SSR analysis of cultivated groundnut (Arachis hypogaea L.) germplasm resistant to rust and late leaf spot diseases

Abstract

Cultivated groundnut (Arachis hypogaea L.) is an agronomically and economically important oilseed crop grown extensively throughout the semi-arid tropics of Asia, Africa and Latin America. Rust (Puccinia arachidis) and late leaf spot (LLS, Phaseoisariopsis personata) are among the major diseases causing significant yield loss in groundnut. The development of varieties with high levels of resistance has been constrained by adaptation of disease isolates to resistance sources and incomplete resistance in resistant sources. Despite the wide range of morphological diversity observed in the cultivated groundnut gene pool, molecular marker analyses have thus far been unable to detect a parallel level of genetic diversity. However, the recent development of simple sequence repeat (SSR) markers presents new opportunities for molecular diversity analysis of cultivate groundnut. The current study was conducted to identify diverse disease resistant germplasm for the development of mapping populations and for their introduction into breeding programs. Twenty-three SSRs were screened across 22 groundnut genotypes with differing levels of resistance to rust and LLS. Overall, 135 alleles across 23 loci were observed in the 22 genotypes screened. Twelve of the 23 SSRs (52%) showed a high level of polymorphism, with PIC values ‡0.5. This is the first report detecting such high levels of genetic polymorphism in cultivated groundnut. Multi-dimensional scaling and cluster analyses revealed three well-separated groups of genotypes. Locus by locus AMOVA and Kruskal-Wallis one-way ANOVA identified candidate SSR loci that may be valuable for mapping rust and LLS resistance. The molecular diversity analysis presented here provides valuable information for groundnut breeders designing strategies for incorporating and pyramiding rust and late leaf spot resistances and for molecular biologists wishing to create recombinant inbred line populations to map these traits.

Identification of QTLs for pod and kernel traits in cultivated peanut by bulked segregant analysis

“…The low level of polymorphism might be due to the low molecular diversity among the parental genotypes. This was in agreement with the previous findings as low level of polymorphism among cultivated groundnut Kochert et al 1991;PaikRo et al 1992;Stalker et al 1994;He and Prakash, 1997;Hopkins et al 1999;Herselman et al 2003;Moretzsohn et al 2004;Mace et al 2006). However, this may be an underestimate of the diversity present in the population, as small (2 bp) differences in size may have not been distinguished reliably using short PAGE gels.…”

“…However, a low level of variation has been observed at the DNA level using random amplified polymorphic DNA (RAPD) Subramanian et al 2000;Mondal et al 2005), inter simple sequence repeat (ISSR) (Raina et al 2001), amplified fragment length polymorphism (AFLP) (Herselman, 2003), and SSR (Mace et al 2006) markers. Of the major DNA marker types, SSR markers have been the most successful at identifying molecular variation within the cultivated peanut species (Hopkins et al 1999;Ferguson et al 2004).…”

“…Markers for resistance to root-knot nematode (Garcia et al 1995;Burow et al 1996;Choi et al 1999), late leaf spot (Stalker and Mozingo, 2001;Mondal et al 2005;Mace et al 2006), the aphid vector causing groundnut rosette disease (Herselman et al 2004), seed infection by Aspergillus flavus (Yong et al 2005) and early leaf spot (Burow et al 2008) have been indentified. However, no markers have been identified for pod-and kernel-related traits.…”

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

“…Simple sequence repeat (SSR) markers have been proven to be more efficient in revealing the diversity in cultivated peanut (Mace et al 2006;Tang et al 2007;Cuc et al 2008) 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 and LD in peanut.…”

Genetic variability in banana diploids and nonparametric statistics of fragments associated with natural fruit finger drop

“…In order to improve breeding programs, molecular markers have played a key role in indirect selection of genotypes with resistance to pests and diseases, by associating bands or alleles of interest via nonparametric methods (Mace et al, 2006;Mondal and Badigannavar, 2010;Singh et al, 2013). Although these methods are somewhat limited, with restricted inferences (Whitely and Ball, 2002;Cowan, 1992), they may be used when data do not follow normal distribution and have shown to be useful in association studies, especially for orphan crops that have very limited genomic resources including genetic maps with sufficient marker coverage, which are pre-requisites for a conventional mapping approach.…”