Genomics and transcriptomics identify quantitative trait loci affecting growth-related traits in silver pomfret (Pampus argenteus)

IF 2.2 2区 生物学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Comparative Biochemistry and Physiology D-Genomics & Proteomics Pub Date : 2025-01-13 DOI:10.1016/j.cbd.2025.101414
Cheng Zhang , Shun Zhang , Guanlin Wang , Xiang Huang , Shanliang Xu , Danli Wang , Chunyang Guo , Yajun Wang
{"title":"Genomics and transcriptomics identify quantitative trait loci affecting growth-related traits in silver pomfret (Pampus argenteus)","authors":"Cheng Zhang ,&nbsp;Shun Zhang ,&nbsp;Guanlin Wang ,&nbsp;Xiang Huang ,&nbsp;Shanliang Xu ,&nbsp;Danli Wang ,&nbsp;Chunyang Guo ,&nbsp;Yajun Wang","doi":"10.1016/j.cbd.2025.101414","DOIUrl":null,"url":null,"abstract":"<div><div><em>Pampus argenteus</em>, a species distributed throughout the Indo-West Pacific, plays a significant role in the yield of aquaculture species. However, cultured <em>P. argenteus</em> has always been characterised by unbalanced growth synchronisation among individuals, slow growth rate, and lack of excellent germplasm resources. Therefore, we conducted mass selection for fast-growing strain <em>P. argenteus</em> for several consecutive years. Various genetic improvement programs have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In the present study, we combined bulked segregant analysis and transcriptome sequencing to identify candidate single nucleotide polymorphisms (SNPs) and key genes for growth-related traits in <em>P. argenteus</em>. A total of 7,280,936 SNPs and 2,212,379 insertions/deletions were identified in the extreme phenotypes of the fast-growing and slow-growing groups. Based on the examination of SNP frequency differences and sliding-window analysis, 42 SNPs were identified as candidate markers. Moreover, 14 of the 42 SNPs linked to growth-related traits were confirmed to be credible SNPs, and eight growth-related genes were screened, namely myb-binding protein 1 A, insulin A/B chains, α-1B adrenoceptor, engulfment and cell motility protein 3, myosin light chain kinase family member 4, insulin receptor located, unconventional myosin-9b, and matrilin-1. An optimal three-factor model (SNP4&amp;SNP12&amp;SNP14) was constructed using the generalized multifactor dimensionality reduction method, and its accuracy was verified as 67.72 %. These results may benefit genetic studies and accelerate genetic improvement of fast-growing strains of <em>P. argenteus</em>.</div></div>","PeriodicalId":55235,"journal":{"name":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","volume":"54 ","pages":"Article 101414"},"PeriodicalIF":2.2000,"publicationDate":"2025-01-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Comparative Biochemistry and Physiology D-Genomics & Proteomics","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1744117X25000024","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Pampus argenteus, a species distributed throughout the Indo-West Pacific, plays a significant role in the yield of aquaculture species. However, cultured P. argenteus has always been characterised by unbalanced growth synchronisation among individuals, slow growth rate, and lack of excellent germplasm resources. Therefore, we conducted mass selection for fast-growing strain P. argenteus for several consecutive years. Various genetic improvement programs have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In the present study, we combined bulked segregant analysis and transcriptome sequencing to identify candidate single nucleotide polymorphisms (SNPs) and key genes for growth-related traits in P. argenteus. A total of 7,280,936 SNPs and 2,212,379 insertions/deletions were identified in the extreme phenotypes of the fast-growing and slow-growing groups. Based on the examination of SNP frequency differences and sliding-window analysis, 42 SNPs were identified as candidate markers. Moreover, 14 of the 42 SNPs linked to growth-related traits were confirmed to be credible SNPs, and eight growth-related genes were screened, namely myb-binding protein 1 A, insulin A/B chains, α-1B adrenoceptor, engulfment and cell motility protein 3, myosin light chain kinase family member 4, insulin receptor located, unconventional myosin-9b, and matrilin-1. An optimal three-factor model (SNP4&SNP12&SNP14) was constructed using the generalized multifactor dimensionality reduction method, and its accuracy was verified as 67.72 %. These results may benefit genetic studies and accelerate genetic improvement of fast-growing strains of P. argenteus.

Abstract Image

查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
基因组学和转录组学鉴定了影响银鲳鱼生长相关性状的数量性状位点。
阿根廷种(Pampus argenteus)是分布于印度-西太平洋的一种鱼类,在水产养殖品种的产量中起着重要作用。然而,人工养殖的阿根廷种一直存在个体间生长同步不平衡、生长速度慢、缺乏优质种质资源等特点。因此,我们连续几年对快速生长的种属进行了大量筛选。各种基因改良程序通过选择性压力改变了它的基因组序列,留下了可以在基因组水平上检测到的核苷酸信号。在本研究中,我们将散装分离分析和转录组测序相结合,以鉴定阿根廷种单核苷酸多态性(snp)和生长相关性状的关键基因。在快速生长组和缓慢生长组的极端表型中,共鉴定出7,280,936个snp和2,212,379个插入/缺失。根据SNP频率差异和滑动窗口分析,鉴定出42个SNP作为候选标记。此外,42个与生长相关性状相关的snp中有14个被证实为可信snp,并筛选了8个生长相关基因,分别是myb结合蛋白1a、胰岛素A/B链、α-1B肾上腺素受体、吞噬和细胞运动蛋白3、肌球蛋白轻链激酶家族成员4、胰岛素受体定位、非常规肌球蛋白9b和matrilin-1。采用广义多因素降维法构建了最优三因素模型(SNP4&SNP12&SNP14),验证其准确率为67.72%。这些结果可能有助于遗传学研究和加速快速生长菌株的遗传改良。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 去求助
来源期刊
CiteScore
5.10
自引率
3.30%
发文量
69
审稿时长
33 days
期刊介绍: Comparative Biochemistry & Physiology (CBP) publishes papers in comparative, environmental and evolutionary physiology. Part D: Genomics and Proteomics (CBPD), focuses on “omics” approaches to physiology, including comparative and functional genomics, metagenomics, transcriptomics, proteomics, metabolomics, and lipidomics. Most studies employ “omics” and/or system biology to test specific hypotheses about molecular and biochemical mechanisms underlying physiological responses to the environment. We encourage papers that address fundamental questions in comparative physiology and biochemistry rather than studies with a focus that is purely technical, methodological or descriptive in nature.
期刊最新文献
Transcriptomic and metabolomic analyses provide insights into the energy metabolism and signaling regulation of byssus secretion in winged pearl oyster Pteria penguin Pyraclostrobin-induced toxic effects in the gills of common carp (Cyprinus carpio L.): Mechanisms unveiled through biochemical, molecular, and metabolomic analyses Dorsomorphin (DM) inhibits the ovarian development of Portunus trituberculatus by acting on the BMP signaling pathway Synergistic integration of transcriptomics and metabolomics analyses provides novel insights into the mechanisms underlying unsynchronized growth of greater amberjack (Seriola dumerili) Long-term thermal stress reshapes the tolerance of head kidney of Hong Kong catfish (Clarias fuscus) to acute heat shock by regulating energy metabolism and immune response
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1