# Genome-wide association study of pre-harvest sprouting resistance and grain color in common wheat (Triticum aestivum L.)

## TL;DR

This study identifies genetic loci and markers linked to pre-harvest sprouting resistance and grain color in wheat, offering tools for breeding more resistant varieties.

## Contribution

The study discovers new QTLs and KASP markers for pre-harvest sprouting resistance and grain color in wheat.

## Key findings

- Twelve stable QTLs for pre-harvest sprouting resistance and twelve for grain color were identified.
- Six new QTLs for PHS resistance were discovered, explaining 5.8–10.0% of phenotypic variation.
- Four common QTLs influence both PHS resistance and grain color, including major loci on chromosomes 3B and 3D.

## Abstract

Pre-harvest sprouting (PHS) is a serious problem in wheat production globally. Grain color (GC) has a notable impact on PHS resistance, red grains typically show higher resistance compared to white grains. To understand the genetic factors influencing PHS and GC, a genome-wide association study (GWAS) was conducted on a natural population of 235 wheat cultivars using a 90 K single nucleotide polymorphism (SNP) arrays.

A strong correlation between PHS and GC was observed, with the highest correlation coefficient of 0.85 (P < 0.0001). Association mapping was performed using four different models (BLINK, FarmCPU, MMLM and MLM) in the GAPIT along with MLM model in the Tassel. The study identified twelve stable quantitative trait loci (QTLs) related to PHS resistance and another twelve stable QTLs associated with GC. Notably, six QTLs for PHS resistance were newly discovered, explaining 5.8–10.0% of the phenotypic variation. Additionally, four common QTLs were identified that are linked to both PHS resistance and GC. Among these, Qphs.hbaas-3B.2/Qgc.hbaas-3B.2 and Qphs.hbaas-3D/Qgc.hbaas-3D were recognized as major loci significantly affecting both traits, likely associated with the genes Tamyb-B1 and Tamyb-D1, respectively. The other two new QTLs on chromosome 2B explained 7.0–10.0% of phenotypic variation in PHS resistance and 4.7–7.4% of phenotypic variation in GC. Furthermore, six candidate genes associated with PHS resistance were predicted, warranting further investigation. Three KASP markers IACX5850, Tdurum_contig11028_236 and wsnp_Ex_c269_518324 linked to three QTLs (Qphs.hbaas-2B.2, Qphs.hbaas-2B.4, and Qphs.hbaas-7B.2) are applicable for marker-assisted selection in wheat breeding to enhance PHS resistance.

This study provides valuable genetic loci and KASP markers that can enhance PHS resistance in wheat breeding programs and offers insights for discovering PHS resistance genes.

The online version contains supplementary material available at 10.1186/s12870-025-07039-y.