将全基因组关联研究的荟萃分析与猪基因型-组织表达资源相结合,揭示猪初产年龄的遗传结构

Qing Lin, Xueyan Feng, Tingting Li, Xiangchun Pan, Shuqi Diao, Yahui Gao, Xiaolong Yuan, Jiaqi Li, Xiangdong Ding, Zhe Zhang
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引用次数: 0

摘要

初产年龄(AFF)是一个遗传率低、在养猪业中非常重要的繁殖性状。为了提高全基因组关联研究(GWAS)的统计能力并进一步探索初产年龄的遗传本质,我们首先利用约克郡的三个种群进行了 GWAS meta 分析,然后整合了猪基因型-组织表达(PigGTEx)资源来解释其潜在的调控机制。此外,我们还利用 GWAS 统计摘要将猪的 AFF 与人类的初生年龄(AFB)进行了比较。我们在 GWAS meta 分析中发现了 18 个独立变异,在基于基因的关联分析中发现了 8 个与 AFF 显著相关的基因。通过整合 PigGTEx 资源,我们对 34 个猪组织进行了转录组关联研究(TWAS)和共聚焦分析。在全转录组关联研究中,我们发现了 18 对重要的基因-组织配对,如子宫中的 DCAF6 和血液中的 CREG1。在共定位分析中,我们发现了 111 个潜在的候选组织-基因对,如 GJD4 和 LYPLAL1。我们发现,同源基因 CHST10 可能是 AFB 中人与 AFF 中猪之间的潜在候选基因。总之,整合 GWAS meta 分析和 PigGTEx 资源是解读复杂性状遗传结构的有效方法。我们发现,DCAF6、CREG1、GJD4 和 LYPLAL1 是猪 AFF 的可靠性较高的候选基因。比较分析表明,CHST10 可能在人和猪的 AFB/AFF 中发挥潜在的关键作用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

Integrating meta-analysis of genome-wide association study with Pig Genotype-Tissue Expression resources uncovers the genetic architecture for age at first farrowing in pigs

Integrating meta-analysis of genome-wide association study with Pig Genotype-Tissue Expression resources uncovers the genetic architecture for age at first farrowing in pigs

Age at first farrowing (AFF) is a reproductive trait with low heritability and high importance in the pig industry. To enhance the statistical power of genome-wide association study (GWAS) and further explore the genetic nature of AFF, we first conducted GWAS meta-analysis using three Yorkshire populations, and then integrated the Pig Genotype-Tissue Expression (PigGTEx) resources to interpret their potential regulatory mechanism. Additionally, we compared the AFF in pig with the age at first birth (AFB) of human using GWAS summary statistics. We detected 18 independent variants in GWAS meta-analysis and 8 genes in gene-based association analysis significantly associated with AFF. By integrating the PigGTEx resource, we conducted transcriptome-wide association study (TWAS) and colocalization analysis on 34 pig tissues. In TWAS, we detected 18 significant gene-tissue pairs, such as DCAF6 in uterus and CREG1 in blood. In colocalization, we found 111 potential candidate tissue-gene pairs, such as GJD4 and LYPLAL1. We found that the homologous gene, CHST10, might be the potential candidate gene between humans in AFB and pigs in AFF. In conclusion, integrating GWAS meta-analysis and PigGTEx resources is a meaningful way to decipher the genetic architecture of complex traits. We found that DCAF6, CREG1, GJD4, and LYPLAL1 are candidate genes with high reliability for AFF in swine. The comparative analysis showed that CHST10 might play a potentially critical role in AFB/AFF across human and pigs.

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