Identification and Validation of a SNP Marker Linked to the Gene HsBvm-1 for Nematode Resistance in Sugar Beet

Abstract

The beet-cyst nematode (Heterodera schachtii Schmidt) is one of the major pests of sugar beet. The identification of molecular markers associated with nematode tolerance would be helpful for developing tolerant varieties. The aim of this study was to identify single nucleotide polymorphism (SNP) markers linked to nematode tolerance from the Beta vulgaris ssp. maritima source WB242. A WB242-derived F2 population was phenotyped for host-plant nematode reaction revealing a 3:1 segregation ratio of the tolerant and susceptible phenotypes and suggesting the action of a gene designated as HsBvm-1. Bulked segregant analysis (BSA) was used. The most tolerant and susceptible individuals were pooled and subjected to restriction site associated DNA sequencing (RAD-Seq) analysis, which identified 7,241 SNPs. A subset of 384 candidate SNPs segregating between bulks were genotyped on the 20 most-tolerant and most-susceptible individuals, identifying a single marker (SNP192) showing complete association with nematode tolerance. Segregation of SNP192 confirmed the inheritance of tolerance by a single gene. This association was further validated on a set of 26 commercial tolerant and susceptible varieties, showing the presence of the SNP192 WB242-type allele only in the tolerant varieties. We identified and mapped on chromosome 5 the first nematode tolerance gene (HsBvm-1) from Beta vulgaris ssp. maritima and released information on SNP192, a linked marker valuable for high-throughput, marker-assisted breeding of nematode tolerance in sugar beet.