Plant & Animal Genomes XI Conference

January 11-15, 2003
Town & Country Convention Center
San Diego, CA

Poster: Genome Sequencing & ESTs
            

MINING THE HORTRESEARCH APPLE EST DATABASE - IN SILICO TISSUE EXPRESSION ANALYSIS OF RESISTANCE GENE CANDIDATES AND RESISTANCE GENE CLASSES

¹ The Horticulture and Food Research Institute of New Zealand Limited, Private Bag 92169, Auckland, New Zealand

² The Horticulture and Food Research Institute of New Zealand Limited, Private Bag 11030, Palmerston North, New Zealand

³ The Horticulture and Food Research Institute of New Zealand Limited, Private Bag 1401, Havelock North, New Zealand

HortResearch has combined resources in molecular genetics, bioinformatics and germplasm to develop an integrated project to mine, map and use major resistance (R) genes effective against apple pathogens and pests. An in-house customised bioinformatic system queried in silico through a web-based interface was used to mine a database containing 120,000 apple ESTs derived from 49 cDNA libraries. Query based systems linked to this database (involving Blast searches, motif and keyword searches, and an automated annotation system) were used to identify candidate R genes. These genes encompass a number of different classes or domains. This includes 1) a class containing nucleotide binding site and leucine rich repeats with either a coiled coil domain, a Toll/Interleukin-like receptor domain or no recognised 5' domain, 2) serine/threonine protein kinase domains with homology to the Pto and Xa21 genes 3) putative external leucine rich repeat domains with homology to the Cf and Xa21 genes and 4) a class with similarity to the multiple transmembrane domain-like structure of the Mlo gene. Several hundred candidate R gene ESTs were identified. The candidate ESTs identified are being used to identify molecular markers linked to resistance genes recognised by segregation of their resistance phenotype. These markers are facilitating projects in marker-assisted breeding and map-based molecular identification of the genes responsible for the resistance phenotype. We will present information on the distribution and frequency of candidate R genes in cDNA libraries from different tissue types and the relative frequencies of the different types of resistance gene classes or domains identified.