TITLE:
High-throughput simple sequence repeat (SSR) markers development for the kelp grouper (Epinephelus bruneus) and cross-species amplifications for Epinephelinae species
AUTHORS:
Satoshi Kubota, Qi Liu, Kanonkporn Kessuwan, Nobuaki Okamoto, Takashi Sakamoto, Yoji Nakamura, Yuya Shigenobu, Takuma Sugaya, Motohiko Sano, Susumu Uji, Kazuharu Nomura, Akiyuki Ozaki
KEYWORDS:
Kelp Grouper; Epinephelus bruneus; Repeat Motif; Simple Sequence Repeat (SSR); 454 Pyrosequencing; Cross-Species Amplification
JOURNAL NAME:
Advances in Bioscience and Biotechnology,
Vol.5 No.2,
January
24,
2014
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, dito 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).