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

• Published in: PloS one Vol. 12; no. 3; p. e0174150
• Main Authors: Arnau, Gemma, Bhattacharjee, Ranjana, Mn, Sheela, Chair, Hana, Malapa, Roger, Lebot, Vincent, K, Abraham, Perrier, Xavier, Petro, Dalila, Penet, Laurent, Pavis, Claudie
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 29.03.2017; Public Library of Science (PLoS)
• Subjects: Adaptation; Africa; Agricultural sciences; Agriculture; Anthracnose; Asia; Bayes Theorem; Bayesian analysis; Biodiversity; Biodiversity and Ecology; Biology and Life Sciences; Breeding; Caribbean Region; Collections; Colletotrichum - pathogenicity; Colletotrichum - physiology; Conservation; Crops; Crops, Agricultural; Cultivars; Dioscorea - classification; Dioscorea - genetics; Dioscorea - microbiology; Disease resistance; Disease Resistance - genetics; Domestication; Earth Sciences; Ecology and Environmental Sciences; Environmental Sciences; Food; Food supply; Genetic aspects; Genetic diversity; Genetic Markers; Genetic resources; Genetic Variation; Genetics; Genotype & phenotype; Genotyping; Germplasm; Life Sciences; Microsatellite Repeats; Microsatellites; Microsatellites (Genetics); People and places; Phylogeny; Phylogeography; Plant Breeding; Plant Diseases - genetics; Plant Diseases - microbiology; Ploidies; Ploidy; Population genetics; Population structure; Principal Component Analysis; Vegetal Biology; Yams; Southeast Asia; France; Guadeloupe; West Africa
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0174150

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.