Submitted to: Genetica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/27/2010
Publication Date: 3/27/2011
Citation: Belamkar, V., Gomez, M., Ayers, J., Payton, P.R., Puppala, N., Burow, M. 2011. A first insight into population structure and linkage disequilibrium in the US Peanut Mini-core Collection. Genetica. 139:411-429. Interpretive Summary: Peanut (Arachis hypogaea L.) is a globally important crop as both a primary source of protein and oil. As a member of the Fabaceae, peanut is capable of utilizing atmospheric nitrogen by symbiotic nitrogen fixation. Thus, in addition to being a food crop, peanut is capable of increasing the fertility of the soil. Cultivated peanut is a highly selfing tetraploid species and its origin is thought to be the results of a single hybridization event between two wild species, A. duranensis (A genome) and A. ipaensis (B genome), giving rise to a wild diploid hybrid, followed by a chromosome duplication event. Domestication of this wild allotetraploid is hypothesized to have resulted in the present day cultivated peanut (Arachis hypogaea L.). As result of this domestication, a genetic bottleneck has been created and resulted in limited molecular level polymorphism. This lack of polymorphism in domesticated peanut is a major hindrance to development of genomic resources in peanut, and many other polyploidy crop species. However, it is expected that the selfing nature of peanut and the genetic bottleneck would be advantageous for linkage-disequilibrium (LD)-based mapping, as they would result in high amounts of LD and thus genome-wide association studies would become feasible with fewer genetic markers as compared to an open-pollinated crop such as maize. In the present study, the population structure and the extent of linkage disequilibrium in the U.S. peanut minicore collection is being investigated with simple sequence repeat markers, and to the best of our knowledge this is the first report giving insight of LD in the peanut genome. The objectives of the present study are:(1) to evaluate the genetic diversity and population structure of the U.S. peanut mincore collection, and (2) characterize linkage disequilibrium in the peanut genome as a first step towards dtermining the feasibility of performing association mapping in peanut. Our findings, although preliminary, suggest that LD mapping is a viable, cost-effective approach to identify genetic regions in peanut associated with traits of interest. Utimately, this technology and the use of novel germplasm and new populations will result in improved cultivars derived from marker assisted selection.
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 U.S. peanut mini-core collection, diploid progenitors A. duranensis (AA) and A. ipae¨nsis (BB), a component line of the tetraploid variety Florunner, and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker alleles amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. 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 the last containing diploid progenitors and TxAG-6. Similarly, model-based clustering identified four subgroups - fastigiata and hypogaea subspecies, a third consisting of diploid progenitors and TxAG-6, and a fourth containing individuals of both subspecies or of mixed ancestry. Analysis of molecular variance (AMOVA) revealed statistically-significant (p < 0.0001) genetic variance of 16.87% among subgroups. Of SSR markers pairs, 12.60% revealed significant LD (at r² = 0.05). At the significance threshold of p = 0.01, some syntenic marker pairs separated by distances <50 cM, beyond 50 cM, and non-synthenic marker pairs were found in strong LD, in accord with LD extending to great distances in self pollinated crops. The proportion of marker pairs in linkage disequilibrium within the entire A. hypogaea species was approximately twice that within the fastigiata subspecies. The implications of these finding with regard to the possibility of using association mapping for detection of genome-wide SSR marker-phenotype association are discussed.