Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene.
Nucleotide variability and linkage disequilibrium patterns in the porcine MUC4 gene.
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猪MUC4基因的核苷酸变异性和连锁不平衡模式
DOI：
10.1186/1471-2156-13-57
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发表时间：
2012-07-13
期刊：
影响因子：
2.9
通讯作者：
Huang L
中科院分区：
文献类型：
--
作者：
Yang M;Yang B;Yan X;Ouyang J;Zeng W;Ai H;Ren J;Huang L
MUC4是一种膜锚定糖蛋白，是覆盖气管、结肠和宫颈等多种组织上皮表面的粘液的主要成分。MUC4在表面上皮细胞的润滑和保护、细胞的增殖和分化、免疫反应、细胞黏附和肿瘤的发生等方面发挥着重要作用。为了深入了解猪MUC4基因的进化，我们调查了该基因在中国地方品种和西方商业品种中的核苷酸变异性和连锁不平衡(LD)。对来自11个中国品种和3个西方品种的5头野猪和307头家猪共53个包含MUC4基因的SNPs进行了基因分型。对这些品种的MUC4基因核苷酸变异、单倍型系统发育和LD范围进行了分析。中国品种和西方品种在MUC4基因座上都存在相当大的核苷酸多样性。杜洛克和大白猪等西方猪品种的核苷酸多样性与许多中国猪品种相当，因此人工选择生产瘦肉型猪肉并没有降低西方商业品种MUC4的遗传变异性。单倍型系统发育分析表明，MUC4在中国猪和西方猪中进化不同。品种间遗传分化的树状图大体上反映了这些品种的人口历史和地理分布。中国品种和西方品种的LD模式出人意料地相似，其中LD通常延伸不到20 kb。这与西方商业品种推定的高LD范围(超过100 kb)不同。少数中国和西方品种的Tajima‘d、Fu和Li’s D统计均为显著阳性，提示MUC4在国内品种中可能经历了平衡选择。然而，我们告诫说，重要的统计数据可能会因SNP确定过程而向上偏向。中国和西方品种具有相似的核苷酸多样性，但在MUC4区域进化不同。西方品种在MUC4基因座上表现出异常低的LD，反映了猪基因组核苷酸变异的复杂性。这一发现表明，需要高密度(例如1SNP/10 kb)标记来捕捉这些区域的潜在因果变异。
MUC4 is a type of membrane anchored glycoprotein and serves as the major constituent of mucus that covers epithelial surfaces of many tissues such as trachea, colon and cervix. MUC4 plays important roles in the lubrication and protection of the surface epithelium, cell proliferation and differentiation, immune response, cell adhesion and cancer development. To gain insights into the evolution of the porcine MUC4 gene, we surveyed the nucleotide variability and linkage disequilibrium (LD) within this gene in Chinese indigenous breeds and Western commercial breeds. A total of 53 SNPs covering the MUC4 gene were genotyped on 5 wild boars and 307 domestic pigs representing 11 Chinese breeds and 3 Western breeds. The nucleotide variability, haplotype phylogeny and LD extent of MUC4 were analyzed in these breeds. Both Chinese and Western breeds had considerable nucleotide diversity at the MUC4 locus. Western pig breeds like Duroc and Large White have comparable nucleotide diversity as many of Chinese breeds, thus artificial selection for lean pork production have not reduced the genetic variability of MUC4 in Western commercial breeds. Haplotype phylogeny analyses indicated that MUC4 had evolved divergently in Chinese and Western pigs. The dendrogram of genetic differentiation between breeds generally reflected demographic history and geographical distribution of these breeds. LD patterns were unexpectedly similar between Chinese and Western breeds, in which LD usually extended less than 20 kb. This is different from the presumed high LD extent (more than 100 kb) in Western commercial breeds. The significant positive Tajima’D, and Fu and Li’s D statistics in a few Chinese and Western breeds implied that MUC4 might undergo balancing selection in domestic breeds. Nevertheless, we cautioned that the significant statistics could be upward biased by SNP ascertainment process. Chinese and Western breeds have similar nucleotide diversity but evolve divergently in the MUC4 region. Western breeds exhibited unusual low LD extent at the MUC4 locus, reflecting the complexity of nucleotide variability of pig genome. The finding suggests that high density (e.g. 1SNP/10 kb) markers are required to capture the underlying causal variants at such regions.
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影响因子：
11.2
作者：
Singh, AP;Moniaux, N;Batra, SK
通讯作者：
Batra, SK
影响因子：
2.4
作者：
Esteve, A.;Ojeda, A.;Perez-Enciso, M.
通讯作者：
Perez-Enciso, M.
影响因子：
3.3
作者：
Ojeda, Ana;Rozas, Julio;Perez-Enciso, Miguel
通讯作者：
Perez-Enciso, Miguel
影响因子：
4.5
作者：
Ren J;Duan Y;Qiao R;Yao F;Zhang Z;Yang B;Guo Y;Xiao S;Wei R;Ouyang Z;Ding N;Ai H;Huang L
通讯作者：
Huang L
影响因子：
1.8
作者：
Jacobsen M;Cirera S;Joller D;Esteso G;Kracht SS;Edfors I;Bendixen C;Archibald AL;Vogeli P;Neuenschwander S;Bertschinger HU;Rampoldi A;Andersson L;Fredholm M;Jørgensen CB
通讯作者：
Jørgensen CB