Median Joining Network

Median Joining Networ

NADH1 gene alignment

NADH1 gene alignmen

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

<div><p>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 (<i>iHS</i> and <i>Rsb</i>) 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.</p></div

Manhattan plots of genome-wide autosomal <i>Rsb</i> analyses of Kenana cattle.

<p>(A) European taurine (Holstein-Friesian and Jersey), (B) African taurine (N’Dama), (C) East African shorthorn zebu, (D) Sheko and (E) Asian zebu (Nelore). One-tailed Z-test is applied and the significance threshold is set at–log₁₀ (one-tailed <i>P</i>-value) = 4.</p

PCA plots showing the genetic relationship between cattle breeds.

<p>(A) all cattle breeds and (B) Butana and Kenana cattle.</p

Manhattan plots of genome-wide autosomal <i>Rsb</i> analyses of Butana cattle.

<p>(A) European taurine (Holstein-Friesian and Jersey), (B) African taurine (N’Dama), (C) East African shorthorn zebu, (D) Sheko, and (E) Asian zebu (Nelore). One-tailed Z-test is applied and the significance threshold is set at–log₁₀ (one-tailed <i>P</i>-value) = 4.</p

Significantly enriched functional term clusters and their enrichment scores following DAVID analysis for genes identified in Butana and Kenana candidate regions.

<p>Significantly enriched functional term clusters and their enrichment scores following DAVID analysis for genes identified in Butana and Kenana candidate regions.</p

ADMIXTURE bar plots of genomic membership proportions from <i>K</i> = 2 to <i>K</i> = 4.

<p>Each sample is represented by a vertical line divided into <i>K</i> colours. HOL: Holstein, JER: Jersey, NDM: N’Dama, NEL: Nelore, SHK: Sheko, KEN: Kenana, BUT: Butana.</p

Manhattan plots of genome-wide <i>iHS</i> analyses on (A) Butana and (B) Kenana cattle.

<p>two-tailed Z-test is applied and the significance threshold is set at–log₁₀ (two-tailed <i>P</i>-value) = 4.</p

Additional file 1 of Exploring genetic diversity and variation of Ovar-DRB1 gene in Sudan Desert Sheep using targeted next-generation sequencing

Additional file 1. Fig S1. Neighbor-joining (NJ) tree constructed from the nucleotide sequence that only encoded the antigen-binding site (ABS) by all reported Ovar-DRB1 alleles and the four new ones (From Ovar-DRB1*Sudan1 to Ovar-DRB1*Sudan4) detected in the Sudan desert sheep breed. Numbers are bootstrap percentages that support each node. Bootstrapping was carried up with 1000 replicates to assess the reliability of individual branches. Abrag (AB), Ashgar (AS), Buze´e, Hamari (H), Kabashi (K), and Watish (W). Breeds where alleles were detected are indicated between brackets