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Development of a SNP marker set related to crown gall disease in grapevines by a genome wide association study

  • Kim, Dae-Gyu (Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University) ;
  • Jang, Hyun A (Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University) ;
  • Lim, Dong Jun (National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Hur, Youn Young (National Institute of Horticultural and Herbal Science, Rural Development Administration) ;
  • Lee, Kyo-Sang (Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University) ;
  • Min, Jiyoung (Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University) ;
  • Oh, Sang-Keun (Department of Applied Biology, College of Agriculture & Life Sciences, Chungnam National University)
  • Received : 2020.08.10
  • Accepted : 2020.08.24
  • Published : 2020.09.01

Abstract

Grapes (Vitis spp. L.) are the third most produced fruit in the world. Crown gall disease caused by Agrobacterium vitis forms galls in the stems of the grapevines and reduces the vitality of the fruit trees, resulting in reduced yields. This pathogen has occurred in vineyards worldwide and caused serious economic losses. It is a soil-borne disease, so Agrobacterium vitis can survive for several years in vineyards and is difficult to control. Additionally, since there is no effective chemical control method, the most effective control method is the breeding of resistant varieties. To make the resistant variety, marker-assisted selection (MAS) enables fast breeding with low cost. In this study, we applied a genome-wide association study (GWAS), by combining phenotyping and genotyping-by-sequencing (GBS), for the development of a single nucleotide polymorphism (SNP) marker set related to crown gall disease using 350 grapevine varieties. As a result of the GBS based genotyping analysis, about 58,635 SNPs were obtained. In addition, the phenotypic analysis showed 35.2% resistance, 73% moderate susceptibility and 16.4% highly susceptibility. Moreover, after confirmation, two genes (VvARF4 and VvATL6-like) were shown to be related to crown gall disease based on the results of GWAS analysis, using the phenotypic data, and GBS. High-resolution melting analysis (HRMA) was performed using the Luna® Universal Probe with real-time PCR to distinguish the melting peaks of the resistant and susceptible varieties. Our data show that these SNP markers are expected to be helpful in evaluating resistance against grapevine crown gall disease and in breeding.

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