Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Abstract

The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

Parentage Analysis in Giant Grouper (Epinephelus lanceolatus) Using Microsatellite and SNP Markers from Genotyping-by-Sequencing Data

“…However, although 72 microsatellite markers have been developed for giant grouper so far [ 43 , 45 , 46 , 47 ], only a few of them have been applied in parentage related analysis [ 48 , 49 ]. For groupers, moreover, the development of SNP markers has only been reported for identification of growth traits in potato grouper ( E. tukula ) [ 50 ] and orange-spotted grouper ( E. coioides ) [ 51 ], while the application of SNPs for parentage analysis in groupers has not yet been reported.…”

Utilizing ISSRseq genotyping to assist growth selection in tomato grouper (Cephalopholis sonnerati) without broodstock information

“…In the past, the marker-assisted selection often required detailed experimental designs and higher costs and development time (Hsu et al, 2021;Luo et al, 2021;Weng et al, 2021;Yang et al, 2020). Particularly when there are fewer molecular markers, a lack of genomic information, or insufficient broodstock information, the effectiveness of these methods can be limited (Hsu et al, 2021;Luo et al, 2021;Weng et al, 2021;Yang et al, 2020). However, broader applications have become possible due to the widespread use and reduced cost of high-throughput sequencing technologies (Hsu et al, 2021;Luo et al, 2021;Weng et al, 2021;Yang et al, 2020).…”

“…Traditional breeding methods often involve the mixed culture of broodstocks and natural mating, which can be time‐consuming and inefficient. Conventional selection breeding can be particularly challenging for grouper species with long generation times (Hsu et al, 2021; Weng et al, 2021; Yang et al, 2020). As a result, various breeding strategies have been employed for grouper species, including hybridization and molecular marker‐assisted breeding.…”

“…These examples underscore the importance of breeding in the aquaculture industry, particularly for grouper species. Molecular marker‐assisted breeding has emerged as a promising approach to overcome the challenges of traditional breeding methods, offering a more targeted and efficient selection process (Hsu et al, 2021; Weng et al, 2021; Yang et al, 2019; Yang et al, 2020).…”

“…They are now widely used in fisheries and aquaculture research (Hsu et al, 2022; Wong et al, 2022; You et al, 2020). Molecular markers can be employed to track the inheritance of traits within populations, providing valuable information for breeding programs (Chen et al, 2022; Chu et al, 2021; Hsu et al, 2021). The successful application of molecular markers in various aquaculture species has facilitated the development of improved strains with enhanced growth rates and other desirable traits (You et al, 2020; Wong et al, 2022).…”