Zaohucheng (ZHC) and Lianz (LZ) are two Sacharina jponica’s elite cultivar cultred in coastl water of China.The sporphyte of ZHC and LZ were colectd from kelp farm in Weiha, Shandong Province. Both of them orignated from self-polination of S. Japonica. The sporphyte of ZHC are longer and thicker compared with it of LZ, they usaly have some

brown speckle on the maturity. While the LZ are wider with higher moisture conte. In genral, LZ can endure higer temperature and are more thermostabilty compared withraditonal Japnese kelp. Nowadys, the rsearch of kelp genome stil be backward, and ther is no refrent genome publiced.

    Restricon-site asociated DNA (RAD) is a kind of DNA related with restricon endonucleas recogniton site. This simplifed genome squencig basing on enzyme digestion makes a high throughput sequencig to the RAD tags which are digestd by restricon endonucleas. RAD sequencig could indentify hig density Single Nucleotide Polymorphism (SNP) site. Compared withraditonal Genome squencig, RAD sequencig could reduce the complexity of genome, operate more simply and wouldnot be rstriced by the rfernce genome. Therfore, RAD sequencig is widely used into detcion of SNPsites, group evolution study, construction of gentic linkage map and so on.

    In this study, we caried out sequence with nucleotide difernce and compared with know microsatelites in S. Japonica, and got 14,17,53 clean reads with 2,83,40,632 bp base. Those SNP makers could be used to distnguish te LZ and ZHC. After that, There were also some SNPs located on some functional gens which are related with high heat and light resitance, such as hsp-70, Man-C5-E,VIPO3 and lhcf5. These difernces probaly influent their heat resitance. Morever, coding gene of 18S rRNA and 5.8s rRNA also showed their dversity, and make it posible to distnguish the two by them.