Genome-Wide Association Mapping of Canopy Coverage in Soybean.

Water-limited conditions reduce crop production, and transpiration (T). Faster establishment of a closed canopy reduces soil surface evaporation (Es), which consequently increases transpiration (T) relative to Es and increase the amount of water available for biomass production. Canopy coverage was estimated using digital imaging with camera mounted on a monopod. Objective of this study was to identify the SNPs associated with canopy coverage and their rate. In this study, apanel of 373 MG IV soybean genotypes was grown in 5 environments for phenotyping. The marker data consisted of over 42,000 SNPs obtained from the Illumina Infinium SoySNP50K iSelect SNP Beadchip. After filtration for quality control, 31,260 SNPs were used for association mapping. To control the false positives due to population stratification, FarmCPU model was used for association analysis, which not only reduce the false positives and but also reduce the false negatives. Analysis with the FarmCPU model identified several environment-specific SNPs, and SNPs that were common in more than one environment, which were significantly associated with canopy coverage and rate. Most of identified significant SNPs were located within a gene or very close to genes that may have some association with faster canopy closure. In the future, favorable alleles from significant SNPs may be used to identify the parental genotypes for a breeding program.