This document summarizes an ongoing project to create a genomic reference resource for African cattle (GRRFAC). The project aims to sequence 600-700 samples from 40 African cattle breeds. So far, 71 samples have been sequenced with 225 more planned by end of 2019. Analysis of sequences shows 38 million SNPs identified across samples. The document also summarizes assessments of ascertainment bias in commercial SNP chips for African cattle, finding lower linkage between chip SNPs and sequence variants in African populations compared to European cattle. Finally, genome-wide scans have identified signatures of selection in African cattle related to heat tolerance, trypanotolerance, and other adaptive traits.

1. African cattle genomic reference resource, SNP
assays, and signatures of selection
Speaker name: Abdulfatai Tijjani
Speaker organisation/s: ILRI – Addis Ababa
Investigators: Karen Marshall (ILRI), Kellie Watson (CTLGH), James
Prendergast (Roslin) and Olivier Hanotte (ILRI)
CTLGH Annual Meeting, Edinburgh, 24-25 September 2019

2.  Genomic reference resource for African cattle (GRRFAC)
 Assessment of the commercial Bovine HD SNP chip
 Genome-wide scans for signatures of positive selection in African cattle
Outline

3. GRRFAC – Objectives
 to facilitate the generation of a set of sequences and genotype information on African cattle, for
use by African and international research communities in cattle genomics for the ultimate benefit
of African livestock keepers
 We aim to collate between 600 and 700 sequences of African cattle samples covering up to 40
African indigenous breeds. This will comprise about 300 new sequences that we envisaged to
generate by the end of 2019, while the remaining sequences will be obtained from other sources
including public databases and ILRI collaborators including the 1000 Bull genome project in which
ILRI is a consortium member
Facilitate the capacity building of African researchers in the field of genomics

4. GRRFAC – project update
National partners
Total number of African national partners 13
Cattle breeds
Total number of breeds 40
The number currently classified as taurine 8
The number currently classified as zebu 28
Number currently classified as zebu x taurine crosses 4
Cattle Samples
Total number of samples 1500
Total number of samples with sequence generated under this project 71
Additional samples planned to have new sequence by the end of 2019 225
A summary of the current status of the resource

5. GRRFAC – project update
Indigenous African cattle Breeds and countries where samples were collected
GRRFAC collaborators
Country Research partner
Senegal Ecole Inter Etats des Sciences et Médecine
Vétérinaires de Dakar (EISMV)
Malawi (LAUNAR)
Burkina Faso Institut de l’Environnement et de Recherches
Agricoles (INERA), Ouagadougougou
Chad National High Institute of Sciences and
Techniques, Abeche
Togo Universite de Lome
Sudan University of Khartoum
Ethiopia Ethiopian Biodervisity Institute (EBI)
Rwanda Rwanda Agricultural Board
Kenya National Environment Management Agency
(NEMA)
Madagascar Ministère de l’Elevage
Ghana University of Ghana
Guinea Central Vétérinaire de Dianostic (LCVD)
Nigeria Centre for Genomic Research and Innovation
(CGRI), NABDA
Benin Laboratoire de Biotechnologie Animale et
de Technologie des Viandes
 13 African partners, 40 African cattle breeds and
about 1500 samples

6. GRRFAC – project update
principal component analysis of the currently
collated African cattle samples/breeds in
relation to reference cattle breeds.
 13 African partners, 40 African cattle breeds and
about 1500 samples
 Whole genome sequences of up to 380 samples is
already in our database and the generation of
new sequences is on-going
 Sequences are being mapped to the latest Bos
taurus reference genome assembly (ARS-UCD1.2)
for variants discovery and further analyses
 About 38 million SNPs identified in all samples
and PCA of these samples shown

7.  to test the hypothesis that a meaningful proportion of African cattle SNPs remain unrepresented
on the existing BovineHD SNP panel, resulting in ascertainment bias when utilized in the study
involving African indigenous cattle
we will investigate the relative genome-wide correlation between BovineHD-SNPs and sequence
variants within appropriate genomic windows. A significant and meaningful difference between
European and African genotypes in terms of the sequence-based polymorphism which are (and are
not) in LD with SNPs contained in the BovineHD would suggest there is a benefit in developing a
supplementary SNP assay for African cattle.
Assessment of the commercial Bovine
HD SNP chip - Objectives

8. Our plan is to calculate the R-
squared values between
BovineHD SNP genotypes and
the sequence variants of
African cattle breeds (mainly
N’dama and Boran) and to
compare these values to that
obtained in European Bos
taurus.
Assessment of
the commercial
Bovine HD SNP
chip - Update
Breed Country Number samples Status
N’dama Senegal 19 30 x sequence data available on 9
animals; 10 additional samples
already submitted for sequencing
N’dama Guinea 15 15 samples already submitted for
sequencing
N’dama Nigeria 15 15 samples already submitted for
sequencing / Access and benefit-
sharing agreement for ILRI use of
data in negotiation/
N’dama Kenya 1 (used to
generate
reference
genome)
Access and benefit-sharing
agreement in negotiation
Boran (Improved) Kenya 15 Access and benefit-sharing
agreement obtained/ sequences of 6
samples have been generated under
different ILRI project
Boran (Orma) Kenya 15 Access and benefit-sharing
agreement in negotiation/15 samples
for sequencing are being identified
Boran Ethiopia 20 Access and benefit-sharing
agreement obtained /20 samples for
sequencing are being identified

9. Bovine HD SNP chip - Update
preliminary assessments reveal lower proportions of SNPs
captured on the SNP chip are in high linkage disequilibrium with
the sequence variants in African cattle population when
compared to the European Bos taurus
West African taurine
 Muturu
 N’dama
 Baoule
 Ghana Shorthorn
African zebu
 Ethiopian Boran
 Afar
 Bale
 Semien
Bos indicus
 Gir
 Nellore
 Brahman
European Bos taurus
 Holstein

10.  Genome-wide investigation of signature of positive selection underpinning adaptability/resilience
and productivity traits in African indigenous cattle
 Initial focus is on thermotolerance , trypanotolerance and milk production traits
 Several widely used selection scan approaches will be adopted for this investigation, including
1. Within-population tests (e.g. Integrated Haplotype Score (iHS), Composite Likelihood Ratio
(CLR), pooled heterozygosity (Hp), and
2. Between-population tests (eg. Population differentiation (FST), Cross-population Extended
Haplotype Homozygosity (XPEHH), Cross-population Composite Likelihood Ratio (XPCLR)
and Haplotype differentiation (hapFLK))
Signature of Selection analysis : Objectives

11. Signature of Selection analysis : Update
comparative genome-wide
selection scan of the genome
of African indigenous
Trypanotolerant cattle
population based on
population differentiation
(FST) test.
Chr Start end
2 61489617 61524285 MCM6 cell cycle
7 50736654 50743097 TMEM173 innate immune res[ponse
7 49921360 50255751 CTNNA1 Leukocyte transendothelial migration
11 7203304 7233720 IL18RAP Cytokine-cytokine Receptor interaction
11 7165278 7193294 IL18R1 Cytokine-cytokine Receptor interaction
19 27879985 27895903 PFAS Purine metabolism
19 40524612 40546357 CDC6 cell cycle
21 67549224 67603033 TRAF3 innate immune res[ponse
Position (bp) overlapping
gene
function
West African taurine
 Muturu
 N’dama
 Baoule
 Ghana Shorthorn

12. comparative genome-wide selection scan of the genome of
African indigenous cattle breeds based on population
differentiation (FST) test, for investigation of the genomic
regions under position selection due to adaption to heat
stress.
Signature of Selection analysis : Update
Chr Start end
1 3824601 3833406 SOD1 protein polyubiquitination
5 47564309 47624668 IRAK3 response to lipopolysaccharide
7 49825961 49830306 EGR1 response to hypoxia, glucose
7 60743594 60752561 GRPEL2 protein folding
7 49894161 49909804 HSPA9 protein folding
7 51435093 51510425 PFDN1 protein folding
7 53035569 53054126 RNF14 protein polyubiquitination
10 70906350 70915756 DACT1 regulation of protein stability
18 14051588 14127897 CBFA2T3 response to hypoxia
19 40559946 40595285 RARA cellular response to lipopolysaccharide
26 22130152 22301533 BTRC protein polyubiquitination
Position (bp) overlapping
gene
function

13. Continued efforts are being undertaken to ensure the resource is compliant re-access and benefit-
sharing legislation of provider countries (i.e. the African partner countries), as well as user countries
(Kenya and the United Kingdom)
Discussions with partners are on-going in relation to establishing a consortium around the obtained
samples and data generated.
 sequencing of more samples are expected soonest and much more samples are being prepared for
sequencing
 further downstream analysis will be performed to meet set objectives
Going forward . . . . . .

14. Olivier Hanotte
Karen Marshall
 James Prendergast
Kellie Watson
Acknowledgements

15. CTLGH Funders

16. www.ctlgh.org