Genetic diversity, linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers.
Genetic diversity, linkage disequilibrium and selection signatures in chinese and Western pigs revealed by genome-wide SNP markers.
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全基因组 SNP 标记揭示中国和西方猪的遗传多样性、连锁不平衡和选择特征
DOI：
10.1371/journal.pone.0056001
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Ren J
中科院分区：
文献类型：
--
作者：
Ai H;Huang L;Ren J
为了在基因组水平上研究中国猪和西方猪的群体结构、连锁不平衡（LD）模式和选择特征，我们利用猪60 K SNP芯片对来自18个不同群体的304头无关动物进行了基因分型。我们证实了中国猪和西方猪之间的分歧进化，并显示了不同的拓扑结构的测试群体。获得了两个中国猪种中西方猪基因渐渗的证据。纯合性分析表明，历史近亲繁殖减少了几个中国品种的遗传变异。我们发现中国猪和西方猪的群体内LD程度大致相当。然而，种群间LD是更长的西方猪与中国猪相比，平均r2 0.3值为125 kb的西方猪和只有10.5 kb的中国猪。这一发现表明，在中国猪的全基因组关联研究和基因组选择中，需要更高密度的标记来捕获具有因果变异的LD。此外，我们在两个对比样本上使用FST离群值检验来观察整个基因组以确定选择下的候选基因座：藏猪与低地猪和束带猪与非束带猪。有趣的是，我们强调了几个基因，包括ADAMTS12，SIM1和NOS1，这些基因在藏猪中显示出自然选择的特征，并且可能对遗传适应高海拔很重要。我们的研究结果与以前的报告的比较表明，藏猪，藏人和牦牛的高海拔适应的潜在遗传基础可能是彼此不同的。此外，我们确定了最强的定向选择信号在EDNRB位点在中国腰带猪，支持EDNRB作为一个有前途的候选基因的白色带毛色在中国猪。总而言之，我们的发现推进了对中国和西方猪的基因组生物学的理解。
To investigate population structure, linkage disequilibrium (LD) pattern and selection signature at the genome level in Chinese and Western pigs, we genotyped 304 unrelated animals from 18 diverse populations using porcine 60 K SNP chips. We confirmed the divergent evolution between Chinese and Western pigs and showed distinct topological structures of the tested populations. We acquired the evidence for the introgression of Western pigs into two Chinese pig breeds. Analysis of runs of homozygosity revealed that historical inbreeding reduced genetic variability in several Chinese breeds. We found that intrapopulation LD extents are roughly comparable between Chinese and Western pigs. However, interpopulation LD is much longer in Western pigs compared with Chinese pigs with average r2 0.3 values of 125 kb for Western pigs and only 10.5 kb for Chinese pigs. The finding indicates that higher-density markers are required to capture LD with causal variants in genome-wide association studies and genomic selection on Chinese pigs. Further, we looked across the genome to identify candidate loci under selection using FST outlier tests on two contrast samples: Tibetan pigs versus lowland pigs and belted pigs against non-belted pigs. Interestingly, we highlighted several genes including ADAMTS12, SIM1 and NOS1 that show signatures of natural selection in Tibetan pigs and are likely important for genetic adaptation to high altitude. Comparison of our findings with previous reports indicates that the underlying genetic basis for high-altitude adaptation in Tibetan pigs, Tibetan peoples and yaks is likely distinct from one another. Moreover, we identified the strongest signal of directional selection at the EDNRB loci in Chinese belted pigs, supporting EDNRB as a promising candidate gene for the white belt coat color in Chinese pigs. Altogether, our findings advance the understanding of the genome biology of Chinese and Western pigs.
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影响因子：
3.7
作者：
Ramos AM;Crooijmans RP;Affara NA;Amaral AJ;Archibald AL;Beever JE;Bendixen C;Churcher C;Clark R;Dehais P;Hansen MS;Hedegaard J;Hu ZL;Kerstens HH;Law AS;Megens HJ;Milan D;Nonneman DJ;Rohrer GA;Rothschild MF;Smith TP;Schnabel RD;Van Tassell CP;Taylor JF;Wiedmann RT;Schook LB;Groenen MA
通讯作者：
Groenen MA
DOI：
10.1098/rspb.2006.3514
发表时间：
2006-07-22
影响因子：
4.7
作者：
Fang, Meiying;Andersson, Leif
通讯作者：
Andersson, Leif
影响因子：
3.3
作者：
Heifetz, EM;Fulton, JE;Soller, M
通讯作者：
Soller, M
影响因子：
3.3
作者：
Foll, Matthieu;Gaggiotti, Oscar
通讯作者：
Gaggiotti, Oscar
影响因子：
4.5
作者：
Bigham A;Bauchet M;Pinto D;Mao X;Akey JM;Mei R;Scherer SW;Julian CG;Wilson MJ;López Herráez D;Brutsaert T;Parra EJ;Moore LG;Shriver MD
通讯作者：
Shriver MD