Feature Analysis Of EST-SSR And Marker Development In Cucumber

Recently,SSR is one of the most popular molecular markers since its relative abundance,wild genome coverage,multi-allelic nature,reproducibility and codominant inheritance.With the emergence of sequenced genome,developed ESTs and available public sequence database,which all provided abundant resources for the development of SSR marker.Cucumis belongs to Cucumis genus,which is a kind of vegetable crops with high economic value.The development of the available EST-SSR markers in cucumber has a significant role,Here,we firstly download EST-SSR sequences in cucumber database and then analysis their distribution characteristics.Finally,we evaluated their application based on the phylogeny analysis.The main results are listed belows:In total,there were 381,022 ESTs generated by assembling 513,801 ESTs from cucumber database.Following on the criteria-5 units as the minimum repeat and base sequence of length 1-6 bp,a sum of 15,665 SSR loci was received.The frequency is 4.11%and the EST containing SSR loci frequency is 3.05%.Trinucleotide was the most abundant,with a frequency of 45.67%,followed by dinucleotide(28.01%)and mononucleotide(22.31%)motifs.98.56%the length of EST-SSR locus range 10-30 bp.A subset of 146 primers were randomly selected to investigate the polymorphism of EST-SSRs in 19 accessions worldwide.In total,88 primer pairs amplified fragments around the expected band size,and 58 no obvious PCR amplicons were eliminated from the following analysis.For the 88 primers with successful amplification,28 pairs of primer revealed polymorphism among the tested cucumber genotypes,the proportion of polymorphic primers was 19.18%.These polymorphic loci were confined to cucumber chromosome 1-7.In addition,we use the 28 polymorphism EST-SSR markers to performe the system cluster analysis,which can be clustered all the 19 accessions into two major groups European-American and Chinese-Japanese ecotypes at the similarity level of 0.55.The latter could be divided into three ecotypes:south China ecotype,north China ecotype and hybrid China ecotype,similar to the previous studies based on the geographical distribution and ecological characters.The function of genes corresponding to 28 polymorphic EST-SSR markers were analysed and found that 6 genes are functional factors,12 related to protein or enzyme function,3 related to binding and repairing function,7 unknown.