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

Te-Hua Hsu,Chang-Wen Huang,Hung-Tai Lee,Yu-Ting Chiu,Hong-Yi Gong

doi:10.3390/biology10010036

Te-Hua Hsu, Chang-Wen Huang + Show 3 more

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https://doi.org/10.3390/biology10010036

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Journal: Biology	Publication Date: Jan 7, 2021
Citations: 5	License type: CC BY 4.0

Affiliation: National Taiwan Ocean University

Abstract

Simple SummaryThe potato grouper is a novel aquaculture species in Taiwan. Due to the lack of genetic information concerning this species, we have developed molecular markers based on transcriptome sequencing and further characterized their association with gene diversity and growth traits of this species. Ultimately, these markers could be utilized as accurate and efficient tools for genetic management and marker-assisted selection of potato grouper with distinct growth traits.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.

Highlights

With the increase in the global population, the annual demand for animal-based protein has risen, which includes increasing requirements for aquaculture
We discovered that the available molecular markers form a close genetic relationship, meaning that they had low genetic diversity and commonality and a smaller number of markers
The common economic aquaculture grouper species—orange-spotted grouper, giant grouper, and hybrid grouper (E. fuscoguttatus × E. lanceolatus)—have been evaluated for growth trait performance, virus resistance, dietary supplementation, and temperature challenge, and the results have revealed some underlying molecular mechanisms [80,81,82,83]

Summary

Introduction

With the increase in the global population, the annual demand for animal-based protein has risen, which includes increasing requirements for aquaculture. Conventional long-term selective breeding programs, such as those of Atlantic salmon (Salmo salar) [7], rainbow trout (Oncorhynchus mykiss) [8], and Nile tilapia (Oreochromis niloticus) [9], may cause stock inbreeding because candidate broodstock is always chosen from a few phenotypes of interest (e.g., fast growth) [10]. This impairs genetic diversity and may cause an unexpected loss of essential characteristics, such as disease resistance [11,12]. The use of MAS in Atlantic salmon breeding programs increases efficiency [16,17,18] and has allowed various vital genetic traits to be improved and combined [19,20]

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