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

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 frst 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 frst high-density linkage map that resulted in 1,913 SNPs mapped to 14 linkage groups, spanning a length of 1,410cM and a density of 1 marker per 0.73cM. This map can be used for many further genetic and genomic studies in napiergrass and related species.

Genetic map files for Elephant grass genetic map.
Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach)

# Marker files:
Sex averaged map: map_NG_final_geneticmap_1913.txt
Female map: map_female_selected899_lm.txt
Male map: map_male_selected1073_nn.txt 

# Sequence and locus information.
All reference based pipelines used the pearl millet genome v1 as explained in the manuscript. Sequences for the reference pipelines can be extracted based on the location of the SNPs. For denovo based pipelines, either the sequences or the locus and denovo map are included.

Freebayes (F)
- 1_freebayes_48.vcf.gz

GATK (G)
- 2_gatk_48.vcf.gz

Samtools (St)
- 3_samtools_48.vcf.gz

GBS-SNP-CROP (C)
- 4_snpcrop.hmp.txt

TASSEL (T)
- 5_tassel.hmp.txt.gz

Stacks (St)
- 6a_stacks_loc.gz
- 6b_stacks_snp.vcf.gz

denovo GBS-SNP-CROP (dC)
- 7a_denovo_SNP_CROP.hmp.txt
- 7b_snpcrop_MockRef2PP.MockRef_Genome.fasta

denovo Stacks (dS)
- 8a_denovo_stacks.loc
- 8b_denovo_stacks_sequences.tsv

denovo TASSEL (dT)
- 9_denovo_tassel_uneak.fas

# Comparison between elephant grass and pearl millet genome:
- Filterdp20_Elephantgrass.vcf.gz