{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T17:17:49Z","timestamp":1787937469422,"version":"build-2784847793"},"reference-count":73,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T00:00:00Z","timestamp":1776902400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004608","name":"Natural Science Foundation of Jiangsu Province","doi-asserted-by":"publisher","award":["BK20230102"],"award-info":[{"award-number":["BK20230102"]}],"id":[{"id":"10.13039\/501100004608","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["2025AIYJSZX-YB006"],"award-info":[{"award-number":["2025AIYJSZX-YB006"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100012226","name":"Fundamental Research Funds for the Central Universities","doi-asserted-by":"publisher","award":["KTYQ2025036"],"award-info":[{"award-number":["KTYQ2025036"]}],"id":[{"id":"10.13039\/501100012226","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["W2431030"],"award-info":[{"award-number":["W2431030"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42277113"],"award-info":[{"award-number":["42277113"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42477122"],"award-info":[{"award-number":["42477122"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42325704"],"award-info":[{"award-number":["42325704"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["42090064"],"award-info":[{"award-number":["42090064"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Guangxi Science and Technology Program","award":["GuiKeAA24010003"],"award-info":[{"award-number":["GuiKeAA24010003"]}]},{"DOI":"10.13039\/501100012166","name":"National Key Research and Development Program of China","doi-asserted-by":"publisher","award":["2022YFF1001804"],"award-info":[{"award-number":["2022YFF1001804"]}],"id":[{"id":"10.13039\/501100012166","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Rhizosphere microbiome critically influences plant growth and health, yet the genetic mechanisms underlying host regulation of microbiome composition remain unclear. Here, we analyzed whole-genome genotype and 16S rhizosphere microbiome data from 432 globally sourced eggplant accessions (Solanum melongena L.). Eggplant population structure corresponded to geographic origins, with rhizosphere microbiomes varying significantly among subpopulations. Host genetics explains 9%\u201339% of the variation in individual microbial taxa abundance, with core taxa more affected by host genetic variation. Microbial genome-wide association studies (mGWAS) identified 1235 significant genetic variants associated with 46 core microbial taxa, revealing key regulatory loci including chr10:7799021 near MYB113 (associated with Stenotrophomonas, P\u2009=\u20092.16\u2009\u00d7\u200910\u221215) and chr10:19786889 near BLH9 (associated with Mycobacterium, P\u2009=\u20091.24\u2009\u00d7\u200910\u221212), as well as a chromosome 5 locus with specific regulatory effects on Rhizobiales. These microbiome-associated genetic variants were enriched in secondary metabolic pathways, including anthocyanin biosynthesis, benzoxazinoid biosynthesis, and brassinosteroid biosynthesis, indicating that hosts regulate microbial communities through complex metabolic networks. Notably, genetic loci controlling microbial community structure underwent strong directional selection across eggplant subpopulations from different geographic origins, providing evidence for host\u2013microbe coadaptive evolution. This study elucidates genetic regulatory patterns of eggplant rhizosphere microbiomes, enriching the theoretical framework of plant\u2013microbe coevolution, with broad implications for microbiome-assisted crop improvement and sustainable agriculture.<\/jats:p>","DOI":"10.1093\/hr\/uhag163","type":"journal-article","created":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T11:31:34Z","timestamp":1776771094000},"source":"Crossref","is-referenced-by-count":0,"title":["Genetic dissection of the eggplant rhizosphere microbiome enables microbiome-assisted breeding"],"prefix":"10.1093","volume":"13","author":[{"given":"Yarong","family":"Li","sequence":"first","affiliation":[{"name":"Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University , Nanjing ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weiliu","family":"Li","sequence":"additional","affiliation":[{"name":"Vegetable Research Institute , Guangxi Academy of Agricultural Sciences, Nanning 530007,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guiyun","family":"Gan","sequence":"additional","affiliation":[{"name":"Vegetable Research Institute , Guangxi Academy of Agricultural Sciences, Nanning 530007,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5030-1686","authenticated-orcid":false,"given":"Xiaofang","family":"Wang","sequence":"additional","affiliation":[{"name":"Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University , Nanjing ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0766-1541","authenticated-orcid":false,"given":"Yaoyao","family":"Wu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University , Nanjing 211800 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yangchun","family":"Xu","sequence":"additional","affiliation":[{"name":"Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University , Nanjing ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexandre","family":"Jousset","sequence":"additional","affiliation":[{"name":"Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University , Nanjing ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0697-5696","authenticated-orcid":false,"given":"Yikui","family":"Wang","sequence":"additional","affiliation":[{"name":"Vegetable Research Institute , Guangxi Academy of Agricultural Sciences, Nanning 530007,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5662-9620","authenticated-orcid":false,"given":"Qirong","family":"Shen","sequence":"additional","affiliation":[{"name":"Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University , Nanjing ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5331-739X","authenticated-orcid":false,"given":"Gaofei","family":"Jiang","sequence":"additional","affiliation":[{"name":"Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University , Nanjing ,","place":["China"]},{"name":"Vegetable Research Institute , Guangxi Academy of Agricultural Sciences, Nanning 530007,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7967-4897","authenticated-orcid":false,"given":"Zhong","family":"Wei","sequence":"additional","affiliation":[{"name":"Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Key Lab of Organic-Based Fertilizers of China, Jiangsu Collaborative Innovation Center for Solid Organic Wastes, Educational Ministry Engineering Center of Resource-Saving Fertilizers, Nanjing Agricultural University , Nanjing ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,4,23]]},"reference":[{"key":"2026082812263021800_ref1","doi-asserted-by":"crossref","first-page":"1196","DOI":"10.1111\/nph.13312","article-title":"The importance of the microbiome of the plant holobiont","volume":"206","author":"Vandenkoornhuyse","year":"2015","journal-title":"New Phytol"},{"key":"2026082812263021800_ref2","doi-asserted-by":"crossref","first-page":"1469","DOI":"10.1016\/j.cell.2025.01.035","article-title":"Exploring the plant microbiome: a pathway to climate-smart crops","volume":"188","author":"Ge","year":"2025","journal-title":"Cell"},{"key":"2026082812263021800_ref3","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1038\/s41586-025-09264-9","article-title":"Functional regimes define soil microbiome response to environmental change","volume":"644","author":"Lee","year":"2025","journal-title":"Nature"},{"key":"2026082812263021800_ref4","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1038\/nature11336","article-title":"Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota","volume":"488","author":"Bulgarelli","year":"2012","journal-title":"Nature"},{"key":"2026082812263021800_ref5","doi-asserted-by":"crossref","first-page":"e00041","DOI":"10.1128\/msystems.00041-24","article-title":"The role of plant host genetics in shaping the composition and functionality of rhizosphere microbiomes","volume":"10","author":"Negre Rodr\u00edguez","year":"2025","journal-title":"mSystems"},{"key":"2026082812263021800_ref6","doi-asserted-by":"crossref","first-page":"1379","DOI":"10.1016\/j.molp.2023.08.004","article-title":"RIN enhances plant disease resistance via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota","volume":"16","author":"Yang","year":"2023","journal-title":"Mol Plant"},{"key":"2026082812263021800_ref7","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/s41477-021-00897-y","article-title":"Plant flavones enrich rhizosphere oxalobacteraceae to improve maize performance under nitrogen deprivation","volume":"7","author":"Yu","year":"2021","journal-title":"Nat Plants"},{"key":"2026082812263021800_ref8","doi-asserted-by":"crossref","first-page":"676","DOI":"10.1038\/s41587-019-0104-4","article-title":"NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice","volume":"37","author":"Zhang","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2026082812263021800_ref9","doi-asserted-by":"crossref","first-page":"932","DOI":"10.1111\/nph.13286","article-title":"Transcriptional networks in plant immunity","volume":"206","author":"Tsuda","year":"2015","journal-title":"New Phytol"},{"key":"2026082812263021800_ref10","doi-asserted-by":"crossref","first-page":"372","DOI":"10.1016\/S1360-1385(01)02019-2","article-title":"Signal transmission in the plant immune response","volume":"6","author":"N\u00fcrnberger","year":"2001","journal-title":"Trends Plant Sci"},{"key":"2026082812263021800_ref11","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1146\/annurev-arplant-050718-100423","article-title":"Molecular and environmental regulation of root development","volume":"70","author":"Motte","year":"2019","journal-title":"Annu Rev Plant Biol"},{"key":"2026082812263021800_ref12","doi-asserted-by":"crossref","DOI":"10.1002\/imt2.210","article-title":"Ms Gene and Mr Gene: microbial-mediated spatiotemporal communication between plants","volume":"3","author":"Lv","year":"2024","journal-title":"iMeta"},{"key":"2026082812263021800_ref13","doi-asserted-by":"crossref","first-page":"5320","DOI":"10.1038\/ncomms6320","article-title":"Genome-wide association study of Arabidopsis thaliana leaf microbial community","volume":"5","author":"Horton","year":"2014","journal-title":"Nat Commun"},{"key":"2026082812263021800_ref14","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1038\/s41467-023-44335-3","article-title":"Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis","volume":"15","author":"Su","year":"2024","journal-title":"Nat Commun"},{"key":"2026082812263021800_ref15","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1038\/s41477-024-01654-7","article-title":"Heritable microbiome variation is correlated with source environment in locally adapted maize varieties","volume":"10","author":"He","year":"2024","journal-title":"Nat Plants"},{"key":"2026082812263021800_ref16","doi-asserted-by":"crossref","first-page":"3181","DOI":"10.1038\/s41396-021-00993-z","article-title":"Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome","volume":"15","author":"Deng","year":"2021","journal-title":"ISME J"},{"key":"2026082812263021800_ref17","doi-asserted-by":"crossref","first-page":"602","DOI":"10.1016\/j.foodchem.2018.06.093","article-title":"Health benefits and bioactive compounds of eggplant","volume":"268","author":"G\u00fcrb\u00fcz","year":"2018","journal-title":"Food Chem"},{"key":"2026082812263021800_ref18","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1016\/j.ympev.2012.02.006","article-title":"Phylogeographic relationships among Asian eggplants and new perspectives on eggplant domestication","volume":"63","author":"Meyer","year":"2012","journal-title":"Mol Phylogenet Evol"},{"key":"2026082812263021800_ref19","doi-asserted-by":"crossref","DOI":"10.1016\/j.syapm.2020.126106","article-title":"Plant microbiota modified by plant domestication","volume":"43","author":"Mart\u00ednez-Romero","year":"2020","journal-title":"Syst Appl Microbiol"},{"key":"2026082812263021800_ref20","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1038\/s43705-022-00094-8","article-title":"Exploring rhizo-microbiome transplants as a tool for protective plant-microbiome manipulation","volume":"2","author":"Jiang","year":"2022","journal-title":"ISME COMMUN"},{"key":"2026082812263021800_ref21","doi-asserted-by":"crossref","first-page":"uhad272","DOI":"10.1093\/hr\/uhad272","article-title":"A QTL of eggplant shapes the rhizosphere bacterial community, co-responsible for resistance to bacterial wilt","volume":"11","author":"Gong","year":"2024","journal-title":"Hortic Res"},{"key":"2026082812263021800_ref22","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1038\/nature03288","article-title":"Functional cartography of complex metabolic networks","volume":"433","author":"Guimer\u00e0","year":"2005","journal-title":"Nature"},{"key":"2026082812263021800_ref23","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1111\/j.1365-313X.2007.03373.x","article-title":"Regulation of the anthocyanin biosynthetic pathway by the TTG1\/bHLH\/Myb transcriptional complex in Arabidopsis seedlings","volume":"53","author":"Gonzalez","year":"2008","journal-title":"Plant J"},{"key":"2026082812263021800_ref24","doi-asserted-by":"crossref","first-page":"3069","DOI":"10.1111\/pce.13074","article-title":"Combined transcriptomic and proteomic analysis constructs a new model for light-induced anthocyanin biosynthesis in eggplant (Solanum melongena L.)","volume":"40","author":"Li","year":"2017","journal-title":"Plant Cell Environ"},{"key":"2026082812263021800_ref25","doi-asserted-by":"crossref","first-page":"465","DOI":"10.1111\/tpj.14230","article-title":"Bell1-like homeobox genes regulate inflorescence architecture and meristem maintenance in rice","volume":"98","author":"Ikeda","year":"2019","journal-title":"Plant J"},{"key":"2026082812263021800_ref26","doi-asserted-by":"crossref","first-page":"1126","DOI":"10.1111\/tpj.13924","article-title":"Bel1-like homeodomain 11 regulates chloroplast development and chlorophyll synthesis in tomato fruit","volume":"94","author":"Meng","year":"2018","journal-title":"Plant J"},{"key":"2026082812263021800_ref27","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2023.112301","article-title":"A conserved Brassinosteroid-mediated BES1-CERP-EXPA3 signaling cascade controls plant cell elongation","volume":"42","author":"Zhu","year":"2023","journal-title":"Cell Rep"},{"key":"2026082812263021800_ref28","doi-asserted-by":"crossref","first-page":"1667","DOI":"10.1111\/tpj.16455","article-title":"Analysis of &gt;3400 worldwide eggplant accessions reveals two independent domestication events and multiple migration-diversification routes","volume":"116","author":"Barchi","year":"2023","journal-title":"Plant J"},{"key":"2026082812263021800_ref29","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1111\/nph.16890","article-title":"Host selection shapes crop microbiome assembly and network complexity","volume":"229","author":"Xiong","year":"2021","journal-title":"New Phytol"},{"key":"2026082812263021800_ref30","doi-asserted-by":"crossref","first-page":"e00764","DOI":"10.1128\/mBio.00764-17","article-title":"Drought stress results in a compartment-specific restructuring of the rice root-associated microbiomes","volume":"8","author":"Santos-Medell\u00edn","year":"2017","journal-title":"mBio"},{"key":"2026082812263021800_ref31","doi-asserted-by":"crossref","first-page":"8413","DOI":"10.1038\/ncomms9413","article-title":"Trophic network architecture of root-associated bacterial communities determines pathogen invasion and plant health","volume":"6","author":"Wei","year":"2015","journal-title":"Nat Commun"},{"key":"2026082812263021800_ref32","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.tplants.2022.08.012","article-title":"Plant microbiota dysbiosis and the Anna Karenina principle","volume":"28","author":"Arnault","year":"2023","journal-title":"Trends Plant Sci"},{"key":"2026082812263021800_ref33","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2201285119","article-title":"Plant genetic effects on microbial hubs impact host fitness in repeated field trials","volume":"119","author":"Brachi","year":"2022","journal-title":"P Natl Acad Sci USA"},{"key":"2026082812263021800_ref34","doi-asserted-by":"crossref","first-page":"3116","DOI":"10.1038\/s41467-025-58080-2","article-title":"Core microbes regulate plant-soil resilience by maintaining network resilience during long-term restoration of Alpine grasslands","volume":"16","author":"Du","year":"2025","journal-title":"Nat Commun"},{"key":"2026082812263021800_ref35","doi-asserted-by":"crossref","first-page":"e00313","DOI":"10.1128\/mSystems.00313-18","article-title":"Core microbiota in agricultural soils and their potential associations with nutrient cycling","volume":"4","author":"Jiao","year":"2019","journal-title":"mSystems"},{"key":"2026082812263021800_ref36","doi-asserted-by":"crossref","first-page":"1038","DOI":"10.1111\/gcb.16024","article-title":"Core microbiota drive functional stability of soil microbiome in reforestation ecosystems","volume":"28","author":"Jiao","year":"2022","journal-title":"Glob Chang Biol"},{"key":"2026082812263021800_ref37","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/j.envexpbot.2015.05.012","article-title":"Multiple functional roles of anthocyanins in plant-environment interactions","volume":"119","author":"Landi","year":"2015","journal-title":"Environ Exp Bot"},{"key":"2026082812263021800_ref38","first-page":"15","article-title":"A comprehensive comparative genomic analysis revealed that plant growth promoting traits are ubiquitous in strains of Stenotrophomonas","volume":"15","author":"Zhao","year":"2024","journal-title":"Front Microbiol"},{"key":"2026082812263021800_ref39","first-page":"465","article-title":"Assessment of phytohormones producing capacity of Stenotrophomonas maltophilia SSA and its interaction with Zea mays L","volume":"44","author":"Naz","year":"2025","journal-title":"Pak J Bot"},{"key":"2026082812263021800_ref40","doi-asserted-by":"crossref","first-page":"933","DOI":"10.1111\/nph.17397","article-title":"Repressors of anthocyanin biosynthesis","volume":"231","author":"LaFountain","year":"2021","journal-title":"New Phytol"},{"key":"2026082812263021800_ref41","doi-asserted-by":"crossref","first-page":"74","DOI":"10.1016\/j.plgene.2018.05.001","article-title":"Exogenous ABA and endogenous ABA affects \u2018Kyoho\u2019 grape berry coloration in different pathway","volume":"14","author":"Saito","year":"2018","journal-title":"Plant Gene"},{"key":"2026082812263021800_ref42","doi-asserted-by":"crossref","first-page":"655","DOI":"10.1007\/s00203-007-0286-x","article-title":"Orchid-associated bacteria produce indole-3-acetic acid, promote seed germination, and increase their microbial yield in response to exogenous auxin","volume":"188","author":"Tsavkelova","year":"2007","journal-title":"Arch Microbiol"},{"key":"2026082812263021800_ref43","doi-asserted-by":"crossref","first-page":"3110","DOI":"10.1038\/s41564-024-01865-w","article-title":"Estimates of microbiome heritability across hosts","volume":"9","author":"Morris","year":"2024","journal-title":"Nat Microbiol"},{"key":"2026082812263021800_ref44","doi-asserted-by":"crossref","first-page":"156","DOI":"10.1038\/s41588-020-00763-1","article-title":"Large-scale association analyses identify host factors influencing human gut microbiome composition","volume":"53","author":"Kurilshikov","year":"2021","journal-title":"Nat Genet"},{"key":"2026082812263021800_ref45","doi-asserted-by":"crossref","first-page":"5913","DOI":"10.1038\/s41467-022-33238-4","article-title":"GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet","volume":"13","author":"Wang","year":"2022","journal-title":"Nat Commun"},{"key":"2026082812263021800_ref46","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1111\/ele.12630","article-title":"The interconnected rhizosphere: high network complexity dominates rhizosphere assemblages","volume":"19","author":"Shi","year":"2016","journal-title":"Ecol Lett"},{"key":"2026082812263021800_ref47","doi-asserted-by":"crossref","first-page":"7286","DOI":"10.1038\/s41467-025-62550-y","article-title":"Photosynthate distribution determines spatial patterns in the rhizosphere microbiota of the maize root system","volume":"16","author":"Schultes","year":"2025","journal-title":"Nat Commun"},{"key":"2026082812263021800_ref48","doi-asserted-by":"crossref","first-page":"1150","DOI":"10.1038\/s41564-021-00941-9","article-title":"Host preference and invasiveness of commensal bacteria in the lotus and Arabidopsis root microbiota","volume":"6","author":"Wippel","year":"2021","journal-title":"Nat Microbiol"},{"key":"2026082812263021800_ref49","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1186\/s40168-023-01669-w","article-title":"Relative abundance data can misrepresent heritability of the microbiome","volume":"11","author":"Bruijning","year":"2023","journal-title":"Microbiome"},{"key":"2026082812263021800_ref50","first-page":"2401","article-title":"Dissection of rhizosphere microbiome and exploiting strategies for sustainable agriculture","volume":"242","author":"Xun","year":"2024","journal-title":"new"},{"key":"2026082812263021800_ref51","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1038\/nrmicro.2017.171","article-title":"Rhizobia: from saprophytes to endosymbionts","volume":"16","author":"Poole","year":"2018","journal-title":"Nat Rev Microbiol"},{"key":"2026082812263021800_ref52","doi-asserted-by":"crossref","first-page":"768","DOI":"10.1038\/s41586-025-09057-0","article-title":"A kinase mediator of rhizobial symbiosis and immunity in Medicago","volume":"643","author":"Wang","year":"2025","journal-title":"Nature"},{"key":"2026082812263021800_ref53","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1038\/s41467-017-00262-8","article-title":"Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence","volume":"8","author":"Yeoh","year":"2017","journal-title":"Nat Commun"},{"key":"2026082812263021800_ref54","doi-asserted-by":"crossref","first-page":"839","DOI":"10.1038\/s41467-024-45207-0","article-title":"Microbiome convergence enables siderophore-secreting-rhizobacteria to improve iron nutrition and yield of peanut intercropped with maize","volume":"15","author":"Wang","year":"2024","journal-title":"Nat Commun"},{"key":"2026082812263021800_ref55","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1038\/s41579-024-01079-1","article-title":"Harnessing the plant microbiome for sustainable crop production","volume":"23","author":"Compant","year":"2025","journal-title":"Nat Rev Microbiol"},{"key":"2026082812263021800_ref56","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1080\/10409230802341296","article-title":"SSB as an organizer\/mobilizer of genome maintenance complexes","volume":"43","author":"Shereda","year":"2008","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"2026082812263021800_ref57","doi-asserted-by":"crossref","first-page":"1952","DOI":"10.1111\/jipb.13338","article-title":"Arabidopsis mitochondrial single-stranded DNA-binding proteins SSB1 and SSB2 are essential regulators of mtDNA replication and homologous recombination","volume":"64","author":"Qian","year":"2022","journal-title":"J Integr Plant Biol"},{"key":"2026082812263021800_ref58","doi-asserted-by":"crossref","first-page":"1321","DOI":"10.1093\/pcp\/pcab097","article-title":"Arabidopsis SSB1, a mitochondrial single-stranded DNA-binding protein, is involved in ABA response and mitochondrial RNA splicing","volume":"62","author":"Qian","year":"2021","journal-title":"Plant Cell Physiol"},{"key":"2026082812263021800_ref59","doi-asserted-by":"crossref","first-page":"uhaf248","DOI":"10.1093\/hr\/uhaf248","article-title":"Graph pan-genome advances genetic discoveries and the improvement of eggplant","volume":"13","author":"Yu","year":"2026","journal-title":"Hortic Res"},{"key":"2026082812263021800_ref60","doi-asserted-by":"crossref","first-page":"2174","DOI":"10.1111\/pbi.13897","article-title":"Host genetic determinants drive compartment-specific assembly of tea plant microbiomes","volume":"20","author":"Tan","year":"2022","journal-title":"Plant Biotechnol J"},{"key":"2026082812263021800_ref61","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1038\/nature11237","article-title":"Defining the core Arabidopsis thaliana root microbiome","volume":"488","author":"Lundberg","year":"2012","journal-title":"Nature"},{"key":"2026082812263021800_ref62","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1038\/nature25973","article-title":"Environment dominates over host genetics in shaping human gut microbiota","volume":"555","author":"Rothschild","year":"2018","journal-title":"Nature"},{"key":"2026082812263021800_ref63","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2026082812263021800_ref64","doi-asserted-by":"crossref","first-page":"1274","DOI":"10.1111\/1755-0998.13321","article-title":"A high-quality genome assembly of the eggplant provides insights into the molecular basis of disease resistance and chlorogenic acid synthesis","volume":"21","author":"Li","year":"2021","journal-title":"Mol Ecol Resour"},{"key":"2026082812263021800_ref65","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1038\/ng.608","article-title":"Common SNPs explain a large proportion of heritability for human height","volume":"42","author":"Yang","year":"2010","journal-title":"Nat Genet"},{"key":"2026082812263021800_ref66","doi-asserted-by":"crossref","first-page":"1655","DOI":"10.1101\/gr.094052.109","article-title":"Fast model-based estimation of ancestry in unrelated individuals","volume":"19","author":"Alexander","year":"2009","journal-title":"Genome Res"},{"key":"2026082812263021800_ref67","doi-asserted-by":"crossref","first-page":"D590","DOI":"10.1093\/nar\/gks1219","article-title":"The SILVA ribosomal RNA gene database project: improved data processing and web-based tools","volume":"41","author":"Quast","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2026082812263021800_ref68","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2104429118","article-title":"Defining and quantifying the core microbiome: challenges and prospects","volume":"118","author":"Neu","year":"2021","journal-title":"P Natl Acad Sci USA"},{"key":"2026082812263021800_ref69","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1186\/1471-2105-13-113","article-title":"Molecular ecological network analyses","volume":"13","author":"Deng","year":"2012","journal-title":"BMC Bioinform"},{"key":"2026082812263021800_ref70","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1186\/s40168-021-01040-x","article-title":"Joint contributions of the gut microbiota and host genetics to feed efficiency in chickens","volume":"9","author":"Wen","year":"2021","journal-title":"Microbiome"},{"key":"2026082812263021800_ref71","doi-asserted-by":"crossref","first-page":"821","DOI":"10.1038\/ng.2310","article-title":"Genome-wide efficient mixed-model analysis for association studies","volume":"44","author":"Zhou","year":"2012","journal-title":"Nat Genet"},{"key":"2026082812263021800_ref72","doi-asserted-by":"crossref","first-page":"D587","DOI":"10.1093\/nar\/gkac963","article-title":"KEGG for taxonomy-based analysis of pathways and genomes","volume":"51","author":"Kanehisa","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026082812263021800_ref73","doi-asserted-by":"crossref","first-page":"1733","DOI":"10.1016\/j.molp.2023.09.010","article-title":"TBtools-II: a \u201cone for all, all for one\u201d bioinformatics platform for biological big-data mining","volume":"16","author":"Chen","year":"2023","journal-title":"Mol Plant"}],"container-title":["Horticulture Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/hr\/advance-article-pdf\/doi\/10.1093\/hr\/uhag163\/68142395\/uhag163.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hr\/article-pdf\/13\/9\/uhag163\/68142395\/uhag163.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/hr\/article-pdf\/13\/9\/uhag163\/68142395\/uhag163.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T16:26:47Z","timestamp":1787934407000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/hr\/article\/doi\/10.1093\/hr\/uhag163\/8661319"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,23]]},"references-count":73,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2026,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/hr\/uhag163","relation":{},"ISSN":["2052-7276"],"issn-type":[{"value":"2052-7276","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,9]]},"published":{"date-parts":[[2026,4,23]]},"article-number":"uhag163"}}