5337_CR92","doi-asserted-by":"publisher","first-page":"4340","DOI":"10.1038\/ncomms5340","volume":"5","author":"X Qi","year":"2014","unstructured":"Qi X, Li MW, Xie M, Liu X, Ni M, Shao G, Song C, Kay-Yuen Yim A, Tao Y, Wong FL, Isobe S, Wong CF, Wong KS, Xu C, Li C, Wang Y, Guan R, Sun F, Fan G, Xiao Z, Zhou F, Phang TH, Liu X, Tong SW, Chan TF, Yiu SM, Tabata S, Wang J, Xu X, Lam HM (2014) Identification of a novel salt tolerance gene in wild soybean by whole-genome sequencing. Nat Commun 5:4340. https:\/\/doi.org\/10.1038\/ncomms5340","journal-title":"Nat Commun"},{"key":"5337_CR93","doi-asserted-by":"publisher","first-page":"1534","DOI":"10.3389\/fpls.2017.01534","volume":"8","author":"L Qian","year":"2017","unstructured":"Qian L, Hickey LT, Stahl A, Werner CR, Hayes B, Snowdon RJ, Voss-Fels KP (2017) Exploring and harnessing haplotype diversity to improve yield stability in crops. Front Plant Sci 8:1534. https:\/\/doi.org\/10.3389\/fpls.2017.01534","journal-title":"Front Plant Sci"},{"key":"5337_CR94","doi-asserted-by":"publisher","first-page":"107","DOI":"10.1186\/1471-2229-14-107","volume":"14","author":"L Qin","year":"2014","unstructured":"Qin L, Hao C, Hou J, Wang Y, Li T, Wang L, Ma Z, Zhang X (2014) Homologous haplotypes, expression, genetic effects, and geographic distribution of the wheat yield gene TaGW2. BMC Plant Biol 14:107. https:\/\/doi.org\/10.1186\/1471-2229-14-107","journal-title":"BMC Plant Biol"},{"key":"5337_CR95","doi-asserted-by":"publisher","first-page":"902","DOI":"10.1038\/s42003-023-05258-3","volume":"6","author":"P Ramu","year":"2023","unstructured":"Ramu P, Srivastava RK, Sanyal A, Fengler K, Cao J, Zhang Y, Nimkar M, Gerke J, Shreedharan S, Llaca V, May G, Peterson-Burch B, Lin H, King M, Das S, Bhupesh V, Mandaokar A, Maruthachalam K, Krishnamurthy P, Babu R (2023) Improved pearl millet genomes representing the global heterotic pool offer a framework for molecular breeding applications. Commun Biol 6:902. https:\/\/doi.org\/10.1038\/s42003-023-05258-3","journal-title":"Commun Biol"},{"key":"5337_CR219","doi-asserted-by":"publisher","unstructured":"Radecka-Janusik M, Piechota U, Piaskowska D, S\u0142owacki P, Bartosiak S, Czembor P (2024) Haplotype-based association mapping of genomic regions associated with Zymoseptoria tritici resistance using 217 diverse wheat genotypes. BMC Plant Biol 24:682. https:\/\/doi.org\/10.1186\/s12870-024-05400-1","DOI":"10.1186\/s12870-024-05400-1"},{"key":"5337_CR220","doi-asserted-by":"publisher","unstructured":"Ragsdale AP, Gravel S (2019) Unbiased estimation of linkage disequilibrium from unphased data. Mol Biol Evol 37:923\u2013932. https:\/\/doi.org\/10.1093\/molbev\/msz265","DOI":"10.1093\/molbev\/msz265"},{"key":"5337_CR96","doi-asserted-by":"publisher","first-page":"3119","DOI":"10.1111\/pbi.14590","volume":"23","author":"A Raza","year":"2025","unstructured":"Raza A, Zaman QU, Shabala S, Tester M, Munns R, Hu Z, Varshney RK (2025) Genomics-assisted breeding for designing salinity-smart future crops. Plant Biotechnol J 23:3119\u20133151. https:\/\/doi.org\/10.1111\/pbi.14590","journal-title":"Plant Biotechnol J"},{"key":"5337_CR221","doi-asserted-by":"publisher","unstructured":"Ren Z, Gao J, Li L, Cai X, Huang W, Chao D et al (2005) A rice quantitative trait locus for salt tolerance encodes a sodium transporter. Nat Genet 37:1141\u20131146. https:\/\/doi.org\/10.1038\/ng1643","DOI":"10.1038\/ng1643"},{"key":"5337_CR97","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.jare.2015.01.008","volume":"7","author":"MN Saad","year":"2016","unstructured":"Saad MN, Mabrouk MS, Eldeib AM, Shaker OG (2016) Identification of rheumatoid arthritis biomarkers based on single nucleotide polymorphisms and haplotype blocks: a systematic review and meta-analysis. J Adv Res 7:1\u201316. https:\/\/doi.org\/10.1016\/j.jare.2015.01.008","journal-title":"J Adv Res"},{"key":"5337_CR98","doi-asserted-by":"publisher","first-page":"425","DOI":"10.1086\/338688","volume":"70","author":"DJ Schaid","year":"2002","unstructured":"Schaid DJ, Rowland CM, Tines DE, Jacobson RM, Poland GA (2002) Score tests for association between traits and haplotypes when linkage phase is ambiguous. Am J Hum Genet 70:425\u2013434. https:\/\/doi.org\/10.1086\/338688","journal-title":"Am J Hum Genet"},{"issue":"4","key":"5337_CR99","doi-asserted-by":"publisher","first-page":"529","DOI":"10.2135\/cropsci1980.0011183X002000040028x","volume":"20","author":"WT Schapaugh","year":"1980","unstructured":"Schapaugh WT (1980) Relationships between harvest indices and other plant characteristics in soybeans. Crop Sci 20(4):529","journal-title":"Crop Sci"},{"key":"5337_CR100","doi-asserted-by":"publisher","first-page":"589490","DOI":"10.3389\/fgene.2020.589490","volume":"11","author":"D Sehgal","year":"2020","unstructured":"Sehgal D, Mondal S, Crespo-Herrera L, Velu G, Juliana P, Huerta-Espino J, Shrestha S, Poland J, Singh R, Dreisigacker S (2020) Haplotype-based, genome-wide association study reveals stable genomic regions for grain yield in CIMMYT spring bread wheat. Front Genet 11:589490. https:\/\/doi.org\/10.3389\/fgene.2020.589490","journal-title":"Front Genet"},{"key":"5337_CR101","doi-asserted-by":"publisher","first-page":"10082","DOI":"10.1038\/s41598-021-87964-8","volume":"11","author":"R Selvaraj","year":"2021","unstructured":"Selvaraj R, Singh AK, Singh VK, Abbai R, Habde SV, Singh UM, Kumar A (2021) Superior haplotypes towards development of low glycemic index rice with preferred grain and cooking quality. Sci Rep 11:10082. https:\/\/doi.org\/10.1038\/s41598-021-87964-8","journal-title":"Sci Rep"},{"key":"5337_CR102","doi-asserted-by":"publisher","first-page":"10813","DOI":"10.3390\/ijms251910813","volume":"25","author":"M Shi","year":"2024","unstructured":"Shi M, Sun J, Jiang F, Shaw RK, Ijaz B, Fan X (2024) Mining of oil content genes in recombinant maize inbred lines with introgression from temperate and tropical germplasm. Int J Mol Sci 25:10813. https:\/\/doi.org\/10.3390\/ijms251910813","journal-title":"Int J Mol Sci"},{"key":"5337_CR103","doi-asserted-by":"publisher","first-page":"92","DOI":"10.1186\/s12870-017-1044-0","volume":"17","author":"Y Shi","year":"2017","unstructured":"Shi Y, Gao L, Wu Z, Zhang X, Wang M, Zhang C, Zhang F, Zhou Y, Li Z (2017) Genome-wide association study of salt tolerance at the seed germination stage in rice. BMC Plant Biol 17:92. https:\/\/doi.org\/10.1186\/s12870-017-1044-0","journal-title":"BMC Plant Biol"},{"key":"5337_CR104","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1038\/ng.3518","volume":"48","author":"L Si","year":"2016","unstructured":"Si L, Chen J, Huang X, Gong H, Luo J, Hou Q, Zhou T, Lu T, Zhu J, Shangguan Y, Chen E, Gong C, Zhao Q, Jing Y, Zhao Y, Li Y, Cui L, Fan D, Lu Y, Weng Q, Wang Y, Zhan Q, Liu K, Wei X, An K, An G, Han B (2016) OsSPL13 controls grain size in cultivated rice. Nat Genet 48:447\u2013456. https:\/\/doi.org\/10.1038\/ng.3518","journal-title":"Nat Genet"},{"key":"5337_CR222","doi-asserted-by":"publisher","unstructured":"Si Y, Tian S, Niu J, Lu Q, Shang Q, Ma S et al (2025) The TaNHLP1-TaRACK1A module regulates tillering via abscisic acid signaling in wheat. Nat Commun 16:7336. https:\/\/doi.org\/10.1038\/s41467-025-62654-5","DOI":"10.1038\/s41467-025-62654-5"},{"key":"5337_CR105","doi-asserted-by":"publisher","first-page":"8621","DOI":"10.1038\/s41598-020-65588-8","volume":"10","author":"A Singh","year":"2020","unstructured":"Singh A, Singh Y, Mahato AK, Jayaswal PK, Singh S, Singh R, Yadav N, Singh AK, Singh PK, Singh R, Kumar R, Septiningsih EM, Balyan HS, Singh NK, Rai V (2020) Allelic sequence variation in the Sub1A, Sub1B and Sub1C genes among diverse rice cultivars and its association with submergence tolerance. Sci Rep 10:8621. https:\/\/doi.org\/10.1038\/s41598-020-65588-8","journal-title":"Sci Rep"},{"key":"5337_CR106","doi-asserted-by":"publisher","first-page":"972","DOI":"10.3389\/fpls.2017.00972","volume":"8","author":"N Singh","year":"2017","unstructured":"Singh N, Singh B, Rai V, Sidhu S, Singh AK, Singh NK (2017) Evolutionary insights based on SNP haplotypes of red pericarp, grain size and starch synthase genes in wild and cultivated rice. Front Plant Sci 8:972. https:\/\/doi.org\/10.3389\/fpls.2017.00972","journal-title":"Front Plant Sci"},{"key":"5337_CR107","doi-asserted-by":"publisher","first-page":"2482","DOI":"10.1111\/pbi.13422","volume":"18","author":"P Sinha","year":"2020","unstructured":"Sinha P, Singh VK, Saxena RK, Khan AW, Abbai R, Chitikineni A, Desai A, Molla J, Upadhyaya HD, Kumar A, Varshney RK (2020) Superior haplotypes for haplotype-based breeding for drought tolerance in pigeonpea (Cajanus cajan L.). Plant Biotechnol J 18:2482\u20132490. https:\/\/doi.org\/10.1111\/pbi.13422","journal-title":"Plant Biotechnol J"},{"key":"5337_CR223","doi-asserted-by":"publisher","unstructured":"Sivabharathi R, Rajagopalan VR, Suresh R, Sudha M, Karthikeyan G, Jayakanthan M, Raveendran M (2024) Haplotype-based breeding: a new insight in crop improvement. Plant Sci 346:112129. https:\/\/doi.org\/10.1016\/j.plantsci.2024.112129","DOI":"10.1016\/j.plantsci.2024.112129"},{"key":"5337_CR108","doi-asserted-by":"publisher","first-page":"3741","DOI":"10.3390\/cimb46040233","volume":"46","author":"J Song","year":"2024","unstructured":"Song J, Tang L, Fan H, Xu X, Peng X, Cui Y, Wang J (2024) Enhancing yield and improving grain quality in Japonica rice: targeted EHD1 editing via CRISPR-CAS9 in low-latitude adaptation. Curr Issues Mol Biol 46:3741\u20133751. https:\/\/doi.org\/10.3390\/cimb46040233","journal-title":"Curr Issues Mol Biol"},{"key":"5337_CR109","doi-asserted-by":"publisher","first-page":"767","DOI":"10.1534\/genetics.110.122549","volume":"186","author":"FW Stearns","year":"2010","unstructured":"Stearns FW (2010) One hundred years of pleiotropy: a retrospective. Genetics 186:767\u2013773. https:\/\/doi.org\/10.1534\/genetics.110.122549","journal-title":"Genetics"},{"key":"5337_CR110","doi-asserted-by":"publisher","first-page":"848","DOI":"10.1126\/science.1136678","volume":"315","author":"BE Stranger","year":"2007","unstructured":"Stranger BE, Forrest MS, Dunning M et al (2007) Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science 315:848\u2013853. https:\/\/doi.org\/10.1126\/science.1136678","journal-title":"Science"},{"key":"5337_CR111","doi-asserted-by":"publisher","first-page":"165256","DOI":"10.1016\/j.scitotenv.2023.165256","volume":"898","author":"Q Su","year":"2023","unstructured":"Su Q, Rohila JS, Ranganathan S, Karthikeyan R (2023) Rice yield and quality in response to daytime and nighttime temperature increase\u2014A meta-analysis perspective. Sci Total Environ 898:165256. https:\/\/doi.org\/10.1016\/j.scitotenv.2023.165256","journal-title":"Sci Total Environ"},{"key":"5337_CR112","doi-asserted-by":"publisher","first-page":"211","DOI":"10.1007\/s00122-010-1437-z","volume":"122","author":"Z Su","year":"2011","unstructured":"Su Z, Hao C, Wang L, Dong Y, Zhang X (2011) Identification and development of a functional marker of TaGW2 associated with grain weight in bread wheat (Triticum aestivum L.). Theor Appl Genet 122:211\u2013223. https:\/\/doi.org\/10.1007\/s00122-010-1437-z","journal-title":"Theor Appl Genet"},{"key":"5337_CR113","doi-asserted-by":"publisher","first-page":"124","DOI":"10.13057\/biodiv\/d170118","volume":"17","author":"A Sulistyo","year":"2016","unstructured":"Sulistyo A, Sumartini S (2016) Evaluation of soybean genotypes for resistance to rust disease (Phakopsora pachyrhizi). Biodiversitas 17:124\u2013128. https:\/\/doi.org\/10.13057\/biodiv\/d170118","journal-title":"Biodiversitas"},{"key":"5337_CR114","doi-asserted-by":"publisher","first-page":"4265","DOI":"10.1038\/s41467-022-31844-w","volume":"13","author":"X Sun","year":"2022","unstructured":"Sun X, Xiong H, Jiang C, Zhang D, Yang Z, Huang Y, Zhu W, Ma S, Duan J, Wang X, Liu W, Guo H, Li G, Qi J, Liang C, Zhang Z, Li J, Zhang H, Han L, Zhou Y, Peng Y, Li Z (2022) Natural variation of DROT1 confers drought adaptation in upland rice. Nat Commun 13:4265. https:\/\/doi.org\/10.1038\/s41467-022-31844-w","journal-title":"Nat Commun"},{"key":"5337_CR115","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1016\/j.cj.2018.10.007","volume":"7","author":"M Tang","year":"2019","unstructured":"Tang M, Zhang Y, Liu Y, Tong C, Cheng X, Zhu W, Li Z, Huang J, Liu S (2019) Mapping loci controlling fatty acid profiles, oil and protein content by genome-wide association study in Brassica napus. Crop J 7:217\u2013226. https:\/\/doi.org\/10.1016\/j.cj.2018.10.007","journal-title":"Crop J"},{"key":"5337_CR116","doi-asserted-by":"publisher","first-page":"1884","DOI":"10.1093\/plphys\/kiac550","volume":"191","author":"V Thakro","year":"2023","unstructured":"Thakro V, Malik N, Basu U, Srivastava R, Narnoliya L, Daware A, Varshney N, Mohanty JK, Bajaj D, Dwivedi V, Tripathi S, Jha UC, Dixit GP, Singh AK, Tyagi AK, Upadhyaya HD, Parida SK (2023) A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea. Plant Physiol 191:1884\u20131912. https:\/\/doi.org\/10.1093\/plphys\/kiac550","journal-title":"Plant Physiol"},{"key":"5337_CR117","doi-asserted-by":"publisher","first-page":"1088","DOI":"10.1086\/421249","volume":"74","author":"A Thomas","year":"2004","unstructured":"Thomas A, Camp NJ (2004) Graphical modeling of the joint distribution of alleles at associated loci. Am J Hum Genet 74:1088\u20131101. https:\/\/doi.org\/10.1086\/421249","journal-title":"Am J Hum Genet"},{"key":"5337_CR118","doi-asserted-by":"publisher","first-page":"148","DOI":"10.1007\/s12284-010-9053-8","volume":"3","author":"MJ Thomson","year":"2010","unstructured":"Thomson MJ, de Ocampo M, Egdane J et al (2010) Characterizing the Saltol quantitative trait locus for salinity tolerance in Oryza sativa. Rice 3:148\u2013160. https:\/\/doi.org\/10.1007\/s12284-010-9053-8","journal-title":"Rice"},{"key":"5337_CR119","doi-asserted-by":"publisher","first-page":"984527","DOI":"10.3389\/fpls.2022.984527","volume":"13","author":"L Tong","year":"2022","unstructured":"Tong L, Yan M, Zhu M, Yang J, Li Y, Xu M (2022) ZmCCT haplotype H5 improves yield, stalk-rot resistance, and drought tolerance in maize. Front Plant Sci 13:984527. https:\/\/doi.org\/10.3389\/fpls.2022.984527","journal-title":"Front Plant Sci"},{"issue":"20","key":"5337_CR120","doi-asserted-by":"publisher","first-page":"375","DOI":"10.9734\/ijpss\/2023\/v35i203818","volume":"35","author":"A Topno","year":"2023","unstructured":"Topno A, Williams M, Sakthi AR, Bharathi A, Ranjani RV, Suresh R, Sudha M, Boopathi NM, Raveendran M (2023) Exploitation of allelic variation and superior haplotypes for OsMIT3 regulating tiller number in rice. Int J Plant Soil Sci 35(20):375\u2013382. https:\/\/doi.org\/10.9734\/ijpss\/2023\/v35i203818","journal-title":"Int J Plant Soil Sci"},{"key":"5337_CR224","doi-asserted-by":"publisher","unstructured":"Uecker H, Setter D, Hermisson J (2015) Adaptive gene introgression after secondary contact. J Math Biol 70:1523\u20131580. https:\/\/doi.org\/10.1007\/s00285-014-0802-y","DOI":"10.1007\/s00285-014-0802-y"},{"key":"5337_CR121","doi-asserted-by":"publisher","first-page":"1097","DOI":"10.1038\/ng.2725","volume":"45","author":"Y Uga","year":"2013","unstructured":"Uga Y, Sugimoto K, Ogawa S, Rane J, Ishitani M, Hara N, Kitomi Y, Inukai Y, Ono K, Kanno N, Inoue H, Takehisa H, Motoyama R, Nagamura Y, Wu J, Matsumoto T, Takai T, Okuno K, Yano M (2013) Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions. Nat Genet 45:1097\u20131102. https:\/\/doi.org\/10.1038\/ng.2725","journal-title":"Nat Genet"},{"key":"5337_CR122","doi-asserted-by":"publisher","first-page":"969","DOI":"10.1038\/nbt.3943","volume":"35","author":"RK Varshney","year":"2017","unstructured":"Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A et al (2017) Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol 35:969\u2013976. https:\/\/doi.org\/10.1038\/nbt.3943","journal-title":"Nat Biotechnol"},{"key":"5337_CR225","doi-asserted-by":"publisher","unstructured":"Varshney RK, Roorkiwal M, Sun S, Bajaj P, Chitikineni A, Thudi M et al (2021) A chickpea genetic variation map based on the sequencing of 3,366 genomes. Nature 599:622\u2013627. https:\/\/doi.org\/10.1038\/s41586-021-04066-1","DOI":"10.1038\/s41586-021-04066-1"},{"key":"5337_CR123","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1086\/505313","volume":"79","author":"CJ Verzilli","year":"2006","unstructured":"Verzilli CJ, Stallard N, Whittaker JC (2006) Bayesian graphical models for genome-wide association studies. Am J Hum Genet 79:100\u2013112. https:\/\/doi.org\/10.1086\/505313","journal-title":"Am J Hum Genet"},{"key":"5337_CR226","doi-asserted-by":"publisher","unstructured":"Villiers K, Voss-Fels KP, Dinglasan E, Jacobs B, Hickey L, Hayes BJ (2024) Evolutionary computing to assemble standing genetic diversity and achieve long-term genetic gain. Plant Genome 17:e20467. https:\/\/doi.org\/10.1002\/tpg2.20467","DOI":"10.1002\/tpg2.20467"},{"key":"5337_CR125","doi-asserted-by":"publisher","first-page":"1553","DOI":"10.1111\/pbi.13569","volume":"19","author":"A Wang","year":"2021","unstructured":"Wang A, Shu X, Jing X, Jiao C, Chen L, Zhang J, Ma L, Jiang Y, Yamamoto N, Li S, Deng Q, Wang S, Zhu J, Liang Y, Zou T, Liu H, Wang L, Huang Y, Li P, Zheng A (2021) Identification of rice (Oryza sativa L.) genes involved in sheath blight resistance via a genome-wide association study. Plant Biotechnol J 19:1553\u20131566. https:\/\/doi.org\/10.1111\/pbi.13569","journal-title":"Plant Biotechnol J"},{"key":"5337_CR126","doi-asserted-by":"publisher","first-page":"1503","DOI":"10.1111\/nph.14688","volume":"215","author":"C Wang","year":"2017","unstructured":"Wang C, Yang Q, Wang W, Li Y, Guo Y, Zhang D, Ma X, Song W, Zhao J, Xu M (2017a) A transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize. New Phytol 215:1503\u20131515. https:\/\/doi.org\/10.1111\/nph.14688","journal-title":"New Phytol"},{"key":"5337_CR127","doi-asserted-by":"publisher","first-page":"2731","DOI":"10.1111\/pce.13400","volume":"41","author":"F Wang","year":"2018","unstructured":"Wang F, Longkumer T, Catausan SC et al. (2018) Genome-wide association and gene validation studies for early root vigor to improve direct seeding of rice. Plant Cell Environ 41:2731\u20132743. https:\/\/doi.org\/10.1111\/pce.13400","journal-title":"Plant Cell Environ"},{"key":"5337_CR128","doi-asserted-by":"publisher","first-page":"903","DOI":"10.1093\/aob\/mcy218","volume":"124","author":"J Wang","year":"2019","unstructured":"Wang J, Wang R, Mao X, Li L, Chang X, Zhang X, Jing R (2019) TaARF4 genes are linked to root growth and plant height in wheat. Ann Bot 124:903\u2013915. https:\/\/doi.org\/10.1093\/aob\/mcy218","journal-title":"Ann Bot"},{"key":"5337_CR129","doi-asserted-by":"publisher","first-page":"950","DOI":"10.1038\/ng.2327","volume":"44","author":"S Wang","year":"2012","unstructured":"Wang S, Wu K, Yuan Q, Liu X, Liu Z, Lin X, Zeng R, Zhu H, Dong G, Qian Q, Zhang G, Fu X (2012) Control of grain size, shape and quality by OsSPL16 in rice. Nat Genet 44:950\u2013954. https:\/\/doi.org\/10.1038\/ng.2327","journal-title":"Nat Genet"},{"key":"5337_CR227","doi-asserted-by":"publisher","unstructured":"Wang S, Feng J, Ren W, Huang B, Zhou L, Wen Y et al (2016) Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology. Sci Rep 6:19444. https:\/\/doi.org\/10.1038\/srep19444","DOI":"10.1038\/srep19444"},{"key":"5337_CR130","doi-asserted-by":"publisher","first-page":"1998","DOI":"10.3389\/fpls.2016.01998","volume":"7","author":"X Wang","year":"2017","unstructured":"Wang X, Pang Y, Wang C, Chen K, Zhu Y, Shen C, Ali J, Xu J, Li Z (2017b) New candidate genes affecting rice grain appearance and milling quality detected by genome-wide and gene-based association analyses. Front Plant Sci 7:1998. https:\/\/doi.org\/10.3389\/fpls.2016.01998","journal-title":"Front Plant Sci"},{"key":"5337_CR131","doi-asserted-by":"publisher","first-page":"17203","DOI":"10.1038\/s41598-017-17347-5","volume":"7","author":"X Wang","year":"2017","unstructured":"Wang X, Pang Y, Zhang J, Wu Z, Chen K, Ali J, Ye G, Xu J, Li Z (2017c) Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content. Sci Rep 7:17203. https:\/\/doi.org\/10.1038\/s41598-017-17347-5","journal-title":"Sci Rep"},{"key":"5337_CR132","doi-asserted-by":"publisher","unstructured":"Wang Y, Wang X, Zhai L, Zafar S, Shen C, Zhu S, Chen K, Wang Y, Xu J (2024) A novel Effective Panicle Number per Plant 4 haplotype enhances grain yield by coordinating panicle number and grain number in rice. Crop J 12(1):202\u2013212. https:\/\/doi.org\/10.1016\/j.cj.2023.11.003","DOI":"10.1016\/j.cj.2023.11.003"},{"key":"5337_CR134","doi-asserted-by":"publisher","first-page":"890","DOI":"10.1007\/s00122-002-1051-9","volume":"105","author":"M Wissuwa","year":"2002","unstructured":"Wissuwa M, Wegner J, Ae N, Yano M (2002) Substitution mapping of Pup1: a major QTL increasing phosphorus uptake of rice from a phosphorus-deficient soil. Theor Appl Genet 105:890\u2013897. https:\/\/doi.org\/10.1007\/s00122-002-1051-9","journal-title":"Theor Appl Genet"},{"key":"5337_CR135","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2229-11-1","volume":"11","author":"S Worch","year":"2011","unstructured":"Worch S, Rajesh K, Harshavardhan VT, Pietsch C, Korzun V, Kuntze L, B\u00f6rner A, Wobus U, R\u00f6der MS, Sreenivasulu N (2011) Haplotyping, linkage mapping and expression analysis of barley genes regulated by terminal drought stress influencing seed quality. BMC Plant Biol 11:1. https:\/\/doi.org\/10.1186\/1471-2229-11-1","journal-title":"BMC Plant Biol"},{"key":"5337_CR136","doi-asserted-by":"publisher","first-page":"e0146383","DOI":"10.1371\/journal.pone.0146383","volume":"11","author":"Z Wu","year":"2016","unstructured":"Wu Z, Wang B, Chen X, Wu J, King GJ, Xiao Y, Liu K (2016) Evaluation of linkage disequilibrium pattern and association study on seed oil content in Brassica napus using ddRAD sequencing. PLoS ONE 11:e0146383. https:\/\/doi.org\/10.1371\/journal.pone.0146383","journal-title":"PLoS ONE"},{"key":"5337_CR137","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1111\/nph.14400","volume":"214","author":"G Xu","year":"2017","unstructured":"Xu G, Wang X, Huang C, Xu D, Li D, Tian J, Chen Q, Wang C, Liang Y, Wu Y, Yang X, Tian F (2017) Complex genetic architecture underlies maize tassel domestication. New Phytol 214:852\u2013864. https:\/\/doi.org\/10.1111\/nph.14400","journal-title":"New Phytol"},{"key":"5337_CR138","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1007\/BF00564199","volume":"2","author":"K Xu","year":"1996","unstructured":"Xu K, Mackill DJ (1996) A major locus for submergence tolerance mapped on rice chromosome 9. Mol Breed 2:219\u2013224. https:\/\/doi.org\/10.1007\/BF00564199","journal-title":"Mol Breed"},{"key":"5337_CR139","doi-asserted-by":"publisher","first-page":"705","DOI":"10.1038\/nature04920","volume":"442","author":"K Xu","year":"2006","unstructured":"Xu K, Xu X, Fukao T, Canlas P, Maghirang R, Heuer S, Ismail AM, Bailey J, Ronald PC, Mackill DJ (2006) Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice. Nature 442:705\u2013708. https:\/\/doi.org\/10.1038\/nature04920","journal-title":"Nature"},{"key":"5337_CR140","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1007\/s004380051217","volume":"263","author":"K Xu","year":"2000","unstructured":"Xu K, Xu X, Ronald PC, Mackill DJ (2000) A high-resolution linkage map of the vicinity of the rice submergence tolerance locus Sub1. Mol Gen Genet 263:681\u2013689. https:\/\/doi.org\/10.1007\/s004380051217","journal-title":"Mol Gen Genet"},{"key":"5337_CR141","doi-asserted-by":"publisher","first-page":"651","DOI":"10.1270\/jsbbs.19087","volume":"69","author":"L Xu","year":"2019","unstructured":"Xu L, Guo L, You H, Zhang O, Xiang X (2019) Novel haplotype combinations reveal enhanced seedling vigor traits in rice that can accurately predict dry biomass accumulation in seedlings. Breed Sci 69:651\u2013657. https:\/\/doi.org\/10.1270\/jsbbs.19087","journal-title":"Breed Sci"},{"key":"5337_CR143","doi-asserted-by":"publisher","first-page":"16969","DOI":"10.1073\/pnas.1310949110","volume":"110","author":"Q Yang","year":"2013","unstructured":"Yang Q, Li Z, Li W, Ku L, Wang C, Ye J, Li K, Yang N, Li Y, Zhong T, Li J, Chen Y, Yan J, Yang X, Xu M (2013) CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the post-domestication spread of maize. Proc Natl Acad Sci USA 110:16969\u201316974. https:\/\/doi.org\/10.1073\/pnas.1310949110","journal-title":"Proc Natl Acad Sci USA"},{"key":"5337_CR144","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/1471-2156-9-90","volume":"9","author":"Y Yang","year":"2008","unstructured":"Yang Y, Li SS, Chien JW, Andriesen J, Zhao LP (2008) A systematic search for SNPs\/haplotypes associated with disease phenotypes using a haplotype-based stepwise procedure. BMC Genet 9:90. https:\/\/doi.org\/10.1186\/1471-2156-9-90","journal-title":"BMC Genet"},{"key":"5337_CR145","doi-asserted-by":"publisher","first-page":"1057","DOI":"10.1007\/s00122-012-1895-6","volume":"125","author":"Z Yang","year":"2012","unstructured":"Yang Z, Bai Z, Li X, Wang P, Wu Q, Yang L, Li L, Li X (2012) SNP identification and allelic-specific PCR markers development for TaGW2, a gene linked to wheat kernel weight. Theor Appl Genet 125:1057\u20131068. https:\/\/doi.org\/10.1007\/s00122-012-1895-6","journal-title":"Theor Appl Genet"},{"key":"5337_CR200","doi-asserted-by":"publisher","unstructured":"Yu J, Pressoir G, Briggs WH et al (2006) A unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203\u2013208. https:\/\/doi.org\/10.1038\/ng1702","DOI":"10.1038\/ng1702"},{"key":"5337_CR146","doi-asserted-by":"publisher","first-page":"2286","DOI":"10.1111\/pbi.13140","volume":"17","author":"F Yu","year":"2019","unstructured":"Yu F, Liang K, Fang T, Zhao H, Han X, Cai M, Qiu F (2019) A group VII ethylene response factor gene, ZmEREB180, coordinates waterlogging tolerance in maize seedlings. Plant Biotechnol J 17:2286\u20132298. https:\/\/doi.org\/10.1111\/pbi.13140","journal-title":"Plant Biotechnol J"},{"key":"5337_CR147","doi-asserted-by":"publisher","first-page":"9958","DOI":"10.1038\/s41598-020-66604-7","volume":"10","author":"J Yuan","year":"2020","unstructured":"Yuan J, Wang X, Zhao Y, Khan NU, Zhao Z, Zhang Y, Wen X, Tang F, Wang F, Li Z (2020) Genetic basis and identification of candidate genes for salt tolerance in rice by GWAS. Sci Rep 10:9958. https:\/\/doi.org\/10.1038\/s41598-020-66604-7","journal-title":"Sci Rep"},{"key":"5337_CR148","doi-asserted-by":"publisher","first-page":"221","DOI":"10.1017\/S1479262115000544","volume":"15","author":"JS Yumnam","year":"2017","unstructured":"Yumnam JS, Rai M, Tyagi W (2017) Allele mining across two low-P tolerant genes PSTOL1 and PupK20-2 reveals novel haplotypes in rice genotypes adapted to acidic soils. Plant Genet Resour 15:221\u2013229. https:\/\/doi.org\/10.1017\/S1479262115000544","journal-title":"Plant Genet Resour"},{"key":"5337_CR230","doi-asserted-by":"publisher","unstructured":"Zhang F, Deng H (2010) Confounding from cryptic relatedness in haplotype-based association studies. Genetica 138:945\u2013950. https:\/\/doi.org\/10.1007\/s10709-010-9476-6","DOI":"10.1007\/s10709-010-9476-6"},{"key":"5337_CR149","doi-asserted-by":"publisher","first-page":"787","DOI":"10.1016\/j.molp.2021.02.003","volume":"14","author":"F Zhang","year":"2021","unstructured":"Zhang F, Wang C, Li M, Cui Y, Shi Y, Wu Z, Hu Z, Wang W, Xu J, Li Z (2021) The landscape of gene\u2013CDS\u2013haplotype diversity in rice: properties, population organization, footprints of domestication and breeding, and implications for genetic improvement. Mol Plant 14:787\u2013804. https:\/\/doi.org\/10.1016\/j.molp.2021.02.003","journal-title":"Mol Plant"},{"key":"5337_CR150","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1186\/s12284-019-0351-5","volume":"12","author":"F Zhang","year":"2019","unstructured":"Zhang F, Zeng D, Zhang CS, Lu JL, Chen TJ, Xie JP, Zhou YL (2019) Genome-wide association analysis of the genetic basis for sheath blight resistance in rice. Rice 12:93. https:\/\/doi.org\/10.1186\/s12284-019-0351-5","journal-title":"Rice"},{"key":"5337_CR151","doi-asserted-by":"publisher","first-page":"447","DOI":"10.3389\/fpls.2018.00447","volume":"9","author":"GM Zhang","year":"2018","unstructured":"Zhang GM, Zheng TQ, Chen Z, Wang YL, Wang Y, Shi YM, Wang CC, Zhang LY, Ma JT, Deng LW, Li W, Xu TT, Liang CZ, Xu JL, Li ZK (2018a) Joint exploration of favourable haplotypes for mineral concentrations in milled grains of rice (Oryza sativa L.). Front Plant Sci 9:447. https:\/\/doi.org\/10.3389\/fpls.2018.00447","journal-title":"Front Plant Sci"},{"key":"5337_CR152","doi-asserted-by":"publisher","first-page":"e1009114","DOI":"10.1371\/journal.pgen.1009114","volume":"16","author":"H Zhang","year":"2020","unstructured":"Zhang H, Goettel W, Song Q, Jiang H, Hu Z, Wang ML, An YC (2020a) Selection of GmSWEET39 for oil and protein improvement in soybean. PLoS Genet 16:e1009114. https:\/\/doi.org\/10.1371\/journal.pgen.1009114","journal-title":"PLoS Genet"},{"key":"5337_CR153","doi-asserted-by":"publisher","first-page":"7335","DOI":"10.1073\/pnas.102186799","volume":"99","author":"K Zhang","year":"2002","unstructured":"Zhang K, Deng M, Chen T, Waterman MS, Sun F (2002) A dynamic programming algorithm for haplotype block partitioning. Proc Natl Acad Sci USA 99:7335\u20137339. https:\/\/doi.org\/10.1073\/pnas.102186799","journal-title":"Proc Natl Acad Sci USA"},{"key":"5337_CR154","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1186\/s12870-020-02473-6","volume":"20","author":"L Zhang","year":"2020","unstructured":"Zhang L, Liu P, Wu J, Qiao L, Zhao G, Jia J, Gao L, Wang J (2020b) Identification of a novel ERF gene, TaERF8, associated with plant height and yield in wheat. BMC Plant Biol 20:263. https:\/\/doi.org\/10.1186\/s12870-020-02473-6","journal-title":"BMC Plant Biol"},{"key":"5337_CR155","doi-asserted-by":"publisher","first-page":"1044","DOI":"10.1111\/pbi.14017","volume":"21","author":"Q Zhang","year":"2023","unstructured":"Zhang Q, Xie J, Zhu X, Ma X, Yang T, Khan NU, Zhang S, Liu M, Li L, Liang Y, Pan Y, Li D, Li J, Li Z, Zhang H, Zhang Z (2023) Natural variation in Tiller Number 1 affects its interaction with TIF1 to regulate tillering in rice. Plant Biotechnol J 21:1044\u20131057. https:\/\/doi.org\/10.1111\/pbi.14017","journal-title":"Plant Biotechnol J"},{"key":"5337_CR156","doi-asserted-by":"publisher","first-page":"1032","DOI":"10.1111\/tpj.13828","volume":"93","author":"Z Zhang","year":"2018","unstructured":"Zhang Z, Zhang X, Lin Z, Wang J, Xu M, Lai J, Yu J, Lin Z (2018b) The genetic architecture of nodal root number in Zea mays. Plant J 93:1032\u20131044. https:\/\/doi.org\/10.1111\/tpj.13828","journal-title":"Plant J"},{"key":"5337_CR231","doi-asserted-by":"publisher","unstructured":"Zhao Z, Shi T (2025) Haplotype-resolved assembly in polyploid plants: methods, challenges, and implications for evolutionary and breeding research. Genes 16:636. https:\/\/doi.org\/10.3390\/genes16060636","DOI":"10.3390\/genes16060636"},{"issue":"35","key":"5337_CR157","doi-asserted-by":"publisher","first-page":"9326","DOI":"10.1073\/pnas.1701762114","volume":"114","author":"C Zhao","year":"2017","unstructured":"Zhao C, Liu B, Piao S, Wang X, Lobell DB, Huang Y, Huang M, Yao Y, Bassu S, Ciais P, Durand J-L, Elliott J, Ewert F, Janssens IA, Li T, Lin E, Liu Q, Martre P, M\u00fcller C, Peng S, Pe\u00f1uelas J, Ruane AC, Wallach D, Wang T, Wu D, Liu Z, Zhu Y, Zhu Z, Asseng S (2017) Temperature increase reduces global yields of major crops in four independent estimates. Proc Natl Acad Sci U S A 114(35):9326\u20139331. https:\/\/doi.org\/10.1073\/pnas.1701762114","journal-title":"Proc Natl Acad Sci U S A"},{"key":"5337_CR158","doi-asserted-by":"publisher","first-page":"870","DOI":"10.1016\/j.cj.2023.01.004","volume":"11","author":"L Zhao","year":"2023","unstructured":"Zhao L, Wang C, Wang T, Liu J, Qiao Q, Yang Y, Hu P, Zhang L, Zhao S, Chen D, Ren Y, Zhang N, Dong Z, Chen F (2023) Identification of the candidate gene controlling tiller angle in common wheat through genome-wide association study and linkage analysis. Crop J 11:870\u2013877. https:\/\/doi.org\/10.1016\/j.cj.2023.01.004","journal-title":"Crop J"},{"key":"5337_CR159","doi-asserted-by":"publisher","first-page":"332","DOI":"10.3389\/fpls.2018.00332","volume":"9","author":"Y Zhao","year":"2018","unstructured":"Zhao Y, Zhao W, Jiang C, Wang X, Xiong H, Todorovska EG, Yin Z, Chen Y, Wang X, Xie J, Pan Y, Rashid MAR, Zhang H, Li J, Li Z (2018) Genetic architecture and candidate genes for deep-sowing tolerance in Oryza sativa revealed by non-syn GWAS. Front Plant Sci 9:332. https:\/\/doi.org\/10.3389\/fpls.2018.00332","journal-title":"Front Plant Sci"},{"key":"5337_CR160","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1186\/s12864-021-07391-x","volume":"22","author":"H Zhong","year":"2021","unstructured":"Zhong H, Liu S, Meng X, Sun T, Deng Y, Kong W, Peng Z, Li Y (2021) Uncovering the genetic mechanisms regulating panicle architecture in Oryza sativa with GPWAS and GWAS. BMC Genom 22:86. https:\/\/doi.org\/10.1186\/s12864-021-07391-x","journal-title":"BMC Genom"}],"container-title":["Theoretical and Applied Genetics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00122-026-05337-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00122-026-05337-z","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/s00122-026-05337-z.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T02:57:55Z","timestamp":1792724275000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/article\/10.1007\/s00122-026-05337-z"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,23]]},"references-count":184,"journal-issue":{"issue":"11","published-print":{"date-parts":[[2026,11]]}},"alternative-id":["5337"],"URL":"https:\/\/doi.org\/10.1007\/s00122-026-05337-z","relation":{},"ISSN":["0040-5752","1432-2242"],"issn-type":[{"value":"0040-5752","type":"print"},{"value":"1432-2242","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,23]]},"assertion":[{"value":"5 March 2025","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"26 July 2026","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"23 October 2026","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","label":"Conflict of interest","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":2,"name":"Ethics","label":"Ethics approval","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":3,"name":"Ethics","label":"Consent to participate","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"Not applicable.","order":4,"name":"Ethics","label":"Consent for publication","group":{"name":"EthicsHeading","label":"Declarations"}}],"article-number":"310"}}