整合基因组和转录组筛选调控北京鸭脂肪沉积的候选基因

doi:10.16431/j.cnki.1671-7236.2025.04.002

摘要/Abstract

摘要： 【目的】利用北京鸭(Pekin duck)与绿头野鸭(Mallard duck)基因组重测序数据、转录组数据以及血浆生化指标筛选调控北京鸭脂肪沉积相关候选基因。【方法】分别选取3只42日龄北京鸭公鸭与绿头野鸭公鸭，采集翅下静脉血并分离血浆，测定北京鸭与绿头野鸭血浆甘油三酯(TG)、磷脂(PLIP)等12项生化指标。基于30只北京鸭、41只绿头野鸭的基因组重测序数据，利用固定指数(F_ST)、跨群体扩展单倍型纯合(cross population extended haplotype homozygosity，XP-EHH)以及Tajima’D检验检测北京鸭潜在的受选择区间。基于3种滑动窗口/步长模式，保证至少一种方法可以筛选到北京鸭的驯化基因。提取试验鸭肝脏样本总RNA并进行转录组测序，通过差异表达基因分析筛选北京鸭和绿头野鸭肝脏组织的差异表达基因，并对其进行KEGG通路富集分析。选取差异表达基因与北京鸭驯化基因的交集，筛选出调控鸭脂肪沉积的候选基因。【结果】血浆生化指标检测结果显示，北京鸭血浆中低密度脂蛋白胆固醇(LDL-C)和葡萄糖(GLU)含量显著低于绿头野鸭(P＜0.05)，TG含量显著高于绿头野鸭(P＜0.05)。共筛选到了2 681个北京鸭驯化基因和455个肝脏组织差异表达基因。差异表达基因显著富集在甘油脂代谢(glycerolipid metabolism)和甘油磷脂代谢(glycerophospholipid metabolism)等代谢通路上，筛选到2个在北京鸭驯化过程中受到强烈选择的肝脏组织差异表达基因：ACSL5和ELOVL3。【结论】本研究筛选到了2个在北京鸭和绿头野鸭肝脏组织中差异表达的基因ELOVL3和ACSL5，二者在北京鸭驯化过程中经历了强烈的正向选择，可能是调控鸭脂肪沉积的关键候选基因。研究结果为解析鸭脂质沉积调控机制和精准调控北京鸭的脂质沉积水平提供理论依据,为鸭脂肪沉积的进一步研究提供借鉴。

关键词: 北京鸭; 转录组; 基因组; 驯化; 肝脏; 脂质代谢

Abstract: 【Objective】 The purpose of this experiment was to use the genome resequencing data,transcriptome data,and plasma biochemical indicators of Pekin ducks and Mallard ducks to screen for candidate genes related to fat deposition in Pekin ducks.【Method】 Three 42-day-old Pekin ducks and Mallard ducks were selected to collect and separate the blood plasma from wings,and 12 biochemical indexes such as triglyceride (TG) and phospholipid (PLIP) were determined.Based on the genome resequencing data of 30 Pekin ducks and 41 Mallard ducks,various methods such as fixation index (F_ST),cross population extended haplotype homozygosity (XP-EHH),and Tajima’s D test were used to detect potential selective intervals in Pekin ducks.Using three sliding window/step size models,it was ensured that at least one method could be used to filter out the domestication genes of Pekin ducks.Total RNA was extracted from duck liver samples and transcriptome sequencing was performed.Differential expression genes in liver tissues of Pekin ducks and Mallard ducks were screened by differential expression gene analysis and the KEGG pathway enrichment analysis was performed.The intersection of differentially expressed genes and domestication genes of Pekin ducks was selected to screen out candidate genes regulating duck fat deposition.【Result】 The results of plasma biochemical indices showed that the contents of low density lipoprotein cholesterol (LDL-C) and glucose (GLU) in plasma of Pekin ducks were significantly lower than those of Mallard ducks (P＜0.05),and the content of TG was significantly higher than that of Mallard ducks (P＜0.05).A total of 2 681 domestication genes of Pekin ducks and 455 differentially expressed genes in liver were screened.Differentially expressed genes were significantly enriched in metabolic pathways such as glycerolipid metabolism and glycerophospholipid metabolism.Two differentially expressed genes in liver that were strongly selected during the domestication process of Pekin ducks were identified:ACSL5 and ELOVL3.【Conclusion】 This study identified two differentially expressed genes in liver of Pekin ducks and Mallard ducks,namely ELOVL3 and ACSL5.These two genes underwent strong positive selection during the domestication process of Pekin ducks and might be key candidate genes regulating fat deposition in ducks.The results of this study provided a theoretical basis for elucidating the regulatory mechanism of lipid deposition in ducks and precisely regulating the lipid deposition levels in Pekin ducks,offering a reference for further research on duck fat deposition.

Key words: Pekin duck; transcriptome; genome; domestication; liver; lipid metabolism

中图分类号:

S834⁺.81

刘嗣睿, 刘洪飞, 刘大鹏, 牟启铭, 唐贺贺, 张鹤, 张永福, 侯水生, 周正奎. 整合基因组和转录组筛选调控北京鸭脂肪沉积的候选基因[J]. 中国畜牧兽医, 2025, 52(4): 1468-1477.

LIU Sirui, LIU Hongfei, LIU Dapeng, MU Qiming, TANG Hehe, ZHANG He, ZHANG Yongfu, HOU Shuisheng, ZHOU Zhengkui. Screening of Candidate Genes Regulating Fat Deposition in Pekin Ducks by Integrating Genome and Transcriptome[J]. China Animal Husbandry and Veterinary Medicine, 2025, 52(4): 1468-1477.

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