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

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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 simple sequence repeat marker VMC7f2 on chromosome 18—a marker that is associated with multiple disease 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 SNP 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. The Vitis9KSNP array was more cost-efficient than all other approaches tested for marker discovery and genotyping, enabling the genotyping of 1317 informative SNPs within the span of 1 week and at a cost of 11 cents per SNP. From a total of 1,446 high quality, informative markers segregating in 03-3004, we developed a haplotype signature of 15 multiplexed SNP markers linked with Ren4 in 03-3004, 5 of which were linked in 05-3010, and 6 of which were 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. Since this is the first application of the Vitis9KSNP array in a breeding program, some suggestions are provided for application of genotyping arrays. 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.

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Acknowledgments

This project was funded by the American Vineyard Foundation. Development of the Vitis9KSNP array and its application in genotyping of the parents and 18 progeny was funded by a grant from USDA-ARS to Ed Buckler and Doreen Ware.

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Author notes

  1. Molly Cadle-Davidson

    Present address: SRC Advanced Technologies Initiative, 7502 Round Pond Road, North Syracuse, NY, 13212, USA

  2. Sean Myles

    Present address: Department of Plant and Animal Sciences, Nova Scotia Agricultural College, Truro, NS, B2N 5E3, Canada

Authors and Affiliations

  1. USDA-ARS Grape Genetics Research Unit, 630 W. North St, Geneva, NY, 14456, USA

    Siraprapa Mahanil, Molly Cadle-Davidson, Christopher Owens & Lance Cadle-Davidson

  2. USDA-ARS San Joaquin Valley Agricultural Sciences Center, 9611 South Riverbend Avenue, Parlier, CA, 93648-9757, USA

    David Ramming

  3. Department of Horticultural Sciences, New York State Agricultural Experiment Station, 630 W. North St, Geneva, NY, 14456, USA

    Amanda Garris

  4. Department of Genetics, Stanford University, 300 Pasteur Dr, Stanford, CA, 94305, USA

    Sean Myles

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  1. Siraprapa Mahanil
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Correspondence to Lance Cadle-Davidson.

Additional information

Communicated by C. Gebhardt.

S. Mahanil and D. Ramming equally contributed to this study.

Mention of trade names or commercial products is solely for the purpose of providing specific information and does not imply recommendation or endorsement by the U.S. Department of Agriculture. USDA is an equal opportunity provider and employer.

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Mahanil, S., Ramming, D., Cadle-Davidson, M. et al. Development of marker sets useful in the early selection of Ren4 powdery mildew resistance and seedlessness for table and raisin grape breeding. Theor Appl Genet 124, 23–33 (2012). https://doi.org/10.1007/s00122-011-1684-7

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