Signatures of positive selection in African Butana and Kenana dairy zebu cattle

Abstract

Butana and Kenana are two types of zebu cattle found in Sudan. They are unique amongst African indigenous zebu cattle because of their high milk production. Aiming to understand their genome structure, we genotyped 25 individuals from each breed using the Illumina BovineHD Genotyping BeadChip. Genetic structure analysis shows that both breeds have an admixed genome composed of an even proportion of indicine (0.75 ± 0.03 in Butana, 0.76 ± 0.006 in Kenana) and taurine (0.23 ± 0.009 in Butana, 0.24 ± 0.006 in Kenana) ancestries. We also observe a proportion of 0.02 to 0.12 of European taurine ancestry in ten individuals of Butana that were sampled from cattle herds in Tamboul area suggesting local crossbreeding with exotic breeds. Signatures of selection analyses (iHS and Rsb) reveal 87 and 61 candidate positive selection regions in Butana and Kenana, respectively. These regions span genes and quantitative trait loci (QTL) associated with biological pathways that are important for adaptation to marginal environments (e.g., immunity, reproduction and heat tolerance). Trypanotolerance QTL are intersecting candidate regions in Kenana cattle indicating selection pressure acting on them, which might be associated with an unexplored level of trypanotolerance in this cattle breed. Several dairy traits QTL are overlapping the identified candidate regions in these two zebu cattle breeds. Our findings underline the potential to improve dairy production in the semi-arid pastoral areas of Africa through breeding improvement strategy of indigenous local breeds.

Genome-wide analysis of goat genetic diversity and production systems in Uganda

“…Our findings indicated that pathways associated with production and mechanisms of environmental adaptation, such as immune response, male reproduction, energy production and heat stress, may be under selection in Ugandan goat breeds. This is in agreement with findings in East African Short -horn Zebu cattle Bahbahani et al, 2017;Bahbahani et al, 2018), South African cattle (Makina et al, 2015) and indigenous goats in Morocco and Egypt . Gene ontology analysis shows that multiple pathways are expressed in the Ugandan goat breeds, which may indicate an adaptation to varied environmental conditions.…”

Genomic signatures of divergent selection for production and adaptation in domestic goats (Capra hircus)

“…There were ve (Rsb = 3, iHS = 2) candidate regions that spanned no annotated genes ( Supplementary Table S2). Such regions have been designated as "gene deserts" and have also been reported by other investigators [12,13,14,15]. Genome-wide, we identi ed 258 genes (di = 13, Rsb = 115, iHS = 130) mapping to 36 (di = 4, Rsb = 19, iHS = 13) candidate selection regions that were de ned by 287 signi cant SNPs ( Supplementary Table S2).…”

“…The grouping was based on a priori knowledge of the breeding history and geographic-environmental origin of the breeds. Such a pooling strategy has been implemented previously [13,15,37]. Sample pooling offers several advantages.…”

Novel and known signals of selection for fat deposition in domestic sheep breeds from Africa and Eurasia

“…Inter-population analyses of the six fat- vs. thin-tail groups (Table 1) were performed using the Extended Haplotype Homozygosity (EHH) – derived statistic Rsb [15], as in Bahbahani et al [16–17]. To identify statistically significant SNPs under selection in each of the six pair-wise comparisons (positive Rsb value), one-sided P -values (fat- vs. thin-tail group) were derived as −logl0(1-Φ( Rsb )), where Φ( Rsb ) represents the Gaussian cumulative distribution function.…”