Signatures of Selection in Admixed Dairy Cattle in Tanzania

Abstract

Multiple studies have investigated selection signatures in domestic cattle and other species. However, there is a dearth of information about the response to selection in genomes of highly admixed crossbred cattle in relation to production and adaptation to tropical environments. In this study, we evaluated 839 admixed crossbred cows sampled from two major dairy regions in Tanzania namely Rungwe and Lushoto districts, in order to understand their genetic architecture and detect genomic regions showing preferential selection. Animals were genotyped at 150,000 SNP loci using the Geneseek Genomic Profiler (GGP) High Density (HD) SNP array. Population structure analysis showed a large within-population genetic diversity in the study animals with a high degree of variation in admixture ranging between 7 and 100% taurine genes (dairyness) of mostly Holstein and Friesian ancestry. We explored evidence of selection signatures using three statistical methods (iHS, XP-EHH, and pcadapt). Selection signature analysis identified 108 candidate selection regions in the study population. Annotation of these regions yielded interesting genes potentially under strong positive selection including ABCG2, ABCC2, XKR4, LYN, TGS1, TOX, HERC6, KIT, PLAG1, CHCHD7, NCAPG, and LCORL that are involved in multiple biological pathways underlying production and adaptation processes. Several candidate selection regions showed an excess of African taurine ancestral allele dosage. Our results provide further useful insight into potential selective sweeps in the genome of admixed cattle with possible adaptive and productive importance. Further investigations will be necessary to better characterize these candidate regions with respect to their functional significance to tropical adaptations for dairy cattle.

Keywords: SNP; XP-EHH; admixture; crossbred cattle; iHS; pcadapt; selection signatures.

FIGURE 1

Distribution of minor allele frequencies (MAF) for the Tanzanian crossbred cattle and reference breeds. Subpopulations are indicated as AT, African Taurine; ET, European Taurine; Indicine and Tanzanian crossbred cattle (TZ), respectively. SNPs were SNPs were binned into 5 categories based on the MAF; [0, 0.1], [0.1, 0.2], [0.2, 0.3], [0.3, 0.4], and [0.4, 0.5].

FIGURE 2

Principal Component Analysis (PCA) plot showing clustering of Tanzanian crossbred cattle and reference breeds. Each point represents an individual animal colored as per the breed.

FIGURE 3

ADMIXTURE bar plot showing breed proportions at assumed ancestry (cluster) K = 2–8. Short vertical lines at the bottom of each horizontal bar delimit individuals of different populations. Tanzanian crossbred cattle populations are divided according to the sampling locations (Lushoto and Rungwe) while reference breeds are labeled as Friesian (FR), Holstein (HO), Guernsey (GN),Jersey (JE), Norwegian Red (NR), Gir (GI), East African Shorthorn Zebu (ZB), and N’Dama (ND).

FIGURE 4

Distribution of standardized iHS scores in the Tanzanian crossbred cattle versus EASZ comparison. The dashed line corresponds to the false discovery rate (FDR) at 1% threshold.

FIGURE 5

Distribution of standardized XP-EHH scores in the Tanzanian crossbred cattle versus the EASZ comparison.

FIGURE 6

Proportion of variance explained by 10 principal components for combined dataset of Tanzanian crossbred cattle, East African Shorthorn Zebu (EASZ) and N’Dama.

FIGURE 7

Manhattan plot of genomic selection regions detected using pcadapt for combined dataset of Tanzanian crossbred cattle, East African Shorthorn Zebu and N’Dama. The dashed line corresponds to the 1% false discovery rate (FDR) threshold.

FIGURE 8

Local ancestral allele dosage on BTA 14 sweep region detected by iHS at 23.28 – 26.99 Mb for Tanzanian crossbred cattle. The dashed vertical lines delimit selective sweep region. The y-axis is the average ancestral allele dosage estimate for 324 unrelated individuals.