Genome-Wide Microsatellites in : Development, Distribution, Characterization, and Polymorphism

Overview

Journal Animals (Basel)

Date 2025 Jan 8

PMID 39765613

Authors

Chao Peng

Congqiang Luo

Guangqing Xiang

Jiezhen Huang

Liye Shao

Haihong Huang

Sigang Fan

Affiliations

Soon will be listed here.

Abstract

The yellowfin seabream () is an economically important commercial mariculture fish in China and Southeast Asia. Only a few simple sequence repeats (SSRs) of have been isolated and reported, which has hindered breeding progress. A total of 318,862 SSRs were isolated and characterized from the genome in this study. All SSRs were 9,069,670 bp in length, accounting for 1.32% of the genome. The density and frequency of SSRs were 468.40 loci/Mb and 13,323.19 bp/Mb, respectively. The major SSRs were dinucleotides (accounting for 76.92%), followed by trinucleotides (15.75%). The most abundant SSR motif was (AC)n (168,390, accounting for 53%), with the highest frequency (245.78 loci/Mb) and density (7304.18 bp/Mb). Most SSRs were located in non-coding regions, such as intergenic regions (34.54%) and introns (56.91%). SSR-containing exons were distributed into 51 gene ontology (GO) terms and significantly enriched in immunity- and growth-related pathways. A total of 217,791 SSR markers were successfully designed. Nine SSR markers were amplified in 29 individuals, and eight of them possess high polymorphism. The cross-species transferability of 33 out of the 37 tested loci were successfully amplified in . These results lay the foundation for the molecular marker-assisted breeding and genetic information assessment of .

Citing Articles

Genomic Insights into the Population Genetics and Adaptive Evolution of Yellow Seabream () with Whole-Genome Resequencing.

Li Y, Yang J, Fang Y, Zhang R, Cai Z, Shan B Animals (Basel). 2025; 15(5).

PMID: 40076030 PMC: 11898413. DOI: 10.3390/ani15050745.

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