基于全基因组关联研究鉴定蛋黄水分含量的候选基因组区域。

Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study.

机构信息

Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, 100193, Beijing, China.

出版信息

BMC Genomics. 2023 Mar 14;24(1):110. doi: 10.1186/s12864-023-09221-8.

DOI:10.1186/s12864-023-09221-8

PMID:36918797

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10015838/

Abstract

BACKGROUND

Eggs represent important sources of protein and are widely loved by consumers. Egg yolk taste is an important index for egg selection, and the moisture content of the egg yolk affects the taste. To understand the molecular mechanism underlying egg yolk moisture content, this study determined the phenotype and heritability of egg yolk water content and conducted a genome-wide association study (GWAS) using a mixed linear model.

RESULTS

We determined the phenotype and heritability of thermogelled egg yolk water content (TWC) and found that the average TWC was 47.73%. Moreover, significant variations occurred (41.06-57.12%), and the heritability was 0.11, which indicates medium-low heritability. Through the GWAS, 48 single nucleotide polymorphisms (SNPs) related to TWC (20 significantly, 28 suggestively) were obtained, and they were mainly located on chromosomes 10 and 13. We identified 36 candidate genes based on gene function and found that they were mainly involved in regulating fat, protein, and water content and embryonic development. FGF9, PIAS1, FEM1B, NOX5, GLCE, VDAC1, IGFBP7, and THOC5 were involved in lipid formation and regulation; AP3S2, GNPDA1, HSPA4, AP1B1, CABP7, EEF1D, SYTL3, PPP2CA, SKP1, and UBE2B were involved in protein folding and hydrolysis; and CSF2, SOWAHA, GDF9, FSTL4, RAPGEF6, PAQR5, and ZMAT5 were related to embryonic development and egg production. Moreover, MICU2, ITGA11, WDR76, BLM, ANPEP, TECRL, EWSR1, and P4HA2 were related to yolk quality, while ITGA11, WDR76, BLM, and ANPEP were potentially significantly involved in egg yolk water content and thus deserve further attention and research. In addition, this study identified a 19.31-19.92 Mb genome region on GGA10, and a linkage disequilibrium analysis identified strong correlations within this region. Thus, GGA10 may represent a candidate region for TWC traits.

CONCLUSION

The molecular genetic mechanism involved in TWC was revealed through heritability measurements and GWAS, which identified a series of SNPs, candidate genes, and candidate regions related to TWC. These results provide insights on the molecular mechanism of egg yolk moisture content and may aid in the development of new egg traits.

摘要

背景

鸡蛋是蛋白质的重要来源，深受消费者喜爱。蛋黄口感是鸡蛋选择的重要指标，而蛋黄水分含量会影响口感。为了了解蛋黄水分含量的分子机制，本研究采用混合线性模型确定了蛋黄水分的表型和遗传力，并进行了全基因组关联研究（GWAS）。

结果

我们确定了热凝胶蛋黄水分含量（TWC）的表型和遗传力，发现平均 TWC 为 47.73%。此外，存在显著的变化（41.06-57.12%），遗传力为 0.11，表明遗传力中等偏低。通过 GWAS，获得了与 TWC 相关的 48 个单核苷酸多态性（SNP）（20 个显著，28 个提示），它们主要位于第 10 和 13 号染色体上。我们根据基因功能确定了 36 个候选基因，并发现它们主要参与调节脂肪、蛋白质和水分含量以及胚胎发育。FGF9、PIAS1、FEM1B、NOX5、GLCE、VDAC1、IGFBP7 和 THOC5 参与脂质形成和调节；AP3S2、GNPDA1、HSPA4、AP1B1、CABP7、EEF1D、SYTL3、PPP2CA、SKP1 和 UBE2B 参与蛋白质折叠和水解；CSF2、SOWAHA、GDF9、FSTL4、RAPGEF6、PAQR5 和 ZMAT5 与胚胎发育和产蛋有关。此外，MICU2、ITGA11、WDR76、BLM、ANPEP、TECRL、EWSR1 和 P4HA2 与蛋黄质量有关，而 ITGA11、WDR76、BLM 和 ANPEP 可能与蛋黄水分含量显著相关，因此值得进一步关注和研究。此外，本研究在 GGA10 上鉴定了一个 19.31-19.92 Mb 的基因组区域，连锁不平衡分析表明该区域内存在很强的相关性。因此，GGA10 可能代表 TWC 性状的候选区域。