SNP 指纹图谱用于快速生长的太平洋牡蛎(Crassostrea gigas)"海达 1 号 "品种的种质鉴定

IF 2.6 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Zihao Zhang, Ben Yang, Liting Ren, Qi Li, Shikai Liu
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引用次数: 0

摘要

太平洋牡蛎(Crassostrea gigas)是具有重要经济意义的全球水产养殖物种。为了培育出具有快速生长和其他理想性状的多个品系,人们开展了选择性育种计划。然而,由于牡蛎的表型可塑性强,在选择性育种的品系中进行精确的种质鉴定存在挑战。在这项工作中,我们确定了三个快速生长太平洋牡蛎品系的选择特征,这三个品系分别来源于从中国、日本和韩国采集的野生种群,并将其用于开发基于SNP的分子指纹图谱,以精确鉴定种质。我们对来自三个选育品系和一个野生种群的 59 只牡蛎进行了全基因组重测序,以进行全基因组 SNP 分析。利用这些 SNPs 进行的种群结构分析表明,选育品系之间存在显著的遗传分化。根据 FST 指数,我们从三个选育品系中分别鉴定出 41、49 和 36 个品系特异性 SNPs。考虑到正向选择过程中基因组中出现的 "搭便车效应",我们为三个品系分别确定了两个、三个和两个分子指纹。我们用 42 个具有不同遗传背景的牡蛎群体对中国选育品系(即 "海大 1 号 "品种)的分子指纹进行了验证,结果表明种质鉴定的准确率超过 96%。这项工作为精确鉴定 "海大1号 "品种和其他两个选育品系的种质提供了可靠的工具,对吉贝的种质保存和育种设计具有重要价值。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
SNP Fingerprinting for Germplasm Identification of the Fast-Growing Pacific oyster (Crassostrea gigas) “Haida No. 1” Variety

The Pacific oyster (Crassostrea gigas) is a global aquaculture species of economic significance. Selective breeding programs have been conducted to produce multiple strains with fast growth as well as other desirable traits. However, due to the phenotypic plasticity of oysters, challenges existed for precise germplasm identification among selectively bred strains. In this work, we identified selection signatures of three fast-growing Pacific oyster strains originated from wild populations collected from China, Japan, and Korea, respectively, which were used for development of SNP-based molecular fingerprinting for precise identification of germplasm. We performed whole-genome resequencing of 59 oysters from three selectively bred strains and a wild population for genome-wide SNP analyses. Population structure analysis with these SNPs revealed significant genetic differentiation among the selectively bred strains. Based on the FST index, we identified 41, 49, and 36 strain-specific SNPs from the three selectively bred strains. Taking into account the “hitch-hiking effect” that occurs in the genome during positive selection, we identified two, three, and two molecular fingerprints for the three strains, respectively. We validated the molecular fingerprints of the China selectively bred strain (i.e., “Haida No. 1” variety) with a separate population of 42 oysters with diverse genetic background, demonstrating the accuracy of germplasm identification of over 96%. This work provides a reliable tool for precise germplasm identification of the "Haida No. 1" variety as well as other two selectively bred strains, which is valuable in germplasm conservation and breeding design in the C. gigas.

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来源期刊
Marine Biotechnology
Marine Biotechnology 工程技术-海洋与淡水生物学
CiteScore
4.80
自引率
3.30%
发文量
95
审稿时长
2 months
期刊介绍: Marine Biotechnology welcomes high-quality research papers presenting novel data on the biotechnology of aquatic organisms. The journal publishes high quality papers in the areas of molecular biology, genomics, proteomics, cell biology, and biochemistry, and particularly encourages submissions of papers related to genome biology such as linkage mapping, large-scale gene discoveries, QTL analysis, physical mapping, and comparative and functional genome analysis. Papers on technological development and marine natural products should demonstrate innovation and novel applications.
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