Integrating genomics and transcriptomics to identify candidate genes for high-altitude adaptation and egg production in Nixi chicken.

IF 1.6 3区农林科学 Q2 AGRICULTURE, DAIRY & ANIMAL SCIENCE

British Poultry Science Pub Date : 2024-06-26 DOI:10.1080/00071668.2024.2367228

C Deng, M Li, T Wang, W Duan, A Guo, G Ma, F Yang, F Dai, Q Li

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引用次数: 0

Abstract

1. This study combined genome-wide selection signal analysis with RNA-sequencing to identify candidate genes associated with high altitude adaptation and egg production performance in Nixi chickens (NXC).2. Based on the whole-genome data from 20 NXC (♂:10; ♀:10), the population selection signal was analysed by sliding window analysis. The selected genes were screened by combination with the population differentiation statistic (F_ST). The sequence diversity statistic (θπ). RNA-seq was performed on the ovarian tissues of NXC (n = 6) and Lohmann laying hens (n = 6) to analyse the differentially expressed genes (DEGs) between the two groups. The functional enrichment analysis of the selected genes and differentially expressed genes was performed.3. There were 742 genes under strong positive selection and 509 differentially expressed genes screened in NXC. Integrated analysis of the genome and transcriptome revealing 26 overlapping genes. The candidate genes for adaptation to a high-altitude environment, as well as for egg production, disease resistance, vision and pigmentation in NXC were preliminarily screened.4. The results provided theoretical guidance for further research on the genetic resource protection and utilisation of NXC.

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整合基因组学和转录组学，鉴定尼西鸡高海拔适应性和产蛋量的候选基因

1.本研究将全基因组选择信号分析与 RNA 测序相结合，以鉴定与尼西鸡（NXC）高海拔适应性和产蛋性能相关的候选基因。 2. 基于 20 只尼西鸡（♂:10；♀:10）的全基因组数据，通过滑动窗口分析法分析种群选择信号。结合种群分化统计量（FST）对筛选出的基因进行筛选。序列多样性统计量（θπ）。对 NXC（n = 6）和 Lohmann 蛋鸡（n = 6）的卵巢组织进行 RNA-seq 分析，以分析两组之间的差异表达基因（DEGs）。对筛选出的基因和差异表达基因进行了功能富集分析。在 NXC 中筛选出了 742 个强阳性选择基因和 509 个差异表达基因。对基因组和转录组进行综合分析，发现了 26 个重叠基因。初步筛选出 NXC 适应高海拔环境以及产蛋、抗病、视觉和色素的候选基因。 4.研究结果为进一步开展 NXC 遗传资源保护和利用研究提供了理论指导。

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来源期刊

British Poultry Science 农林科学-奶制品与动物科学

CiteScore

3.90

自引率

5.00%

发文量

审稿时长

4.5 months

期刊介绍： From its first volume in 1960, British Poultry Science has been a leading international journal for poultry scientists and advisers to the poultry industry throughout the world. Over 60% of the independently refereed papers published originate outside the UK. Most typically they report the results of biological studies with an experimental approach which either make an original contribution to fundamental science or are of obvious application to the industry. Subjects which are covered include: anatomy, embryology, biochemistry, biophysics, physiology, reproduction and genetics, behaviour, microbiology, endocrinology, nutrition, environmental science, food science, feeding stuffs and feeding, management and housing welfare, breeding, hatching, poultry meat and egg yields and quality.Papers that adopt a modelling approach or describe the scientific background to new equipment or apparatus directly relevant to the industry are also published. The journal also features rapid publication of Short Communications. Summaries of papers presented at the Spring Meeting of the UK Branch of the WPSA are published in British Poultry Abstracts .