Characterization Of SSR Loci In Jujube Genome And Development Of SSR Primers

Jujube (Ziziphus jujuba Mill.) is one of the most representative fruit tree in China andhas very important economic value. SSRs (Simple Sequence Repeat) are repeatingsequences of1-6base pairs (bp) and also the important part of the genome. To understandthe distribution and characterization of SSRs will help to explore the genome evolution andstructure. Meanwhile, the development of SSR primers will contribute to analysis ofgenetic diversity, identification of variety and molecular breeding. Hence, the distributionof SSR loci in jujube genome was searched and analyzed, then using the same SSR criteria,SSRs characterization of jujube genome was compared with that of apple, pear, grape andother species. SSR primers were designed according to SSR loci,6jujube cultivars wereused for primers screening and20cultivars were used to verify its polymorphism. Theversatility of jujube SSR primers was also verified among different species of8families.The main results were as follows:1. Using the MISA program,70.83%of scaffold sequences (2144) contained SSRloci among3027ones (90.00%of estimated genome size). A total of436676SSRs wereobserved and the average distance between SSRs was0.93kb, in which the main type wasperfect SSR (401456).480types of motifs were found in jujube genome, and thedominant motifs types were mononucleotide, dinucleotide and trinucleotide repeats. Thenumber of monomucleotide repeats was maximum (283301), followed by dinucleotideand trinucleotide repeats (106537and38168), tetrabucleotide, pentanucleotide andhexanucleotide repeats were the least, accounting for3.84%of all SSRs.2. A/T was the main motifs type in mononucleotide repeats, accounting for98.48%;the main motifs type was AT/AT in dinucleotide repeats (74.33%); the predominant motifstypes was AAT/ATT in trinucleotide repeats (64.17%); the predominant motifs types wereAAAT/ATTT, AAAAT/ATTTT and AAAAAG/CTTTTT in tetrabucleotide, penta-nucleotide and hexanucleotide repeats.3. The genomic data of apple, pear, grape, peach, strawberry, plum and mulberry wasdownloaded from NCBI database, and then based on the same search parameters jujubeSSRs were compared with those species. The result showed that the density of SSRs indifferent species genome was different, and the density of SSR in jujube genome (387/Mb)was the largest.4. The Primer3.0software was used to design SSR primers of jujube, and then78928 pairs of primers were successfully designed, accounting for51.46%of all SSR loci (exceptfor mononucleotide repeats), and then30565pairs of primers were screened by using theseries of principles. Among them, two types of dinucleotide and trinucleotide repeats werethe main motifs types, acounting for81.48%and13.39%, respectively.5.1000pairs of primers with randomly selected were rescreened by using6cultivars.725primers were proved to effective and511primers were polymorphic. The main motifstypes were dinucleotide (243primers) and trinucleotide repeats (232primers).6.16pairs SSR primers selected randomly were used for20jujube varieties to verifythe effective and high polymorphism.68polymorphic bands were amplified, and theaverage polymorphic fragments of each pair primer was4.25, and the PIC values werebetween0.51-0.72with an average of0.61. The result showed that16pairs primers werehighly efficient primers.7.64pairs SSR primers selected randomly were used to verify the transferability ofthe primers among15species of8families.35primers were polymorphic primers.107polymorphic bands were amplified, and the average polymorphic fragments of each pairprimer were3.06, and the PIC values were ranged from0.20to0.70, the average was0.48.The results proved that SSR primers of jujube had transferability among other species.8、The clustering results of15species showed that jujube (wild jujube) is closelyrelated with the species of family Rosaceae.