NDLI: Population structure and marker–trait association analysis of the US peanut (Arachis hypogaea L.) mini-core collection

Content Provider	Springer Nature Link
Author	Wang, Ming Li Sukumaran, Sivakumar Barkley, elle A. Chen, Zhenbang Chen, Charles Y. Guo, Baozhu Pittman, Roy N. Stalker, H. Thomas Holbrook, C. Corley Pederson, Gary A. Yu, Jianming
Copyright Year	2011
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 United States. To determine the population structure and its impact on marker–trait association, this mini-core collection was assessed by genotyping 94 accessions with 81 SSR markers and two functional SNP markers from fatty acid desaturase 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. Genetic diversity and population structure analysis identified four major subpopulations that are related to four botanical varieties. Model comparison with different levels of population structure and kinship control was conducted for each trait and association analyses with the selected models verified that the functional SNP from the FAD2A gene is significantly associated with oleic acid (C18:1), linoleic acid (C18:2), and oleic-to-linoleic (O/L) ratio across this diverse collection. Even though the allele distribution of FAD2A was structured among the four subpopulations, the effect of FAD2A gene remained significant after controlling population structure and had a likelihood-ratio-based R 2 (R LR 2 ) value of 0.05 (oleic acid), 0.09 (linoleic acid), and 0.07 (O/L ratio) because the FAD2A alleles were not completely fixed within subpopulations. Our genetic analysis demonstrated that this peanut mini-core panel is suitable for association mapping. Phenotypic characterization for seed quality traits and association testing of the functional SNP from FAD2A gene provided information for further breeding and genetic research.
Starting Page	1307
Ending Page	1317
Page Count	11
File Format	PDF
ISSN	00405752
Journal	Theoretical and Applied Genetics
Volume Number	123
Issue Number	8
e-ISSN	14322242
Language	English
Publisher	Springer-Verlag
Publisher Date	2011-08-07
Publisher Place	Berlin/Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Biochemistry Plant Breeding/Biotechnology Biotechnology Plant Genetics & Genomics Agriculture Plant Biochemistry
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine Biotechnology Agronomy and Crop Science

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