Genetic Variation and Population Structure of Oryza glaberrima and Development of a Mini-Core Collection Using DArTseq

Frontiers in Plant Science
Marie-Noelle NdjiondjopMarilyn L Warburton

Abstract

The sequence variation present in accessions conserved in genebanks can best be used in plant improvement when it is properly characterized and published. Using low cost and high density single nucleotide polymorphism (SNP) assays, the genetic diversity, population structure, and relatedness between pairs of accessions can be quickly assessed. This information is relevant for different purposes, including creating core and mini-core sets that represent the maximum possible genetic variation contained in the whole collection. Here, we studied the genetic variation and population structure of 2,179 Oryza glaberrima Steud. accessions conserved at the AfricaRice genebank using 27,560 DArTseq-based SNPs. Only 14% (3,834 of 27,560) of the SNPs were polymorphic across the 2,179 accessions, which is much lower than diversity reported in other Oryza species. Genetic distance between pairs of accessions varied from 0.005 to 0.306, with 1.5% of the pairs nearly identical, 8.0% of the pairs similar, 78.1% of the pairs moderately distant, and 12.4% of the pairs very distant. The number of redundant accessions that contribute little or no new genetic variation to the O. glaberrima collection was very low. Using the maximum length sub-tree me...Continue Reading

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Citations

Mar 7, 2019·PloS One·Margaretha A VeltmanM Eric Schranz
Dec 24, 2018·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Marie Noelle NdjiondjopKassa Semagn
Nov 13, 2018·Molecular Breeding : New Strategies in Plant Improvement·Marie Noelle NdjiondjopDule Zhao
Oct 7, 2020·Plants·Michael HalewoodCharlotte Lusty

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Methods Mentioned

BETA
genotyping
PCA

Software Mentioned

DArTseq
DARwin
MSTRAT
STRUCTURE
XLSTAT
molecular evolutionary genetics analysis ( MEGA )
DArTsoft
Core Hunter
Dissimilarity Analysis and Representation for windows ( DARwin )
ARLEQUIN

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