Genetic analysis of selective breeding population and introduced population in Litopenaeus vannamei using SSRs and SNPs

IF 1 Q4 GENETICS & HEREDITY

Gene Reports Pub Date : 2025-05-13 DOI:10.1016/j.genrep.2025.102251

Chaoan Guo , Shuo Fu , Yuan Zhang , Guangbo Wu , Xiaoxun Zhou , Jianyong Liu

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Abstract

Knowledge of genetic information is crucial for stabilizing diversity and planning selection processes. This study evaluates the genetic diversity of six Litopenaeus vannamei populations (two breeding and four introduced, totaling 180 individuals) using data from 12 microsatellite markers and whole-genome resequencing. After resequencing and filtering, 14,136,203 loci were used for genetic diversity analysis. In SSR analysis, the average observed and expected heterozygosity of the six populations was 0.411 (0.339 to 0.459) and 0.508 (0.402 to 0.558), respectively. Among them, the diversity of SIS in the populations was the highest and XH-F was the lowest. In SNP analysis, the average observed and expected heterozygosity of the six populations was 0.283 (0.252 to 0.312) and 0.292 (0.291 to 0.293), respectively. SIS heterozygosity level was the lowest, but the polymorphism was high, with more low-frequency loci. In population differentiation analysis, the results of the two markers were similar. Both molecular markers were able to classify different populations of L. vannamei. PCA analysis showed that there were obvious differences among different groups. In phylogenetic tree and ancestral estimation analysis, SSR can only classify six populations into three groups. When the K value increases, SSR may face limitations that prevent further subdivision of the population into six groups. In contrast, SNPs exhibit stronger discriminative ability and can clearly divide these six populations into six groups. The results generated from this study will contribute to enriching the genetic resources of L. vannamei and provide important reference information for its artificial breeding and genetic improvement.

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利用ssr和snp对凡纳滨对虾选育群体和引种群体进行遗传分析

遗传信息的知识对于稳定多样性和规划选择过程至关重要。本研究利用12个微卫星标记和全基因组重测序数据，对6个凡纳滨对虾（Litopenaeus vannamei）种群（2个育种种群和4个引种种群，共180个个体）的遗传多样性进行了评价。经过重测序和筛选，共有14136203个位点用于遗传多样性分析。SSR分析结果表明，6个群体的平均观察杂合度和期望杂合度分别为0.411（0.339 ~ 0.459）和0.508（0.402 ~ 0.558）。其中，SIS在种群中的多样性最高，XH-F最低。在SNP分析中，6个群体的平均观察杂合度和预期杂合度分别为0.283（0.252 ~ 0.312）和0.292（0.291 ~ 0.293）。SIS杂合度最低，多态性高，低频位点较多。在群体分化分析中，两个标记的结果相似。这两种分子标记都能对南美扁豆的不同居群进行分类。PCA分析显示，不同组间存在明显差异。在系统发育树和祖先估计分析中，SSR只能将6个群体划分为3个类群。当K值增加时，SSR可能会面临限制，从而阻止群体进一步细分为6个群体。相比之下，snp表现出更强的区分能力，可以清楚地将这6个种群划分为6个群体。本研究结果将有助于丰富凡纳梅的遗传资源，并为其人工育种和遗传改良提供重要参考信息。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Gene Reports Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

3.30

自引率

7.70%

发文量

246

审稿时长

49 days

期刊介绍： Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.