SSR and SNP Discovery in Endive (Cichorium endivia) and Common Chicory (C. intybus).

The common chicory (Cichorium intybus) and endive (C. endivia), herbaceous plants, are cultivated for their leaves used as salad or cooked, and rich in many vitamins and minerals including vitamins A, B9 (folate) and K. The objective of this research is to discover SNPs and SSRs in order to expedite new common chicory and endive variety development through marker-assisted selection. SNPs and SSRs were postulated from public ESTs stored in GenBank. DNASTAR Lasergene Genomics Suite was used for EST assembly and SNP discovery. From 53,973 ESTs of C. intybus, 7,326 contigs were assembled, and 1,076 SNPs were postulated from 361 non-redundant contigs. From 30,171 ESTs of C. endivia, 2,668 contigs were assembled, and only 48 SNPs identified from 38 contigs. SSRLocator was used for SSR discovery. From 53,973 ESTs of C. intybus, a total of 923 SSRs with di-nucleotide repeat motif were found ranging from 6 to 24 repeats, most of which were 6 – 9 repeats (77.7%); 3,714 SSRs with tri-nucleotide repeat motif that ranged 4 - 12 repeats, most with 4 - 7 repeats (97.5%); 135 SSRs with tetra-nucleotide repeat motif ranged 4 - 8 repeats, most having 4 repeats (69.9%); and 319 pentra-nucleotide repeat motif with 3-5 repeats. From 30,171 ESTs of C. endivia, a total of 425 SSRs with di-nucleotide repeat motif were found ranging from 6 to 20 repeats, most of which were 6 – 9 repeats (77.4%); 2,016 SSRs with tri-nucleotide repeat motif that ranged 6 - 12 repeats, most with 4 - 7 repeats (97.2%); 63 SSRs with tetra-nucleotide repeat motif of 4 - 9 repeats, most having 4 - 5 repeats (66.7%); and 152 pentra-nucleotide repeat motif with 3-5 repeats. The validation of SNPs and SSRs are in progress in various genotypes of C. intybus and C. endivia.