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. 2017 Mar 29;12(3):e0174150.
doi: 10.1371/journal.pone.0174150. eCollection 2017.

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

Gemma Arnau  1 , Ranjana Bhattacharjee  2 , Sheela Mn  3 , Hana Chair  4 , Roger Malapa  5 , Vincent Lebot  6 , Abraham K  3 , Xavier Perrier  4 , Dalila Petro  7 , Laurent Penet  7 , Claudie Pavis  7
Affiliations

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

Gemma Arnau et al. PLoS One. .

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.

Figures

Fig 1A
Fig 1A. Diagram showing the relationships among 367 accessions of D. alata based on Principal Coordinate Analysis (PCoA) using 24 microsatellites.
Clones originated from Vanuatu are colored in green and those from CTCRI (India) in red. The accessions of the CRB-PT and the IITA are colored in orange and pink, respectively. 1B. Diagram showing the relationships among 83 polyploid accessions of D. alata based on Principal Coordinate Analysis(PCoA) using 24 microsatellites. Tetraploids accessions are colored in green and triploids in blue.
Fig 2
Fig 2. Dendrogram showing the relationships among 284 diploid accessions of D. alata based on UPGMA analysis using 24 microsatellites.
Fig 3
Fig 3. Structure of the genetic diversity of the 284 diploid accessions of D. alata at K = 6.
See this image and copyright information in PMC

References

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