Identification of Genes and SNPs Related to Body Colors by Transcriptome Profiling in Leopard Coral Grouper (Plectropomus leopardus Lacépède)

IF 0.7 4区农林科学 Q4 FISHERIES

Journal of Applied Ichthyology Pub Date : 2023-05-05 DOI:10.1155/2023/4135906

Yucong Hong, K. Sun, Xiaowen Zhu, Xufeng Zhu, Qiuxia Deng, Yang Huang, Ruijuan Hao, Chunhua Zhu

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引用次数: 0

Abstract

Body colors are an important trait for the survival and reproduction of animals. In this study, transcriptomes and related single nucleotide polymorphisms (SNPs) of black- and red-colored Plectropomus leopardus (Lacépède) were identified to investigate important molecules and SNP markers associated with body color formation. In the comparison of red- and black-colored groups, 489 differential expressed genes (DEGs) were detected and among them, 236 up- and 253 down-regulated genes were found in the red-colored group. Gene ontology (GO) analysis of DEGs showed that pigmentation associated terms including pigment granule, pigmentation, melanin metabolic process, tyrosine metabolic process, pigment metabolic process, and pigmentation cell differentiation were enriched. Kyoto encyclopedia of genes and genomes (KEGG) analysis of DEGs presented that melanin related pathways (tyrosine metabolism and melanogenesis) were enriched. Furthermore, lipid metabolism and immune-related metabolism were also enriched. A total of 1,048,575 SNPs were detected from the transcriptome, and among them, 627,172 SNPs were located in the gene region. A total of 1323 SNPs were identified as differential SNPs in the comparison of black- and red-colored groups and were located in 1127 genes. Among the 1127 genes, 20 genes were identified as DEGs and were comprised of 9 SNPs with a potential role in body color selective breeding in fish farming.

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LeopardCoralGrouper（PlectropomusleopardusLacépède）体色相关基因和SNPs的转录组鉴定

体色是动物生存和繁殖的重要特征。在本研究中，鉴定了黑色和红色豹子（Lacépède）的转录组和相关单核苷酸多态性（SNPs），以研究与体色形成相关的重要分子和SNP标记。在红色和黑色组的比较中，检测到489个差异表达基因（DEG），其中，在红色组中发现236个上调基因和253个下调基因。DEG的基因本体论分析表明，色素颗粒、色素沉着、黑色素代谢过程、酪氨酸代谢过程、色素代谢过程和色素沉着细胞分化等色素沉着相关术语丰富。京都基因和基因组百科全书（KEGG）对DEG的分析表明，黑色素相关途径（酪氨酸代谢和黑色素生成）得到了丰富。此外，脂质代谢和免疫相关代谢也得到了丰富。从转录组中共检测到1048575个SNPs，其中627172个SNPs位于基因区。在黑色和红色组的比较中，共有1323个SNPs被鉴定为差异SNPs，位于1127个基因中。在1127个基因中，有20个基因被鉴定为DEG，由9个SNPs组成，在鱼类养殖的体色选择育种中具有潜在作用。

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来源期刊

Journal of Applied Ichthyology 生物-海洋与淡水生物学

CiteScore

2.30

自引率

11.10%

发文量

审稿时长

3-8 weeks

期刊介绍： The Journal of Applied Ichthyology publishes articles of international repute on ichthyology, aquaculture, and marine fisheries; ichthyopathology and ichthyoimmunology; environmental toxicology using fishes as test organisms; basic research on fishery management; and aspects of integrated coastal zone management in relation to fisheries and aquaculture. Emphasis is placed on the application of scientific research findings, while special consideration is given to ichthyological problems occurring in developing countries. Article formats include original articles, review articles, short communications and technical reports.