{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T11:02:39Z","timestamp":1789383759759,"version":"build-2803163510"},"reference-count":61,"publisher":"MDPI AG","issue":"18","license":[{"start":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T00:00:00Z","timestamp":1789171200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan","award":["BR24992903"],"award-info":[{"award-number":["BR24992903"]}]},{"award":["BR24992903"],"award-info":[{"award-number":["BR24992903"]}],"id":[{"id":"https:\/\/ror.org\/05tyne317","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Reliable identification of genomic regions controlling complex agronomic traits across variable growing seasons remains a major challenge in soybean genetics and breeding. Here, a diverse panel of 252 soybean accessions was evaluated over six consecutive growing seasons (2018\u20132023) for flowering time, maturity, plant height, number of seeds per plant, seed yield per plant, and thousand-seed weight. Whole-genome resequencing and variant filtering yielded 2,019,772 high-quality SNPs, and association signals were evaluated using Inclusive Integrative Input Multiple-locus Random-SNP-effect Mixed Linear Model (IIIVmrMLM), Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), and Multi-Locus Mixed Model (MLMM) together with linkage disequilibrium (LD)-based locus consolidation. Cross-model prioritization retained 21 high-confidence loci supported by all three GWAS models and distributed across 10 chromosomes. Among the identified loci, 18 overlapped or co-localized with previously reported SoyBase genes and QTLs, whereas three (q.VER2.13-1, q.YP.01-1, and q.TSW.15-1) showed no positional overlap with known genes and QTLs and were therefore considered presumably novel. These three loci were associated with flowering time, yield per plant, and thousand-seed weight, accounting for 1.60%, 2.13%, and 5.53% of phenotypic variation, respectively. Ten loci co-localized with genomic regions containing established soybean regulators, including E2, E3, GmDt2, and POWR1, support the biological plausibility of the association results. Integration of genomic position, functional annotation, and tissue-expression evidence prioritized 112 candidate genes across 18 loci. These findings provide a focused set of genomic loci and candidate genes for independent validation and further investigation of the genetic basis of soybean adaptation and yield formation under variable continental growing conditions.<\/jats:p>","DOI":"10.3390\/plants15182800","type":"journal-article","created":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T09:34:01Z","timestamp":1789378441000},"page":"2800","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi-Season Multi-Model GWAS Prioritizes Stable Genomic Loci and Candidate Genes for Six Agronomic Traits in Soybean Under Conditions in Southeastern Kazakhstan"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-4310-5753","authenticated-orcid":false,"given":"Alibek","family":"Zatybekov","sequence":"first","affiliation":[{"name":"Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5987-2952","authenticated-orcid":false,"given":"Yuliya","family":"Genievskaya","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Chao","family":"Fang","sequence":"additional","affiliation":[{"name":"School of Life Science, Guangzhou University, Guangzhou 510006, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Zixuan","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, College of Life Sciences, Zhejiang University, Hangzhou 310058, China"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"given":"Svetlana","family":"Didorenko","sequence":"additional","affiliation":[{"name":"Department of Oil Crop, Kazakh Research Institute of Agriculture and Plant Growing, Almalybak 040909, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"data-curation","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9748-507X","authenticated-orcid":false,"given":"Saule","family":"Abugalieva","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8590-1745","authenticated-orcid":false,"given":"Yerlan","family":"Turuspekov","sequence":"additional","affiliation":[{"name":"Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"project-administration","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,12]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s12571-010-0108-x","article-title":"Crops that feed the World 2. Soybean\u2013worldwide production, use, and constraints caused by pathogens and pests","volume":"3","author":"Hartman","year":"2011","journal-title":"Food Secur."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Zatybekov, A., Abugalieva, S., Didorenko, S., Gerasimova, Y., Sidorik, I., Anuarbek, S., and Turuspekov, Y. (2017). GWAS of agronomic traits in soybean collection included in breeding pool in Kazakhstan. BMC Plant Biol., 17.","DOI":"10.1186\/s12870-017-1125-0"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"161","DOI":"10.1186\/s13059-017-1289-9","article-title":"Genome-wide association studies dissect the genetic networks underlying agronomical traits in soybean","volume":"18","author":"Fang","year":"2017","journal-title":"Genome Biol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1289","DOI":"10.1002\/csc2.20349","article-title":"Association mapping identifies and confirms loci for soybean seed weight","volume":"61","author":"Kaler","year":"2021","journal-title":"Crop Sci."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"E2155","DOI":"10.1073\/pnas.1117982109","article-title":"Positional cloning and characterization of the soybean maturity gene E1","volume":"109","author":"Xia","year":"2012","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"395","DOI":"10.1534\/genetics.110.125062","article-title":"A map-based cloning strategy employing a residual heterozygous line reveals that the GIGANTEA gene is involved in soybean maturity and flowering","volume":"188","author":"Watanabe","year":"2011","journal-title":"Genetics"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Xu, M., Xu, Z., Liu, B., Kong, F., Tsubokura, Y., Watanabe, S., Xia, Z., Harada, K., Kanazawa, A., and Yamada, T. (2013). Genetic variation in four maturity genes affects photoperiod responses in soybean. BMC Plant Biol., 13.","DOI":"10.1186\/1471-2229-13-91"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"198","DOI":"10.1104\/pp.109.150607","article-title":"The soybean stem growth habit gene Dt1 is an ortholog of TERMINAL FLOWER1","volume":"153","author":"Liu","year":"2010","journal-title":"Plant Physiol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"3051","DOI":"10.1038\/s41467-022-30314-7","article-title":"POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean","volume":"13","author":"Goettel","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/ng.3819","article-title":"Natural variation at the soybean J locus improves adaptation to the tropics and enhances yield","volume":"49","author":"Lu","year":"2017","journal-title":"Nat. Genet."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"981","DOI":"10.1111\/jipb.13021","article-title":"Molecular mechanisms for the photoperiodic regulation of flowering in soybean","volume":"63","author":"Lin","year":"2021","journal-title":"J. Integr. Plant Biol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1038\/nbt.3096","article-title":"Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean","volume":"33","author":"Zhou","year":"2015","journal-title":"Nat. Biotechnol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"256","DOI":"10.1111\/pbi.13682","article-title":"Progress in soybean functional genomics over the past decade","volume":"20","author":"Zhang","year":"2022","journal-title":"Plant Biotechnol. J."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"629","DOI":"10.1016\/j.gpb.2021.08.005","article-title":"GAPIT Version 3: Boosting power and accuracy for genomic association and prediction","volume":"19","author":"Wang","year":"2021","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1016\/j.tplants.2017.08.011","article-title":"Genomic selection in plant breeding: Methods, models, and perspectives","volume":"22","author":"Crossa","year":"2017","journal-title":"Trends Plant Sci."},{"key":"ref_16","doi-asserted-by":"crossref","unstructured":"Khan, M.H.U., Wang, S., Wang, J., Ahmar, S., Saeed, S., Khan, S.U., Xu, X., Chen, H., Bhat, J.A., and Feng, X. (2022). Applications of artificial intelligence in climate-resilient smart-crop breeding. Int. J. Mol. Sci., 23.","DOI":"10.3390\/ijms231911156"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"e20268","DOI":"10.1002\/tpg2.20268","article-title":"Genome-wide association analysis identified consistent QTL for seed yield in a soybean diversity panel tested across multiple environments","volume":"15","author":"Ayalew","year":"2022","journal-title":"Plant Genome"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Xavier, A., Hall, B., Casteel, S., Muir, W., and Rainey, K.M. (2021). Comparing a Mixed Model Approach to Traditional Stability Estimators for Mapping Genotype by Environment Interactions and Yield Stability in Soybean [Glycine max (L.) Merr.]. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.630175"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"825","DOI":"10.1038\/ng.2314","article-title":"An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations","volume":"44","author":"Segura","year":"2012","journal-title":"Nat. Genet."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"giy154","DOI":"10.1093\/gigascience\/giy154","article-title":"BLINK: A package for the next level of genome-wide association studies with both individuals and markers in the millions","volume":"8","author":"Huang","year":"2019","journal-title":"GigaScience"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1016\/j.molp.2022.02.012","article-title":"A compressed variance component mixed model for detecting QTNs and QTN-by-environment and QTN-by-QTN interactions in genome-wide association studies","volume":"15","author":"Li","year":"2022","journal-title":"Mol. Plant"},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1007\/s10681-007-9449-8","article-title":"BLUP for phenotypic selection in plant breeding and variety testing","volume":"161","author":"Piepho","year":"2008","journal-title":"Euphytica"},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1111\/1467-842X.00163","article-title":"The analysis of crop variety evaluation data in Australia","volume":"43","author":"Smith","year":"2001","journal-title":"Aust. N. Z. J. Stat."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"55","DOI":"10.9787\/PBB.2017.5.2.55","article-title":"Current status and future prospects of soybean production in Kazakhstan","volume":"5","author":"Makulbekova","year":"2017","journal-title":"Plant Breed. Biotechnol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1391","DOI":"10.18280\/ijdne.180612","article-title":"Influence of climate conditions and biofertilizers on soybean yield in Southeastern Kazakhstan","volume":"18","author":"Kenenbayev","year":"2023","journal-title":"Int. J. Des. Nat. Ecodyn."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"565","DOI":"10.18699\/VJGB-23-68","article-title":"Genome-wide association study for charcoal rot resistance in soybean harvested in Kazakhstan","volume":"27","author":"Zatybekov","year":"2023","journal-title":"Vavilov J. Genet. Breed."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"e36135","DOI":"10.1016\/j.heliyon.2024.e36135","article-title":"Assessment of the genetic parameters of soybean genotypes for precocity and productivity in the various cultivation conditions","volume":"10","author":"Kipshakbayeva","year":"2024","journal-title":"Heliyon"},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Doszhanova, B., Zatybekov, A., Didorenko, S., Fang, C., Abugalieva, S., and Turuspekov, Y. (2024). Genome-Wide Association Study of Seed Quality and Yield Traits in a Soybean Collection from Southeast Kazakhstan. Agronomy, 14.","DOI":"10.3390\/agronomy14112746"},{"key":"ref_29","doi-asserted-by":"crossref","unstructured":"Mazkirat, S., Didorenko, S., Bulatova, K., Baizhanov, Z., Babissekova, D., Khalbayeva, S., Tukenov, A., Yespembetova, A., Saparbayeva, N., and Shavrukov, Y. (2026). Integrative haplotype and SNP-based GWAS supports the identification of stable genomic loci controlling yield-related traits in soybean. Front. Plant Sci., 17.","DOI":"10.3389\/fpls.2026.1929722"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"D843","DOI":"10.1093\/nar\/gkp798","article-title":"SoyBase, the USDA-ARS soybean genetics and genomics database","volume":"38","author":"Grant","year":"2010","journal-title":"Nucleic Acids Res."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Severin, A.J., Woody, J.L., Bolon, Y.T., Joseph, B., Diers, B.W., Farmer, A.D., Muehlbauer, G.J., Nelson, R.T., Grant, D., and Specht, J.E. (2010). RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptome. BMC Plant Biol., 10.","DOI":"10.1186\/1471-2229-10-160"},{"key":"ref_32","first-page":"86","article-title":"An integrated transcriptome atlas of the crop model Glycine max and its use in comparative analyses in plants","volume":"63","author":"Libault","year":"2010","journal-title":"Plant J."},{"key":"ref_33","unstructured":"Ravelombola, W., Qin, J., Shi, A., Nice, L., Bao, Y., Lorenz, A., and Chen, P. (2021). Integrating GWAS and transcriptomics for candidate gene prioritization in soybean. Front. Plant Sci., 12."},{"key":"ref_34","doi-asserted-by":"crossref","unstructured":"Gai, Y., Liu, S., Zhang, Z., Wei, J., Wang, H., Liu, L., Bai, Q., Qin, Q., Zhao, C., and Zhang, S. (2025). Integrative approaches to soybean resilience, productivity, and utility: A review of genomics, computational modeling, and economic viability. Plants, 14.","DOI":"10.3390\/plants14050671"},{"key":"ref_35","doi-asserted-by":"crossref","unstructured":"Yan, L., Hofmann, N., Li, S., Ferreira, M.E., Song, B., Jiang, G., Ren, S., Quigley, C., Fickus, E., and Cregan, P. (2017). Identification of QTL with large effect on seed weight in a selective population of soybean with genome-wide association and fixation index analyses. BMC Genom., 18.","DOI":"10.1186\/s12864-017-3922-0"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1038\/hdy.2008.108","article-title":"QTL analyses of seed weight during the development of soybean (Glycine max L. Merr.)","volume":"102","author":"Teng","year":"2009","journal-title":"Heredity"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"467","DOI":"10.1038\/s41576-019-0127-1","article-title":"Benefits and limitations of genome-wide association studies","volume":"20","author":"Tam","year":"2019","journal-title":"Nat. Rev. Genet."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"2831","DOI":"10.1105\/tpc.114.126938","article-title":"Dt2 Is a Gain-of-Function MADS-Domain Factor Gene That Specifies Semideterminacy in Soybean","volume":"26","author":"Ping","year":"2014","journal-title":"Plant Cell"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"557","DOI":"10.1098\/rstb.2007.2170","article-title":"Marker-assisted selection: An approach for precision plant breeding in the twenty-first century","volume":"363","author":"Collard","year":"2008","journal-title":"Philos. Trans. R. Soc. B"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"jkab117","DOI":"10.1093\/g3journal\/jkab117","article-title":"Meta-GWAS for quantitative trait loci identification in soybean","volume":"11","author":"Shook","year":"2021","journal-title":"G3"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"101010","DOI":"10.1016\/j.xplc.2024.101010","article-title":"TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean","volume":"5","author":"Li","year":"2024","journal-title":"Plant Commun."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Dai, D., Huang, L., Zhang, X., Liu, J., Zhang, S., Yuan, X., Chen, X., and Xue, C. (2024). Detection of Candidate Genes and Development of KASP Markers for Pod Length and Pod Width by Combining Genome-Wide Association and Transcriptome Sequencing in Vegetable Soybean. Agronomy, 14.","DOI":"10.3390\/agronomy14112654"},{"key":"ref_43","doi-asserted-by":"crossref","unstructured":"Zhao, X., Zhu, H., Liu, F., Wang, J., Zhou, C., Yuan, M., Zhao, X., Li, Y., Teng, W., and Han, Y. (2024). Integrating Genome-Wide Association Study, Transcriptome and Metabolome Reveal Novel QTL and Candidate Genes That Control Protein Content in Soybean. Plants, 13.","DOI":"10.3390\/plants13081128"},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Kumawat, G., Gupta, S., Ratnaparkhe, M.B., Maranna, S., and Satpute, G.K. (2016). QTLomics in soybean: A way forward for translational genomics and breeding. Front. Plant Sci., 7.","DOI":"10.3389\/fpls.2016.01852"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"100005","DOI":"10.1016\/j.xplc.2019.100005","article-title":"Enhancing genetic gain through genomic selection: From livestock to plants","volume":"1","author":"Xu","year":"2020","journal-title":"Plant Commun."},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Widener, J.N., Graef, G.L., Lipka, A.E., and Jarquin, D. (2021). An assessment of the factors influencing the prediction accuracy of genomic prediction models across multiple environments. Front. Genet., 12.","DOI":"10.3389\/fgene.2021.689319"},{"key":"ref_47","unstructured":"Fehr, W.R., and Caviness, C.E. (1977). Stages of Soybean Development, Cooperative Extension Service, Agriculture and Home Economics Experiment Station, Iowa State University of Science and Technology. Special Report 80."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1881","DOI":"10.1534\/genetics.107.074229","article-title":"Computing heritability and selection response from unbalanced plant breeding trials","volume":"177","author":"Piepho","year":"2007","journal-title":"Genetics"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"525","DOI":"10.2135\/cropsci2018.06.0376","article-title":"Estimating broad-sense heritability with unbalanced data from agricultural cultivar trials","volume":"59","author":"Schmidt","year":"2019","journal-title":"Crop Sci."},{"key":"ref_50","unstructured":"R Core Team (2026, August 14). R: A Language and Environment for Statistical Computing, Available online: https:\/\/www.R-project.org\/."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1038\/s41588-020-0604-7","article-title":"Stepwise selection on homeologous PRR genes controlling flowering and maturity during soybean domestication","volume":"52","author":"Lu","year":"2020","journal-title":"Nat. Genet."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows\u2013Wheeler transform","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"giab008","DOI":"10.1093\/gigascience\/giab008","article-title":"Twelve years of SAMtools and BCFtools","volume":"10","author":"Danecek","year":"2021","journal-title":"GigaScience"},{"key":"ref_54","unstructured":"Broad Institute (2026, August 14). Picard Toolkit. Available online: https:\/\/broadinstitute.github.io\/picard\/."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"McKenna","year":"2010","journal-title":"Genome Res."},{"key":"ref_56","first-page":"11.10.1","article-title":"From FastQ data to high-confidence variant calls: The Genome Analysis Toolkit best practices pipeline","volume":"43","author":"Carneiro","year":"2013","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/s13742-015-0047-8","article-title":"Second-generation PLINK: Rising to the challenge of larger and richer datasets","volume":"4","author":"Chang","year":"2015","journal-title":"GigaScience"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"4414","DOI":"10.3168\/jds.2007-0980","article-title":"Efficient methods to compute genomic predictions","volume":"91","author":"VanRaden","year":"2008","journal-title":"J. Dairy Sci."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"794","DOI":"10.1016\/j.molp.2023.03.011","article-title":"SoyOmics: A deeply integrated database on soybean multi-omics","volume":"16","author":"Liu","year":"2023","journal-title":"Mol. Plant"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"qzae080","DOI":"10.1093\/gpbjnl\/qzae080","article-title":"SoyOD: An Integrated Soybean Multi-omics Database for Mining Genes and Biological Research","volume":"22","author":"Li","year":"2024","journal-title":"Genom. Proteom. Bioinform."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"D1639","DOI":"10.1093\/nar\/gkad786","article-title":"SoyMD: A platform combining multi-omics data with various tools for soybean research and breeding","volume":"52","author":"Yang","year":"2024","journal-title":"Nucleic Acids Res."}],"container-title":["Plants"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2800\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T10:03:34Z","timestamp":1789380214000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2223-7747\/15\/18\/2800"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,12]]},"references-count":61,"journal-issue":{"issue":"18","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["plants15182800"],"URL":"https:\/\/doi.org\/10.3390\/plants15182800","relation":{},"ISSN":["2223-7747"],"issn-type":[{"value":"2223-7747","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,12]]}}}