Genotyping by sequencing provides new insights into the diversity of Napier grass (Cenchrus purpureus) and reveals variation in genome-wide LD patterns between collections

We report on the development of genome-wide and sequence-based molecular markers for 105 Napier grass accessions held in the International Livestock Research Institute genebank using the DArTseq platform

Meki S. Muktar; Abel Teshome; Jean Hanson; Alemayehu T. Negawo; Ermias Habte; Jean-Baka Domelevo Entfellner; Ki-Won Lee; Chris S. Jones

2019

Scholarcy highlights

  • Napier grass Morrone syn
  • The genotyping by sequencing approach, which enabled the identification of high quality genome-wide simple sequence repeat and single nucleotide polymorphism markers, has recently been applied to Napier grass leading to the construction of the first high density linkage map in this species
  • The collection from the International Livestock Research Institute forage genebank represents a diverse set of genotypes assembled from a range of environments and origins which is maintained in situ at the Bishoftu and Ziway sites in Ethiopia
  • The SilicoDArT and SNP markers identified in our study, in conjunction with SSR and SNP markers developed by Paudel et al. and Wang et al., serve to enhance the data resources available for Napier grass improvement using marker assisted breeding
  • The genetic diversity analysis revealed the presence of considerable variation in the Napier grass collection maintained in the ILRI genebank and identified some unique materials from the EMBRAPA collection, showing the suitability of the population for further genetic and marker-trait association studies
  • The minor allele frequency of the markers was greater than 5% and the missing values were less than 10%
  • A fast rate of linkage disequilibrium-decay was observed across the Napier grass A′ genome and the LD decayed more slowly in the ILRI collection when compared to the EMBRAPA collection, suggesting that the materials from ILRI contain long haplotype blocks, in which a large amount of variation may be stacked which could potentially be released by crossing
  • A fast rate of linkage disequilibrium-decay was observed across the Napier grass A′ genome and the LD decayed more slowly in the International Livestock Research Institute collection when compared to the EMBRAPA collection, suggesting that the materials from ILRI contain long haplotype blocks, in which a large amount of variation may be stacked which could potentially be released by crossing

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