Abstract
Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = − 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops.
Highlights
ObjectivesThe objectives of this study were to (1) compare different dissimilarity matrices and hierarchical clustering methods for evaluating genetic diversity in white Guinea yam, (2) assess the genetic diversity and differentiation in a population of white Guinea yam using morphological, molecular and combined data
The dissimilarity coefficient, as well as clustering method used for genetic diversity analysis, have implications on the r esults[23,25], the choice of an appropriate coefficient and hierarchical clustering method is critical for determining the accuracy of the genetic variability among individuals
The UPGMA method was observed to give high cophenetic correlation coefficients for most of the dissimilarity matrices across the molecular, morphological, and combined data, demonstrating that there is a good representation of the dissimilarity matrices and distances in the form of dendrograms
Summary
The objectives of this study were to (1) compare different dissimilarity matrices and hierarchical clustering methods for evaluating genetic diversity in white Guinea yam, (2) assess the genetic diversity and differentiation in a population of white Guinea yam using morphological, molecular and combined data
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