ScHsc70 gene SNP markers screening and correlation analysis for high temperature resistance of Sinonovacula constricta new variety “Shenzhe NO. 1”

To obtain single nucleotide polymorphism (SNP) markers of heat shock protein 70 (ScHsc70) gene related to heat tolerance traits in Sinonovacula constricta, the full-length sequence of ScHsc70 gene was cloned by direct sequencing. The results showed that theScHsc 70 gene was 4 048 bp, including 6 introns and 7 exons, and the coding region was 1 950 bp. The high temperature resistance group and control group from a new variety of razor clam were established, and six potential SNPs Rs1 (g.588 C > T), Rs2 (g.840 C > T), Rs3 (g.885 T > A), Rs4 (g.1233 A > G), Rs5 (g.1467 T > G), Rs6 (g.1482 T > C) were screened from the exon region of ScHSc70 gene by PCR product direct sequencing. SNPs genotyping was performed on the high temperature tolerant population and the control population of the new variety " Shenzhe No.1” by Sanger sequencing. The results of genetic diversity analysis showed that the polymorphism information content (PIC) of the two populations was between 0.111 2 and 0.371 8, and the average polymorphism information content of the control population was 0.267 0, which is higher than that of the high temperature resistant populations (0.236 5). Association analysis results showed that the genotype frequency and allele frequency of Rs1, Rs3 and Rs4 were significantly different between control group and high temperature tolerant group. Haploid linkage disequilibrium analysis showed that SNPs markers of ScHsc70 gene could form 2 haploid blocks and 7 haplotypes, among which CCT haplotypes were significantly correlated with high temperature tolerance traits. It was found that Rs2 and Rs3 were in a linkage state (r² = 0.86, LOD = 25.56, Dx = 1.0), and could be used as SNP markers for the Genetic breeding of S. constricta for high temperature tolerance. In summary, Rs1, Rs3, Rs4 and haplotype CCT can be used as candidate auxiliary molecular markers for high temperature tolerance breeding of razor clam, which lays a theoretical foundation for the subsequent functional verification of resistance-related SNPs.