ARS | Publication request: Development of marker sets useful in the early selection of Ren4 powdery mildew resistance and seedlessness for table and raisin grape breeding

Submitted to: Journal of Theoretical and Applied Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: August 12, 2011
Publication Date: January 15, 2012
Citation: Mahanil, S., Ramming, D.W., Cadle-Davidson, M., Owens, C.L., Garris, A., Myles, S., Cadle Davidson, L.E. 2012. Development of marker sets useful in the early selection of Ren4 powdery mildew resistance and seedlessness for table and raisin grape breeding. Journal of Theoretical and Applied Genetics. 124:23-33.

Interpretive Summary: DNA markers can be used to detect the presence or absence of disease resistance genes in grape breeding lines. Here we describe the application of DNA markers linked to a strong powdery mildew resistance gene, named Resistance to Erysiphe necator 4 (Ren4), which we have domesticated from the Asian wild species Vitis romanetii. Ren4 resides on chromosome 18, near genes providing downy mildew resistance and seedlessness. The DNA markers we developed for this chromosome region will enable grape breeders to discard seeded, susceptible seedlings. This improved efficiency will allow breeders to focus on evaluation of more elite lines. The use of Ren4 in new grape varieties will enable fungicide applications to be drastically reduced in commercial production.

Technical Abstract: The single, dominant powdery mildew resistance locus Ren4 from Vitis romanetii prevents hyphal growth by Erysiphe necator. Previously, we showed that when introgressed into V. vinifera in the modified BC2 population 03-3004, Ren4 was linked with the SSR marker VMC7f2 on chromosome 18, which is also associated with downy mildew resistance and seedlessness. However, in the current study this marker was monomorphic in related breeding populations 05-3010 and 07-3553. To enhance marker assisted selection at this locus, we developed multiplexed SNPlex markers using three approaches: conversion of bulked segregant analysis AFLP markers, sequencing of candidate genes and regions flanking known V. vinifera SNPs, and hybridization to the Vitis9KSNP genotyping array. From 1317 high-quality, informative markers segregating in 03-3004, we developed 15 additional SNPlex markers linked with Ren4 in 03-3004, 5 linked in 05-3010, and 6 linked in 07-3553. Two of these populations segregated for seedlessness, which was tightly linked with Ren4 in 03-3004 (2 cM) but not in 05-3010 (22 cM). Chromosomal rearrangements were detected among these three populations and the reference genome PN40024. Our results provide novel markers for tracking and pyramiding this unique resistance gene and for further functional characterization of this region on chromosome 18 encoding multiple disease resistance and seedlessness. Since this is the first application of the Vitis9KSNP array in a breeding program, some suggestions are provided for application of genotyping arrays.