Abstract
Genetic response in hop to fungal pathogen infection has been evaluated at the chromosomal level through QTL analyses but very little information exists on the expression of genes during infection periods. Raw GBS reads and phenotypic data from a previously published QTL analysis along with a newly assembled PacBio-derived hop reference genome were used to re-evaluate resistance to races v4/v6 of powdery mildew (PM; Podosphaera humuli). QTL analyses revealed two tightly linked regions of association on a single linkage group. The three SNP markers most tightly linked to PM resistance (found on contig 000559F) were observed downstream from a putative R-gene locus for powdery mildew resistance. This 230 kb region contained a series of seven putative R-genes surrounded by seven putative peroxidase-3 genes downstream and seven putative glucan endo-1,3-beta-glucosidase upstream and an expressed F-box domain protein. RNAseq data showed all putative R-genes along with all putative glucan endo-1,3-beta-glucosidase genes were expressed under diseased conditions, while none of the peroxidase genes were expressed. The second region contained three SNPs found on contig 002916F next to two putative R-genes. RNAseq data showed complex expression of exons contained in putative isoforms of R-genes. This preliminary information will prove valuable information for development of precise markers located either within or next to genes responsible for race v4/v6 PM resistance.
Highlights
Introduction10 Page 2 of 15 replacement therapy (Hemachandra et al 2012)
Hop (Humulus lupulus L. var lupulus) is a diploid (2n = 2x = 18 ? XX/XY) dioecious perennial crop species used principally for beer bittering and flavoring alternate uses include replacement of antibiotics in poultry (Bortoluzzi et al 2014), anticancer (Miranda et al 1999; Jiang et al 2018), metabolic disorder (Miranda et al 2016) and estrogen10 Page 2 of 15 replacement therapy (Hemachandra et al 2012)
Blocks within replications were maintained for interval mapping (IM) and composite interval mapping (CIM) analyses in QTL studies and for association studies
Summary
10 Page 2 of 15 replacement therapy (Hemachandra et al 2012) It is produced on six meters tall trellis under wide row spacing (three to five meters) between rows in most countries with the exception of Great Britain where some hops are produced under 2.5 m low-trellis using hops bred for these conditions (Neve 1991). Pathogen resistance to chemical treatments has been documented (Klein 1994; Gent et al 2008) and efforts towards implementation of physical control methods such as springtime pruning are limited due to the potential spread of virus and viroid’s using mechanical pruning With these factors in mind, it follows that the most economical means of controlling fungal diseases is to produce hop cultivars that are resistant to fungal pathogens
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