Development and use of an expressed sequenced tag library in quinoa (Chenopodium quinoa Willd.) for the discovery of single nucleotide polymorphisms

Quinoa (Chenopodium quinoa Willd.) is a widely consumed food crop and a primary protein source for many of the indigenous inhabitants of the Andean region of South America. In this study, we report the development of immature seed and floral expressed sequenced tag (EST) libraries and the identification of single nucleotide polymorphisms (SNPs) for quinoa. A total of 424 cDNA clones derived from immature seed and floral tissue were sequenced and analyzed for homology with known gene sequences. Three hundred and eleven of the clones were identified as homologues of known plant proteins, 38 were homologous to Arabidopsis proteins with no known function and 75 do not share significant homology with any protein in the queried databases. Interestingly, several of the annotated ESTs were present in relatively high abundance and have putative functions related to plant defense. Based on EST sequence information, fragments of 34 ESTs were amplified and sequenced in five quinoa accessions and one related weed species, C. berlandieri. Analysis of the quinoa EST sequences revealed a total of 51 SNPs in 20 EST sequences, including 38 single-base changes and 13 insertions-deletions (indels), with an average 1 SNP per 462 base pairs (bp) and 1 indel per 1812 bp. When the C. berlandieri accession was included in the analysis, 29 of the EST clones screened had at least one SNP present and an additional 81 SNPs were identified, bringing the total number of SNPs discovered to 132 (1 per 179 bp). The EST clones and SNP markers identified in this manuscript are of particular value in ongoing efforts to characterize gene expression and regulation associated with seed development, while the SNPs identified have immediate application for genetic mapping experiments, germplasm development, and the investigation of evolutionary relationships within the genus Chenopodium.