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United States Department of Agriculture

Agricultural Research Service

Research Project: GENETIC IMPROVEMENT OF FRUIT CROPS THROUGH FUNCTIONAL GENOMICS AND BREEDING Title: Genomic analysis reveals candidate genes for PPV resistance in apricot (Prunus armeniaca L.)

Authors
item Zuriaga, Elena -
item Soriano, Jose -
item Zhebentyayeva, Tetyana -
item Romero, Carlos -
item Dardick, Christopher
item Canizares, Joaquin -
item Bandenes, Maria -

Submitted to: Molecular Plant Pathology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 7, 2013
Publication Date: May 14, 2013
Citation: Zuriaga, E., Soriano, J., Zhebentyayeva, T., Romero, C., Dardick, C.D., Canizares, J., Bandenes, M. 2013. Genomic analysis reveals candidate genes for PPV resistance in apricot (Prunus armeniaca L.). Molecular Plant Pathology. DOI:10.1111/mpp.12037.

Interpretive Summary: Plum pox virus (PPV) is a serious problem in stone fruits causing severe disease symptoms and fruit loss. A few apricot varieties have been identified which are immune to the virus. Previously, genetic mapping studies have been conducted to find the location of the gene in hopes to enable efficient marker assistant selection for PPV resistant varieties. This work has led to the first detailed genetic maps. Here, we sequenced the chromosomal interval to identify which genes are present in the region and find differences between PPV resistant and susceptible varieties. The results revealed a set of likely candidate genes, some of which have been shown to confer virus resistance in other plant species. These findings represent significant progress towards understanding natural resistance mechanisms to PPV in stone fruit species.

Technical Abstract: Sharka disease, caused by Plum pox virus (PPV), is the most important disease affecting Prunus species. A major PPV resistance locus (PPVres) was previously mapped to the upper part of apricot (Prunus armeniaca) linkage group 1. In this study, a physical map of the PPVres locus in the PPV resistant cultivar 'Goldrich' was constructed. BAC clones belonging to the resistant haplotype contig were sequenced using 454/GS-FLX Titanium technology. Concurrently, whole genome of 7 apricot varieties (3 PPVresistant and 4 PPV susceptible) and 2 PPV susceptible apricot relatives (P. sibirica var.davidiana and P. mume) were obtained using Illumina-HiSeq2000 platform. Single nucleotide polymorphisms (SNPs) within mapped interval, recorded from alignments against the peach genome, allowed us to narrow down the PPVres locus to an approximately196kb region. Searches for SNPs and deletion/insertion polymorphisms linked in coupling with the resistance led to the identification of 68 variants within 23 predicted transcripts according to peach genome annotation. Candidate resistance genes were ranked combining data from variant calling and predicted functions inferred from sequence homology. Altogether, results suggest that members of a cluster of meprin and TRAF-C homology domain (MATHd) containing proteins are the most likely candidate genes for PPV resistance in apricot. Interestingly, MATHd proteins are hypothesized to control long-distance movement (LDM) of potyviruses in Arabidopsis and restriction for LDM is also a major component of PPV resistance in apricot. Nevertheless, further research will still be necessary to unambiguously identify the gene(s) conferring PPV resistance in apricot.

Last Modified: 10/20/2014