Identification of Candidate Genes Associated with X-disease Resistance in Chokecherry (Prunus virginiana L.) through Comparative Genomics

Recent advances in sequencing technology accelerate the completion of whole genome sequencing for a few model species; however, whole genome sequences of many other species still remain unsequenced including chokecherry, a unique Prunus species for both genetics and disease resistance research due to its tetraploid nature and known-variations in X-disease resistance (a destructive disease of stone fruit trees). One quantitative trait locus (QTL) located on a genetic linkage group of chokecherry was recently detected to be associated with X-disease resistance. In this study, the DNA walking strategy was used to extend, clone, and sequence the flanking regions of the identified SSR marker linked to X-disease resistance. A total of 4748 bp chokecherry DNA sequence that includes the SSR marker was sequenced. As a query sequence, the 4748 bp DNA was aligned with the whole genome sequence of peach (Prunus persica) using BLASTN (http://www.phytozome.net/search.php). One sequence in feature 1 in scaffold 2 in peach genome showed a high similarity (90.5% identity percentage and E-value =0) with the chokecherry sequence among 14 identified scaffolds. The target region (homologous to 4748 chokecherry DNA) on scaffold 2 was extended to 400 kb (200 kb of each direction) as a candidate region for further analysis. Twenty eight transcripts were identified in this region. Functional annotation was conducted through Pfam, gene ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG). Seventeen (of 28) transcripts showed function annotation information. Of which, seven transcripts code plant transposase, one codes protein kinase with serine/threonine/tyrosine kinase (STYKc) domain and leucine rich repeat (LRR) domain, one codes plant transposon, and others involve in coding of zinc finger protein, pentatricopeptide repeat protein, and short chain dehydrogenase protein. Determination of functions and structures of potential resistance (R) genes in this region are underway. Identification of candidate genes/regions will certainly open perspectives for plant molecular breeding.