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. 2023 May 31;18(5):e0286480.
doi: 10.1371/journal.pone.0286480. eCollection 2023.

Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers

Joseph Innocent Massawe  1   2 , Gladness Elibariki Temu  2
Affiliations

Unravelling the genetic diversity of water yam (Dioscorea alata L.) accessions from Tanzania using simple sequence repeat (SSR) markers

Joseph Innocent Massawe et al. PLoS One. .

Abstract

Water yam (Dioscorea alata L.) is among the most cultivated species used as a source of food and income for small-scale farmers in Tanzania. However, little is documented about Dioscorea species available in Tanzania, including their genetic diversity. This study used ten polymorphic microsatellite markers to determine the genetic diversity and relationship of 63 D. alata accessions from six major producing regions. Results revealed a polymorphic information content (PIC) of 0.63, while the number of alleles per locus ranged from 4 to 12 with a mean of 7.60. The expected heterozygosity ranged from 0.20to 0.76, with a mean of 0.53, which suggests moderate genetic diversity of D. alata accessions. Kagera region had the highest mean number of (1.5) private alleles. Analysis of molecular variance revealed that 54% of the variation was attributed to within individual, 39% was attributed to among individual while among population contributed 7% of the total variation. The highest Nei's genetic distance (0.43) was for accessions sampled from Kilimanjaro and Mtwara regions. Principal coordinate analysis and cluster analysis using Unweighted Paired Group Method using Arithmetic (UPGMA) grouped D. alata accessions into two major clusters regardless of geographical origin and local names. The Bayesian structure analysis confirmed the two clusters obtained in UPGMA and revealed an admixture of D. alata accessions in all six regions suggesting farmers' extensive exchange of planting materials. These results are helpful in the selection of D. alata accessions for breeding programs in Tanzania.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Map of Tanzania showing regions and study sites where yam samples were collected.
Fig 2
Fig 2. Principal coordinate analysis (PCoA) showing the relationship among 63 D. alata accessions using 10 SSR markers.
Group A contained accessions collected from all five regions while group B had accessions from Kagera, Lindi and Morogoro. Coord. 1 and Coord. 2 represent the first and second coordinates respectively.
Fig 3
Fig 3. UPGMA cluster analysis of 63 D. alata accessions based on 10 SSR markers, using MEGA-X software.
A1 and A2 are sub-clusters of cluster A while B1 and B2 represent sub-clusters of cluster B.
Fig 4
Fig 4. Structure of the genetic diversity of 63 D. alata accessions based on Bayesian analysis of 10 SSR markers at K = 2.
The vertical bar represents yam accessions assigned into two clusters.
See this image and copyright information in PMC

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