Comparative Genomics Analysis between V. shuttleworthii and V. vinifera grapes

• Author(s): Bradeley, F; Huang, Wensheng; Hunter, Wayne; Lu, J.; Ren, Zhongbo;
• Abstract: Vitis shuttleworthii is a grape species native to the southeastern United States that is known for its resistance to major grape diseases and pests. To identify and isolate the genes linked to disease resistance in V. shuttleworthii, a clone was used to produce a cDNA library derived from leaves and flowers during anthesis. The expressed sequence tags, ESTs, were then used to conduct comparative, in silico analysis. Phase I of this project analyzed 12,936 ESTs which generated a set of 12,008 quality scored ESTs. These produced a set of 5,766 unigenes after assembly. Among these 5,766 V. shuttleworthii unigenes, 157 produced full-length protein sequences. The 157 contigs were compared by BLASTX analyses against the V. vinifera unigene set which contains a total of 23,871 unigenes generated from 139,380 ESTs (TIGR database). Of these, 153 had significant similarity to known Vitis proteins (E value -30). Then the 5,766 V. shuttleworthii unigene set was compared to the current set of genes from the wine grape; of the 23,871 V. vinifera unigenes using BLASTN, roughly 27%, or 1,588 of these sequences did not have a significant identity match (E value ' -10). Comparison of the translated protein sequences identified 1,086 sequences which did not have homologs in the Vitis unigene set (BLASTX, E value ' -10). Furthermore, when these1,086 unique sequences were compared by BLASTX against the 119,971 Arabidopsis protein database, a unique set of only 428 proteins from V. shuttleworthii was identified. These had no significant matches (E value -20). Further comparison of these unique proteins by BLASTX analyses to the grape V. viniferea unigene set, to our surprise, showed that none of them were found to be homologous to any of the 23,871 sequences in the grape database. Comparing the unique set of 428 sequences to known disease resistance gene families in other crop plants identified 54 putative candidates significantly linked to disease resistance. These candidates are being further characterized for their potential usefulness as genetic markers linked to disease resistance for grape breeding programs, and to identify their role(s) in disease resistance pathways. A unique microarray has been produced (LuVs) and which is being used to examine expression of these genes in relation to disease resistance in grapes.
• Publication Date: Jan 2006
• Journal: Acta Horticulturae