Development of single nucleotide polymorphisms in key genes of taurine and betaine metabolism in Crassostrea hongkongensis and their association with content-related traits

Background Taurine and betaine are important nutrients in Crassostrea hongkongensis and have many important biological properties. To investigate the characteristics of taurine and betaine contents and identify SNPs associated with traits in the C.hongkongensis, we cloned the full-length cDNA of key genes in taurine and betaine (unpublished data) metabolism, determined taurine and betaine content and gene expression in different tissues and months of specimen collection, and developed SNPs in the gene coding region. Results We cloned the full-length cDNA of cysteine dioxygenase (ChCDO) and cysteine sulfite decarboxylase (ChCSAD), which are key genes involved in taurine metabolism in C. hongkongensis, and found that betaine and taurine contents and the expression of key genes were regulated by seawater salinity. A total of 47 SNP markers were developed in the coding regions of ChCSAD, ChCDO, ChCDH, ChBADH, and ChBHMT using gene fragment resequencing and FLDAS-PCR. Through association analysis in a population of C. hongkongensis in the Maowei Sea, Guangxi, nine SNPs were found to be associated with taurine content, and one SNP was associated with betaine content. Haploid and linkage disequilibrium analyses showed that SNPs in ChCDO formed one linkage group with three haplotypes: ACACA, GTTTG, and GTACA. The average taurine content of the corresponding individuals was 873.88, 838.99, and 930.72 ng/g, respectively, indicating the GTACA haplotype has a significant advantage in terms of taurine content. Conclusions We identified SNPs associated with taurine and betaine contents in C.hongkongensis for the first time, and found the GTACA haplotype in the ChCDO coding region has a significant advantage in taurine content. These loci and haplotypes can serve as potential molecular markers for the molecular breeding of C. hongkongensis.