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全基因组贝叶斯扫描分析西非牛的适应性遗传分化。

A whole genome Bayesian scan for adaptive genetic divergence in West African cattle.

机构信息

INRA, UMR de Génétique Animale et Biologie Intégrative, 78350 Jouy-en-Josas, France.

出版信息

BMC Genomics. 2009 Nov 21;10:550. doi: 10.1186/1471-2164-10-550.

DOI:10.1186/1471-2164-10-550
PMID:19930592
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2784811/
Abstract

BACKGROUND

The recent settlement of cattle in West Africa after several waves of migration from remote centres of domestication has imposed dramatic changes in their environmental conditions, in particular through exposure to new pathogens. West African cattle populations thus represent an appealing model to unravel the genome response to adaptation to tropical conditions. The purpose of this study was to identify footprints of adaptive selection at the whole genome level in a newly collected data set comprising 36,320 SNPs genotyped in 9 West African cattle populations.

RESULTS

After a detailed analysis of population structure, we performed a scan for SNP differentiation via a previously proposed Bayesian procedure including extensions to improve the detection of loci under selection. Based on these results we identified 53 genomic regions and 42 strong candidate genes. Their physiological functions were mainly related to immune response (MHC region which was found under strong balancing selection, CD79A, CXCR4, DLK1, RFX3, SEMA4A, TICAM1 and TRIM21), nervous system (NEUROD6, OLFM2, MAGI1, SEMA4A and HTR4) and skin and hair properties (EDNRB, TRSP1 and KRTAP8-1).

CONCLUSION

The main possible underlying selective pressures may be related to climatic conditions but also to the host response to pathogens such as Trypanosoma(sp). Overall, these results might open the way towards the identification of important variants involved in adaptation to tropical conditions and in particular to resistance to tropical infectious diseases.

摘要

背景

西非的牛群在经历了几波从遥远的驯化中心的迁徙后，最近在西非定居，这给它们的环境条件带来了巨大的变化，特别是通过接触新的病原体。西非牛种群因此代表了一个有吸引力的模型，可以揭示对适应热带条件的基因组反应。本研究的目的是在一个新收集的数据集（包括 36320 个 SNPs，在 9 个西非牛种群中进行了基因分型）中，在全基因组水平上识别适应性选择的痕迹。

结果

在对种群结构进行了详细分析之后，我们通过一个先前提出的包括扩展的贝叶斯程序，对 SNP 分化进行了扫描，以提高对受选择的基因座的检测能力。基于这些结果，我们确定了 53 个基因组区域和 42 个强候选基因。它们的生理功能主要与免疫反应有关（MHC 区域受到强烈的平衡选择，CD79A、CXCR4、DLK1、RFX3、SEMA4A、TICAM1 和 TRIM21）、神经系统（NEUROD6、OLFM2、MAGI1、SEMA4A 和 HTR4）和皮肤和毛发特性（EDNRB、TRSP1 和 KRTAP8-1）。

结论

主要的潜在选择压力可能与气候条件有关，但也可能与宿主对寄生虫（如锥虫）等病原体的反应有关。总的来说，这些结果可能为鉴定与适应热带条件有关的重要变异体，特别是对热带传染病的抗性，开辟了道路。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/52ee0f0c2656/1471-2164-10-550-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/0e876727eaf5/1471-2164-10-550-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/8962a98e24ff/1471-2164-10-550-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/4abe95fd2c88/1471-2164-10-550-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/e715f0f9413e/1471-2164-10-550-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/4068eb0511ef/1471-2164-10-550-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/52ee0f0c2656/1471-2164-10-550-6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/0e876727eaf5/1471-2164-10-550-1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/8962a98e24ff/1471-2164-10-550-2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/4abe95fd2c88/1471-2164-10-550-3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/e715f0f9413e/1471-2164-10-550-4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/4068eb0511ef/1471-2164-10-550-5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4fcc/2784811/52ee0f0c2656/1471-2164-10-550-6.jpg

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