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.

Figure 1

Venn diagram showing concordant napiergrass SNPs called by five reference-based SNP callers, SAMtools, GBS-SNP-CROP, GATK, FreeBayes, and TASSEL. Numbers in parenthesis after the program name shows the total number of SNPs called by each program.

Figure 2

Genotyping by sequencing single nucleotide polymorphism (GBS-SNP) marker distribution for the 14 linkage groups of napiergrass. A black bar means a GBS-SNP marker. A blue bar represents segregation distortion region. The left scale plate represents genetic distance (centiMorgan as unit).

Figure 3

Circos plot of the mapped TASSEL de-novo UNEAK napiergrass markers with pearl millet reference genome. Pearl millet pseudomolecules start with “PM” and are color coded for each pseudomolecule. Napiergrass linkage groups start with “LG” and are in green color. Each line corresponds to tags that showed significant BLAST hits to the pearl millet genome (>80% identity and >50 bp length).

Figure 4

Syntenic regions between napiergrass linkage groups and the pearl millet genome. PM01 to PM07 are pearl millet pseudomolecules, LG01 to LG14 are napiergrass linkage groups. The small dots represent significant BLAST hits of mapped UNEAK tags to the pearl millet genome (>80% identity and >50 bp length).