Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu.
Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu.
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DOI：
10.3389/fgene.2017.00068
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发表时间：
2017
影响因子：
3.7
通讯作者：
Hanotte O
中科院分区：
文献类型：
--
作者：
Bahbahani H;Tijjani A;Mukasa C;Wragg D;Almathen F;Nash O;Akpa GN;Mbole-Kariuki M;Malla S;Woolhouse M;Sonstegard T;Van Tassell C;Blythe M;Huson H;Hanotte O
东非短角瘤牛（EASZ）是亚洲瘤牛×非洲牛磺酸牛的古老杂交种，因其对非洲环境的适应性而受到当地农民的青睐。这些适应性的遗传控制尚未清楚地了解。在这里，我们对来自肯尼亚（KEASZ）的92个EASZ样本进行了基因分型，其中有超过770，000个SNP，并对10个KEASZ样本的基因组进行了测序。我们观察到一个均匀混合的常染色体组结构，在种群中的牛磺酸。基于全基因组SNP分析（meta-SS、Rsb、iHS和ΔAF）和合并杂合性（Hp）全基因组序列分析，鉴定了总共101个和165个正选择的候选区域，其中35个区域在它们之间共享。在这些区域内共检测到142个功能变体，其中30个和26个分别被归类为来自非洲牛磺酸和非洲瘤牛磺酸。对乌干达和尼日利亚的瘤牛×牛磺酸混合牛群体进行的高密度全基因组SNP分析表明，其中25个区域在KEASZ和乌干达牛之间共享，7个区域在KEASZ、乌干达和尼日利亚牛之间共享。共同候选区域的识别使我们能够精细映射18个区域。这些区域与生殖和环境胁迫相关的基因和QTL（例如，免疫力和热应激），这表明，在繁殖和存活能力方面，杂交牛的基因组已经被独特地选择以最大化杂交适合度。
The East African Shorthorn Zebu (EASZ) cattle are ancient hybrid between Asian zebu × African taurine cattle preferred by local farmers due to their adaptability to the African environment. The genetic controls of these adaptabilities are not clearly understood yet. Here, we genotyped 92 EASZ samples from Kenya (KEASZ) with more than 770,000 SNPs and sequenced the genome of a pool of 10 KEASZ. We observe an even admixed autosomal zebu × taurine genomic structure in the population. A total of 101 and 165 candidate regions of positive selection, based on genome-wide SNP analyses (meta-SS, Rsb, iHS, and ΔAF) and pooled heterozygosity (Hp) full genome sequence analysis, are identified, in which 35 regions are shared between them. A total of 142 functional variants, one novel, have been detected within these regions, in which 30 and 26 were classified as of zebu and African taurine origins, respectively. High density genome-wide SNP analysis of zebu × taurine admixed cattle populations from Uganda and Nigeria show that 25 of these regions are shared between KEASZ and Uganda cattle, and seven regions are shared across the KEASZ, Uganda, and Nigeria cattle. The identification of common candidate regions allows us to fine map 18 regions. These regions intersect with genes and QTL associated with reproduction and environmental stress (e.g., immunity and heat stress) suggesting that the genome of the zebu × taurine admixed cattle has been uniquely selected to maximize hybrid fitness both in terms of reproduction and survivability.