High-throughput simple sequence repeat (SSR) markers development for the kelp grouper (<i>Epinephelus bruneus</i>) and cross-species amplifications for Epinephelinae species

Abstract

The kelp grouper (Epinephelus bruneus), belonging to one of the largest genera among the subfamily Epinephelinae, is a commercially important fish in Japan. There are limited data about the genomics of this species. To provide tools for addressing both population genetics studies and gene mapping, di-to pentanucleotide simple sequence repeat (SSR) markers were developed using 454 pyrosequencing. Among the 1466 SSR markers developed, 1244 primer sets produced strong PCR products, of which 905 (72.7%) were polymorphic in kelp grouper. Cross-species utility of the 905 polymorphic SSR markers was tested in four additional Epinephelinae species of Hyporthodus septemfasciatus, Plectropomus leopardus, Epinephelus lanceolatus and Epinephelus coioides. Results revealed that, respectively, 401 (44.3%), 136 (15.0%), 434 (49.0%) and 538 (59.4%) SSRs showed specific polymorphic products. Of these, 40 SSR markers (33 di-, 1 tri-and 6 tetra-nucleotides) showed polymorphism in all species tested. Additionally, three AGAT SSR motifs which accounted for 42.9% of the nondi-nucleotide markers were found in the 40 SSR markers. This indicates that the AGAT SSR motif has a high potential as a highly versatile SSR marker in grouper Epinephelinae. The SSR markers developed in this study can be employed to obtain reliable genetic variability estimates for groupers (Epinephelinae).

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

“…A total of 2348 microsatellite-enriched segments from the kelp grouper were developed using next-generation sequencing (NGS) by the GS FLX system (Roche, Switzerland) (denoted as the EBR series) (Kubota et al 2014 ) and 889 simple tandem repeats (STR) markers were obtained from the NCBI database of a cross section of species in the subfamily Epinephelinae (denoted as the STR series) (Chapman et al 1999 ; Dong et al 2008 ; Liu et al 2008 ; Lo and Yue 2007 ; Mokhtar et al 2011 ; Ramirez et al 2006 ; Renshaw et al 2010 ; Rivera et al 2003 ; Zeng et al 2008 ; Zhao et al 2009a , b ; Zhu et al 2005 ). In total, 1867 SSR markers (1466 EBR markers and 401 STR markers) were designed using the TROLL program at http://wsmartins.net/websat/ (Martins et al 2009 ) under the default settings and considering a product size of 100–250 bp.…”

Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus)

“…A total of 2348 microsatellite-enriched segments from the kelp grouper were developed using next-generation sequencing (NGS) by the GS FLX system (Roche, Switzerland) (denoted as the EBR series) (Kubota et al 2014) and 889 simple tandem repeats (STR) markers were obtained from the NCBI database of a cross section of species in the subfamily Epinephelinae (denoted as the STR series) (Chapman et al 1999;Dong et al 2008;Liu et al 2008;Lo and Yue 2007;Mokhtar et al 2011;Ramirez et al 2006;Renshaw et al 2010;Rivera et al 2003;Zeng et al 2008;Zhao et al 2009a, b;Zhu et al 2005). In total, 1867 SSR markers (1466 EBR markers and 401 STR markers) were designed using the TROLL program at http://wsmartins.net/websat/ (Martins et al 2009) under the default settings and considering a product size of 100-250 bp.…”

Assessment of genetic diversity and phylogenetic relationship among grouper species Epinephelus spp. from the Saudi waters of the Arabian Gulf

“…This study gave the first detailed analysis of the level of genetic variation and genetic relationship among the genotypes of grouper species Epinephelus spp. on the Arabian Gulf coast of Saudi Arabia revealed by ISSR (dominant) and SSR (co-dominant) molecular markers that have been proven to be valuable for the determination of genetic diversity and taxonomic discrimination of the species ( Kubota et al, 2014 , Bernard et al, 2016 , Hassanien and Al-Rashada, 2019 , Oliveira et al, 2019 ).…”

“…Microsatellite analysis has been proofed to offer the best estimation of genetic diversity (by producing a greater amount of polymorphism) and a better understanding of intra‐ and interspecific variability among and within these Epinephelus spp. ( Koedprang et al, 2007 , An et al, 2014 , Kubota et al, 2014 ). In the current investigation, the average number of alleles (A = 9.72) was lower than that found in E. coioides populations using microsatellite markers (Ec_122, Ec_154, and Ec_158) ( Wang, et al, 2011 ).…”