Identification of Genomic Loci Associated with the Photochemical Reflectance Index by Genome-Wide Association Study in Soybean.

The photochemical reflectance index (PRI) is determined from canopy spectral reflectance measurements and can provide important information about photosynthesis. The PRI can be used to assess the epoxidation state of xanthophyll pigments, which provides information on nonphotochemical quenching (NPQ) and the amount of energy used for photosynthesis. Genome-wide association analyses were conducted to identify single-nucleotide polymorphisms (SNPs) and genomic loci associated with PRI using data from a soybean [ (L.) Merr.] diversity panel grown under field conditions over 2 yr. Based on a mixed linear model (MLM), 31 unique candidate SNPs that identify 15 putative loci on 11 chromosomes were identified. Several candidate genes known to be associated with NPQ, photosynthesis, and sugar transport processes were identified in the proximity of 10 putative loci. Violaxanthin de-epoxidase, one of the identified genes, is directly involved in the xanthophyll cycle, which plays a major role in NPQ. This study is the first to identify genomic loci for PRI and illustrates the potential of canopy spectral reflectance measurements for high-throughput phenotyping of a photosynthesis related trait. Significant SNPs, candidate genes, and genotypes contrasting for PRI identified in this study may prove useful for crop improvement efforts.