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

Abstract

Napier grass is an important tropical forage-grass and of growing potential as an energy crop. One-hundred-five Napier grass accessions, encompassing two independent collections, were subjected to genotyping by sequencing which generated a set of high-density genome-wide markers together with short sequence reads. The reads, averaging 54 nucleotides, were mapped to the pearl millet genome and the closest genes and annotation information were used to select candidate genes linked to key forage traits. 980 highly polymorphic SNP markers, distributed across the genome, were used to assess population structure and diversity with seven-subgroups identified. A few representative accessions were selected with the objective of distributing subsets of a manageable size for further evaluation. Genome-wide linkage disequilibrium (LD) analyses revealed a fast LD-decay, on average 2.54 kbp, in the combined population with a slower LD-decay in the ILRI collection compared with the EMBRAPA collection, the significance of which is discussed. This initiative generated high-density markers with a good distribution across the genome. The diversity analysis revealed the existence of a substantial amount of variation in the ILRI collection and identified some unique materials from the EMBRAPA collection, demonstrating the potential of the overall population for further genetic and marker-trait-association studies.

Genotyping-By-Sequencing Reveals Population Structure and Genetic Diversity of a Buffelgrass (Cenchrus ciliaris L.) Collection

“…Analysis of molecular variance (AMOVA) was conducted to determine the contribution of, among, and within cluster variation to the total variation using GenAlex 6.5 [32]. The STRUCTURE software [33,34] was used to analyze population structure as described elsewhere [35], with modifications as follows: The burn-in time and number of iterations were set to 30,000, with three repetitions testing the probability of K = 2-20 subpopulations. The results of the run were uploaded to the software "Structure harvester" [36] and the optimal number of subpopulations was determined by the Evanno method [37].…”

Forage Performance and Detection of Marker Trait Associations with Potential for Napier Grass (Cenchrus purpureus) Improvement

“…For genetic analysis, leaf sample collection, DNA extraction, and genotyping were conducted, as described previously by Muktar et al [12].…”

“…In addition, the simple ANOVA model, which assumes that genotypes are independent, was employed to test the association of each marker with the trait. The collection was genotyped using the DArTseq platform (http://www.diversityarrays.com) to generate genome wide (SNP and SilicoDArT) markers, as described previously [12]. The genome-wide marker data, together with the phenotype data for annual dry weight production and metabolizable energy, were used in the marker-trait association analysis.…”

“…The DArTseq genotyping platform [52] produces short sequence reads, averaging about 55 nt in length, corresponding to each of the SilicoDArT and SNP markers [12]. In this study, the short sequence reads corresponding to the associated markers were compared with previously reported Napier grass genomic [30] and transcriptome [31] sequences.…”

“…Napier grass has limited genomic information available, and, until recently, only a handful of molecular markers have been applied, mainly in studies targeting the assessment of genetic diversity. Although the recent advances in the genotyping by sequencing (GBS) approach have enabled the generation of a large number of high-density genome-wide markers [12][13][14], this species still lacks a reference genome. Hence, the reference genome sequence of pearl millet [15], a closely related species to Napier grass, has been used for mapping the genome-wide markers.…”