A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines.
A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines.
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DOI：
10.1186/s12711-023-00815-0
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发表时间：
2023-06-15
影响因子：
4.1
通讯作者：
Jungnickel, Melissa K. K.
中科院分区：
文献类型：
--
作者：
Desire, Suzanne;Johnsson, Martin;Ros-Freixedes, Roger;Chen, Ching-Yi;Holl, Justin W. W.;Herring, William O. O.;Gorjanc, Gregor;Mellanby, Richard J. J.;Hickey, John M. M.;Jungnickel, Melissa K. K.
全基因组关联研究（GWAS）旨在确定参与表型表达的基因组区域，但确定致病变异是困难的。猪组合注释依赖性消耗（pCADD）评分提供了遗传变体的预测后果的量度。将pCADD引入GWAS管道可能有助于识别它们。我们的目标是识别与腰部深度和肌肉pH值相关的基因组区域，并识别感兴趣的区域以进行精细绘图和进一步的实验工作。使用来自四个商业品系的329，964头猪的去回归育种值（dEBV），使用约40，000个单核苷酸多态性（SNP）的基因型对这两个性状进行GWAS。使用插补序列数据来鉴定与具有最高pCADD分数的前导GWAS SNP处于强（0.80）连锁不平衡的SNP。15个不同的区域与腰部深度和腰部pH值在全基因组的意义。染色体1，2，5，7和16上的区域，解释了0.06%和3.55%之间的加性遗传方差，并与腰部深度密切相关。只有一小部分的肌肉pH值的加性遗传方差归因于SNPs。我们的pCADD分析的结果表明，高分pCADD变体富含错义突变。SSC 1上两个接近但不同的区域与腰部深度相关，pCADD在其中一个品系的MC 4 R基因中鉴定出先前鉴定的错义变体。对于腰部pH，pCADD鉴定RNF 25基因（SSC 15）中的同义变体为肌肉pH关联的最可能候选者。错义突变的PRKAG 3基因已知影响糖原含量没有优先考虑pCADD的腰部pH值。对于腰部深度，我们确定了几个强有力的候选区域，进一步统计精细映射，在文献中得到支持，和两个新的区域。对于腰部肌肉pH值，我们确定了一个先前确定的相关区域。我们发现混合证据的效用pCADD作为启发式精细映射的扩展。下一步是进行更复杂的精细定位和表达数量性状基因座（eQTL）分析，然后通过干扰CRISPR测定在体外询问候选变体。在线版本包含补充材料，可通过10.1186/s12711-023-00815-0获得。
Genome-wide association studies (GWAS) aim at identifying genomic regions involved in phenotype expression, but identifying causative variants is difficult. Pig Combined Annotation Dependent Depletion (pCADD) scores provide a measure of the predicted consequences of genetic variants. Incorporating pCADD into the GWAS pipeline may help their identification. Our objective was to identify genomic regions associated with loin depth and muscle pH, and identify regions of interest for fine-mapping and further experimental work. Genotypes for ~ 40,000 single nucleotide morphisms (SNPs) were used to perform GWAS for these two traits, using de-regressed breeding values (dEBV) for 329,964 pigs from four commercial lines. Imputed sequence data was used to identify SNPs in strong ( 0.80) linkage disequilibrium with lead GWAS SNPs with the highest pCADD scores. Fifteen distinct regions were associated with loin depth and one with loin pH at genome-wide significance. Regions on chromosomes 1, 2, 5, 7, and 16, explained between 0.06 and 3.55% of the additive genetic variance and were strongly associated with loin depth. Only a small part of the additive genetic variance in muscle pH was attributed to SNPs. The results of our pCADD analysis suggests that high-scoring pCADD variants are enriched for missense mutations. Two close but distinct regions on SSC1 were associated with loin depth, and pCADD identified the previously identified missense variant within the MC4R gene for one of the lines. For loin pH, pCADD identified a synonymous variant in the RNF25 gene (SSC15) as the most likely candidate for the muscle pH association. The missense mutation in the PRKAG3 gene known to affect glycogen content was not prioritised by pCADD for loin pH. For loin depth, we identified several strong candidate regions for further statistical fine-mapping that are supported in the literature, and two novel regions. For loin muscle pH, we identified one previously identified associated region. We found mixed evidence for the utility of pCADD as an extension of heuristic fine-mapping. The next step is to perform more sophisticated fine-mapping and expression quantitative trait loci (eQTL) analysis, and then interrogate candidate variants in vitro by perturbation-CRISPR assays. The online version contains supplementary material available at 10.1186/s12711-023-00815-0.
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不同肌肉特征猪品种胸最长肌的比较转录组分析
影响因子：
3.7
作者：
Cai C;Li M;Zhang Y;Meng S;Yang Y;Gao P;Guo X;Cao G;Li B
通讯作者：
Li B
DOI：
10.1186/s12711-021-00661-y
发表时间：
2021-10-07
期刊：
Genetics, selection, evolution : GSE
影响因子：
--
作者：
Bian C;Prakapenka D;Tan C;Yang R;Zhu D;Guo X;Liu D;Cai G;Li Y;Liang Z;Wu Z;Da Y;Hu X
通讯作者：
Hu X
影响因子：
16.6
作者：
Kern C;Wang Y;Xu X;Pan Z;Halstead M;Chanthavixay G;Saelao P;Waters S;Xiang R;Chamberlain A;Korf I;Delany ME;Cheng HH;Medrano JF;Van Eenennaam AL;Tuggle CK;Ernst C;Flicek P;Quon G;Ross P;Zhou H
通讯作者：
Zhou H
影响因子：
9.2
作者：
Chang CC;Chow CC;Tellier LC;Vattikuti S;Purcell SM;Lee JJ
通讯作者：
Lee JJ
影响因子：
1.8
作者：
Galve, A.;Burgos, C.;Lopez-Buesa, P.
通讯作者：
Lopez-Buesa, P.