vavilovВавиловский журнал генетики и селекцииVavilov Journal of Genetics and Breeding2500-3259Institute of Cytology and Genetics of Siberian Branch of the RAS10.18699/vjgb-26-06vavilov-4979Research ArticleГЕНЕТИКА И СЕЛЕКЦИЯ РАСТЕНИЙPLANT GENETICS AND BREEDINGЛокус сои qDTF-7 как пример генетической гетерогенности, ассоциированной с продолжительностью цветения и созреванияSoybean locus qDTF-7 as an example of genetic heterogeneity associated with flowering and maturity timehttps://orcid.org/0000-0003-2858-1479ПерфильевР. Н.Perfil’evR. N.

Новосибирск

Novosibirsk

ШматоваМ. И.ShmatovaM. I.

Новосибирск

Novosibirsk

https://orcid.org/0000-0003-1000-8228ЩербаньА. Б.ShcherbanA. B.

Новосибирск

Novosibirsk

https://orcid.org/0000-0001-8590-847XСалинаЕ. А.SalinaE. A.

Новосибирск

Novosibirsk

Федеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наукРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of SciencesRussian FederationФедеральный исследовательский центр Институт цитологии и генетики Сибирского отделения Российской академии наук; Курчатовский геномный центр ИЦиГ СО РАНРоссияInstitute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences; Kurchatov Genomic Center of ICG SB RASRussian Federation2026050320263014352Copyright © Перфильев Р.Н., Шматова М.И., Щербань А.Б., Салина Е.А., 20262026Перфильев Р.Н., Шматова М.И., Щербань А.Б., Салина Е.А.Perfil’ev R.N., Shmatova M.I., Shcherban A.B., Salina E.A.This work is licensed under a Creative Commons Attribution 4.0 License.https://vavilov.elpub.ru/jour/article/view/4979

В настоящее время полногеномный анализ ассоциаций (GWAS) стал стандартным подходом для идентификации локусов количественных признаков, ассоциированных с различными фенотипическими признаками. При последующем изучении локуса, т.е. поиске гена и мутации, которые влияют на признак, можно столкнуться с разными проблемами. Одна из проблем – генетическая (или локусная) гетерогенность, ситуация, когда аллели из разных близко расположенных генов в одном локусе влияют на один признак. Ранее с помощью GWAS на хромосоме 3 сои мы обнаружили локус qDTF-7, ассоциированный с продолжительностью цветения в условиях Новосибирска. Первоначально для данного локуса в качестве наиболее вероятного гена-кандидата мы определили GmTOE1, ортолог TOE1 (TARGET OF EAT 1), известного регулятора цветения у арабидопсиса. У GmTOE1 были обнаружены четыре основных гаплотипа, которые ассоциированы с цветением и созреванием сои и, вероятно, связаны с адаптацией сои к северным широтам. Однако этот ген демонстрировал очень слабую ассоциацию с цветением сои в Новосибирской области по сравнению с Орловской, что указывало на наличие в составе локуса другого гена, который может влиять на цветение сои. Повторно проанализировав гены в составе локуса qDTF-7, мы примерно на 21 т.п.н. выше гена GmTOE1 обнаружили GmRVE8c, ортолог гена RVE8 (REVEILLE 8), который вовлечен в процессы развития у арабидопсиса в качестве компонента циркадных ритмов. Изучив естественное нуклеотидное разнообразие GmRVE8c, мы выявили четыре основных гаплотипа, которые возникли из-за трех однонуклеотидных замен и одной делеции длиной 19 п.н., приводящей к сдвигу рамки считывания. Для определения трех гаплотипов GmRVE8chap1, 3, 4, преобладающих в современных сортах сои, мы разработали ДНК-маркеры. С помощью этих маркеров мы генотипировали 129 сортообразцов сои, для которых ранее изучили продолжительность развития в условиях Новосибирской и Орловской областей. В результате с помощью наших сведений и данных из SoyOmics мы обнаружили ассоциацию гаплотипов GmRVE8chap3 и GmRVE8chap4 с поздним цветением и созреванием сои. Раннеспелый гаплотип GmRVE8chap1 преобладает в сортообразцах из северных регионов и, вероятно, связан с адаптацией сои к северным широтам. Гаплотип GmRVE8chap4 полностью сцеплен с раннеспелым аллелем GmTOE1С, а гаплотип GmRVE8chap3 сильно сцеплен с позднеспелым аллелем GmTOE1T. Кроме того, результат ANOVA показывает наличие взаимодействия GmRVE8c с главным регулятором цветения сои – геном E1. Данное взаимодействие выражается более сильным эффектом гаплотипов GmRVE8chap3, 4 на цветение и созревание на генетическом фоне аллеля e1-as в сравнении с E1. Все это формирует достаточно комплексный и интересный локус, который может выступать как возможный пример генетически гетерогенного локуса.

Genome-wide association studies (GWAS) have become a standard approach for identifying quantitative trait loci associated with diverse phenotypic traits. Further investigation of the locus – specifically, the search for the causal gene and mutation – may present various challenges. One of the challenges is genetic heterogeneity (or locus heterogeneity), when alleles from different closely located genes can influence the same trait. Recently, using GWAS, we found the qDTF-7 locus on soybean chromosome 3, which is associated with flowering time under Novosibirsk conditions. Initially, we identified GmTOE1, an ortholog of TOE1 (TARGET OF EAT1), a known flowering-time regulator in Arabidopsis, as the most likely candidate gene for this locus. Four major haplotypes were identified in GmTOE1, which are associated with soybean flowering and maturity and are likely to provide soybean adaptation to northern latitudes. However, this gene showed only a very weak association with soybean flowering in the Novosibirsk region compared to the Oryol region, suggesting the presence of another gene within the locus that influences flowering time. We therefore re-analyzed genes in the qDTF-7 locus and identified GmRVE8c, an Arabidopsis RVE8 (REVEILLE 8) ortholog, located ~21 kb upstream of GmTOE1; RVE8 is a circadian clock component involved in plant development. After studying the natural variation of the GmRVE8c genes, we found four major haplotypes that arose due to three nonsynonymous substitutions and one 19-bp deletion leading to a frameshift. To identify three haplotypes, GmRVE8chap1, 3, 4, which are predominant in improved soybean cultivars, we developed DNA markers. Using these markers, we genotyped 129 soybean accessions, the developmental time of which had been studied in the Novosibirsk and Oryol regions. Using our data and data from SoyOmics, we found the GmRVE8chap3 and GmRVE8chap4 haplotypes to be associated with late flowering and maturity in soybean. The early-maturing haplotype GmRVE8chap1 is predominant in cultivars from northern regions and is likely associated with the adaptation of soybean to high latitudes. The GmRVE8chap4 haplotype is in complete linkage with the early-maturing allele GmTOE1C, whereas the GmRVE8chap3 haplotype shows strong linkage with the late maturing allele GmTOE1T . Furthermore, the ANOVA results indicate an interaction between GmRVE8c and E1, the major regulator of flowering in soybean. This interaction is manifested as a stronger effect of the GmRVE8chap3,4 haplotypes on flowering and maturity in the genetic background of the e1-as allele compared with E1. Together, these findings define a complex and intriguing locus, which may serve as a possible example of a genetically heterogeneous locus.

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The authors declare that there are no conflicts of interest present.