Association analysis of baking and milling quality traits in an elite soft red winter wheat population

Authors: GAIRE, RUPESH - Purdue University; HUANG, MOA - The Ohio State University; SNELLER, CLAY - The Ohio State University; GRIFFEY, CARL - Virginia Polytechnic Institution & State University; Brown-Guedira, Gina; MOHAMMADI, MOHSEN - Purdue University

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/1/2019
Publication Date: 6/10/2019
Citation: Gaire, R., Huang, M., Sneller, C., Griffey, C., Brown Guedira, G.L., Mohammadi, M. 2019. Association analysis of baking and milling quality traits in an elite soft red winter wheat population. Crop Science. 59:1085–1094.

Interpretive Summary: Though grain yield is the most important trait for wheat growers, milling and baking industries demand high quality grain for various end products. To accelerate breeding of wheat cultivars with high grain quality, an understanding of the genetic basis of quality traits is necessary. Genome-wide association studies (GWAS) were conducted to identify DNA markers associated with milling and baking quality traits in soft red winter wheat (SRWW). Seven quality traits were evaluated in two locations and two years for 270 elite SRWW lines. These traits include flour yield, softness equivalent, flour protein and four solvent (lactose, sodium carbonate, sucrose, and water) retention capacity measurements. In this study, 27,449 single nucleotide polymorphisms markers were developed. A linear mixed model in GWAS, accounting for population structure and kinship was fitted to identify 18 regions on 12 different chromosomes associated with the quality traits. Only one of these associations seems to be a previously identified gene, whereas others are novel associations. The most significant associations for quality traits were identified in chromosomes 1B, 2A, 2B, 4B, 5A 7A, and 7D. Candidate gene searches, facilitated by the wheat genome assembly, led us to the identification of putative genes related to SRWW quality traits including fasciclin-like arabinogalactan. The results of this study can be used in developing high quality SRWW varieties for the Eastern region of the US.

Technical Abstract: Though grain yield is the most important trait for growers, milling and baking industries demand high quality and scab-free grains for various end products. To accelerate breeding of wheat cultivars with high grain quality, genetic dissection of quality traits is necessary. Genome-wide association studies (GWAS) were conducted to identify genomic regions responsible for milling and baking quality traits in soft red winter wheat (SRWW). Seven quality traits were evaluated in two locations and two years for 270 elite SRWW lines. These traits include flour yield, softness equivalent, flour protein and four solvent (lactose, sodium carbonate, sucrose, and water) retention capacity measurements. In this study, 27,449 single nucleotide polymorphisms markers were developed by using both genotyping-by-sequencing and 90K SNP array technologies. A linear mixed model in GWAS, accounting for population structure and kinship was fitted to identify 18 (-logP = 4.0) genomic regions on 12 different chromosomes associated with the quality traits. Only one of these associations seems to be previously identified QTL, whereas others are novel associations. The most significant associations for quality traits were identified in chromosomes 1B, 2A, 2B, 4B, 5A 7A, and 7D. Candidate gene searches, facilitated by the wheat genome assembly, led us to the identification of putative genes related to SRWW quality traits including fasciclin-like arabinogalactan. The results of this study can be used in developing high quality SRWW varieties for the Eastern region of the US.