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ARS Home » Southeast Area » Tifton, Georgia » Crop Genetics and Breeding Research » Research » Publications at this Location » Publication #351730

Research Project: Genetic Enhancement and Management of Warm-season Species for Forage, Turf and Renewable Energy

Location: Crop Genetics and Breeding Research

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

item PAUDEL, DEV - University Of Florida
item KANNAN, BASKARAN - University Of Florida
item YANG, YIPING - University Of Florida
item Harris-Shultz, Karen
item THUDI, MAHENDAR - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item VARSHNEY, RAJEEV - International Crops Research Institute For Semi-Arid Tropics (ICRISAT) - India
item ALTPETER, FREDY - University Of Florida
item WANG, JIANPING - University Of Florida

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/13/2018
Publication Date: 9/26/2018
Citation: Paudel, D., Kannan, B., Yang, Y., Harris-Shultz, K.R., Thudi, M., Varshney, R., Altpeter, F., Wang, J. 2018. Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach.). Scientific Reports. 8:14419.

Interpretive Summary: Napiergrass is a tropical perennial grass used for forage and has potential for use as a lignocellulosic feedstock for fuel ethanol. Improvement of napiergrass for agronomic traits such as flowering time, abiotic and biotic stress tolerance, etc. has been limited and few genetic resources exist for napiergrass. In this study millions of sequencing reads were generated for napiergrass and the largest resulting contigs (overlapping reads) were aligned to the genome of pear millet. From these sequences, 5339 simple sequence repeat (SSR) markers were created which will be useful for napiergrass breeding. Furthermore, a linkage map was constructed using single nucleotide polymorphism markers in napiergrass using the progeny of a cross between two napiergrass parents. The linkage map will be used for the identification of genomic regions in napiergrass that are associated with traits of interest. Thus, this study provided genetic resources for napiergrass and identified regions of similarity that exist between the napiergrass linkage groups and the pearl millet chromosomes.

Technical Abstract: Napiergrass, Cenchrus purpureus (Schumach.) Morrone, is a tropical forage grass and a promising lignocellulosic biofuel feedstock due to its high biomass yield, persistence, and nutritive value. However, genetic improvement of napiergrass has lagged behind other crops due to a lack of genomic resources and an absence of a genetic linkage map. In this study, next-generation sequencing was used to survey the genome of napiergrass. The genome sequence of napiergrass displayed high synteny to the genome of pearl millet. From the napiergrass sequences, a total of 5,339 SSRs were identified and characterized. Furthermore, SNP markers were identified from a bi-parental population using genotyping by sequencing. Multiple programs (TASSEL, GBS-SNP-CROP, STACKS, Freebayes, Samtools, and GATK) were used for de-novo and reference based single nucleotide polymorphism (SNP) identification. The resulting SNPs allowed the first high density consensus linkage map to be constructed with 1,917 SNP markers on 14 linkage groups, spanning a length of 1473.94 cM and a density of 1 marker per 0.76 cM. This map can be used for many further genetic and genomic studies in napiergrass and related species.