Novel Genomic Loci and Potential Candidate Genes Identified for Chlorophyll, Carotenoids and Photochemical Reflectance Index Traits.

Photosynthetic capacity is important for biomass production and ultimately grain yield. Leaf chlorophyll and carotenoids play important roles in light absorption and photoprotection and targeted selection for leaf chlorophyll and carotenoids may offer avenues to improve abiotic stress tolerance. The amount of solar radiation that is absorbed by a leaf is closely related to its chlorophyll concentration, which generally is positively related with photosynthetic rate. In plants, carotenoids play important roles in photosynthesis as accessory pigments and in photoprotection. As accessory pigments, carotenoids are involved in light harvesting and energy transfer to chlorophyll. The photochemical reflectance index (PRI), determined from canopy spectral reflectance measurements, can be used to assess the epoxidation state of xanthophyll pigments, which provides information on non-photochemical quenching (NPQ) and the amount of energy used for photosynthesis. A genome-wide associating mapping approach was employed using 31,253 single nucleotide polymorphisms (SNPs) to identify genetic loci associated with extract-based chlorophyll and carotenoids concentration, and canopy spectral reflectance based assessments of chlorophyll, carotenoid and PRI in soybean [Glycine max (L.) Merr.]. These analyses revealed a tractable number of common SNP markers, genetic loci and candidate genes associated with chlorophyll, carotenoids and PRI. In this study, we examine the relationships of the genomic loci and putative candidate genes identified for these traits.  This analysis may provide novel insights about the importance of the identified genetic loci/genes for soybean photosynthetic characteristics, and facilitate prioritization for future research and crop improvement efforts.