Genome wide association study of the whiteness and colour related traits of flour and dough sheets in common wheat

Abstract

Flour whiteness and colour are important factors that influence the quality of wheat flour and end-use products. In this study, a genome wide association study focusing on flour and dough sheet colour using a high density genetic map constructed with 90K single nucleotide polymorphism arrays in a panel of 205 elite winter wheat accessions was conducted in two different locations in 2 years. Eighty-six significant marker-trait associations (MTAs) were detected for flour whiteness and the brightness index (L* value), the redness index (a* value), and the yellowness index (b* value) of flour and dough sheets (P < 10–4) on homologous group 1, 2, 5 and 7, and chromosomes 3A, 3B, 4A, 6A and 6B. Four, three, eleven, eleven MTAs for the flour whiteness, L* value, a* value, b* value, and one MTA for the dough sheet L* value were identified in more than one environment. Based on MATs, some important new candidate genes were identified. Of these, two candidate genes, TraesCS5D01G004300 and Gsp-1D, for BS00000020_51 were found in wheat, relating to grain hardness. Other candidate genes were associated with proteins, the fatty acid biosynthetic process, the ketone body biosynthetic process, etc.

Genome-Wide Association Study Reveals the Genetic Basis of Five Quality Traits in Chinese Wheat

“…Additionally, the evaluation of wheat quality traits necessitates the large-scale production of seeds to be ground into flour, which is one of challenges to traditional QTL mapping. With the rapid development of genome sequencing technology and high-density SNP arrays for genotyping (e.g., 9, 35, 55, 90, 660, and 820), the genome-wide association study (GWAS) has become an increasingly popular and promising alternative to linkage mapping for elucidating the genetic basis of complex traits, especially quality traits ( Yu et al, 2006 ; Zhu et al, 2008 ; Ji et al, 2021 ). This method enables the use of natural populations without interbreeding to produce progeny, making it convenient for phenotype and genotype identifications.…”

Conditional QTL mapping for seed germination and seedling traits under salt stress and candidate gene prediction in wheat

“…To identify the position of important QTL loci on a physical map and possible candidate genes, significant markers detected in this study were used to identify putative candidate genes according to the method of Ji 53 . A BLAST (Basic Local Alignment Search Tool) search was performed on the International Wheat Genome Sequencing Consortium database (wheat Chinese Spring IWGSC RefSeq v1.1 and v2.1 genome assembly; http://www.wheatgenome.org/ ) using the sequence of the significant DArT markers identified by QTL mapping.…”

“…A BLAST (Basic Local Alignment Search Tool) search was performed on the International Wheat Genome Sequencing Consortium database (wheat Chinese Spring IWGSC RefSeq v1.1 and v2.1 genome assembly; http://www.wheatgenome.org/ ) using the sequence of the significant DArT markers identified by QTL mapping. When a DArT marker sequence from the IWGSC was 100% identical to any wheat contig, the sequence was extended 2 Mb for each marker using the IWGSC BLAST results 53 . Then, the extended sequence was used to run a BLAST search at the National Center for Biotechnology Information (NCBI) database ( http://www.ncbi.nlm.nih.gov ) and Ensembl Plants ( http://plants.ensembl.org/Triticum_aestivum/Tools/Blast ) to confirm possible candidate genes and functions 53 .…”

“…When a DArT marker sequence from the IWGSC was 100% identical to any wheat contig, the sequence was extended 2 Mb for each marker using the IWGSC BLAST results 53 . Then, the extended sequence was used to run a BLAST search at the National Center for Biotechnology Information (NCBI) database ( http://www.ncbi.nlm.nih.gov ) and Ensembl Plants ( http://plants.ensembl.org/Triticum_aestivum/Tools/Blast ) to confirm possible candidate genes and functions 53 .…”

“…org/) using the sequence of the significant DArT markers identified by QTL mapping. When a DArT marker sequence from the IWGSC was 100% identical to any wheat contig, the sequence was extended 2 Mb for each marker using the IWGSC BLAST results 53 . Then, the extended sequence was used to run a BLAST search at the National Center for Biotechnology Information (NCBI) database (http:// www.…”