Genomic basis of European ash tree resistance to ash dieback fungus

Abstract

15Populations of European ash trees (Fraxinus excelsior) are being devastated by the invasive alien 16 fungus Hymenoscyphus fraxineus, which causes ash dieback (ADB). We sequenced whole 17 genomic DNA from 1250 ash trees in 31 DNA pools, each pool containing trees with the same 18 ADB damage status in a screening trial and from the same seed-source zone. A genome-wide 19 association study (GWAS) identified 3,149 single nucleotide polymorphisms (SNPs) associated 20 with low versus high ADB damage. Sixty-one of the 203 most significant SNPs were in, or close 21 to, genes with putative homologs already known to be involved in pathogen responses in other 22 plant species. We also used the pooled sequence data to train a genomic prediction (GP) model, 23 cross-validated using individual whole genome sequence data generated for 75 healthy and 75 24 damaged trees from a single seed source. Using the top 30% of our genomic estimated breeding 25 values from 200 SNPs, we could predict tree health with over 90% accuracy. We infer that ash 26 dieback resistance in F. excelsior is a polygenic trait that should respond well to both natural 27 selection and breeding, which could be accelerated using GP. 28 29

Genomic prediction in the wild: A case study in Soay sheep

“…Attempts to use genomic prediction in an ecological context remain very rare compared to its application in breeding or medicine, although some examples are now described (Stocks et al, 2019, Gienapp et al, 2019, Bosse et al, 2017. As far as we are aware this is the first genomic prediction study in a wild population that considers either multiple traits with different genetic architectures or different genomic prediction methods.…”

“…First, being able to estimate an individual's breeding value and/or phenotype before it is expressed means it should be possible to predict (and test) how different individuals will respond to a future environmental event. A good example of this comes from a genomic prediction study of ash trees experiencing an outbreak of ash dieback, a disease caused by the fungus Hymenoscyphus fraxineus (Stocks et al, 2019). Being able to identify which young plants are most resistant to dieback could be an essential tool in re-establishing populations devastated by disease.…”

Will natural resistance result in populations of ash trees remaining in British woodlands after a century of ash dieback disease?

“…The current hypothesis is that, probably in part, resistance (or at least the ability to escape the disease) is conferred by earlier spring leaf flushing and earlier autumn leaf senescence [11,22]. It is possible that there could be other resistance mechanisms and a genome-wide association study suggests that there are genetic associations with ADB damage, some of which are known to be associated with pathogen responses in plants [64]. If the fungus does develop a means to overcome current resistance mechanisms, then the future of the ash would be less clear.…”

The viability of a breeding programme for ash in the British Isles in the face of ash dieback

“…A report of a GWAS based on the Forest Research mass screening trial (see above) is available as a pre-print (Stocks et al, 2019…”

“…Whilst a breeding programme based on phenotypic selection is likely to be effective, more research is needed to understand how efficiently breeding could be accelerated using screening for genetic markers. This will involve better understanding of the genetic basis of ADB resistance, including further testing of the loci identified by Stocks et al (2019) and investigating the geographic distribution of their alleles. We also need to understand more about the susceptibility of juvenile versus mature trees and how these are correlated.…”