PDF(Pubmed)
Abstract：
Identifying genetic markers of economically valuable traits has practical benefits for the meat goat industry. To better understand the genomic variations influencing body conformation traits, a genome-wide association study was performed on Tashi goats, an indigenous Chinese goat breed. A total of 155 Tashi goats were phenotyped for eight body conformation traits: body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Then, 100 Tashi goats were randomly selected for whole-genome sequencing and genotyped. We obtained 1676.4 Gb of raw data with an average sequencing depth of 6.2X. Clean reads were aligned to the ARS1.2 reference genome, and 11,257,923 single nucleotide polymorphisms (SNPs) were identified. The structure analysis showed that these Tashi goats were almost not genetically related. The 109, 20, 52, 14, 62, 51, 70, and 7 SNPs were significantly associated with body height, body length, chest depth, chest width, chest girth, rump width, rump height, and cannon bone circumference. Within the ±500 kb region of significant SNPs, 183 genes were annotated. The most significantly enriched KEGG pathway was \"olfactory transduction\", and the most significantly enriched gene ontology (GO) terms were \"cellular process\", \"cellular anatomical entity\", and \"molecular transducer activity\". Interestingly, we found several SNPs on chromosomes 10 and 11 that have been identified multiple times for all eight body conformation traits located in two fragments (114 kb and 1.03 Mb). In chr.10:25988403-26102739, the six SNPs were tightly linked, the TACTAG genotype was the highest at 91.8%, and the FNTB (Farnesyltransferase, CAAX Box Beta) and CHURC1 (Churchill Domain Containing 1) genes were located. In chr.11:88216493-89250659, ten SNPs were identified with several dependent linkage disequilibrium (LD) blocks, and seven related genes were annotated, but no significant SNP was located in them. Our results provide valuable biological information for improving growth performance with practical applications for genomic selection in goats.
摘要：
鉴定具有经济价值的性状的遗传标记对肉山羊工业具有实际的益处。为了更好地了解影响身体构象性状的基因组变异，对扎西山羊进行了全基因组关联研究，中国本土山羊品种。总共对155只扎西山羊进行了八个身体构象特征的表型分析：身高，身体长度,胸部深度,胸部宽度,胸围,臀部宽度,臀部高度,和大炮骨围。然后，随机选择100只Tashi山羊进行全基因组测序和基因分型。我们获得了1676.4Gb的原始数据，平均测序深度为6.2X。将干净的读数与ARS1.2参考基因组进行比对，并鉴定了11,257,923个单核苷酸多态性（SNP）。结构分析表明，这些扎西山羊几乎没有遗传关系。109、20、52、14、62、51、70和7个SNP与身高显著相关，身体长度,胸部深度,胸部宽度,胸围,臀部宽度,臀部高度,和大炮骨围。在显著SNP的±500kb区域内，对183个基因进行了注释。最显著富集的KEGG途径是“嗅觉转导”，最显著丰富的基因本体论(GO)术语是“细胞过程”，“细胞解剖实体”，和“分子传感器活动”。有趣的是,我们在10号和11号染色体上发现了几个SNP，这些SNP已被多次鉴定为位于两个片段（114kb和1.03Mb）中的所有八个身体构象性状。在chr.10：25988403-26102739中，六个SNP紧密相连，TACTAG基因型最高，为91.8%，和FNTB(法尼基转移酶，定位CAAXBoxBeta)和CHURC1(Churchill结构域包含1)基因。在chr.11：88216493-89250659中，十个SNP被鉴定为具有几个依赖的连锁不平衡（LD）块，并注释了七个相关基因，但没有显著的SNP位于他们。我们的结果为改善山羊的生长性能提供了有价值的生物学信息，并将其应用于山羊的基因组选择。
