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United States Department of Agriculture

Agricultural Research Service

Research Project: CONSERVATION, CHARACTERIZATION, AND EVALUATION OF CROP GENETIC RESOURCES AND ASSOCIATED INFORMATION

Location: Plant Genetic Resources Conservation Unit

Title: Population structure and marker-trait association analysis of the U.S. Peanut (Arachis hypogaea L.) mini-core collection

Authors
item Wang, Ming
item Sukumaran, Siva -
item Barkley, Noelle
item Chen, Zhenbang -
item Chen, Charles
item Guo, Baozhu
item Pittman, Roy
item Stalker, H Thomas -
item Holbrook, C
item Pederson, Gary
item Yu, Jianming -

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 16, 2011
Publication Date: August 7, 2011
Repository URL: http://handle.nal.usda.gov/10113/57656
Citation: Wang, M.L., Sukumaran, S., Barkley, N.L., Chen, Z., Chen, C.Y., Guo, B., Pittman, R.N., Stalker, H., Holbrook Jr, C.C., Pederson, G.A., Yu, J. 2011. Population structure and marker-trait association analysis of the U.S. Peanut (Arachis hypogaea L.) mini-core collection. Journal of Theoretical and Applied Genetics. 123:1307-1317.

Interpretive Summary: Cultivated peanut is one of the most important oilseed and nutritional crops in the world. To efficiently utilize the germplasm collection, a peanut mini-core containing 112 accessions was established in the U.S. The genetic diversity and population structure of this mini-core collection was assessed by genotyping 94 accessions with 81 SSR markers and two functional SNP markers from fatty acid desturase 2. Seed quality traits including oil content, fatty acid composition, flavonoids, and resveratrol were obtained through nuclear magnetic resonance, gas chromatography, and high performance liquid chromatography analysis. Marker-trait association analysis was performed. Genetic diversity and population structure analysis identified four major subpopulations that are related with four botanical varieties. Candidate-gene association analysis verified that one functional SNP from FAD2A gene is significantly associated with oleic acid, linoleic acid, and oleic to linoleic (O/L) ratio but there is no functional mutation identified for FAD2B gene within this mini-core collection. There were no other associations between markers and seed quality traits identified in this study. The U.S. peanut mini-core collection is useful for peanut breeding and genetic studies. Additional markers and traits need to be added to this panel to further explore marker-trait associations in peanut.

Technical Abstract: Peanut (Arachis hypogaea L.) is one of the most important oilseed and nutritional crops in the world. To efficiently utilize the germplasm collection, a peanut mini-core containing 112 accessions was established in the U.S. The genetic diversity and population structure of this mini-core collection was assessed by genotyping 94 accessions with 81 SSR markers and two functional SNP markers from fatty acid desturase 2 (FAD2). Seed quality traits (including oil content, fatty acid composition, flavonoids, and resveratrol) were obtained through nuclear magnetic resonance (NMR), gas chromatography (GC), and high performance liquid chromatography (HPLC) analysis. Marker-trait association analysis was performed. Genetic diversity and population structure analysis identified four major subpopulations that are related with four botanical varieties. Candidate-gene association analysis verified that one functional SNP from FAD2A gene is significantly associated with oleic acid (C18:1), linoleic acid (C18:2), and oleic to linoleic (O/L) ratio but there is no functional mutation identified for FAD2B gene within this mini-core collection. There were no other associations between SSR markers and seed quality traits identified in this study. Utilization of the U.S. peanut mini-core and association mapping were discussed. Additional markers and traits need to be added to this panel to further explore marker-trait associations in peanut.

Last Modified: 7/25/2014