Progress of Genetic Improvement and the Whole Genome Selection Research Program in Large Yellow Croaker

Large yellow croaker (Larimichthys crocea) is one of the most important maricultured fish species in China. Annual productions of the marketable fish and the fries were 90 thousand tons and more than 2 billion, respectively. The genetic improvement program of this species was started in 2001. Combined with gynogenesis techniques, a new variety namely “Minyou 1” with faster growth rate and higher survival rate have been bred and used in the aquaculture industry in China. On the other hand, the techniques of producing genetically all female population was also established by mating the sex reversed gynogens (neomales, XX��) with the normal females (XX��) for the females grow faster than the males significantly. The output can increase by more than 20% by culturing all female population.

To further improve the breeding effect of large yellow croaker, a new genetic improvement program based on whole-genome selection had been set up in China in 2012. At first, A draft genome sequence was obtained by whole genome sequencing (102.46Gb data in total) with a highly pure individual from gynogen population. The primary assembly comprised 940 Mb, with a contig N50 size of 9.67kb and a scaffold N50 size of 190.7kb. The coverage is more than 90% in the whole genome and 96.8% in code region. Combined with data from transcriptome sequencing, a total of 31,028 genes were predicted. Of them, 25332 genes are homologous to zebrafish and Medaka; 1246 and 894 genes are respectively homologous to zebrafish and Medaka; and 3556 genes are specific in large yellow croaker. Moreover, 57 male individuals and 57 female individuals were re-sequenced to identify SNPs and sex specific markers. Based on sequence comparison, more than 10⁶ SNPs are identified; a 40 Mb fragment showing potential male specific and some short fragments showing potential X-chromosome specific were isolated as well.

More than 30 large yellow croaker families have been constructed to support the plan. A dense SNP-based linkage map is constructing with 10 families in our labotory. All above works can serve as a basis for further whole-genome selection program in large yellow croaker.