基于全基因组序列鉴定的中国沼虾（Monopterus albus）微卫星标记开发及多态性分析

Genome-wide identification of simple sequence repeats and development of polymorphic SSR markers in swamp eel (Monopterus albus).

机构信息

Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei, China.

出版信息

Sci Prog. 2021 Jul-Sep;104(3):368504211035597. doi: 10.1177/00368504211035597.

DOI:10.1177/00368504211035597

PMID:34375541

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10358632/

Abstract

OBJECTIVES

Swamp eel is one model species for sexual reversion and an aquaculture fish in China. One local strain with deep yellow and big spots of has been selected for consecutive selective breeding. The objectives of this study were characterizing the Simple Sequence Repeats (SSRs) of in the assembled genome obtained recently, and developing polymorphic SSRs for future breeding programs.

METHODS

The genome wide SSRs were mined by using MISA software, and their types and genomic distribution patterns were investigated. Based on the available flanking sequences, primer pairs were batched developed, and Polymorphic SSRs were identified by using Polymorphic SSR Retrieval tool. The obtained polymorphic SSRs were validated by using e-PCR and capillary electrophoresis, then they were used to investigate genetic diversity of one breeding population.

RESULTS

A total of 364,802 SSRs were identified in assembled genome. The total length, density and frequency of SSRs were 8,204,641 bp, 10,259 bp/Mb, and 456.16 loci/Mb, respectively. Mononucleotide repeats were predominant among SSRs (33.33%), and AC and AAT repeats were the most abundant di- and tri-nucleotide repeats motifs. A total of 287,189 primer pairs were designed, and a high-density physical map was constructed (359.11 markers per Mb). A total of 871 polymorphic SSRs were identified, and 38 SSRs of 101 randomly selected ones were validated by using e-PCR and capillary electrophoresis. Using these 38 polymorphic SSRs, 201 alleles were detected and genetic diversity level (Na, PIC, , and ) was evaluated.

CONCLUSIONS

The genome-wide SSRs and newly developed SSR markers will provide a useful tool for genetic mapping, diversity analysis studies in swamp eel in the future. The high level of genetic diversity (Na = 5.29, PIC = 0.5068, = 0.4665, = 0.5525) but excess of homozygotes ( = 0.155) in one breeding population provide baseline information for future breeding program.

摘要

目的

鳗鱼是性反转的模式物种之一，也是中国的水产养殖鱼类。中国已选择了一个具有深黄色和大斑点的地方品系进行连续选择性繁殖。本研究的目的是对最近获得的组装基因组中的进行简单序列重复（SSR）特征分析，并开发用于未来繁殖计划的多态性 SSR。

方法

使用 MISA 软件在全基因组范围内挖掘 SSR，研究其类型和基因组分布模式。基于可用的侧翼序列，批量开发引物对，使用多态性 SSR 检索工具鉴定多态性 SSR。使用 e-PCR 和毛细管电泳验证获得的多态性 SSR，然后使用这些 SSR 来研究一个繁殖群体的遗传多样性。

结果

在组装的基因组中共鉴定出 364802 个 SSR。SSR 的总长度、密度和频率分别为 8204641bp、10259bp/Mb 和 456.16 个/Mb。单核苷酸重复是 SSR 中的主要类型（33.33%），而 AC 和 AAT 重复是最丰富的二核苷酸和三核苷酸重复基序。共设计了 287189 对引物，并构建了高密度物理图谱（每 Mb 有 359.11 个标记）。共鉴定出 871 个多态性 SSR，随机选择的 101 个 SSR 中的 38 个通过 e-PCR 和毛细管电泳进行了验证。使用这 38 个多态性 SSR，检测到 201 个等位基因，并评估了遗传多样性水平（Na、PIC、、）。