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首页> 外文期刊>BMC Genomics >Genome wide association and gene enrichment analysis reveal membrane anchoring and structural proteins associated with meat quality in beef
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Genome wide association and gene enrichment analysis reveal membrane anchoring and structural proteins associated with meat quality in beef

机译：基因组宽协会和基因富集分析显示牛肉中肉质相关的膜锚固和结构蛋白

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Meat quality related phenotypes are difficult and expensive to measure and predict but are ideal candidates for genomic selection if genetic markers that account for a worthwhile proportion of the phenotypic variation can be identified. The objectives of this study were: 1) to perform genome wide association analyses for Warner-Bratzler Shear Force (WBSF), marbling, cooking loss, tenderness, juiciness, connective tissue and flavor; 2) to determine enriched pathways present in each genome wide association analysis; and 3) to identify potential candidate genes with multiple quantitative trait loci (QTL) associated with meat quality. The WBSF, marbling and cooking loss traits were measured in longissimus dorsi muscle from 672 steers. Out of these, 495 animals were used to measure tenderness, juiciness, connective tissue and flavor by a sensory panel. All animals were genotyped for 221,077 markers and included in a genome wide association analysis. A total number of 68 genomic regions covering 52 genes were identified using the whole genome association approach; 48% of these genes encode transmembrane proteins or membrane associated molecules. Two enrichment analysis were performed: a tissue restricted gene enrichment applying a correlation analysis between raw associated single nucleotide polymorphisms (SNPs) by trait, and a functional classification analysis performed using the DAVID Bioinformatic Resources 6.8 server. The tissue restricted gene enrichment approach identified eleven pathways including "Endoplasmic reticulum membrane" that influenced multiple traits simultaneously. The DAVID functional classification analysis uncovered eleven clusters related to transmembrane or structural proteins. A gene network was constructed where the number of raw associated uncorrelated SNPs for each gene across all traits was used as a weight. A multiple SNP association analysis was performed for the top five most connected genes in the gene-trait network. The gene network identified the EVC2, ANXA10 and PKHD1 genes as potentially harboring multiple QTLs. Polymorphisms identified in structural proteins can modulate two different processes with direct effect on meat quality: in vivo myocyte cytoskeletal organization and postmortem proteolysis. The main result from the present analysis is the uncovering of several candidate genes associated with meat quality that have structural function in the skeletal muscle.
机译：肉质相关的表型是难以且昂贵的测量和预测，但是如果可以识别出于表型变异的有价值比例的遗传标记，则是基因组选择的理想候选者。本研究的目的是：1）进行战争 - 布拉茨勒剪力（WBSF），大理石，烹饪损失，柔软，脂肪，结缔组织和味道的基因组宽协会分析; 2）确定每个基因组宽关联分析中存在的富集途径; 3）鉴定具有与肉质相关的多种定量性状基因座（QTL）的潜在候选基因。从672个阉牛座中测量WBSF，大理石和烹饪损失特征。其中，使用495只动物来测量感官面板的柔软，脂肪，结缔组织和风味。所有动物都是基因分型对于221,077个标记物并包括在基因组宽关联分析中。使用全基因组关联方法鉴定覆盖52个基因的68个基因组区域的总数;这些基因的48％编码跨膜蛋白或膜相关分子。进行了两种富集分析：组织限制基因富集在具有特征的原始相关单核苷酸多态性（SNP）之间的相关分析，以及使用David BioIncormatic资源6.8服务器进行的功能分类分析。组织限制基因富集方法鉴定了11个途径，包括“内质网膜”，其同时影响多种性状。 David功能分类分析发现与跨膜或结构蛋白相关的11个簇。构建基因网络，其中所有特征的每个基因的原始相关不相关SNP的数量用作重量。对基因特征网络中的前五个最相关基因进行多种SNP关联分析。基因网络鉴定EVC2，ANXA10和PKHD1基因，可能含有多个QTL。结构蛋白中鉴定的多态性可以调节两种不同的过程，直接对肉质有效：在体内肌细胞细胞骨骼组织和后蛋白质溶解中。本分析的主要结果是揭示与骨骼肌中具有结构功能的肉质相关的几种候选基因。

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