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

Date Published: March 29, 2017

Publisher: Public Library of Science

Author(s): Gemma Arnau, Ranjana Bhattacharjee, Sheela MN, Hana Chair, Roger Malapa, Vincent Lebot, Abraham K, Xavier Perrier, Dalila Petro, Laurent Penet, Claudie Pavis, Tzen-Yuh Chiang.

http://doi.org/10.1371/journal.pone.0174150

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.

Partial Text

Yams (Dioscorea sp.) are important food security crops for millions of small-scale farmers in the tropical and subtropical regions of Africa, Asia, the Pacific, the Caribbean and Latin America [1]. Dioscorea alata (known as the “greater yam” or the “winged yam”) is one of the major cultivated species with wide geographical distribution [2]. It is currently second to D. rotundata in production volumes. Several traits of D. alata make it particularly valuable for commercial cultivation. These include high yield potential, ease of propagation, early growth vigour for weed suppression, and long storability of tubers [3, 4]. Tubers possess a high nutritional content with an average crude protein content of 7.4%, starch content of 75–84%, and vitamin C content ranging from 13.0 to 24.7 mg/100g [5].

Seventeen accessions presenting more than 25% of the missing data were removed from the analyses. The total number of accessions analyzed was 367, including 77 from India, 67 from Vanuatu, 89 from Caribbean, 87 from Africa, 13 from New Caledonia and 7 from French Guyana.

This study represents the first approach that comprehensively investigates the genetic diversity within different large collections of D. alata using microsatellite markers. Several other studies on genetic diversity have been conducted on this species using different types of molecular markers including random amplified polymorphism DNAs [30, 55], amplified fragment length polymorphisms [15, 56, 57] and simple sequence repeat (SSR) markers [34, 58]. However, these included accessions from only one or two regions or collections. Lebot et al. [27] evaluated the genetic diversity of 269 accessions of D. alata originating from the South Pacific, Asia and the Caribbean using isozymes. However, due to low polymorphism of these markers, no relationships could be established between these accessions.

Microsatellite markers and a worldwide sample material proved to be effective for identifying polymorphism and for evaluating genetic relationships between yam varieties, clarifying relationships between genetic diversity, geographic origins, and ploidy levels.

 

Source:

http://doi.org/10.1371/journal.pone.0174150

 

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