Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

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.

Detection and application of genome-wide variations in peach for association and genetic relationship analysis

“…CG/GC and CGC/GCG/CGG/CCG/CGC/GCC were the least repeats of di-nucleotide and tri-nucleotide repeats, respectively. The result indicated A/T nucleotide exhibited a strong bias among SSRs, similar with the study reported before [8,19].…”

“…Frequency analysis of various nucleotide repeats of SSRs in the peach genome revealed that mononucleotides were the most abundant SSR (47.36% of the total), followed by di-, tri-, etc (Table 4). However, tetranucleotide repeats were the primary motif in cucumber [24], Chinese jujube [19] and pear [26] and the most abundant in soybean [27] and rice [28]. Among the dinucleotide repeats in peach, AT/TA was the most common, followed by CT/TC (Table 4).…”

Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

“…et Zucc.) [26], Chinese jujube ( Ziziphus jujuba Mill) [34], and Rosa roxburghii Tratt [32]. Here, for the first time, we report a genome survey of P. vera using whole genome shotgun sequencing.…”

“…The average GC content of the P. vera genome was higher than that of wild sweet potato (36.0%) [39], but lower than that of switchgrass (45.5%) [33] and Chinese jujube (48%) [34]. Different GC contents may result in sequencing bias on the Illumina sequencing platform, and can, therefore, seriously affect genome assembly [40, 41].…”

Comparative analyses of simple sequence repeats (SSRs) in 23 mosquito species genomes: Identification, characterization and distribution (Diptera: Culicidae)

“…Whole‐genome SSR detection has been reported in plants such as Oryza minuta and Or. punctata (Wang et al ., ), Sesamum indicum (Wei et al ., ), and Ziziphus jujuba (Xiao et al ., ) and in 30 marine animals (Jiang et al ., ), six species of birds (Huang et al ., ), six species of bovids (Qi et al ., ), Apis cerana (Liu et al ., ) and Tribolium castaneum (Demuth et al ., ). The SSRs in coding sequences (CDs) of 25 insect species have been identified and comparatively analyzed (Behura & Severson, ).…”