# Genetic dissection of gluten characteristics based on single- and multi-locus genome-wide association studies in wheat (Triticum aestivum L.)

## TL;DR

This study identifies genetic factors influencing gluten traits in wheat, offering new tools for breeding better baking wheat.

## Contribution

The study discovers 15 stable QTLs and four KASP markers for gluten traits using GWAS in wheat.

## Key findings

- 15 stable QTLs for gluten traits were identified across multiple environments.
- A major QTL, qGI·1D, was detected by all multi-locus GWAS models.
- Four KASP markers for gluten index were developed and validated.

## Abstract

Gluten protein quantity and quality, crucial factors determining the baking quality of wheat-based foods, are primary targets for wheat breeding. To elucidate their genetic basis, five key gluten traits were investigated utilizing a genome-wide association study (GWAS) approach: wet gluten content (WGC), residual gluten content (RGC), dry gluten content (DGC), water-holding capacity (WHC), and gluten index (GI). Using 48,057 SNPs across 200 wheat accessions, analyses employed one single-locus (SL) model and five multi-locus (ML) models. Genotype primarily influenced these gluten traits, with broad-sense heritability (H2) ranging from 0.85 (DGC) to 0.97 (GI). The SL-GWAS and ML-GWAS models identified 143 and 203 significant marker-trait associations (MTAs), respectively. Of these, 15 stable quantitative trait loci (QTL) were detected in at least three environments using multiple GWAS models. Most notably, qGI·1D for GI, which integrated from 138 significant MTAs, was identified in multi-environments and recognized by all five ML-GWAS models across all environments. This QTL was shown to be co-localized with qWGC·1D, qRGC·1D, and qWHC·1D. Furthermore, five candidate genes related to wheat gluten including TraesCS1A02G317500, TraesCS1A02G466400LC, TraesCS1A02G466500LC, TraesCS1B02G330000, and TraesCS1D02G317300 were indentified. Interestingly, TraesCS1B02G330000 has the PF13016 domain related to gliadins and has collinearity with two other genes, suggesting the genes in the first homologous group encoding gliadins may play an important role in GI. Additionally, four kompetitive allele-specific PCR (KASP) markers (K_AX-108,999,948, K_AX-110,940,435, K_AX-111,216,618 and K_AX-94,670,671) for GI were developed successfully and validated in the natural population. This work elucidates the genetic basis of wheat gluten traits and provides both valuable germplasm and robust molecular tools for breeding applications.

•Wheat gluten plays a crucial role in determining the baking quality of wheat-based foods.•Due to the time-consuming and costly nature of obtaining phenotype data for gluten traits, there has been limited progress in related research•Identified 15 QTLs with gluten-related traits, including a major locus (qGI.1D).•Four KASP markers for GI were developed.

Wheat gluten plays a crucial role in determining the baking quality of wheat-based foods.

Due to the time-consuming and costly nature of obtaining phenotype data for gluten traits, there has been limited progress in related research

Identified 15 QTLs with gluten-related traits, including a major locus (qGI.1D).

Four KASP markers for GI were developed.