Genomic and Field Tools for Cranberry
Vegetable Crops Research Unit
2012 Annual Report
1a.Objectives (from AD-416):
Initiate genomic analysis of cranberry and its relatives that will provide molecular markers to be tied to field variation. Characterize field performance of next genotypes.
1b.Approach (from AD-416):
DNA will be sequenced and evaluated for genomic signatures known from other plant genetic and genomic studies to be associated with field traits. Known trait variation in cranberries and related plants will compare to genomic variation and relationships will be sought to initiate the development of hypotheses to test genomic bases for traits. Field traits important for growers and consumers will be evaluated and field data compared to genomic data.
Roche 454 pyrosequencing data was bioinformatically analyzed. Eleven cranberry plastid contigs were selected for the construction of the plastid genome. A total of 11 contigs were used to assemble and annotate a cranberry plastid genome with a length of 176kb. The longest contig (104,544 bases long) was used as a starting point for the reconstruction of the cranberry plastid genome. The large (LSC) and small (SSC) were represented by single contigs, while the inverted repeat regions (IR) were inferred by connecting nine small contigs. The reconstructed plastid genome was 176,037 bp long, LSC region = 104,544bp, two IR = 34,232bp each, and the SSC region = 3,029bp. The cranberry plastid genome sequence will allow the accumulation of critical data useful for breeding and a suite of other genetic studies.
This research relates to the initiation of genomic analysis of cranberry and its relatives that will provide molecular markers to be tied to field variation.