Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach)

Abstract

Napiergrass (Cenchrus purpureus Schumach) is a tropical forage grass and a promising lignocellulosic biofuel feedstock due to its high biomass yield, persistence, and nutritive value. However, its utilization for breeding has lagged behind other crops due to limited genetic and genomic resources. In this study, next-generation sequencing was first used to survey the genome of napiergrass. Napiergrass sequences displayed high synteny to the pearl millet genome and showed expansions in the pearl millet genome along with genomic rearrangements between the two genomes. An average repeat content of 27.5% was observed in napiergrass including 5,339 simple sequence repeats (SSRs). Furthermore, to construct a high-density genetic map of napiergrass, genotyping-by-sequencing (GBS) was employed in a bi-parental population of 185 F1 hybrids. A total of 512 million high quality reads were generated and 287,093 SNPs were called by using multiple de-novo and reference-based SNP callers. Single dose SNPs were used to construct the first high-density linkage map that resulted in 1,913 SNPs mapped to 14 linkage groups, spanning a length of 1,410 cM and a density of 1 marker per 0.73 cM. This map can be used for many further genetic and genomic studies in napiergrass and related species.

QTL mapping of flowering time and biomass yield in tetraploid alfalfa (Medicago sativa L.)

“…Using this strategy, linkage maps can be constructed by the software designed for diploids such as JoinMap (https://www.kyazma.nl/docs/JM5Manual.pdf). Although the pseudo-testcross strategy uses only a portion of markers of the genome, it is still useful for polyploid species with complex genomes and marker segregation ratios, and the method has been successfully used in various species [28, 29].…”

High-Resolution Linkage Map With Allele Dosage Allows the Identification of Regions Governing Complex Traits and Apospory in Guinea Grass (Megathyrsus maximus)

“…Since genotyping errors are probable, a large Pelloux et al (2007) amount of missing data and a large number of distorted loci may promote the expansion of linkage maps as well as overestimate the recombination fractions and limit the accuracy of the mapping (Cartwright et al, 2007;Gerard et al, 2018). However, SD is a phenomenon commonly found in the genome, and some linkage maps contain distorted markers, including those of grasses such as pearl millet (Sehgal et al, 2012) and napiergrass (Paudel et al, 2018). Therefore, greater knowledge of the occurrence and genetic causes of SD in plants is important for inferring which genes are kept together or separated by SD (Zhu et al, 2006;Anhalt et al, 2008).…”

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

“…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.…”