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

Paudel, D and Kannan, B and Yang, X and Harris-Shultz, K and Thudi, M and Varshney, R K and Altpeter, F and Wang, J (2018) Surveying the genome and constructing a high-density genetic map of napiergrass (Cenchrus purpureus Schumach). Scientific Reports (TSI), 8 (1) (14419). pp. 1-11. ISSN 2045-2322

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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.

Item Type: Article
Divisions: Research Program : Genetic Gains
CRP: UNSPECIFIED
Uncontrolled Keywords: genetic map, napiergrass, genomics, genetics, napiergrass, elephant grass, tropical perennial grass, Africa, napiergrass genome survey, genotyping-by-sequencing, SNPs, pearl millet, Cenchrus purpureus Schumach
Subjects: Mandate crops > Millets > Pearl Millet
Others > Genetics and Genomics
Others > Africa
Depositing User: Mr Ramesh K
Date Deposited: 01 Oct 2018 09:00
Last Modified: 01 Oct 2018 09:47
URI: http://oar.icrisat.org/id/eprint/10883
Official URL: http://dx.doi.org/10.1038/s41598-018-32674-x
Projects: Hatch Project
Funders: Plant Breeders Workgroup, University of Florida and by the USDA National Institute of Food and Agriculture
Acknowledgement: This work was funded in part by the Plant Breeders Workgroup, University of Florida and by the USDA National Institute of Food and Agriculture, Hatch project 1003932. We like to thank William Anderson USDA-ARS, Tifton, GA for providing napiergrass accession N122 and Sun Gro Horticulture, Apopka, FL, for donation of the Fafard #2 potting mix.
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