Identification of targets for introgression from rye (Secale ssp.) into wheat (Triticum aestivum) to increase arabinoxylan content in flour using a genome-wide association study

Among cereal species, rye (Secale cereale L.) has the highest dietary fibre content, particularly arabinoxylans (AX). Thus, rye flour has gained popularity as a bioactive supplement to white wheat flour-based products. An alternative approach to bio-fortifying white wheat flour could be through wheat-rye introgressions. The recent availability of a rye reference genome assembly makes genome-wide association studies (GWAS) possible for this allogamous species, simplifying the identification of AX-associated rye introgression targets. In this work, a collection comprising 317 rye accessions was assembled to investigate the genetic basis of rye grain quality traits, including total AX (TOT-AX), water-extractable AX (WE-AX) and water-unextractable AX (WU-AX) contents, the proportion of WE-AX to TOT-AX, and thousand kernel weight (TKW). The collection was genotyped using a genotyping-by-sequencing (GBS) approach. Genetic diversification based on the regionally predominant end use of rye was phenotypically evident when considering the TKW of rye. The GWAS detected 12 marker-trait associations (MTAs). No MTA for TKW colocalised with an MTA for TOT-AX, WE-AX, or WU-AX contents. Two MTAs for WE-AX and WU-AX contents located on chromosome segment 2RL explained 21–26% of phenotypic variance, and two MTAs for TOT-AX and WU-AX contents colocalised on chromosome segment 7RL explained about 33% of phenotypic variance. Despite the lack of candidate genes with known cell wall-related functions within LD range of these MTAs, these associations deserve further attention as introgression targets for AX-targeted breeding in wheat.