{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T05:19:30Z","timestamp":1787721570383,"version":"build-2784847793"},"reference-count":29,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T00:00:00Z","timestamp":1787529600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006769","name":"Russian Science Foundation","doi-asserted-by":"publisher","award":["21-76-30003-P"],"award-info":[{"award-number":["21-76-30003-P"]}],"id":[{"id":"10.13039\/501100006769","id-type":"DOI","asserted-by":"publisher"}]},{"award":["21-76-30003-P"],"award-info":[{"award-number":["21-76-30003-P"]}],"id":[{"id":"https:\/\/ror.org\/03y2gwe85","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genes"],"abstract":"<jats:p>Background\/Objectives: Soybean first pod insertion height (FPIH) is a key trait established during plant development, but its genetic architecture in Eurasian germplasm remains largely unknown. Methods: We performed a GWAS and fine-mapping for FPIH using 180 Eurasian varieties (SoySNP50K array, imputed to ~4M SNPs) phenotyped in four Russian environments (2021\u20132022), using two models: a residual-based and a covariate-adjusted. SuSiE fine-mapping was applied to refine candidate loci. Results: The covariate-adjusted model demonstrated better control of genomic inflation (\u03bb = 1.08 vs. 1.16) and higher SNP heritability (0.381 vs. 0.014); the lower heritability in the residual-based model was expected, as this model removes environmental main effects and the genetic variance associated with them. Thus, the models are complementary: one captures stable genetic effects, the other highlights environment-dependent signals. SuSiE refined three loci. On chromosome 13, two stable independent signals (Gm13_30553403, Gm13_30909346; PIP \u2265 0.99) were identified near MYB83 and BEN1, consistent across both models. On chromosome 4, the signal shifted to Gm04_36933515 (PIP = 0.9999) near COBL4\/IRX6, although model dependency was observed, and this locus is not currently recommended for marker development. On chromosome 5, the original GWAS SNP was not causal; two tightly linked SNPs (Gm05_38427309 and Gm05_38710046, r2 = 0.714, PIP \u2265 0.99) formed a haplotype block located near ARR1\/ARR2 and a B-box\/CCT domain gene. Crucially, this signal was absent in the residual-based model (max PIP = 0.33), suggesting that the chromosome 5 locus may modulate developmental plasticity rather than exerting a direct main effect on FPIH. However, as we did not perform formal G \u00d7 E testing, we present this as a hypothesis requiring further validation. The environment-dependent behavior of this locus indicates that it should be used with caution in breeding programs and validated under specific target environments. Conclusions: Chromosome 13 SNPs provide stable genetic associations across environments, whereas the chromosome 5 block requires environment-specific validation. This work provides the first fine-mapped GWAS for FPIH in Russian soybean germplasm and highlights how model choice can uncover or obscure environment-dependent genetic loci affecting plant development.<\/jats:p>","DOI":"10.3390\/genes17090994","type":"journal-article","created":{"date-parts":[[2026,8,24]],"date-time":"2026-08-24T17:20:28Z","timestamp":1787592028000},"page":"994","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["GWAS Fine-Mapping for Soybean First Pod Insertion Height Identifies Candidate Genomic Regions Involved in Plant Development"],"prefix":"10.3390","volume":"17","author":[{"given":"Irina V.","family":"Zorkoltseva","sequence":"first","affiliation":[{"name":"Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Av. 10, Novosibirsk 630090, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9972-9517","authenticated-orcid":false,"given":"Anatoly V.","family":"Kirichenko","sequence":"additional","affiliation":[{"name":"Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Av. 10, Novosibirsk 630090, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dmitriy A.","family":"Potapov","sequence":"additional","affiliation":[{"name":"Siberian Federal Scientific Centre of Agro-BioTechnologies, Russian Academy of Sciences (RAS), Tsentralnaya St. 2b, Krasnoobsk, Novosibirsk 630501, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergey V.","family":"Kiryukhin","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Scientific Institution (FSBSI), Federal Scientific Center of Legumes and Groat Crops, Molodozhnaya St. 10, Orel 302502, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sergey O.","family":"Gurinovich","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Scientific Institution (FSBSI), Federal Scientific Center of Legumes and Groat Crops, Molodozhnaya St. 10, Orel 302502, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Veronika I.","family":"Panarina","sequence":"additional","affiliation":[{"name":"Federal State Budgetary Scientific Institution (FSBSI), Federal Scientific Center of Legumes and Groat Crops, Molodozhnaya St. 10, Orel 302502, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Revmira I.","family":"Polyudina","sequence":"additional","affiliation":[{"name":"Siberian Federal Scientific Centre of Agro-BioTechnologies, Russian Academy of Sciences (RAS), Tsentralnaya St. 2b, Krasnoobsk, Novosibirsk 630501, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena A.","family":"Salina","sequence":"additional","affiliation":[{"name":"Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Av. 10, Novosibirsk 630090, Russia"},{"name":"Kurchatov Genomics Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Av. 10, Novosibirsk 630090, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9478-267X","authenticated-orcid":false,"given":"Gulnara R.","family":"Svishcheva","sequence":"additional","affiliation":[{"name":"Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences (SB RAS), Lavrentiev Av. 10, Novosibirsk 630090, Russia"},{"name":"Vavilov Institute of General Genetics, Russian Academy of Sciences (RAS), Gubkin St. 3, Moscow 119991, Russia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,24]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"36","DOI":"10.9787\/PBB.2017.5.1.36","article-title":"Genetic and Environmental Variation of First Pod Height in Soybean [Glycine max (L.) Merr.]","volume":"5","author":"Kang","year":"2017","journal-title":"Plant Breed. Biotechnol."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Jiang, H., Li, Y., Qin, H., Li, Y., Qi, H., Li, C., Wang, N., Li, R., Zhao, Y., and Huang, S. (2018). Identification of Major QTLs Associated with First Pod Height and Candidate Gene Mining in Soybean. Front. Plant Sci., 9.","DOI":"10.3389\/fpls.2018.01280"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Kuzbakova, M., Khassanova, G., Oshergina, I., Ten, E., Jatayev, S., Yerzhebayeva, R., Bulatova, K., Khalbayeva, S., Schramm, C., and Anderson, P. (2022). Height to first pod: A review of genetic and breeding approaches to improve combine harvesting in legume crops. Front. Plant Sci., 13.","DOI":"10.3389\/fpls.2022.948099"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"e81","DOI":"10.1002\/leg3.81","article-title":"High-throughput NGS-based genotyping and phenotyping: Role in genomics-assisted breeding for soybean improvement","volume":"3","author":"Bhat","year":"2021","journal-title":"Legume Sci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Potapova, N.A., Zorkoltseva, I.V., Zlobin, A.S., Shcherban, A.B., Fedyaeva, A.V., Salina, E.A., Svishcheva, G.R., Aksenovich, T.I., and Tsepilov, Y.A. (2025). Genome-Wide Association Study on Imputed Genotypes of 180 Eurasian Soybean Glycine max Varieties for Oil and Protein Contents in Seeds. Plants, 14.","DOI":"10.3390\/plants14020255"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"1273","DOI":"10.1111\/rssb.12388","article-title":"A simple new approach to variable selection in regression, with application to genetic fine mapping","volume":"82","author":"Wang","year":"2020","journal-title":"J. R. Stat. Soc. Ser. B (Stat. Methodol.)"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Zou, Y., Carbonetto, P., Wang, G., and Stephens, M. (2022). Fine-mapping from summary data with the \u201cSum of Single Effects\u201d model. PLoS Genet., 18.","DOI":"10.1371\/journal.pgen.1010299"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Perfil\u2019ev, R., Shcherban, A., Potapov, D., Maksimenko, K., Kiryukhin, S., Gurinovich, S., Panarina, V., Polyudina, R., and Salina, E. (2023). Impact of Allelic Variation in Maturity Genes E1\u2013E4 on Soybean Adaptation to Central and West Siberian Regions of Russia. Agriculture, 13.","DOI":"10.3390\/agriculture13061251"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1007\/BF00020088","article-title":"Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues","volume":"5","author":"Rogers","year":"1985","journal-title":"Plant Mol. Biol."},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Song, Q., Hyten, D.L., Jia, G., Quigley, C.V., Fickus, E.W., Nelson, R.L., and Cregan, P.B. (2013). Development and evaluation of SoySNP50K, a high-density genotyping array for soybean. PLoS ONE, 8.","DOI":"10.1371\/journal.pone.0054985"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1999","DOI":"10.1534\/g3.115.019000","article-title":"Fingerprinting Soybean Germplasm and Its Utility in Genomic Research","volume":"5","author":"Song","year":"2015","journal-title":"G3 Genes Genomes Genet."},{"key":"ref_12","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_13","doi-asserted-by":"crossref","first-page":"338","DOI":"10.1016\/j.ajhg.2018.07.015","article-title":"A one-penny imputed genome from next-generation reference panels","volume":"103","author":"Browning","year":"2018","journal-title":"Am. J. Hum. Genet."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1880","DOI":"10.1016\/j.ajhg.2021.08.005","article-title":"Fast two-stage phasing of large-scale sequence data","volume":"108","author":"Browning","year":"2021","journal-title":"Am. J. Hum. Genet."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1797","DOI":"10.1007\/s00122-022-04070-7","article-title":"Genotype imputation for soybean nested association mapping population to improve precision of QTL detection","volume":"135","author":"Chen","year":"2022","journal-title":"Theor. Appl. Genet."},{"key":"ref_16","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_17","unstructured":"R Core Team (2025). R: A Language and Environment for Statistical Computing, R Foundation for Statistical Computing. Available online: https:\/\/www.R-project.org\/."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"Wickham","year":"2019","journal-title":"J. Open Source Softw."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"1","DOI":"10.18637\/jss.v082.i13","article-title":"LmerTest Package: Tests in Linear Mixed Effects Models","volume":"82","author":"Kuznetsova","year":"2017","journal-title":"J. Stat. Softw."},{"key":"ref_20","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":"ref_21","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_22","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1002\/gepi.20297","article-title":"Estimation of significance thresholds for genomewide association scans","volume":"32","author":"Dudbridge","year":"2008","journal-title":"Genet. Epidemiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"361","DOI":"10.1002\/gepi.20310","article-title":"A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms","volume":"32","author":"Gao","year":"2008","journal-title":"Genet. Epidemiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1731","DOI":"10.21105\/joss.00731","article-title":"Qqman: An R package for visualizing GWAS results using Q-Q and manhattan plots","volume":"3","author":"Turner","year":"2018","journal-title":"J. Open-Source Softw."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1016\/j.ajhg.2017.08.012","article-title":"Prospects of Fine-Mapping Trait-Associated Genomic Regions by Using Summary Statistics from Genome-wide Association Studies","volume":"101","author":"Benner","year":"2017","journal-title":"Am. J. Hum. Genet."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"559","DOI":"10.1086\/519795","article-title":"PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage Analyses","volume":"81","author":"Purcell","year":"2007","journal-title":"Am. J. Hum. Genet."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"5445","DOI":"10.1038\/s41467-021-25800-3","article-title":"Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics","volume":"12","author":"Dong","year":"2021","journal-title":"Nat. Commun."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"5575","DOI":"10.1007\/s00344-025-11781-w","article-title":"Insights into the Roles of Gibberellin and Cytokinin Levels in Regulating Elongation of Basal Internodes and Lowest Pod Height in Soybean","volume":"44","author":"Thapar","year":"2025","journal-title":"J. Plant Growth Regul."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"e70207","DOI":"10.1002\/tpg2.70207","article-title":"High-resolution quantitative trait loci mapping and pyramiding effects of candidate genes for plant height in soybean","volume":"19","author":"Sha","year":"2026","journal-title":"Plant Genome"}],"container-title":["Genes"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/994\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T04:27:02Z","timestamp":1787718422000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2073-4425\/17\/9\/994"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,24]]},"references-count":29,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["genes17090994"],"URL":"https:\/\/doi.org\/10.3390\/genes17090994","relation":{},"ISSN":["2073-4425"],"issn-type":[{"value":"2073-4425","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,24]]}}}