In silico development of simple sequence repeat markers within the aeschynomenoid/dalbergoid and genistoid clades of the Leguminosae family and their transferability to Arachis hypogaea, groundnut

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. The genetic base of the cultivated groundnut is very narrow as a result of the genetic bottleneck associated with recent polyploidization which makes it critical to determine the levels of genetic diversity within available germplasm collections prior to breeding. In groundnut, the use of SSRs for diversity assessment may offer the potential to reveal genetic variation within the genome of the cultivated species. An alternative bioinformatics, or in silico approach, to identifying SSRs suitable for application in cultivated groundnut is presented, as a low-cost alternative to wet lab SSR identification. All available nucleotide sequences from species within the aeschynomenoid/ dalbergoid and genistoid clades of the Leguminosae family were searched for SSR motifs and primers designed from 109 unique SSRs. Representative accessions from six genera within the aeschynomenoid/dalbergoid and genistoid clades were selected for assessing SSRtransferability rates. In total, 60% of the total cross-genera transfer testing reactions gave prominent and reproducible amplicons, with 51 of the 109 SSRs amplifying in A. hypogaea. These 51 SSRs were further tested against 27 diverse Arachis accessions and 18 revealed polymorphism, demonstrating that the in silico approach to SSR identification and development is a valid strategy in lesser-studied crops.

A high-density genetic map of Arachis duranensis, a diploid ancestor of cultivated peanut

“…Those most recently reported include: 14 by Gimenes et al [27]; 51 by Mace et al [28]; 188 by Proite et al [29]; 104 by Cuc et al [30]; 138 by Yuan et al [31]; 33 by Song et al [32]; 123 by Wang et al [33]; 290 by Liang et al [34]; and 1,571 by Koilkonda et al [35]. Five hundred and ninety-eight of these markers are included in the A. duranensis map (Figure 2).…”

High level of natural variation in a groundnut (Arachis hypogaea L.) germplasm collection assayed by selected informative SSR markers

“…However, recent SSR marker‐based genetic diversity studies revealed relatively moderate level of polymorphism in cultivated groundnuts (Gimenes et al. 2007, Mace et al. 2006, 2007, Kottapalli et al.…”

Identification of stable sources for surrogate traits in Arachis glabrata and marker-trait association for tolerance to water deficit stress

“…SSR markers have been found most successful in identifying molecular variation within the cultivated peanut species (Hopkins et al 1999;Ferguson et al, 2004aFerguson et al, , 2004bMace et al, 2006Mace et al, , 2007Cuc et al, 2008;Varshney et al, 2009;Khedikar et al, 2010;Mondal and Badigannavar, 2010;Gautami et al, 2011;Shirasawa, 2012;Sujay et al, 2012). However, a few RAPD markers have been successfully used in the identification of candidate genes of interest in peanut (Burow et al, 1996;Garcia et al, 1996;Mondal et al, 2007).…”