Genetic diversity of cultivated and wild-type peanuts evaluated with M13-tailed SSR markers and sequencing

Abstract

Thirty-one genomic SSR markers with a M13 tail attached were used to assess the genetic diversity of the peanut mini core collection. The M13-tailed method was effective in discriminating almost all the cultivated and wild accessions. A total of 477 alleles were detected with an average of 15.4 alleles per locus. The mean polymorphic information content (PIC) score was 0.687. The cultivated peanut (Arachis hypogaea L.) mini core produced a total of 312 alleles with an average of 10.1 alleles per locus. A neighbour-joining tree was constructed to determine the interspecific and intraspecific relationships in this data set. Almost all the peanut accessions in this data set classified into subspecies and botanical varieties such as subsp. hypogaea var. hypogaea, subsp. fastigiata var. fastigiata, and subsp. fastigiata var. vulgaris clustered with other accessions with the same classification, which lends further support to their current taxonomy. Alleles were sequenced from one of the SSR markers used in this study, which demonstrated that the repeat motif is conserved when transferring the marker across species borders. This study allowed the examination of the diversity and phylogenetic relationships in the peanut mini core which has not been previously reported.

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

“…The higher average number of bands per primer pair (12.3) witnessed in the study involving minicore and wild species was in accordance with the results of Barkley et al (2007) (15.4 bands per primer pair). The most probable diploid progenitors, A. duranensis and A. ipae¨nsis, were found to have 53 and 43% unique bands respectively.…”

“…Data from our study and another study (Barkley et al 2007) suggest that botanical classification of peanut accessions in GRIN was not accurate in some instances and needs further work. For example, COC132 (PI 497639) was classified in GRIN as subsp.…”

“…For example, COC132 (PI 497639) was classified in GRIN as subsp. fastigiata, but in our molecular analysis was placed in the hypogaea subcluster, and was reported by Barkley et al (2007) to lack flowers on the mainstem, to have a spreading and bunch growth habit, rough pod reticulation, deep strangulation of pods, and a pod shape similar to botanical variety hirsuta. Thus, the authors suggested that the accession is probably A. hypogaea subspecies hypogaea var.…”

“…This is in accord with RFLP data of Burow et al (2009) suggesting presence of either other but unidentified diploid progenitors, or that a significant amount of genetic variation arose after hybridization of A. duranensis and A. ipae¨nsis. Distance-based cluster analysis classified the US minicore collection on the basis of subspecies, hypogaea and fastigiata as observed in the earlier studies (Kottapalli et al 2007;Barkley et al 2007). The further division of fastigiata subcluster into two subgroups representing Valencia genotypes and a mix of Spanish and Valencia genotypes has also been reported in the study conducted by Naito et al (2008) on the germplasm of Japan, as well as by Kottapalli et al (2007).…”

Confirmation and refinement of an autosomal dominant congenital motor nystagmus locus in chromosome 1q31.3–q32.1

“…An M13-tailed primer PCR method was used to genotype the additional markers. 12 Haplotypes were generated using the Cyrillic 2.1 program (Cyrillic Software, Wallingford, Oxfordshire, UK) and confirmed by inspection. The criteria for establishing linkage have been described previously.…”