ARS | Publication request: Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.)

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 15, 2010
Publication Date: October 15, 2010
Citation: Cavagnaro, P.F., Weng, Y., Senalik, D.A., Simon, P.W., Harkins, T.T., Huang, S. 2010. Genome-wide characterization of simple sequence repeats in cucumber (Cucumis sativus L.). Biomed Central (BMC) Genomics. 11:569-588.

Interpretive Summary: The genome of the cucumber cultivar Gy14 has been sequenced. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequence, and in EST sequences of cucumber. Similar analyses were performed in genomic and EST data from seven other plant species, and the results were compared with those of cucumber. A total of 112,073 perfect repeats were detected in cucumber genomic sequence, accounting for 0.9% of the genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellite repeats, the dinucleotide AT motif had the highest cumulative length in the genomic sequences due to its high repeat numbers per SSR. The coding regions (ESTs) of cucumber genome had fewer microsatellites compared to its genomic sequence with trinucleotides predominating in the former. AAG was the most frequent repeat in cucumber ESTs. Overall, AT-rich motifs prevailed in both genomic and EST data. Compared to the other species examined, cucumber genomic sequence had the highest density of SSRs, and was the richest in AT-dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,011 SSR loci, and found unexpectedly high degree of polymorphism (48.07%) between the two genotypes. The level of polymorphism seems to be positively associated with number of repeats. The in silico PCR results were validated experimentally with a subset of these polymorphic markers. More than 6,000 primer pairs flanking SSRs located in gene-coding sequences of the cucumber genome were designed.

Technical Abstract: Cucumber is an important vegetable crop worldwide, but progress in genetic and genomics research in this crop is slow. Recently the genomes of two cucumber genotypes were sequenced, (ibred line ‘9930’ and pickling cultivar ‘Gy14’), which provides a powerful tool for developing markers in large scale. In this study, we surveyed and characterized the distribution and frequency of perfect microsatellites in 203 Mbp assembled Gy14 DNA sequence and in EST sequences of cucumber. Similar analyses were performed in genomic and EST data from seven other plant species. A total of 112,073 perfect repeats were detected in cucumber genomic sequence, accounting for 0.9% of the genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellite repeats, the dinucleotide AT motif had the highest cumulative length in the genomic sequences due to its high repeat numbers per SSR. The coding regions (ESTs) of cucumber genome had fewer microsatellites compared to its genomic sequence with trinucleotides predominating in the former. AAG was the most frequent repeat in cucumber ESTs. We investigated the polymorphism between 9930 and Gy14 at 1,011 SSR loci with in silico PCR, and found unexpectedly high degree of polymorphism between the two lines. The in silico PCR results were validated experimentally. More than 6,000 SSR markers were developed from this study, which is an important contribution to the cucurbit research community.