Genome-wide association mapping of dark green color index using a diverse panel of soybean accessions

Authors: KALER, AVJINDER - University Of Arkansas; Abdel-Haleem, Hussein; FRITSCHI, FELIX - University Of Missouri; Gillman, Jason; Ray, Jeffery - Jeff; Smith, James - Rusty; PURCELL, LARRY - University Of Arkansas

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/6/2020
Publication Date: 3/20/2020
Citation: Kaler, A., Abdel-Haleem, H.A., Fritschi, F.B., Gillman, J.D., Ray, J.D., Smith, J.R., Purcell, L.C. 2020. Genome-wide association mapping of dark green color index using a diverse panel of soybean accessions. Scientific Reports. 10. https://doi.org/10.1038/s41598-020-62034-7.
DOI: https://doi.org/10.1038/s41598-020-62034-7

Interpretive Summary: Nitrogen (N) plays a key role in plants because it is a major component of RuBisCO and chlorophyll. Hence, N is central to both the dark and light reactions of photosynthesis. Genotypic variation in canopy greenness provides insights into the variation of N and chlorophyll concentration, photosynthesis rates, and N2 fixation in legumes. The objective of this study was to identify significant loci associated with the intensity of greenness of the soybean [Glycine max (L.) Merr.] canopy as determined by the Dark Green Color Index (DGCI). A panel of 200 maturity group IV accessions was phenotyped for canopy greenness using DGCI in three environments. Association mapping identified 45 SNPs that were significantly (P = 0.0003) associated with DGCI in three environments, and 16 significant SNPs associated with DGCI averaged across all environments. These SNPs likely tagged 43 putative loci. Out of these 45 SNPs, eight were present in more than one environment. Among the identified loci, 21 were located in regions previously reported for N traits and ureide concentration. Putative loci that were coincident with previously reported genomic regions may be important resources for pyramiding favorable alleles for improved N and chlorophyll concentrations, photosynthesis rates, and N2 fixation in soybean.

Technical Abstract: Nitrogen (N) plays a key role in plants because it is a major component of RuBisCO and chlorophyll. Hence, N is central to both the dark and light reactions of photosynthesis. Genotypic variation in canopy greenness provides insights into the variation of N and chlorophyll concentration, photosynthesis rates, and N2 fixation in legumes. The objective of this study was to identify significant loci associated with the intensity of greenness of the soybean [Glycine max (L.) Merr.] canopy as determined by the dark green color index (DGCI), and to identify genotypes with extreme DGCI values within each maturity group (MG) of the USDA Soybean Collection. A panel of 200 maturity group IV accessions were phenotyped for canopy greenness using DGCI in three environments. Using 34,680 single nucleotide polymorphisms (SNPs) with a minor allele frequency = 5 %, association mapping identified 45 SNPs that were significantly (P = 0.0003) associated with DGCI in three environments, and 16 significant SNPs associated with DGCI averaged across all environments. These SNPs likely tagged 43 putative loci. Out of these 45 SNPs, eight were present in more than one environment. Among the identified loci, 21 were located in regions previously reported for N traits and ureide concentration. Putative loci that were coincident with previously reported genomic regions, and significant SNPs that were present in more than one environment, may be important resources for pyramiding favorable alleles for improved N and chlorophyll concentrations, photosynthesis rates, and N2 fixation ability in soybean.