# Deciphering of Genomic Loci Associated with Alkaline Tolerance in Soybean [Glycine max (L.) Merr.] by Genome-Wide Association Study

## TL;DR

This study identifies genetic regions in soybean associated with tolerance to alkaline soil, which could help improve soybean breeding.

## Contribution

The study reports five new QTLs and seventeen candidate genes linked to alkaline tolerance in soybean.

## Key findings

- Twenty-eight SNPs were found significantly associated with alkaline tolerance in soybean.
- Five stable QTLs (qAT1, qAT4, qAT14, qAT18, qAT20) were identified for the first time in soybean.
- Haplotype analysis revealed four candidate genes with allele variations linked to alkaline tolerance traits.

## Abstract

Alkaline stress is one of the major abiotic constraints that limits plant growth and development. However, the genetic basis underlying alkaline tolerance in soybean [Glycine max (L.) Merr.] remains largely unexplored. In this study, an integrated genomic analysis approach was employed to elucidate the genetic architecture of alkaline tolerance in a diverse panel of 326 soybean cultivars. Through association mapping, we detected 28 single nucleotide polymorphisms (SNPs) significantly associated with alkaline tolerance. By examining the genomic distances around these significant SNPs, five genomic regions were characterized as stable quantitative trait loci (QTLs), which were designated as qAT1, qAT4, qAT14, qAT18, and qAT20. These QTLs are reported here for the first time in soybean. Seventeen putative candidate genes were identified within the physical intervals of these QTLs. Haplotype analysis indicated that four of these candidate genes exhibited significant allele variation associated with alkaline tolerance-related traits, and the haplotype alleles for these four genes varied in number from two to four. The findings of this study may have important implications for soybean breeding programs aimed at enhancing alkaline tolerance.