Research Article: SNP markers tightly linked to root knot nematode resistance in grapevine (Vitis cinerea) identified by a genotyping-by-sequencing approach followed by Sequenom MassARRAY validation

Date Published: February 20, 2018

Publisher: Public Library of Science

Author(s): Harley M. Smith, Brady P. Smith, Norma B. Morales, Sam Moskwa, Peter R. Clingeleffer, Mark R. Thomas, Sara Amancio.

http://doi.org/10.1371/journal.pone.0193121

Abstract

Plant parasitic nematodes, including root knot nematode Meloidogyne species, cause extensive damage to agriculture and horticultural crops. As Vitis vinifera cultivars are susceptible to root knot nematode parasitism, rootstocks resistant to these soil pests provide a sustainable approach to maintain grapevine production. Currently, most of the commercially available root knot nematode resistant rootstocks are highly vigorous and take up excess potassium, which reduces wine quality. As a result, there is a pressing need to breed new root knot nematode resistant rootstocks, which have no impact on wine quality. To develop molecular markers that predict root knot nematode resistance for marker assisted breeding, a genetic approach was employed to identify a root knot nematode resistance locus in grapevine. To this end, a Meloidogyne javanica resistant Vitis cinerea accession was crossed to a susceptible Vitis vinifera cultivar Riesling and results from screening the F1 individuals support a model that root knot nematode resistance, is conferred by a single dominant allele, referred as MELOIDOGYNE JAVANICA RESISTANCE1 (MJR1). Further, MJR1 resistance appears to be mediated by a hypersensitive response that occurs in the root apical meristem. Single nucleotide polymorphisms (SNPs) were identified using genotyping-by-sequencing and results from association and genetic mapping identified the MJR1 locus, which is located on chromosome 18 in the Vitis cinerea accession. Validation of the SNPs linked to the MJR1 locus using a Sequenom MassARRAY platform found that only 50% could be validated. The validated SNPs that flank and co-segregate with the MJR1 locus can be used for marker-assisted selection for Meloidogyne javanica resistance in grapevine.

Partial Text

Plant parasitic nematodes are major soil-borne pests that cause extensive damage to a wide range of crops with an estimated cost of $80 billion (USD) per year [1]. To date, greater than 4100 species of plant parasitic nematodes have been identified and classified as endoparasites (sedentary and migratory), semi-endoparasites and ectoparasites. In many horticultural crops including grapevine, rootstocks resistant to plant parasitic nematodes as well as other pests provide a sustainable approach to limit crop losses [2].

In this manuscript, an F1 mapping population derived from a C2-50 x Riesling cross was used to map the M. javanica ‘pt. 1103P’ resistance locus, MJR1. Results from the nematode-screening assay performed on the parents and F1 individuals indicated that M. javanica ‘pt. 1103P’ resistance is controlled by a single dominant allele, which is derived from the C2-50 female parent. Genetic studies indicate that resistance to M. incognita is conferred by a single dominant allele in the V. champinii rootstocks Harmony, Freedom, Dog Ridge and Ramsey [13]. At this time, it is not clear as to whether the location and identity of root knot nematode resistance locus and gene(s), respectively, is similar in C2-50 and the V. champinii derived rootstocks.

In summary, traditional breeding approaches to develop rootstocks with resistance to plant parasitic nematodes and other soil borne pests is costly, time consuming and dependent upon labor-intensive work including plant propagation and nematode screening. However, employing a marker assisted breeding approach with molecular markers that predict nematode resistance would be an efficient and cost-effective approach. Moreover, marker assisted selection will allow for stacking multiple root knot nematode resistant loci into a single genetic background for producing new rootstocks with durable resistance. Using genetic mapping approaches, results show that MJR1 maps at approximately 100 cM on LG18 in V. cinerea C2-50. In addition, SNPs at the MJR1 locus had high genome wide association. Based on the position of these SNPs from 30711041 to 33954011 on chromosome 18 of the PN40024 reference genome, the estimated size of the MJR1 locus is 3.24 Mb. The resistance mechanism mediated by MJR1 involves localized cell necrosis in the root meristem, which may function to impair nematode migration and giant cell formation. Validated SNPs that cosegregate and the flank the MJR1 locus from 99.2 to 101.4 cM will serve as molecular markers for predicting root knot nematode resistance in V. cinerea C2-50 for rootstock development.

 

Source:

http://doi.org/10.1371/journal.pone.0193121

 

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