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Functional marker detection and analysis on a comprehensive transcriptome of large yellow croaker by next generation
Shijun Xiao1, Zhaofang Han1, Panpan Wang1
1Key Laboratory of Healthy Mariculture for the East China Sea, Ministry of Agriculture; Fisheries College, Jimei University, Xiamen, Fujian, China.
Plos One
|April 25, 2015
Summary
This study presents the first comprehensive transcriptome for large yellow croaker (Larimichthys crocea), identifying valuable genetic markers. These resources aid in improving aquaculture and understanding disease resistance in this economically important fish species.
Area of Science:
- * Aquaculture and Fisheries Science
- * Genomics and Molecular Biology
- * Marine Biology
Background:
- * Large yellow croaker (Larimichthys crocea) is a vital economic fish species in China and Eastern Asia.
- * Overfishing and intensive aquaculture have led to germplasm degeneration and increased disease susceptibility.
- * A comprehensive transcriptome and functional molecular markers were previously lacking for this species.
Purpose of the Study:
- * To generate a comprehensive multi-tissue transcriptome for large yellow croaker.
- * To identify and analyze functional polymorphic simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs).
- * To provide essential genetic resources for improving aquaculture and molecular selection.
Main Methods:
- * RNA-sequencing (RNA-seq) was performed using the Illumina Hiseq2000 platform on multi-tissue samples.
- * Transcriptome assembly and annotation were conducted using nt/nr, InterPro, Gene Ontology (GO), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases.
- * Polymorphic SSRs and SNPs were identified, and their functional impacts were analyzed.
Main Results:
- * A total of 88,103 transcripts were assembled, with 52,782 successfully annotated.
- * 34,576 protein-coding transcripts were found to be shared with other fish species.
- * 1,276 polymorphic SSRs and 261,000 SNPs were discovered, with most SNPs causing synonymous mutations or occurring in 3' UTR regions.
Conclusions:
- * This study provides the first high-throughput analysis of functional polymorphic SSR and SNP markers in large yellow croaker.
- * Genes related to DNA binding, enzyme activity, and signal pathways showed fewer variants, while muscle, cytoskeleton, and immunity genes had more frequent SNP mutations.
- * The generated transcriptomic data and molecular markers offer valuable resources for quantitative trait locus (QTL) identification and molecular breeding in large yellow croaker.
