Understanding the genetic diversity and population structure of yam (Dioscorea alata L.) using microsatellite markers

Abstract

Yams (Dioscorea sp.) are staple food crops for millions of people in tropical and subtropical regions. Dioscorea alata, also known as greater yam, is one of the major cultivated species and most widely distributed throughout the tropics. Despite its economic and cultural importance, very little is known about its origin, diversity and genetics. As a consequence, breeding efforts for resistance to its main disease, anthracnose, have been fairly limited. The objective of this study was to contribute to the understanding of D. alata genetic diversity by genotyping 384 accessions from different geographical regions (South Pacific, Asia, Africa and the Caribbean), using 24 microsatellite markers. Diversity structuration was assessed via Principal Coordinate Analysis, UPGMA analysis and the Bayesian approach implemented in STRUCTURE. Our results revealed the existence of a wide genetic diversity and a significant structuring associated with geographic origin, ploidy levels and morpho-agronomic characteristics. Seventeen major groups of genetically close cultivars have been identified, including eleven groups of diploid cultivars, four groups of triploids and two groups of tetraploids. STRUCTURE revealed the existence of six populations in the diploid genetic pool and a few admixed cultivars. These results will be very useful for rationalizing D. alata genetic resources in breeding programs across different regions and for improving germplasm conservation methods.

Development of a cost‐effective single nucleotide polymorphism genotyping array for management of greater yam germplasm collections

“…Our validation panel was thus representative of the worldwide D. alata diversity.Moreover, a good correlation was obtained between the findings of the previous study of worldwide D. alata diversity ofArnau et al (2017) and the gene pools identified in this study (Appendix B). Our validation panel was thus representative of the worldwide D. alata diversity.Moreover, a good correlation was obtained between the findings of the previous study of worldwide D. alata diversity ofArnau et al (2017) and the gene pools identified in this study (Appendix B).…”

“…Nodes shape and letter, cluster of diversity identified by a bootstrap procedure; red nodes, diploids; green nodes, triploids; blue nodes, tetraploids; edge colors, similarity from gray (0.64) to black (1) with previous genetic diversity studies that already pooled these accessions together and highlighted this intragroup variability in tubers (Arnau et al, 2017;Malapa et al, 2005). Nodes shape and letter, cluster of diversity identified by a bootstrap procedure; red nodes, diploids; green nodes, triploids; blue nodes, tetraploids; edge colors, similarity from gray (0.64) to black (1) with previous genetic diversity studies that already pooled these accessions together and highlighted this intragroup variability in tubers (Arnau et al, 2017;Malapa et al, 2005).…”

“…The CRB-PT collection has been shown to be representative of worldwide D. alata diversity (Arnau et al, 2017). A subset of this ex situ collection has been genotyped in this study.…”

“…However, these descriptors are not reliable enough to rationalize ex situ D. alata collection. Indeed, several studies have revealed that morphological variations are not necessarily linked to geographic origin or genetic lineage (Arnau et al, 2017;Lebot, Trilles, Noyer, & Modesto, 1998;Vandenbroucke et al, 2016). Complementary characterization tools are thus required for the conservation and dynamic management of ex situ collections related to germplasm exchange, the development of core collection or identification of future parents for breeding programs.…”

“…d Cluster of diversity identified by SSR inArnau et al (2017). How to cite this article: Cormier F, Mournet P, Causse S, et alTA B L E B 1Description of the 141 D. alata used as the KASPar assay validation panel In italic, ploidy detected using the percentage of polyploid genotype type on overall heterozygous loci.…”