Soybean is a leguminous plant cultivated in many countries and is considered important in the food industry due to the high levels of oil and protein content in the beans. The high demand for soybeans and its products in the industry requires the expansion of cultivation areas. Despite climatic restrictions, West Siberia is gradually expanding its area of soybean cultivation. In this study, we present the first analysis of the population structure and genetic diversity of the 175 soybean Glycine max breeding lines and varieties cultivated in West Siberia (103 accessions) and other regions of Russia (72 accessions), and we compare them with the cultivated soybean varieties from other geographical locations. Principal component analysis revealed several genetic clusters with different levels of genetic heterogeneity. Studied accessions are genetically similar to varieties from China, Japan, and the USA and are genetically distant to varieties from South Korea. Admixture analysis revealed four ancestry groups based on genetic ancestry and geographical origin, which are consistent with the regions of cultivation and origin of accessions and correspond to the principal component analysis result. Population statistics, including nucleotide diversity, Tajima’s D, and linkage disequilibrium, are comparatively similar to those observed for studied accessions of a different origin. This study provides essential population and genetic information about the unique collection of breeding lines and varieties cultivated in West Siberia and other Russian regions to foster further evolutionary, genome-wide associations and functional breeding studies.

Four maturity genes, namely, E1, E2, E3 and E4, have been found to play major roles in controlling the flowering and maturity time of soybean. Which genotypes of E1–E4 genes provide effective adaptation to the varied conditions of Russia are unknown. To clarify this issue, we have studied the allele variation in soybean E1–E4 genes in terms of both flowering and maturity time under the natural day-length conditions of Central Russia and Western Siberia in a collection of 176 soybean accessions, including 142 Russian and 34 foreign accessions. As a result, a high frequency of previously determined E1–E4 alleles has been identified. The field experiment showed that genotypes with all recessive alleles from e1-nl/e2/e3/e4 and e1-as/e2/e3/e4 provide the effective adaptation of soybean to the mentioned conditions. Cultivars with these genotypes are considered to be most suitable for cultivation in Central Russia and Western Siberia.

The duration of flowering and maturity is an important agricultural trait determining the suitability of a variety for cultivation in the target region. In the present study, we used genome-wide association analysis (GWAS) to search for loci associated with soybean flowering and maturity in the Central and West Siberian regions of Russia. A field experiment was conducted in 2021/2022 at two locations (Orel and Novosibirsk). A germplasm collection of 180 accessions was genotyped using SoySNP50K Illumina Infinium Bead-Chip. From the initial collection, we selected 129 unrelated accessions and conducted GWAS on this dataset using two multi-locus models: FarmCPU and BLINK. As a result, we identified 13 loci previously reported to be associated with duration of soybean development, and 17 new loci. 33 candidate genes were detected in these loci using analysis of co-expression, gene ontology, and literature data, with the best candidates being Glyma.03G177500, Glyma.13G177400, and Glyma.06G213100. These candidate genes code the Arabidopis orthologs TOE1 (TARGET OF EAT 1), SPL3 (SQUAMOSA PROMOTER BINDING PROTEIN LIKE 3), the DELLA protein, respectively. In these three genes, we found haplotypes which may be associated with the length of soybean flowering and maturity, providing soybean adaptation to a northern latitudes.

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, GmRVE8c ^{hap1, 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 GmRVE8c ^hap3 and GmRVE8c ^hap4 haplotypes to be associated with late flowering and maturity in soybean. The early-maturing haplotype GmRVE8c ^hap1 is predominant in cultivars from northern regions and is likely associated with the adaptation of soybean to high latitudes. The GmRVE8c ^hap4 haplotype is in complete linkage with the early-maturing allele GmTOE1 ^C , whereas the GmRVE8c ^hap3 haplotype shows strong linkage with the late maturing allele GmTOE1 ^T . 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 GmRVE8c ^hap3,4 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.