De Novo Transcriptomic Characterization Enables Novel Microsatellite Identification and Marker Development in Betta splendens.

Huapu Chen,Wei Yang,Hai Huang,Guangli Li,Yaorong Wang,Xiaomeng Li,Chunhua Zhu

doi:10.3390/life11080803

Abstract

The wild populations of the commercially valuable ornamental fish species, Betta splendens, and its germplasm resources have long been threatened by habitat degradation and contamination with artificially bred fish. Because of the lack of effective marker resources, population genetics research projects are severely hampered. To generate genetic data for developing polymorphic simple sequence repeat (SSR) markers and identifying functional genes, transcriptomic analysis was performed. Illumina paired-end sequencing yielded 105,505,486 clean reads, which were then de novo assembled into 69,836 unigenes. Of these, 35,751 were annotated in the non-redundant, EuKaryotic Orthologous Group, Swiss-Prot, Kyoto Encyclopedia of Genes and Genomes and Gene Ontology databases. A total of 12,751 SSR loci were identified from the transcripts and 7970 primer pairs were designed. One hundred primer pairs were randomly selected for PCR validation and 53 successfully generated target amplification products. Further validation demonstrated that 36% (n = 19) of the 53 amplified loci were polymorphic. These data could not only enrich the genetic information for the identification of functional genes but also effectively facilitate the development of SSR markers. Such knowledge would accelerate further studies on the genetic variation and evolution, comparative genomics, linkage mapping and molecular breeding in B. splendens.

Highlights

The freshwater Siamese fighting fish (Betta splendens) is native to southeast Asia and represents one of the labyrinth fishes with the highest commercial value
As the commercial breeding and seedling production progresses, it has been reported that the long history of domestication of B. splendens has led to the loss of genetic variation of broodstock [3]
(53,062,092 for female and 52,443,394 for male), which is equal to 13.19 GB of sequencing data

Summary

Introduction

The freshwater Siamese fighting fish (Betta splendens) is native to southeast Asia and represents one of the labyrinth fishes with the highest commercial value. Similar to several other teleost fishes, B. splendens displays unique reproductive and paternal care behaviors and exhibits significant differences in terms of the typical behavior ( known as behavioral typicality) between males and females [1]. Owing to its male-typical behavior and notable attractiveness (e.g., color and scale pattern, shape, diverse fin pattern design and easy culture in poor quality water) [3,4], B. splendens is among the most popular aquarium fish species in the ornamental fish industry. The wild populations and germplasm resources of this species are seriously threatened, mainly because of degradation of natural habitat and contamination from artificially bred fish [4]. There is an urgent need to strengthen biodiversity conservation and population structure management, much greater efforts must be devoted to protect and improve B. splendens germplasm resources

Methods

Results

Discussion

Conclusion