基于转录组数据挖掘牦牛皱胃发育代谢的关键候选基因

doi:10.11843/j.issn.0366-6964.2024.01.016

摘要/Abstract

摘要： 旨在比较不同年龄段牦牛皱胃指数测定、转录组表达谱的变化，挖掘影响牦牛皱胃发育代谢的信号通路和关键基因，为进一步探讨牦牛皱胃发育机制提供理论基础。本研究对1日龄、20日龄、60日龄、15月龄与3岁的牦牛皱胃组织进行转录组测序，对转录组数据进行质控、比对、差异表达基因筛选，并对差异表达基因进行GO功能注释和KEGG富集分析。为进一步验证测序数据的可靠性，随机选取5个差异表达基因进行qRT-PCR验证。结果显示，在发育过程中，瘤胃重的增长最快，其次是瓣胃、网胃和皱胃。转录组结果显示，以1日龄组为对照，在20日龄、60日龄、15月龄和3岁组中分别鉴定到1 310、1 715、1 931和2 199个差异表达基因，4个组共有基因565个；以前一个时间点为对照，20日龄、60日龄、15月龄和3岁组分别鉴定到1 310、861、569和597个差异表达基因，4个对比组共有基因9个。GO功能注释发现，以1日龄组为对照，20日龄、60日龄、15月龄和3岁组分别富集到1 191、2 578、1 117和2 835条显著条目，不同年龄组的前10条显著性GO条目中有共有的，也有各年龄阶段特有的条目。KEGG富集分析结果显示，20日龄、60日龄、15月龄和3岁4个年龄段的前30条显著通路中特有信号通路分别为4、1、3和4条，包括ECM受体相互作用、细胞色素P450对外源性物质的代谢和药物代谢-细胞色素P450等与皱胃发育相关的通路。qRT-PCR结果与测序结果基本一致，表明测序结果可靠。通过对牦牛不同发育阶段皱胃组织的转录组测序及生物信息学分析，筛选到与皱胃发育相关的差异表达候选基因，这些基因主要参与胃粘膜上皮细胞增殖分化、细胞分化和免疫调控等过程，其中GKN1、CXCL17、SCNN1B、SCNN1G、CCL5和IGF2BP3等基因可能在牦牛皱胃发育过程中起着重要作用；进一步筛选到参与皱胃葡萄糖代谢、葡萄糖转运、脂肪酸转运、肽转运等过程相关的信号通路和候选基因，其中GANAB、GBA2、SLC2A1、SLC2A3、SLC2A4、CPT1B、SLC15A1等是与牦牛皱胃组织营养代谢和吸收相关的重要候选基因。

关键词: 不同年龄段, 牦牛, 皱胃, 转录组, 发育, 代谢

Abstract: This study aimed to compare the changes in abomasum index and transcriptome expression profile of yaks at different ages, and to explore the signaling pathways and key genes that affect the development and metabolism of abomasum, so as to provide theoretical basis for further study of development mechanism of abomasum in yaks. Abomasum tissues of yaks at 1 day, 20 days, 60 days, 15 months and 3 years old were selected for transcriptome sequencing. The RNA-Seq data were performed quality-controlled, alignment, differential genes screening; GO and KEGG analysis were conducted for differentially expressed genes(DEGs). To further verify the reliability of sequencing data, 5 DEGs were randomly selected for qRT-PCR verification. The results showed that rumen weight increased the fastest, followed by omasum, reticulum and abomasum during development. Compared with 1 day, 1 310, 1 715, 1 931 and 2 199 DEGs were identified at 20 days, 60 days, 15 months and 3 years old, respectively. A total of 565 DEGs were defined as common DEGs among 4 closed groups. Compared with the previous time point, 1 310, 861, 569 and 597 DEGs were identified at 20 days, 60 days, 15 months and 3 years old, respectively, with a total of 9 common DEGs in the 4 consecutive groups. The GO functional annotation found that, taking 1-day-old group as the control, 1 191, 2 578, 1 117 and 2 835 significant items were enriched in 20-day-old, 60-day-old, 15-month-old and 3-year-old groups, respectively. Among the top 10 significant GO items in different age groups, there were common ones, as well as unique ones in each age group. KEGG enrichment analysis showed that there were 4, 1, 3 and 4 unique signaling pathways in the top 30 significant pathways at 20 days old, 60 days old, 15 months old and 3 years old, respectively, including ECM receptor interaction, cytochrome P450 metabolism of exogenous substances, drug metabolism-cytochrome P450 pathways and other pathways related to abomasum development. The qRT-PCR results were basically consistent with sequencing results, indicating that the sequencing results were reliable. Through transcriptome sequencing and bioinformatics analysis of abomasum tissues at different developmental stages of yaks, the differentially expressed candidate genes related to development and metabolism of abomasum were screened, and these genes were mainly involved in the proliferation and differentiation of gastric epithelial cells, cells differentiation and immune regulation. Among them, GKN1, CXCL17, SCNN1B, SCNN1G, CCL5 and IGF2BP3 may play an important role in the development of abomasum in yaks. The signal pathways and candidate genes involved in glucose metabolism, glucose transport, fatty acid transport and peptide transport in abomasum were further screened. Among them, GANAB, GBA2, SLC2A1, SLC2A3, SLC2A4, CPT1B and SLC15A1 were important candidate genes related to nutrient metabolism and absorption in abomasum of yaks.

Key words: different ages, yak, abomasum, transcriptome, development, metabolism

中图分类号:

S823.85

刘益丽, 唐娇, 闵奇, 杨露, 王泽宁, 胡莲, 赵迪, 江明锋. 基于转录组数据挖掘牦牛皱胃发育代谢的关键候选基因[J]. 畜牧兽医学报, 2024, 55(1): 153-168.

LIU Yili, TANG Jiao, MIN Qi, YANG Lu, WANG Zening, HU Lian, ZHAO Di, JIANG Mingfeng. Mining Key Candidate Genes of Development and Metabolism in Yak Abomasum Based on Transcriptome Data[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 153-168.

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