Abstract
Using genome‐wide single nucleotide polymorphism (SNP) discovery in greater yam (Discorea alata L.), 4,593 good quality SNPs were identified in 40 accessions. One hundred ninety six of these SNPs were selected to represent the overall dataset and used to design a competitive allele specific PCR array (KASPar). This array was validated on 141 accessions from the Tropical Plants Biological Resources Centre (CRB‐PT) and CIRAD collections that encompass worldwide D. alata diversity. Overall, 129 SNPs were successfully converted as cost‐effective genotyping tools. The results showed that the ploidy levels of accessions could be accurately estimated using this array. The rate of redundant accessions within the collections was high in agreement with the low genetic diversity of D. alata and its diversification by somatic clone selection. The overall diversity resulting from these 129 polymorphic SNPs was consistent with the findings of previously published studies. This KASPar array will be useful in collection management, ploidy level inference, while complementing accurate agro‐morphological descriptions.
Highlights
Greater yam (Discorea alata L.) is one of the major cultivated yam spe‐ cies (Discorea spp.) and the most widely spread among tropical and subtropical regions
The resuming of the 141 accessions to 43 unique redundancy groups was related to the nar‐ row D. alata genetic diversity, above all in polyploid germplasm already identified in previous studies
We can hypothesize that the 129 single nucleotide polymorphism (SNP) KASPar array developed for D. alata allow us to accurately assess genetic diversity and the findings may be transferable to other collections
Summary
Molecular markers have been used to characterize D. alata di‐ versity: random amplified polymorphic DNA (RAPD; Asemota, Ramser, Lopez‐Peralta, Weising, & Kahl, 1996), isoenzymes (Lebot et al, 1998), amplified fragment length polymorphism (AFLP; Malapa, Arnau, Noyer, & Lebot, 2005), simple sequence repeats (SSRs; Siqueira, Marconi, Bonatelli, Zucchi, & Veasey, 2011; Sartie, Asiedu, & Franco, 2012; Otoo, Anokye, Asare, & Telleh, 2015; Chaïr et al, 2016; Arnau et al, 2017), plastid sequences (Chaïr et al, 2016), and Diversity Arrays Technology (DArT; Vandenbroucke et al, 2016) These studies generated essential information on the diversity and representativity of the germplasm collections. The main objectives of this study were (a) to identify genome‐ wide polymorphic SNP markers, (b) to develop a cost‐effective SNP genotyping array using KASPar technology and (c) to test its use as a tool in managing yam ex situ collections
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