Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants

Abdulfatai Tijjani; Sumaya Kambal; Endashaw Terefe; Regina Njeru; Moses Ogugo; Gideon Ndambuki; Ayao Missohou; Amadou Traore; Bashir Salim; Chukwunonso Ezeasor; Claire D'andre H; Emmanuel T Obishakin; Boubacar Diallo; Essodina Talaki; Issaka Y Abdoukarim; Oyekanmi Nash; Richard Osei-Amponsah; Simeone Ravaorimanana; Youssouf Issa; Tsadkan Zegeye; Christopher Mukasa; Christian Tiambo; James G D Prendergast; Stephen J Kemp; Jianlin Han; Karen Marshall; Olivier Hanotte

doi:10.1038/s41597-024-03589-2

Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants

Abdulfatai Tijjani, Sumaya Kambal, Endashaw Terefe, Regina Njeru, Moses Ogugo, Gideon Ndambuki, Ayao Missohou, Amadou Traore, Bashir Salim, Chukwunonso Ezeasor, Claire D'andre H, Emmanuel T Obishakin, Boubacar Diallo, Essodina Talaki, Issaka Y Abdoukarim, Oyekanmi Nash, Richard Osei-Amponsah, Simeone Ravaorimanana, Youssouf Issa, Tsadkan ZegeyeChristopher Mukasa, Christian Tiambo, James G D Prendergast, Stephen J Kemp, Jianlin Han, Karen Marshall, Olivier Hanotte

Royal (Dick) School of Veterinary Studies

Research output: Contribution to journal › Article › peer-review

Abstract / Description of output

The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.

Original language	English
Article number	801
Pages (from-to)	1-10
Number of pages	10
Journal	Scientific Data
Volume	11
Issue number	1
Early online date	19 Jul 2024
DOIs	https://doi.org/10.1038/s41597-024-03589-2
Publication status	E-pub ahead of print - 19 Jul 2024

Keywords / Materials (for Non-textual outputs)

Cattle/genetics
Animals
Genome
Genomics
Africa
Breeding
Genetic Variation

Access to Document

10.1038/s41597-024-03589-2

Tijjani_et_al-2024-Scientific_DataAccepted author manuscript, 2.28 MBLicence: Creative Commons: Attribution (CC-BY)
s41597-024-03589-2Final published version, 2.28 MBLicence: Creative Commons: Attribution (CC-BY)

Cite this

Tijjani, A., Kambal, S., Terefe, E., Njeru, R., Ogugo, M., Ndambuki, G., Missohou, A., Traore, A., Salim, B., Ezeasor, C., D'andre H, C., Obishakin, E. T., Diallo, B., Talaki, E., Abdoukarim, I. Y., Nash, O., Osei-Amponsah, R., Ravaorimanana, S., Issa, Y., ... Hanotte, O. (2024). Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants. Scientific Data, 11(1), 1-10. Article 801. Advance online publication. https://doi.org/10.1038/s41597-024-03589-2

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abstract = "The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.",

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author = "Abdulfatai Tijjani and Sumaya Kambal and Endashaw Terefe and Regina Njeru and Moses Ogugo and Gideon Ndambuki and Ayao Missohou and Amadou Traore and Bashir Salim and Chukwunonso Ezeasor and {D'andre H}, Claire and Obishakin, {Emmanuel T} and Boubacar Diallo and Essodina Talaki and Abdoukarim, {Issaka Y} and Oyekanmi Nash and Richard Osei-Amponsah and Simeone Ravaorimanana and Youssouf Issa and Tsadkan Zegeye and Christopher Mukasa and Christian Tiambo and Prendergast, {James G D} and Kemp, {Stephen J} and Jianlin Han and Karen Marshall and Olivier Hanotte",

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Tijjani, A, Kambal, S, Terefe, E, Njeru, R, Ogugo, M, Ndambuki, G, Missohou, A, Traore, A, Salim, B, Ezeasor, C, D'andre H, C, Obishakin, ET, Diallo, B, Talaki, E, Abdoukarim, IY, Nash, O, Osei-Amponsah, R, Ravaorimanana, S, Issa, Y, Zegeye, T, Mukasa, C, Tiambo, C, Prendergast, JGD, Kemp, SJ, Han, J, Marshall, K & Hanotte, O 2024, 'Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants', Scientific Data, vol. 11, no. 1, 801, pp. 1-10. https://doi.org/10.1038/s41597-024-03589-2

TY - JOUR

T1 - Genomic Reference Resource for African Cattle

T2 - Genome Sequences and High-Density Array Variants

AU - Tijjani, Abdulfatai

AU - Kambal, Sumaya

AU - Terefe, Endashaw

AU - Njeru, Regina

AU - Ogugo, Moses

AU - Ndambuki, Gideon

AU - Missohou, Ayao

AU - Traore, Amadou

AU - Salim, Bashir

AU - Ezeasor, Chukwunonso

AU - D'andre H, Claire

AU - Obishakin, Emmanuel T

AU - Diallo, Boubacar

AU - Talaki, Essodina

AU - Abdoukarim, Issaka Y

AU - Nash, Oyekanmi

AU - Osei-Amponsah, Richard

AU - Ravaorimanana, Simeone

AU - Issa, Youssouf

AU - Zegeye, Tsadkan

AU - Mukasa, Christopher

AU - Tiambo, Christian

AU - Prendergast, James G D

AU - Kemp, Stephen J

AU - Han, Jianlin

AU - Marshall, Karen

AU - Hanotte, Olivier

PY - 2024/7/19

Y1 - 2024/7/19

N2 - The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.

AB - The diversity in genome resources is fundamental to designing genomic strategies for local breed improvement and utilisation. These resources also support gene discovery and enhance our understanding of the mechanisms of resilience with applications beyond local breeds. Here, we report the genome sequences of 555 cattle (208 of which comprise new data) and high-density (HD) array genotyping of 1,082 samples (537 new samples) from indigenous African cattle populations. The new sequences have an average genome coverage of ~30X, three times higher than the average (~10X) of the over 300 sequences already in the public domain. Following variant quality checks, we identified approximately 32.3 million sequence variants and 661,943 HD autosomal variants mapped to the Bos taurus reference genome (ARS-UCD1.2). The new datasets were generated as part of the Centre for Tropical Livestock Genetics and Health (CTLGH) Genomic Reference Resource for African Cattle (GRRFAC) initiative, which aspires to facilitate the generation of this livestock resource and hopes for its utilisation for complete indigenous breed characterisation and sustainable global livestock improvement.

KW - Cattle/genetics

KW - Animals

KW - Genome

KW - Genomics

KW - Africa

KW - Breeding

KW - Genetic Variation

U2 - 10.1038/s41597-024-03589-2

DO - 10.1038/s41597-024-03589-2

M3 - Article

C2 - 39030190

SN - 2052-4463

VL - 11

SP - 1

EP - 10

JO - Scientific Data

JF - Scientific Data

IS - 1

M1 - 801

ER -

Genomic Reference Resource for African Cattle: Genome Sequences and High-Density Array Variants

Abstract / Description of output

Keywords / Materials (for Non-textual outputs)

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