Genomic analysis of powdery mildew resistance in a hop (Humulus lupulus L.) bi-parental population segregating for “R6-locus”

Authors: PADGITT-COBB, LILLIAN - Oregon State University; KINGAN, SARAH - Pacific Biosciences Inc; Henning, John

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/20/2019
Publication Date: 12/5/2019
Citation: Padgitt-Cobb, L., Kingan, S.B., Henning, J.A. 2019. Genomic analysis of powdery mildew resistance in a hop (Humulus lupulus L.) bi-parental population segregating for “R6-locus”. Euphytica. 216:10. https://doi.org/10.1007/s10681-019-2543-x.
DOI: https://doi.org/10.1007/s10681-019-2543-x

Interpretive Summary: A hop plant’s response to plant disease has been characterized genetically and evaluated at at the level of leaves and whole plants, but very little is known about the sub-cellular or molecular expression during infection. A genetic mapping study was performed to evaluate resistance to hop powdery mildew, a disease caused by a fungus that attacks the leaves and stems of the plant. The mapping study revealed two regions of DNA that were near each other, or linked, on a single chromosome that controlled resistance or susceptibility to powdery mildew. These regions were adjacent to a putative R-gene locus for powdery mildew resistance. R-genes are genes known to control resistance responses in plants. This putative R-gene region of 230 kb region contained a series of seven putative R-genes that were surrounded by other types of genes known to be involved in fighting fungal infection. Analysis of gene expression showed that many of these genes were expressed under diseased conditions, further implicating their role in determining resistance or susceptibility. The other region linked to disease resistance also contained two putative R-genes. This preliminary information will prove valuable for development of precise markers located either within or next to genes responsible for race v6 PM resistance.

Technical 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. One bi-parental mapping population was created to evaluate resistance to powdery mildew (PM; Podosphaera humuli). Genotyping-by-sequencing and disease phenotyping were performed on this population. QTL analyses revealed two tightly linked regions of association on a single linkage group. The two 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 QTL contained three SNPs found on contig 002916F next to two putative R-genes. This preliminary information will prove valuable for development of precise markers located either within or next to genes responsible for race v6 PM resistance.