Abstract
BackgroundMicrosatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. The whole genome sequencing with next-generation sequencing (NGS) technologies provides large amounts of sequence data to develop numerous microsatellite markers at whole genome scale. SSR markers have great advantage in cross-species comparisons and allow investigation of karyotype and genome evolution through highly efficient computation approaches such as in silico PCR. Here we described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were then use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections.ResultsA total of 39,523 microsatellite loci were identified from the watermelon draft genome with an overall density of 111 SSRs/Mbp, and 32,869 SSR primers were designed with suitable flanking sequences. The dinucleotide SSRs were the most common type representing 34.09 % of the total SSR loci and the AT-rich motifs were the most abundant in all nucleotide repeat types. In silico PCR analysis identified 832 and 925 SSR markers with each having a single amplicon in the cucumber and melon draft genome, respectively. Comparative analysis with these cross-species SSR markers revealed complicated mosaic patterns of syntenic blocks among the genomes of three species. In addition, genetic diversity analysis of 134 watermelon accessions with 32 highly informative SSR loci placed these lines into two groups with all accessions of C.lanatus var. citorides and three accessions of C. colocynthis clustered in one group and all accessions of C. lanatus var. lanatus and the remaining accessions of C. colocynthis clustered in another group. Furthermore, structure analysis was consistent with the dendrogram indicating the 134 watermelon accessions were classified into two populations.ConclusionThe large number of genome wide SSR markers developed herein from the watermelon genome provides a valuable resource for genetic map construction, QTL exploration, map-based gene cloning and marker-assisted selection in watermelon which has a very narrow genetic base and extremely low polymorphism among cultivated lines. Furthermore, the cross-species transferable SSR markers identified herein should also have practical uses in many applications in species of Cucurbitaceae family whose whole genome sequences are not yet available.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-2870-4) contains supplementary material, which is available to authorized users.
Highlights
Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly
Citrullus lanatus includes the cultivated watermelon (C. lanatus var. lanatus) which thrives in West Africa and has been cultivated widely worldwide and the preserving melon (C. lanatus var. citroides) that is grown in Southern Africa [3, 4], and C. colocynthi (‘bitter apple’) is a perennial species grown in sandy areas throughout northern Africa, south-western Asia, and the Mediterranean [2, 5]
The cross-species transferable simple sequence repeats (SSR) were detected in melon and cucumber by in silico polymerase chain reaction (PCR) analysis, and these large number share SSR markers provide a higher level of resolution for comparative mapping to understand genomic relationships among these three species in the Cucurbitaceae family
Summary
Microsatellite markers are one of the most informative and versatile DNA-based markers used in plant genetic research, but their development has traditionally been difficult and costly. We described genome wide development and characterization of SSR markers in the watermelon (Citrullus lanatus) genome, which were use in comparative analysis with two other important crop species in the Cucurbitaceae family: cucumber (Cucumis sativus L.) and melon (Cucumis melo L.). We further applied these markers in evaluating the genetic diversity and population structure in watermelon germplasm collections. The availability of these genomic resources of watermelon have greatly promoted the fundamental researches including the development of molecular markers and genetic map construction [8, 9], gene/QTL mapping [10, 11], molecular breeding, and comparative genomics [12]
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