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This research aims to identify the genetic basis of grain protein content in wheat, which influences nutritional quality.

May 9, 2026BMC Plant Biology0 citationsOpen Access

Identifying candidate genes for grain protein content in wheat (Triticum aestivum L.) by integrated GWAS and transcriptome analysis

JSJunxiu Shang YDYuhong Diao YWYan Qing Wang

Key Points

This research aims to identify the genetic basis of grain protein content in wheat, which influences nutritional quality.
Analyzed 260 spring wheat accessions for crude and soluble protein across four environments.
Conducted genome-wide association study (GWAS) to identify significant genetic loci related to protein content.
Performed transcriptome sequencing of two wheat varieties at five developmental stages to assess gene expression.
Identified 20 genetic loci significantly associated with crude protein (CP) and 23 loci with soluble protein (SP).
Selected four core loci after linkage disequilibrium (LD) analysis for further investigation.
Screened five candidate genes linked to grain protein content, providing resources for future wheat breeding.

Abstract

BACKGROUND: Grain protein content and composition are key determinants of wheat nutritional and processing quality, directly influencing the processing characteristics and nutritional value of flour-based products. This trait is regulated by multiple genes in a coordinated manner and is susceptible to genotype-by-environment interactions, resulting in a complex genetic architecture. Elucidating the genetic basis of grain protein content is therefore of great significance for the breeding of high-quality specialty wheat varieties. RESULTS: In this study, a set of 260 widely collected spring wheat germplasm accessions was used. The crude protein (CP) and soluble protein (SP) contents were measured under four environmental conditions. Using genome-wide association study (GWAS), a total of 20 genetic loci significantly associated with CP and 23 loci significantly associated with SP were identified. Based on the linkage disequilibrium (LD) decay distance (590 kb), LD block analysis was performed, and four core loci located within the LD blocks were selected: two CP-related loci, 2B-161,726,146 and 2D-610,941,094, and two SP-related loci, 1B-562,451,687 and 7A-4,591,015. The medium-gluten wheat Humai 14 (HM14) and strong-gluten wheat Xinchun 48 (XC48), which exhibited significant differences in both CP and SP across the four environments, were selected for transcriptome sequencing at five developmental stages of grain (10, 15, 20, 25, and 30 days after anthesis). A total of 27,499 differentially expressed genes were identified, with two expression peaks observed at 10 and 30 days after anthesis. By integrating GWAS and transcriptomic differentially expressed genes, combined with gene functional annotation and expression pattern analysis, five candidate genes associated with grain protein content were ultimately screened: TaPAE2-like, TaHIP1, TaGlu-B1al-like, Ta1-SST, and Td1-SST-like. CONCLUSIONS: This study provides genetic resources for elucidating the genetic mechanisms of grain protein synthesis in wheat and lays a crucial foundation for molecular marker-assisted breeding.

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