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ARS Home » Southeast Area » Stoneville, Mississippi » Crop Genetics Research » Research » Publications at this Location » Publication #348366
Title: Association mapping identifies loci for canopy coverage in diverse soybean genotypes

Author
item KALER, AVJINDER - University Of Arkansas
item Ray, Jeffery - Jeff
item SCHAPAUGH, WILLIAM - Kansas State University
item DAVIES, MARILYNN - University Of Arkansas
item KING, ANDY - University Of Arkansas
item PURCELL, LARRY - University Of Arkansas

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/19/2018
Publication Date: 4/12/2018
Citation: Kaler, A.S., Ray, J.D., Schapaugh, W.T., Davies, M.K., King, A.C., Purcell, L.C. 2018. Association mapping identifies loci for canopy coverage in diverse soybean genotypes. Molecular Breeding. 38:50. https://doi.org/10.1007/s11032-018-0810-5.
DOI: https://doi.org/10.1007/s11032-018-0810-5

Interpretive Summary: Rapid establishment of canopy coverage decreases soil evaporation relative to transpiration, improves water use efficiency and light interception, and increases soybean competitiveness against weeds. The objective of this study was to identify DNA regions associated with canopy coverage and the rate of increase in canopy coverage. Canopy coverage was evaluated using 373 soybean lines that were grown in five environments. Digital image analysis was used to determine canopy coverage two times during vegetative development for each environment. Over 31,000 molecular markers were used for association analysis to identify important DNA regions with genes affecting canopy coverage. Overall, more than 30 DNA regions associated with canopy coverage traits were identified. Genes identified in these regions included those with reported functions associated with growth and development. Favorable molecular markers may be an important resource for combining genes to improve canopy coverage and for identifying parents for use in breeding programs.

Technical Abstract: Rapid establishment of canopy coverage decreases soil evaporation relative to transpiration (T), improves water use efficiency (WUE) and light interception, and increases soybean competitiveness against weeds. The objective of this study was to identify genomic loci associated with canopy coverage (CC) and the canopy coverage rate of increase (CCR). Canopy coverage was evaluated using a panel of 373 MG IV soybean genotypes that was grown in five environments. Digital image analysis was used to determine canopy coverage two times (CC1 and CC2) during vegetative development approximately 7 to 14 days apart for each environment. After filtration for quality control, 31,260 SNPs with a minor allele frequency (MAF) = 5% were used for association mapping with the FarmCPU model. Analysis identified significant SNP-canopy coverage associations including 41 for CC1, 56 for CC2, and 35 for CCR. Six SNPs for CC1, 11 SNPs for CC2, and six SNPs for CCR were present in at least two environments. The significant SNP-associations likely tagged 38, 50, and 30 different loci, for CC1, CC2, and CCR, respectively. Twelve putative loci were identified in which chromosomal regions associated with canopy coverage from both CC1 and CC2 were coincident. Genes identified using these significant SNPs included those with reported functions associated with growth, developmental, and light responses. Favorable alleles from significant SNPs may be an important resource for pyramiding genes to improve canopy coverage and for identifying parental genotypes for use in breeding programs.