Chancelor B. Clark, Dajian Zhang, Weidong Wang, Jianxin Ma.

Theoretical and Applied Genetics;  December (2023) 136:258

Key message

A locus, dt3, modulating semideterminancy in soybean, was discovered by a combination of genome-wide association studies and linkage mapping with multiple distinct biparental populations.

Abstract

Stem growth habit is a key architectural trait in many plants that contributes to plant productivity and environmental adaptation. In soybean, stem growth habit is classified as indeterminate, semideterminate, or determinate, of which semideterminacy is often considered as a counterpart of the “Green Revolution” trait in cereals that significantly increased grain yields. It has been demonstrated that semideterminacy in soybean is modulated by epistatic interaction between two loci, Dt1 on chromosome 19 and Dt2 on chromosome 18, with the latter as a negative regulator of the former. Here, we report the discovery of a third locus, Dt3, modulating soybean stem growth habit, which was delineated to a ~ 196-kb region on chromosome 10 by a combination of allelic and haplotypic analysis of the Dt1 and Dt2 loci in the USDA soybean Germplasm Collection, genome-wide association studies with three subsets of the collection, and linkage mapping with four biparental populations derived from crosses between one of two elite indeterminate cultivars and each of four semideterminate varieties possessing neither Dt2 nor dt1. These four semideterminate varieties are recessive mutants (i.e., dt3/dt3) in the Dt1/Dt1;dt2/dt2 background. As the semideterminacy modulated by the Dt2 allele has unfavorable pleotropic effects such as sensitivity to drought stress, dt3 may be an ideal alternative for use to develop semideterminate cultivars that are more resilient to such an environmental stress. This study enhances our understanding of the genetic factors underlying semideterminacy and enables more accurate marker-assisted selection for stem growth habit in soybean breeding.

See https://link.springer.com/article/10.1007/s00122-023-04493-w

Fig.4: Genetic and physical maps of the Dt3 region. a Genetic map of the Dt3 region constructed based on linkage analysis. InDel markers are listed on the left side and the genetic distance (centimorgan, cM) between adjacent markers are shown on the right side of the map. b Physical positions of the molecular markers on chromosome 10 according to the soybean reference genome (Wm82.a2)