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ARS Home » Plains Area » Lubbock, Texas » Cropping Systems Research Laboratory » Plant Stress and Germplasm Development Research » Research » Publications at this Location » Publication #327904

Title: A first insight into population structure and linkage disequilibrium in the US peanut minicore collection

item BELAMKAR, VIKAS - Texas A&M University
item GOMEZ SELVARAJ, MICHAEL - Texas A&M University
item AYERS, JAIME - Texas A&M University
item Payton, Paxton
item PUPPALA, NAVEEN - New Mexico State University
item BUROW, MARK - Texas A&M University

Submitted to: Genetica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/25/2011
Publication Date: 3/27/2011
Citation: Belamkar, V., Gomez Selvaraj, M., Ayers, J.L., Payton, P.R., Puppala, N., Burow, M.D. 2011. A first insight into population structure and linkage disequilibrium in the US peanut minicore collection. Genetica. 139(4):411-429. doi:10.1007/s10709-011-9556-2.

Interpretive Summary: Simple sequence repeat (SSR) markers have been proven to be efficient in revealing the diversity in cultivated peanut than other markers used previously (RAPDs, RFLPs, and AFLPs). To date, no study has been published giving substantial information about the performance of single nucleotide polymorphisms (SNPs) for characterizing diversity in peanut. Thus, SSRs are currently the best available resource for diversity studies in peanut. In the present study, the population structure and the extent of linkage disequilibrium in the US peanut minicore collection was investigated with SSR markers, and to the best of our knowledge this is the first report giving insight of linkage disequilibrium in the peanut genome. The objectives of the present study were: (1) to evaluate the genetic diversity and population structure of the US peanut minicore collection, and (2) characterize linkage disequilibrium in the peanut genome as a first step towards determining the feasibility of performing association mapping in peanut.

Technical Abstract: Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaensis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Mode l based clustering identified four subgroups- one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P\0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r2 C 0.1). Of the syntenic marker pairs separated by distances\10 cM, 11–20 cM, 21–50 cM, and[50 cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P B 0.01), in accord with LD extending to great distances in self-pollinated crops. A threshold value of r2[0.035 was found to distinguish mean r2 values of linkage distance groups statistically from the mean r2 values of unlinked markers; LD was found to extend to 10 cM over the entire minicore collection by this criterion. However, there were large differences in r2 values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using association mapping for detection of genome-wide SSR marker-phenotype association are discussed.