| Hop stunt viroid (HSVd) was first detected in hop orchards in Washington State in 2004. A 2012 survey for the presence of HSVd, in three major hop growing regions in Washington State indicated an overall incidence of 17.3 percent. A five year yield study comparing HSVd infected and uninfected hop cultivars 'Glacier' and 'Nugget' revealed that, of those tested, 'Nugget' was the most tolerant hop cultivar to HSVd infection and 'Glacier' was the most severely affected.;In this study, whole genome and RNA sequence analysis identified potential genes associated with expression of hop stunt disease, and identified DNA-markers that distinguish HSVd-tolerant plants from HSVd-sensitive cultivars. Healthy plants and HSVd-infected 'Glacier' and 'Nugget' revealed different gene expression profiles that suggested that a pathogenesis-related protein, thaumatin like protein (TLP), is a candidate marker for hop stunt viroid sensitivity.;TLP was observed to be down regulated 2.6 fold in 'Glacier' infected with HSVd compared to HSVd free 'Glacier'; no change in TLP expression was observed in 'Nugget' between HSVd-infected or HSVd-free plants. RNA sequence analyses were confirmed using qRT-PCR for TLP expression levels normalized to Glyceraldehyde 3-phosphate dehydrogenase (GAPDH).;Alignments of the TLP coding sequence (CDS) and the region immediately up-stream of the TLP CDS for each cultivar revealed no sequence variations 100 bp upstream of the TLP CDS which includes the ATG translation start site, TATA box and the transcriptional start site. However, 23 nucleotide variations exist between 'Glacier' and 'Nugget' in a 397 bp region up stream of the first CAAT cis-regulatory element. (CRE). These variations create eleven unique CRE differences between 'Glacier' and 'Nugget'. Additionally, within the TLP CDS nineteen single nucleotide polymorphisms (SNPs) were observed in 'Glacier' relative to 'Nugget'. Several of these SNPs result in amino acid substitutions. Four of the SNPs within the 'Glacier' TLP CDS result in amino acid substitutions that were not observed in five other cultivars of hop. In total, 42 SNPs were identified that potentially may be used in marker assisted breeding programs to distinguish potential HSVd-tolerant plants from HSVd-sensitive plants. Evaluation of additional hop genotypes will be necessary to confirm this relationship. |
