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.
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 SSR-transferability 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.
Plant Science (2007) 174 (1) 51-60 [doi: 10.1016/j.plantsci.2007.09.014]