AI Article Synopsis
- Swamp eel, an important aquaculture species in China, was the subject of a study aimed at characterizing Simple Sequence Repeats (SSRs) in its genome and developing SSR markers for breeding purposes.
- Using MISA software, the study identified 364,802 SSRs, with a predominance of mononucleotide repeats, and created a total of 287,189 primer pairs to find polymorphic SSRs.
- The findings revealed a high level of genetic diversity in one breeding population, which could be leveraged for future genetic mapping and breeding programs.
Article 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.
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| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10358632 | PMC |
| http://dx.doi.org/10.1177/00368504211035597 | DOI Listing |
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