Abstract
We described and characterized 11 expressed sequence tag (EST)-derived simple sequence repeats (SSR) and seven genomic (G)-derived SSRs in Coreoperca whiteheadi Boulenger. The EST-SSRs comprised 62.2% di-nucleotide repeats, 32.2% tri-nucleotide repeats and 5.5% tetra-nucleotide repeats, whereas the majority of the G-SSRs were tri-nuleotide repeats (81.4%). The number of alleles for the 18 loci ranged from 3 to 6, with a mean of 3.8 alleles per locus. The observed (Ho) and expected heterozygosities (He) values ranged from 0.375 to 1.000, and 0.477 to 0.757, respectively. The polymorphic information content (PIC) values ranged from 0.466 to 0.706. The mean values number of alleles, Ho, He, and PIC of EST-SSRs were higher than those of the G-SSRs. Four microsatellite loci deviated significantly from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction and no significant deviations in linkage disequilibrium (LD) were observed. These loci are the first to be characterized in C. whiteheadi and should be useful in the investigation of a genetic evaluation for conservation. Compared with 11 loci in C. whiteheadi, 37 potential polymorphic EST-SSRs were found in Siniperca chuatsi (Basilewsky), which will provide a valuable tool for mapping studies and molecular breeding programs in S. chuatsi.
Highlights
Coreoperca whiteheadi Boulenger, one of the lower percoid fishes, is found in south China and theRed River of North Vietnam [1,2]
Sequence analysis of all the simple sequence repeats (SSR)-containing clones indicated that tri-nucleotide SSRs were found to be more frequent (81.4%) than di-nucleotide SSRs (18.6%), and no tetra/penta/hexa nucleotide SSRs was identified in the library
37 potential polymorphic expressed sequence tag (EST)-SSRs were found in a sample of 12 wild S. chuatsi individuals (Table 3)
Summary
Coreoperca whiteheadi Boulenger, one of the lower percoid fishes, is found in south China and the. Because of its dire conservation status, the genetic conservation of C. whiteheadi is becoming essential for the sustainable management of natural resources and increasing the production of this species. Microsatellites or simple sequence repeats (SSRs) have become a useful marker system in population genetics analysis, genetic mapping and marker-assisted selection (MAS) of many kinds of fish species because of their co-dominant nature, high allelic polymorphism, high reproducibility and transferability across species [4,5]. The recent development of library enrichment techniques and automated sequencing has made production of these markers simple, rapid, and cost effective [7,8]. We characterized 11 EST-SSRs and seven G-SSRs as a tool to support genetic conservation and breeding programs in C. whiteheadi. 37 potential polymorphic EST-SSRs were found in a sample of 12 wild Siniperca chuatsi (Basilewsky) individuals. All the 122 microsatellites from ESTs were tested for S. chuatsi
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