Development Of CSNP Markers In Zhikong Scallop (Chlamys Farreri) And Their Cross-species Applications

Zhikong scallop (Chlamys farreri) and Yesso scallop (Patinopecten yessoensis) are botheconomically important aquaculture species in China. With the development of scallop farming,genetic improvement has been one of the main focus areas of scallop industry. Molecular markersare powerful tools for genetic studies. Single nucleotide polymorphism (SNP) which representsthe most abundant variation in the genomes, has been widely used in the studies on geneticbreeding. In this study, we screened SNP loci from the consensus contigs between Zhikong scallopand Yesso scallop transcriptomes, and developed cSNP markers in C. farreri using high-resolutionmelting (HRM) assays. We also tested the transferability of these SNP markers in Yesso scallop.Furthermore, with the cSNP markers developed, we analyzed the genetic diversity in C. farreriand P. yessoensis populations.1. Development of cSNP markers in C. farreriThe transcriptomes of the C. farreri and P. yessoensis were first assembled to obtain contigs,respectively. By searching contigs from C. farreri against those from P. yessoensis,8472putativeorthologous contig pairs were identified. From350randomly selected orthologous contigs,124putative SNPs were detected and used to design primers and probes for marker development in C.farreri. Among them,85loci were successfully amplified, of which49could be successfullygenotyped and finally38were polymorphic in the C. farreri populations. These polymorphic loci(including11transversion and27transition) accounted for77.6%of the successfully genotypedloci and30.6%of the124putative SNP loci selected for marker development. Contigscorresponding to35of the polymorphic loci were annotated.2. Cross-species evaluation of the developed cSNP markers in P. yessoensisThe38polymorphic loci were further evaluated for interspecific transferability in P.yessoensis. It turned out that36loci (94.7%) could be amplified successfully, of which28(77.8%) could be successfully genotyped and finally8displayed polymorphisms in P. yessoensis,indicating a transferability rate of21%.In comparison, from the previously developed44SNP loci in Zhikong scallop,23loci couldbe amplified successfully in the same P. yessoensis population, of which9could be successfullygenotyped and only2loci displayed polymorphisms, indicating a transferability rate of4.5%(4.6times lower than that from our approach).3. Genetic diversity analysis for C. farreri and P. yessoensis populationsThe38cSNP markers were used to analyze the genetic diversity in two geographicpopulations Qingdao population and Rongcheng population of C. farreri. For Qingdao population,Horanged from0.043to0.727, whereas Heranged from0.043to0.511. The minor allelefrequency (MAF) ranged from0.022to0.480. Only2loci departed significantly fromHardy-Weinberg equilibrium (HWE). The Shannon’s index is0.599±0.121. For Rongchengpopulation, Ho ranged from0.048to0.727, whereas He ranged from0.050to0.515. The MAFranged from0.025to0.500. Three loci departed significantly from HWE after Bonferronicorrection. The Shannon’s index is0.567±0.147. No significant linkage disequilibrium betweenloci pairs was detected in either population. The Shannon’s index of Qingdao population is higerthan Rongcheng population, indicating that Qingdao population has higher genetic diversity thanRongcheng population. The genetic identity is0.9912and genetic distance is0.0089, indicatingthat the two populations are closely related.Genetic diversity of C. farreri and P. yessoensis populations was compared using the8transferable cSNP markers. For C. farreri population, Ho ranged from0.133to0.468whereas Heranged from0.266to0.494. The minor allele frequency (MAF) ranged from0.156to0.426. Only1loci departed significantly from Hardy-Weinberg equilibrium (HWE). The Shannon’s index is0.593±0.094. For P. yessoensis population, Ho ranged from0.091to0.400, whereas He rangedfrom0.198to0.522. The minor allele frequency (MAF) ranged from0.107to0.131. Two locideparted significantly from HWE after Bonferroni correction. The Shannon’s index is0.479to0.131. The Shannon’s index of C. farreri population is higher than P. yessoensis population,indicating that C. farreri population has higher genetic diversity than P. yessoensis population.