Construction Of Sugarcane Fingerprint And Genetic Diversity Analysis Based On SSR And SNP Markers

Sugarcane(Saccharum spp.),one of the important sugar and energy crop,and plays an important role in sugar supply and clean energy development in China.In recent years,because of the fewer elite parental lines used in breeding applications,the genetic basis of cultivars(lines)become similar gradually,which makes difficult to collect,utilize,identify and variety improvement of sugarcane.Therefore,analyzing the genetic structure and relationship of existing sugarcane germplasm resources,establishing the DNA molecular fingerprinting database are significant to collect,identify and improve the sugarcane variety(line)resources,safeguard the intellectual property and solve the variety disputes.In this study,103 sugarcane germplasms were sequenced by SLAF-seq,and highquality SNP markers were obtained.These SNP markers and published SSR markers were used to analyze the population structure and genetic diversity of the collected sugarcane materials.A Multiplex SNaPshot identification system was developed based on 43 SNP markers(32 core markers and 11 extended markers),and the sugarcane fingerprint database was constructed using SSR markers and core SNP markers,respectively.The main research results are as follows:1.Genetic diversity of sugarcane variety(line)resource populationUsing AP85-441 as reference genome,103 sugarcane germplasm resources were sequenced by SLAF-seq,and 105,325 high-quality SNPs were filtered after SNP identification.Genetic diversity of this sugarcane population was analyzed by these SNPs.Meanwhile,21 pairs of internationally acknowledged SSR primers were used to analyze the genetic diversity of 229 sugarcane germplasms(including the 103 sugarcane on SNP project).The results showed that the distribution of sugarcane germplasm resources was diverse,and the subgroup differentiation was not strictly gathered according to the geographical origin,which indicated that the population has a complex background and good genetic diversity with the adequate hybridization.2.Developed a SNP identification system based on SNaPshot technologyDuring 105,325 SNPs,192 SNPs were selected for the further analysis,with 4-8 SNPs on each chromosome.There were seventy-three remaining after Blast of homology detection.The SNP sites obtained were transformed into PCR primers using Multiplex SNaPshot system.At last,43 SNP markers were transformed and 5 panels were established successfully.180 sugarcane varieties(lines)were selected to verify 43 SNP markers,32 SNPs were identified as core markers and 11 SNPs were identified as extend markers.This system can be used to identify sugarcane varieties(lines).3.Construction of the molecular fingerprint of sugarcane varieties(lines)21 SSR markers and 32 SNP markers were used to analyze the genotypes of sugarcane varieties(lines)and resource materials,and the molecular fingerprint code was constructed,respectively.The biological characteristics,images and other information of each material were collected to construct the molecular fingerprinting database,and the twodimensional code of each member’s fingerprint was generated by online tools,which could be queried by mobile internet devices.