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

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.

Fig. 1

The African continent map shows the sampling countries for high-density genotyping (HD, triangle) and whole-genome sequencing (WGS, circle). East African zebu (EAZ), East African admixed (EAA), Central African zebu (CAZ), Central African Admixed (CAA), West African zebu (WAZ), West African admixed (WAA), Central African taurine (CAT), and West African taurine (WAT).

Fig. 2

An overview of the workflow for sequence mapping and variant discovery pipeline. The pipeline follows the Broad Institute’s recommended Genome Analysis Tool Kit best practices for germline short variant discovery.

Fig. 3

The distribution of coverage and estimated sequence yield for 208 new genomes of indigenous African cattle.

Fig. 4

The distribution of detected SNPs in indigenous African cattle per Bos taurus autosomal chromosomes and along functional categories. (a) Distribution of SNPs per Chromosome. (b) Distribution of SNPs by Functional Category.

Fig. 5

Sequencing quality metrics across 555 (208 new and 347 publicly available) genomes of indigenous African cattle. (a) Minor allele frequency (b) Inbreeding coefficient per individual (c) Variant mean depth (d) Mean depth per individual (e) Variant missingness (f) Missingness per individual.

Fig. 6

Population structure of indigenous African cattle depicted through principal component analysis (PC 1 against PC 2). (a) PCA of 532 samples (41 African cattle breeds), based on the whole-genome sequences, and (b) PCA of 1063 samples (39 African cattle breeds) based on the HD SNP genotypes. Six groups of breeds are denoted by different colours and abbreviated as follows: East African zebu (EAZ), East African admixed (EAA), Centre African zebu (CAZ), West African zebu (WAZ), Centre and West African admixed (CWZ), Centre and West African taurine (CWT). Countries abbreviation: Ethiopia (ETH), Kenya (KEN), Uganda (UGD), Rwanda (RWD), Sudan (SUD), Chad (CHD), Cameroon (CAM), Senegal (SEN), Burkina Faso (BKF), Ghana (GHN), Nigeria (NGR), Gambia (GMB), Guinea (GUN). * Savana (S) Muturu and Forest (F) Muturu.