转录组测序与全基因组重测序的整合揭示了直立冠和垂冠鸡产蛋性能的候选基因。

Integration of transcriptome sequencing and whole genome resequencing reveal candidate genes in egg production of upright and pendulous-comb chickens.

机构信息

State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China.

出版信息

Poult Sci. 2023 Apr;102(4):102504. doi: 10.1016/j.psj.2023.102504. Epub 2023 Jan 16.

DOI:10.1016/j.psj.2023.102504

PMID:36739803

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9932115/

Abstract

Egg production performance plays an important role in the poultry industry across the world. Previous studies have shown a great difference in egg production performance between pendulous-comb (PC) and upright-comb (UC) chickens. However, there are no reports to identify potential candidate genes for egg production in PC and UC chickens. In the present study, 1,606 laying chickens were raised, and the egg laid by individual chicken was collected for 100 d. Moreover, the expression level of estrogen and progesterone hormones was measured at the start-laying and peak-laying periods of hens. Besides, 4 PC and 4 UC chickens were selected at 217 d of age to perform transcriptome sequencing (RNA-seq) and whole genome resequencing (WGS) to screen the potential candidate genes of egg production. The results showed that PC chicken demonstrated better egg production performance (P < 0.05) and higher estrogen and progesterone hormone expression levels than UC chicken (P < 0.05). RNA-seq analysis showed that 341 upregulated and 1,036 downregulated differentially expressed genes (DEGs) were identified in the ovary tissues of PC and UC chickens. These DEGs were mainly enriched in protein-related, lipid-related, and nucleic acids-related biological processes including ribosome, peptide biosynthetic process, lipid transport terms, and catalytic activity acting on RNA which can significantly affect egg production in chicken. The enrichment results of WGS analysis were consistent with RNA-seq. Further, joint analysis of WGS and RNA-seq data was utilized to screen 30 genes and CAMK1D, CLSTN2, MAST2, PIK3C2G, TBC1D1, STK3, ADGRB3, and PPARGC1A were identified as potential candidate genes for egg production in PC and UC chickens. In summary, our study provides a wealth of information for a better understanding of the genetic and molecular mechanism for the future breeding of PC and UC chickens for egg production.

摘要

产蛋性能在世界范围内的家禽养殖业中起着重要作用。先前的研究表明，垂肉型（PC）和直立型（UC）鸡之间的产蛋性能存在很大差异。然而，目前尚无报道鉴定出 PC 和 UC 鸡产蛋的潜在候选基因。本研究饲养了 1606 只产蛋鸡，收集了每只鸡产的蛋，连续收集 100 天。此外，在母鸡开始产蛋和产蛋高峰期测量雌激素和孕激素激素的表达水平。此外，在 217 日龄时选择 4 只 PC 和 4 只 UC 鸡进行转录组测序（RNA-seq）和全基因组重测序（WGS），以筛选产蛋的潜在候选基因。结果表明，PC 鸡表现出更好的产蛋性能（P < 0.05），并且雌激素和孕激素激素的表达水平高于 UC 鸡（P < 0.05）。RNA-seq 分析显示，在 PC 和 UC 鸡的卵巢组织中鉴定出 341 个上调和 1036 个下调的差异表达基因（DEGs）。这些 DEGs 主要富集在蛋白质相关、脂质相关和核酸相关的生物学过程中，包括核糖体、肽生物合成过程、脂质转运和对 RNA 具有显著影响的催化活性的术语可以影响鸡的产蛋量。WGS 分析的富集结果与 RNA-seq 一致。进一步利用 WGS 和 RNA-seq 数据的联合分析筛选出 30 个基因，CAMK1D、CLSTN2、MAST2、PIK3C2G、TBC1D1、STK3、ADGRB3 和 PPARGC1A 被鉴定为 PC 和 UC 鸡产蛋的潜在候选基因。总之，我们的研究为更好地理解 PC 和 UC 鸡产蛋的遗传和分子机制提供了丰富的信息，为未来的 PC 和 UC 鸡产蛋选育提供了参考。