转录组分析揭示鸭嵴垫形成的遗传基础

doi:10.1016/j.jia.2023.09.025

Journal of Integrative Agriculture ›› 2024, Vol. 23 ›› Issue (12): 4172-4185.DOI: 10.1016/j.jia.2023.09.025

转录组分析揭示鸭嵴垫形成的遗传基础

收稿日期:2023-05-19 接受日期:2023-08-01 出版日期:2024-12-20 发布日期:2023-09-24

Transcriptome analysis reveals the genetic basis of crest cushion formation in duck

Lan Huang^{1, 2}, Qixin Guo², Yong Jiang², Zhixiu Wang², Guohong Chen^{1, 2}, Guobin Chang^{1, 2#}, Hao Bai^1#

¹Joint International Research Laboratory of Agriculture and Agri-Product Safety, Ministry of Education/Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
²Key Laboratory of Animal Genetics and Breeding and Molecular Design of Jiangsu Province, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China

Received:2023-05-19 Accepted:2023-08-01 Online:2024-12-20 Published:2023-09-24
About author:Lan Huang, E-mail: dx120200133@stu.yzu.edu.cn; #Correspondence Guobin Chang, E-mail: gbchang1975@yzu.edu.cn; Hao Bai, E-mail: bhowen1027@yzu.edu.cn
Supported by:
This work was supported by the earmarked fund for CARS, China (CARS-42), the earmarked fund for Jiangsu Agricultural Industry Technology System, China (JATS (2022) 331) and the Jiangsu Key Research and Development Program, China (BE2021332).

摘要/Abstract

摘要：

鸟类中很少有能与羽冠的多样性、复杂性和进化性相媲美的形态特征。伴随着动物的进化历程以及环境的变化，颅顶部附属物形态进化迅速，颅顶部附属物的大小、形状和解剖细节可以表现出巨大的差异。润州凤头白鸭因其含有一个球状的羽冠而得名，具有重要的经济和文化价值。目前，关于鸭羽冠形成的分子调控机理研究仍然不够充分。为了探究润州凤头白鸭羽冠的形成机制，更好地对我国地方鸭种质资源挖掘与创新利用，本研究通过转录组测序结合差异表达分析和加权基因共表达网络分析（WGCNA）的分析方法，鉴定了参与润州凤头白鸭羽冠形成和发育的调控基因。结果显示，对胚胎期第28天（E28）凤头组织和头皮组织进行基因表达差异分析，共鉴定到261个差异表达基因（其中表达上调基因112个，表达下调基因139个）；对生长第42天（D42）鸭凤头组织和头皮组织进行基因表达差异分析，共鉴定到361个差异表达基因（其中表达上调基因154个，表达下调基因207个）。WGCNA结果显示，3个模块与E28的凤头组织相关，2个模块与D42凤头组织相关。结合差异表达基因和WGCNA模块基因的Venn分析结果显示，D42和E28阶段分别有145和45个基因与凤头组织的发育相关。GO（Gene Ontology）注释和KEGG（Kyoto Encyclopedia of Genes and Genomes）分析结果显示，差异基因WNT16、BMP2、SLC35F2、SLC6A15、APOBEC2、ABHD6、TNNC2、MYL1和TNNI2主要参与脂肪生成、羽毛结构、组织修复等过程。本研究在转录水平上阐明了嵴状头组织关键发育阶段的表达模式，为嵴垫形成过程中亚表型的形成提供了参考，为嵴垫发育的分子遗传调控机理提供了新的见解。

Abstract:

The Chinese crested duck is a unique duck breed having a bulbous feather shape on its duck head. However, the mechanisms involved in its formation and development are unclear. In the present study, RNA sequencing analysis was performed on the crested tissues of 6 Chinese crested ducks and the scalp tissues of 6 cherry valley ducks (CVs) from 2 developmental stages. This study identified 261 differentially expressed genes (DEGs), 122 upregulated and 139 downregulated, in the E28 stage and 361 DEGs, 154 upregulated and 207 downregulated in the D42 stage between CC and CV ducks. The subsequent results of weighted gene co-expression network analysis (WGCNA) revealed that the turquoise and cyan modules were associated with the crest trait in the D42 stage, meanwhile, the green, brown, and pink modules were associated with the crest trait in the E28 stage. Venn analysis of the DEGs and WGCNA showed that 145 and 45 genes are associated between the D42 and E28 stages, respectively. The expression of WNT16, BMP2, SLC35F2, SLC6A15, APOBEC2, ABHD6, TNNC2, MYL1, and TNNI2 were verified by real-time quantitative PCR. This study provides an approach to reveal the molecular mechanisms underlying the crested trait development.

Key words: crested duck , RNA-sequencing , weighted gene co-expression network analysis , differentially expressed genes

Lan Huang, Qixin Guo, Yong Jiang, Zhixiu Wang, Guohong Chen, Guobin Chang, Hao Bai. 转录组分析揭示鸭嵴垫形成的遗传基础[J]. Journal of Integrative Agriculture, 2024, 23(12): 4172-4185.

Lan Huang, Qixin Guo, Yong Jiang, Zhixiu Wang, Guohong Chen, Guobin Chang, Hao Bai. Transcriptome analysis reveals the genetic basis of crest cushion formation in duck[J]. Journal of Integrative Agriculture, 2024, 23(12): 4172-4185.

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转录组分析揭示鸭嵴垫形成的遗传基础

Transcriptome analysis reveals the genetic basis of crest cushion formation in duck

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