Development of genomewide simple sequence repeat fingerprints and highly polymorphic markers in cucumbers based on next‐generation sequence data

Abstract

AbstractCucumbers are one of the most important vegetable crops worldwide. The molecular markers have substantial potential to improve the efficiency of conventional cucumber breeding. In this study, a total of 101 157 simple sequence repeats (SSRs) were identified across the cucumber 9930 genome. Most (69 526 of 76 103 or 91.36%) SSRs with unique flanking sequences (unique SSRs) had polymorphisms among 103 cucumber genomes; the number of alleles ranged from 2 to 34 with an average of 4.70. Next, we selected 7486 unique SSR loci with polymorphism information content (PIC) ≥0.5 and major allele differences (the size difference between the alleles with the highest and the second highest frequency) ≥3 bp to design primers. The SSR marker polymorphisms were experimentally validated; 50 highly polymorphic SSR markers had polymorphisms with an average PIC of 0.44. PCR analysis also indicated that these SSR markers could be effectively used as molecular markers. The SSR fingerprints and polymorphic SSR markers with large major allele differences could enhance the efficiency of genetic research and marker‐assisted breeding in cucumbers.