Genotyping-by-sequencing (GBS) dataset for 185 accessions of buffel grass (<em>Cenchrus ciliaris</em>)

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Negawo, Alemayehu Teressa; Jones, Chris, 2024, "Genotyping-by-sequencing (GBS) dataset for 185 accessions of buffel grass (Cenchrus ciliaris)", https://hdl.handle.net/20.500.11766.1/FK2/KRKYBD, MELDATA, V1

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Description	This dataset presents 7,506 SNP markers (genotype calls "0", "1" and "2) and 8,345 silicoDArT markers (presence/absence, calls "0" and "1), each on 185 accessions of Cenchrus ciliaris, aka. buffel grass (csv list attached). In both xlsx files, missing genotype calls are encoded "-". SNP calls are encoded as follows: 0 = homozygote in the reference allele, 1 = homozygote in the alternative (SNP) allele, 2 = heterozygote. This GBS information pertains to buffel grass i.e. Cenchrus ciliaris (aka. Pennisetum ciliare), but any mapping information, when present, relates the markers to Setaria italica (foxtail millet) in the "Setaria_italica_v2.0" genome assembly of its Yugu1 strain, with INSDC identifier GCA_000263155.2.
Subject	Agricultural Sciences; Earth and Environmental Sciences; Medicine, Health and Life Sciences
Keyword	genotyping-by-sequencing, buffel grass (cenchrus ciliaris l.), dartseq markers, dartseq analysis, buffel grass (cenchrus)
Related Publication	Negawo, A.T.; Muktar, M.S.; Gutiérrez, R.A.S.; Habte, E.; Muchugi, A.; Jones, C.S. A Genome-Wide Association Study of Biomass Yield and Feed Quality in Buffel Grass (Cenchrus ciliaris L.). Agriculture 2024, 14, 257. https://doi.org/10.3390/agriculture14020257 doi: 10.3390/agriculture14020257
Notes	Type: Dataset; Sub-type(s): Other (Genotyping-by-sequencing (GBS) dataset)
License/Data Use Agreement	Custom Dataset Terms

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	accessions.csv Comma Separated Values - 1.0 KB Published Feb 26, 2024 5 Downloads MD5: 658e7207090905e04df17ee384103149	Access File File Access Public Download Options Comma Separated Values Download Metadata Data File Citation EndNote XML RIS BibTeX
	ILRI_s_GBS_data_on_Buffel_grass_SilicosDArT_markers.xlsx MS Excel Spreadsheet - 6.1 MB Published Feb 26, 2024 4 Downloads MD5: 8b5c47d2e7362a7af6d5abe4c8d6e28e	Access File File Access Public Download Options MS Excel Spreadsheet Download Metadata Data File Citation EndNote XML RIS BibTeX
	ILRI_s_GBS_data_on_Buffel_grass_SNP_markers.xlsx MS Excel Spreadsheet - 5.8 MB Published Feb 26, 2024 6 Downloads MD5: eed362858f3063b90acc53808216c6be	Access File File Access Public Download Options MS Excel Spreadsheet Download Metadata Data File Citation EndNote XML RIS BibTeX

Citation Metadata

Persistent Identifier	hdl:20.500.11766.1/FK2/KRKYBD
Publication Date	2024-02-26
Title	Genotyping-by-sequencing (GBS) dataset for 185 accessions of buffel grass (Cenchrus ciliaris)
Other Identifier	MEL: 42168
Author	Negawo, Alemayehu Teressa (International Livestock Research Institute - ILRI) Jones, Chris (International Livestock Research Institute - ILRI)
Point of Contact	Use email button above to contact. Jones, Chris (International Livestock Research Institute - ILRI)
Description	This dataset presents 7,506 SNP markers (genotype calls "0", "1" and "2) and 8,345 silicoDArT markers (presence/absence, calls "0" and "1), each on 185 accessions of Cenchrus ciliaris, aka. buffel grass (csv list attached). In both xlsx files, missing genotype calls are encoded "-". SNP calls are encoded as follows: 0 = homozygote in the reference allele, 1 = homozygote in the alternative (SNP) allele, 2 = heterozygote. This GBS information pertains to buffel grass i.e. Cenchrus ciliaris (aka. Pennisetum ciliare), but any mapping information, when present, relates the markers to Setaria italica (foxtail millet) in the "Setaria_italica_v2.0" genome assembly of its Yugu1 strain, with INSDC identifier GCA_000263155.2.
Subject	Agricultural Sciences; Earth and Environmental Sciences; Medicine, Health and Life Sciences
Keyword	genotyping-by-sequencing (AGROVOC) http://aims.fao.org/aos/agrovoc/c_86f26167 buffel grass (cenchrus ciliaris l.) dartseq markers dartseq analysis buffel grass (cenchrus) (AGROVOC) http://aims.fao.org/aos/agrovoc/c_1428
Related Publication	Negawo, A.T.; Muktar, M.S.; Gutiérrez, R.A.S.; Habte, E.; Muchugi, A.; Jones, C.S. A Genome-Wide Association Study of Biomass Yield and Feed Quality in Buffel Grass (Cenchrus ciliaris L.). Agriculture 2024, 14, 257. https://doi.org/10.3390/agriculture14020257 doi: 10.3390/agriculture14020257 https://doi.org/10.3390/agriculture14020257 Negawo, A.T.; Assefa, Y.; Hanson, J.; Abdena, A.; Muktar, M.S.; Habte, E.; Sartie, A.M.; Jones, C.S. Genotyping-By-Sequencing Reveals Population Structure and Genetic Diversity of a Buffelgrass (Cenchrus ciliaris L.) Collection. Diversity 2020, 12, 88. https://doi.org/10.3390/d12030088 doi: 10.3390/d12030088 https://doi.org/10.3390/d12030088
Notes	Type: Dataset; Sub-type(s): Other (Genotyping-by-sequencing (GBS) dataset)
Language	English
Producer	International Livestock Research Institute (ILRI) http://www.ilri.org/
Production Date	2024-02-26
Contributor	Data Curator : Alemayehu Teressa Negawo (International Livestock Research Institute - ILRI) Funder : Deutsche Gesellschaft für Internationale Zusammenarbeit - GIZ Funder : CGIAR Research Program on Genebanks Funder : CGIAR Trust Fund Project Manager : Alemayehu Teressa Negawo (International Livestock Research Institute - ILRI)
Deposit Date	2024-02-26
Origin of Historical Sources	DArT genotyping platform

Geospatial Metadata

Geographic Coverage	Ethiopia, Addis Ababa
Geographic Unit	Africa

Social Science and Humanities Metadata

Unit of Analysis	buffel grass accession
Universe	buffel grass (Cenchrus ciliaris) collection
Time Method	panel
Sampling Procedure	DNA extracted from leaf samples of each accession was submitted to genotyping-by-sequencing (GBS) analysis using the DArT platform (Diversity Array Technologies), whereby random markers covering the whole genome have been produced through enzymatic digestion. This dataset is made of 185 accessions, 7,506 SNP (allelic) markers and 8,345 silicoDArT (presence/absence) markers.

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