Genomic differentiation and selection signatures of two elite varieties of Yesso scallop Mizuhopecten yessoensis

IF 3.9 1区农林科学 Q1 FISHERIES

Aquaculture Pub Date : 2022-03-15 DOI:10.1016/j.aquaculture.2021.737842

Jia Lv , Yantong Cai , Pingping Liu , Xiaowen Huang , Zhenli Lv , Rongchao Zhang , Liang Zhao , Lisui Bao , Shi Wang , Jingjie Hu

{"title":"Genomic differentiation and selection signatures of two elite varieties of Yesso scallop Mizuhopecten yessoensis","authors":"Jia Lv , Yantong Cai , Pingping Liu , Xiaowen Huang , Zhenli Lv , Rongchao Zhang , Liang Zhao , Lisui Bao , Shi Wang , Jingjie Hu","doi":"10.1016/j.aquaculture.2021.737842","DOIUrl":null,"url":null,"abstract":"<div>Yesso scallop, Mizuhopecten yessoensis, is one of the most important bivalve species in aquaculture industry. Two selective improved varieties (Haida golden scallop and Zhangzidaohong) have been developed by artificial selection in recent years and exhibit good performance on growth and production traits. However, there's still a lack of comprehensive studies to analyze the population differentiation, genomic linkage disequilibrium patterns, as well as the selection signatures of the two elite varieties of Yesso scallop. In the present study, we performed whole genome resequencing of three groups of Yesso scallop to characterize the genetic changes resulted from selective breeding. A total of 9,534,749 high quality single nucleotide polymorphisms (SNPs) were discovered. The two selective varieties exhibited lower genetic diversity and retained relatively large linkage disequilibrium (LD) blocks compared to the reference population. Despite obvious stratification of the population structure of Yesso scallop, medium degrees of genetic differentiation (Fst < 0.15) was detected among the new varieties and the reference population. We highlighted several genes including LPCAT1 and TRAF reveal signatures of artificial selection and these genes would be potentially important for specific characteristics and improved performance in growth and resistance to diseases. The data and findings generated in our project would provide useful additions to currently available genomic resources for scallops and facilitate further genetic improvement and molecular studies in M.yessoensis.</div>","PeriodicalId":8375,"journal":{"name":"Aquaculture","volume":null,"pages":null},"PeriodicalIF":3.9000,"publicationDate":"2022-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"4","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Aquaculture","FirstCategoryId":"97","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0044848621015052","RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"FISHERIES","Score":null,"Total":0}

引用次数: 4

Abstract

Yesso scallop, Mizuhopecten yessoensis, is one of the most important bivalve species in aquaculture industry. Two selective improved varieties (Haida golden scallop and Zhangzidaohong) have been developed by artificial selection in recent years and exhibit good performance on growth and production traits. However, there's still a lack of comprehensive studies to analyze the population differentiation, genomic linkage disequilibrium patterns, as well as the selection signatures of the two elite varieties of Yesso scallop. In the present study, we performed whole genome resequencing of three groups of Yesso scallop to characterize the genetic changes resulted from selective breeding. A total of 9,534,749 high quality single nucleotide polymorphisms (SNPs) were discovered. The two selective varieties exhibited lower genetic diversity and retained relatively large linkage disequilibrium (LD) blocks compared to the reference population. Despite obvious stratification of the population structure of Yesso scallop, medium degrees of genetic differentiation (Fst < 0.15) was detected among the new varieties and the reference population. We highlighted several genes including LPCAT1 and TRAF reveal signatures of artificial selection and these genes would be potentially important for specific characteristics and improved performance in growth and resistance to diseases. The data and findings generated in our project would provide useful additions to currently available genomic resources for scallops and facilitate further genetic improvement and molecular studies in M.yessoensis.

查看原文本刊更多论文

稻穗扇贝两个优良品种的基因组分化和选择特征

野贝(Mizuhopecten yessoensis)是水产养殖业中最重要的双壳类之一。近年来，通过人工选育培育了海大金扇贝和獐子道红两个选择性改良品种，在生长和生产性状上均表现出良好的性能。然而，目前还缺乏对叶索扇贝两个优良品种群体分化、基因组连锁不平衡模式以及选择特征的综合研究。在本研究中，我们对三组耶索扇贝进行了全基因组重测序，以表征选择性育种导致的遗传变化。共发现9534749个高质量单核苷酸多态性(snp)。与参考群体相比，两个选择品种表现出较低的遗传多样性和较大的连锁不平衡区。尽管叶索扇贝群体结构有明显的分层，但中等程度的遗传分化(Fst <在新品种和参考群体中检测到0.15)。我们强调了包括LPCAT1和TRAF在内的几个基因揭示了人工选择的特征，这些基因可能对特定特征和提高生长和抗病性能具有潜在的重要作用。本项目所获得的数据和发现将为现有的扇贝基因组资源提供有益的补充，并为进一步的扇贝遗传改良和分子研究提供便利。

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分钟内获得全文求助全文

来源期刊

Aquaculture 农林科学-海洋与淡水生物学

CiteScore

8.60

自引率

17.80%

发文量

1246

审稿时长

56 days

期刊介绍： Aquaculture is an international journal for the exploration, improvement and management of all freshwater and marine food resources. It publishes novel and innovative research of world-wide interest on farming of aquatic organisms, which includes finfish, mollusks, crustaceans and aquatic plants for human consumption. Research on ornamentals is not a focus of the Journal. Aquaculture only publishes papers with a clear relevance to improving aquaculture practices or a potential application.