A meta analysis of genome-wide association studies for limb bone lengths in four pig populations.
A meta analysis of genome-wide association studies for limb bone lengths in four pig populations.
复制标题
四个猪群四肢骨长度的全基因组关联研究的荟萃分析
DOI：
10.1186/s12863-015-0257-1
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发表时间：
2015-07-29
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：
Guo Y;Hou L;Zhang X;Huang M;Mao H;Chen H;Ma J;Chen C;Ai H;Ren J;Huang L
肢骨长是猪的一个重要经济性状，它与背膘厚呈负相关，同时也是决定猪臀部和腰部产量的重要因素。此外，四肢骨骼的异常生长导致腿部结构性虚弱。到目前为止，猪石灰骨长度的遗传结构仍然知之甚少。结果对来自白色杜洛克×二花脸F2杂种猪、二花脸猪、莱芜猪和苏台猪的925头、331头、314头和434头猪的右侧胴体的肩胛骨、肱骨、尺骨、股骨和胫骨等5个肢骨的长度进行了测定，并对4个猪群的肢骨长度进行了全基因组关联分析。分别我们在猪SNP 60微珠芯片上对2004头猪进行了62，163个单核苷酸多态性（SNP）的基因分型，并在4个群体中进行了GWAS和GWAS Meta分析。共鉴定出12个和4个与四肢骨长度相关的位点，其中4个位点为首次报道。最显著的位点位于猪染色体（SSC）7上的924-kb（千碱基对）连锁不平衡区，高迁移率族AT-钩1（HMGA 1）似乎是该区域的一个强候选基因。另一个有希望的位点位于SSC 4的中部，多形腺瘤基因1（PLAG 1）是该位点的功能上可能的候选基因。由于5肢骨的长度是高度相关的彼此，大多数显着的位点与所有的5个性状，但是，几个位点表现出特定的影响一肢骨的长度，如在近端的位点SSC 2与肩胛骨的长度。正如预期的那样，Meta分析更强大的识别基因组位点。本研究共检测到16个位点，其中包括4个新位点，HMGA 1和PLAG 1是两个新出现的猪肢骨长度候选基因，值得进一步研究。
BackgroundLimb bone length is an economically important trait in pigs, because it is negatively correlated with backfat thickness, and is also a determinant to the yield of hip and loin. Moreover, abnormal growth of the limb bone leads to leg structural weakness. Until now, the genetic architecture of the pig lime bone length remains poorly understood. The object of this study was to map genomic loci for limb bone length by genome-wide association study (GWAS) on 4 pig populations.ResultsWe measured the lengths of five limb bones including scapula, humerus, ulna, femur and tibia that were dissected from the right-side carcass of 925, 331, 314 and 434 animals from White Duroc × Erhualian F2intercross, Erhualian, Laiwu and Sutai populations, respectively. We genotyped the 2004 pigs for 62,163 single nucleotide polymorphisms (SNPs) on the Porcine SNP60 BeadChip, and performed GWAS and a GWAS meta analysis in the 4 populations. In total, we identified 12 and 4 loci associated with the limb bone lengths at suggestive and genome-wide significant levels respectively, of which 4 loci were reported for the first time. The most prominent locus was identified in a 924-kb (kilo base pairs) linkage disequilibrium block onSus Scrofachromosome (SSC) 7, andHigh Mobility Group AT-hook 1(HMGA1) appears to be a strong candidate gene in this region. Another promising locus is located in the middle of SSC4, andPleiomorphic Adenoma Gene 1(PLAG1) is a functionally plausible candidate gene underlying the locus. Because the lengths of the 5 limb bones are highly correlated to each other, most of significant loci were associated with all of the 5 traits; however, several loci showed specific effect on the length of one limb bone, such as the locus at the proximal end of SSC2 associated with only the scapula length.ConclusionTo our knowledge, this study was the first GWAS meta analysis for limb bone lengths in pigs. As expected, the meta analysis is more powerful to identify genomic loci. A total of 16 loci were identified in this study, including four novel loci.HMGA1 andPLAG1 are two appearing candidate genes for pig limb bone lengths, which warrant further investigations.