Abstract
Chinese jujube (Ziziphus jujuba), an economically important species in the Rhamnaceae family, is a popular fruit tree in Asia. Here, we surveyed and characterized simple sequence repeats (SSRs) in the jujube genome. A total of 436,676 SSR loci were identified, with an average distance of 0.93 Kb between the loci. A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively. Among the mononucleotide repeats, A/T was the most common, whereas AT/TA was the most common dinucleotide repeat. A total of 30,565 primer pairs were successfully designed and screened using a series of criteria. Moreover, 725 of 1,000 randomly selected primer pairs were effective among 6 cultivars, and 511 of these primer pairs were polymorphic. Sequencing the amplicons of two SSRs across three jujube cultivars revealed variations in the repeats. The transferability of jujube SSR primers proved that 35/64 SSRs could be transferred across family boundary. Using jujube SSR primers, clustering analysis results from 15 species were highly consistent with the Angiosperm Phylogeny Group (APGIII) System. The genome-wide characterization of SSRs in Chinese jujube is very valuable for whole-genome characterization and marker-assisted selection in jujube breeding. In addition, the transferability of jujube SSR primers could provide a solid foundation for their further utilization.
Highlights
Microsatellites, or simple sequence repeats (SSR), are iterations of between 1- and 6-bp nucleotide motifs
A large proportion of the SSRs included mononucleotide, dinucleotide and trinucleotide repeat motifs, which accounted for 64.87%, 24.40%, and 8.74% of all repeats, respectively
Among the different types of repeats, mononucleotide repeats (283,301) were the most common, accounting for 64.87% of all repeats, followed by dinucleotides (24.40%), trinucleotides (8.74%), tetranucleotides (1.64%), pentanucleotides (0.21%), and hexanucleotides (0.14%)
Summary
Microsatellites, or simple sequence repeats (SSR), are iterations of between 1- and 6-bp nucleotide motifs. These sequences have been detected in the genomes of numerous organisms and are distributed throughout the entire genome in both coding and non-coding regions [1, 2]. Given their many desirable attributes, including wide genomic distribution, co-dominant inheritance, their multi-allelic nature, and a high level of polymorphisms, SSRs are highly favored molecular markers [3,4,5]. As next-generation sequencing technology has developed, de novo genome
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