Wheat straw decomposition constituents: a genome-wide association study and environmental influence analysis

Adoption of no-till farming in Eastern Washington has been slow due to difficulties managing wheat (Triticum aestivum L.) straw residue in no-till systems. We hypothesize that a genome-wide association study (GWAS) will identify single nucleotide polymorphisms (SNPs) that can assist in understanding the genetic loci associated with straw decomposition. The straw from a panel of 465 soft white winter wheat cultivars in the Pacific Northwest was harvested over two years at three locations throughout Eastern Washington. The samples were analyzed for several decomposition constituents, including neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), cellulose, and hemicellulose using a wet chemistry procedure whereas C was determined using dry combustion. Significant differences among environments were observed for all fiber and chemical constituents, with environment accounting for the largest source of variation across all traits. Broad-sense heritabilities were correspondingly low (H² = 0.03-0.21), reflecting the strong influence of environmental conditions on straw composition. Genotyping was performed using the 90K Illumina SNP chip and a GWAS was conducted using Fixed and random model Circulating Probability Unification (FarmCPU) implemented in the statistical program R. Twenty-three marker-trait associations were identified across 12 chromosomes. Cellulose, NDF, and ADF were the most useful traits for identifying chromosomal loci of interest. Five significant loci were identified on chromosomes 1B, 2B, 4B, 5B, and 6B. Four of those loci were associated with cellulose, three with NDF, and three with ADF. The distribution of the significant SNPs across chromosomes, however, demonstrates the genetic complexity of these straw breakdown constituents.