Microsatellite Genome-Wide Database Development for the Commercial Blackhead Seabream (Acanthopagrus schlegelii)

文献类型： 外文期刊

第一作者： Luo, Xinhui

作者： Luo, Xinhui;Zhang, Lichun;Luo, Xinhui;Chen, Songlin;Luo, Xinhui;Chen, Songlin

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关键词： microsatellite database; genome-wide; whole genome resequencing; Acanthopagrus schlegelii

期刊名称：GENES （ 影响因子：3.5； 五年影响因子：3.9 ）

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年卷期： 2023 年 14 卷 3 期

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收录情况： SCI

摘要： Simple sequence repeats (SSRs), the markers with the highest polymorphism and co-dominance degrees, offer a crucial genetic research resource. Limited SSR markers in blackhead seabream have been reported. The availability of the blackhead seabream genome assembly provided the opportunity to carry out genome-wide identification for all microsatellite markers, and bioinformatic analyses open the way for developing a microsatellite genome-wide database in blackhead seabream. In this study, a total of 412,381 SSRs were identified in the 688.08 Mb genome by Krait software. Whole-genome sequences (10x) of 42 samples were aligned against the reference genome and genotyped using the HipSTR tools by comparing and counting repeat number variation across the SSR loci. A total of 156,086 SSRs with a 2-4 bp repeat were genotyped by HipSTR tools, which accounted for 55.78% of the 2-4 bp SSRs in the reference genome. High accuracy of genotyping was observed by comparing HipSTR tools and PCR amplification. A set of 109,131 loci with a number of alleles >= 3 and with a number of genotyped individuals >= 6 were reserved to constitute the polymorphic SSR database. Fifty-one polymorphic SSR loci were identified through PCR amplification. This strategy to develop polymorphic SSR markers not only obtained a large set of polymorphic SSRs but also eliminated the need for laborious experimental screening. SSR markers developed in this study may facilitate blackhead seabream research, which lays a certain foundation for further gene tagging and genetic linkage analysis, such as marker-assisted selection, genetic mapping, as well as comparative genomic analysis.

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