基于全基因组重测序研究文昌鸡产蛋性能的影响因素

doi:10.11843/j.issn.0366-6964.2024.02.009

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (2): 502-514.doi: 10.11843/j.issn.0366-6964.2024.02.009

基于全基因组重测序研究文昌鸡产蛋性能的影响因素

任钰为¹, 陈星², 林燕宁¹, 黄潇仙¹, 洪玲玲¹, 王峰¹, 孙瑞萍¹, 张艳¹, 刘海隆¹, 郑心力^1*, 晁哲^1*

1. 海南省农业科学院畜牧兽医研究所海南省热带动物繁育与疫病研究重点实验室, 海口 571100;
2. 武汉市农业科学院畜牧兽医研究所, 武汉 430000

收稿日期:2023-07-04 出版日期:2024-02-23 发布日期:2024-02-27
通讯作者: 晁哲,主要从事海南地方畜禽资源保护与利用研究,E-mail:chaozhe@hnaas.org.cn;郑心力,主要从事海南地方畜禽资源保护与利用研究,E-mail:zhengxinli06@163.com
作者简介:任钰为(1986-),女,湖北宜昌人,副研究员,博士,主要从事海南地方畜禽资源保护与利用研究,E-mail:renyuwei@hnaas.org.cn
基金资助:
国家重点研发计划项目(2021YFD1300104);海南省农业科学院院本级科研项目(HNJY2022-55-4R;HAAS2023RCQD04);中央引导地方科技发展专项资金(ZY2022HN09)

Investigating the Influencing Factors of Egg Laying Performance in Wenchang Chickens Based on Whole Genome Resequencing

REN Yuwei¹, CHEN Xing², LIN Yanning¹, HUANG Xiaoxian¹, HONG Lingling¹, WANG Feng¹, SUN Ruiping¹, ZHANG Yan¹, LIU Hailong¹, ZHENG Xinli^1*, CHAO Zhe^1*

1. Key Laboratory of Tropical Animal Breeding and Disease Research, Institute of Animal Science and Veterinary Medicine, Hainan Academy of Agricultural Sciences, Haikou 571100, China;
2. Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan 430000, China

Received:2023-07-04 Online:2024-02-23 Published:2024-02-27

摘要/Abstract

摘要： 旨在通过研究文昌鸡进化过程的特征,深入理解影响产蛋性能的因素,为文昌鸡优良品种选育提供基础。本研究采集35只健康文昌鸡(35周龄,15公,20母)和30只健康江汉鸡(35周龄,10公,20母)的血液组织各3 mL提取DNA,采用全基因组重测序方法建库测序。首先,对于原始测序数据用trimmomatic 软件过滤,获得高质量序列比对到鸡的参考基因组,GATK软件提取变异位点SNPs,设置参数质控去除低质量、假阳性变异位点,进一步采用snpEff对过滤的SNPs进行基因结构和功能注释。然后,比较文昌鸡和江汉鸡的群体结构差异,分别设置评估群体差异参数Fst、ROD、Tajima's D的阈值,筛选受到选择的区域,并对这些区域的基因进行功能富集。结果表明:1)文昌鸡测序获得1.05 Tb clean data,平均每个样本大约29.97 Gb,测序深度大约28×;江汉鸡测序获得1.10 Tb clean data,每个样本大约36.72 Gb,测序深度大约35×;平均比对率>98%。2)两个群体基因结构注释总数均是内含子>基因间区>上下游调控区>编码区;系统进化树和主成分分析显示文昌鸡和江汉鸡亲缘关系较远;文昌鸡的连锁不平衡程度低于江汉鸡。3)与产蛋性能相关基因的功能富集结果主要包括3种必须氨基酸(缬氨酸、亮氨酸、异亮氨酸)代谢途径、钙离子沉积、金属肽酶抗氧化、肾上腺素和催乳素受体活性等功能,而且这些通路的基因都位于受到强烈选择的区域。综上所述,影响文昌鸡产蛋性能的因素主要包括必须氨基酸代谢、矿物质沉积和抗氧化、性腺激素分泌,这3个因素在进化过程中都受到强烈选择,对产蛋性能发挥重要调控作用。从进化分子遗传学角度研究鸡的产蛋机理,不但能够促进理解文昌鸡产蛋性能的进化特征,而且有助于加速高产蛋鸡品种或品系的培育。

关键词: 文昌鸡, 全基因组重测序, 遗传选择, 产蛋性能, 影响因素

Abstract: The purpose of this project was to study the features of the evolution process of Wenchang chickens, to understand the factors affecting the egg production performance, and to provide the basis for the breeding of improved breeds of Wenchang chickens. Blood samples of 3 mL from 35 Wenchang chickens (35 weeks of age, 15 cocks and 20 hens) and 30 Jianghan chickens (35 weeks of age, 10 cocks and 20 hens) were collected, and DNA was extracted, which was used to construct libraries for sequencing by whole genome resequencing (WGS) method. Firstly, the original sequencing data was filtered by trimmomatic software to obtain high-quality sequences for comparison with chicken reference genome. The variation sites was extracted by GATK software, parameters was set for quality control to remove low quality and false positive variation sites, and further snpEff was used to annotate the gene structure and function of filtered SNPs. Then, the population structure difference between Wenchang chickens and Jianghan chickens were compared, and the ranges of Fst top 1%,top 5%, ROD top 1%,top 5%, Tajima's D bottom 1% and Bottom 5% were set to screen the selected regions, and the genes in these regions were enriched functionally. The results showed as follows: 1) A total of 1.05 Tb clean data was obtained for Wenchang chickens, with an average of 29.97 Gb (~28×) per sample; A total of 1.10 Tb of clean data was obtained for Jianghan chicken, with approximately 36.72 Gb (~35×) of each sample. The average mapping rate was more than 98%. 2) The total number of gene structure annotations in both populations was intron>intergene region>upstream and downstream regulatory region>coding region; Phylogenetic tree and principal component analysis showed that Wenchang chickens and Jianghan chickens were distant relatives. The degree of linkage disequilibrium of Wenchang chickens was lower than that of Jianghan chickens. 3) The enrichment pathways of genes related to egg production performance were mainly focused on the metabolic pathways of 3 essential amino acids (valine, leucine, isoleucine), calcium ion deposition, metallopeptidase antioxidant, adrenalin and prolactin receptor activities, and the genes in these pathways were located in strongly selected regions. In summary, the factors influencing the laying performance of Wenchang chickens mainly include essential amino acid metabolism, mineral deposition and antioxidant, endocrine hormone secretion. The 3 factors were strongly selected in the evolutionary process, and they played important roles in regulating egg production performance. The study of egg production mechanism from evolutionary molecular genetics can not only promote the understanding of the evolutionary characteristics of Wenchang chickens, but also help to accelerate the breeding of high-yield laying hens.

Key words: Wenchang chickens, whole genome resequencing(WGS), genetic selection, laying performance, influencing factors

中图分类号:

S831.2

任钰为, 陈星, 林燕宁, 黄潇仙, 洪玲玲, 王峰, 孙瑞萍, 张艳, 刘海隆, 郑心力, 晁哲. 基于全基因组重测序研究文昌鸡产蛋性能的影响因素[J]. 畜牧兽医学报, 2024, 55(2): 502-514.

REN Yuwei, CHEN Xing, LIN Yanning, HUANG Xiaoxian, HONG Lingling, WANG Feng, SUN Ruiping, ZHANG Yan, LIU Hailong, ZHENG Xinli, CHAO Zhe. Investigating the Influencing Factors of Egg Laying Performance in Wenchang Chickens Based on Whole Genome Resequencing[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(2): 502-514.

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基于全基因组重测序研究文昌鸡产蛋性能的影响因素

Investigating the Influencing Factors of Egg Laying Performance in Wenchang Chickens Based on Whole Genome Resequencing

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