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United States Department of Agriculture

Agricultural Research Service

Research Project: ALLIUM, CUCUMIS, AND DAUCUS GERMPLASM ENHANCEMENT, GENETICS, AND BIOCHEMISTRY Title: Genome-wide Characterization of Simple Sequence Repeats in Cucumber (Cucumis Sativus L.)

Authors
item Cavagnaro, Pablo -
item Weng, Yiqun
item Senalik, Douglas
item Yang, Luming -
item Simon, Philipp
item Harkins, Timothy -
item Kodira, Chinnappa -
item Huang, Sanwen -

Submitted to: Biomed Central (BMC) Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: October 15, 2010
Publication Date: October 15, 2010
Citation: Cavagnari, P.F., Weng, Y., Senalik, D.A., Yang, L., Simon, P.W., Harkins, T.T., Kodira, C.D., Huang, S. 2010. Genome-wide Characterization of Simple Sequence Repeats in Cucumber (Cucumis Sativus L.). Biomed Central (BMC) Genomics. Available: http://www.biomedcentral.com/1471-2164/11/569.

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 the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length in genomic sequences. Coding regions (ESTs) of the 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 richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available.

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 the Gy14 cucumber genome sequence, accounting for 0.9% of the assembled Gy14 genome, with an overall density of 551.9 SSRs/Mbp. While tetranucleotides were the most frequent microsatellites, dinucleotide repeats, which had more repeat units than any other SSR type, had the highest cumulative sequence length in genomic sequences. Coding regions (ESTs) of the 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 (although comparable to the density of poplar, grapevine and rice), and was richest in AT dinucleotides. Using an electronic PCR strategy, we investigated the polymorphism between 9930 and Gy14 at 1,006 SSR loci, and found unexpectedly high degree of polymorphism (48.3%) between the two genotypes. The level of polymorphism seems to be positively associated with the number of repeat units in the microsatellite. The in silico PCR results were validated empirically in 660 of the 1,006 SSR loci. In addition, primer sequences for more than 83,000 newly-discovered cucumber microsatellites, and their exact positions in the Gy14 genome assembly were made publicly available.

Last Modified: 11/27/2014
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