A robust SNP-haplotype assay for Bct gene region conferring resistance to beet curly top virus in common bean (Phaseolus vulgaris L.)

Beet curly top virus (BCTV), which is synonymous with curly top virus (CTV), causes significant yield loss in common bean (snap and dry beans) cultivars and several other important crops. Common bean cultivars have been found to be resistant to CTV, but screening for resistance is challenging due to the cyclical nature of epidemics and spotty feeding by the leafhopper that vectors the virus. We used an SNP dataset for the Snap Bean Association Panel (SnAP) agro-inoculated with CTV-Logan (CA/Logan) strain to locate the Bct gene region to a 1.7-Mb interval on chromosome Pv07 using genome-wide association study (GWAS) analysis. Recombinant lines from the SnAP were used to further narrow the Bct region to a 58.0-kb interval. A missense SNP (S07_2970381) in candidate gene Phvul.007G036300 Exonuclease V (EXO5) was identified as the most likely causal mutation, and it was the most significant SNP detected by GWAS in a dry bean population (DBP) naturally infected by the CTV-Worland (Wor) strain. Tm-shift assay markers developed for SNP S07_2970381 and two linked SNPs, S07_2970276 and S07_2966197, were useful for tracking different origins of the Bct EXO5 candidate gene resistance to CTV in common bean. The three SNPs identified four haplotypes, with haplotype 3-1 (Haplo3-1) of Middle American origin associated with the highest levels of CTV resistance. This SNP-haplotype assay will enable breeders to track resistance sources and to develop cultivars with better CTV resistance

Pathogenicity, vegetative compatibility and genetic diversity of <i>Verticillium dahliae</i> isolates from sugar beet

<p>Verticillium wilt of sugar beet is a disease that has received very little attention, but which has been reported to reduce sugar quality. A survey of sugar beet fields with wilt symptoms was conducted in 2007 (5 roots from each of 40 fields) and 2008 (5 roots from each of 45 fields) in Idaho. <i>Verticillium dahliae</i> was isolated from all root samples. From a collection of 106 <i>V. dahliae</i> sugar beet isolates, all were of the <i>MAT1-2</i> mating type. The vegetative compatibility grouping (VCG) was evaluated for 93 of these isolates and 95, 3, 1 and 1% were VCG 4A, VCG 2B, VCG 4B and non-compatible, respectively. All the VCG 4A isolates had the same mitochondrial haplotype based on sequencing of <i>cox3</i> to <i>nad6</i> and <i>cox1</i> to <i>rnl</i> loci, while the VCG 2B isolates had two haplotypes. Pathogenicity tests on sugar beet cultivar ‘Monohikari’ revealed that the VCG 4A isolates produced more foliar symptoms (<i>P</i> < 0.0001) than VCG 1, 1A, 2A, 2B, 3 and 4B isolates, but none of the VCGs consistently reduced root and foliage weight. Since <i>V. dahliae</i> VCG 4A isolates have also been reported as a pathogen of potato in North America, rotating sugar beet fields with potato could be a concern.</p