Genetic diversity of NIP genes in Rynchosporium commune in France and genome wide association study of sensitivity to leaf scald in a French winter barley collection grown in the field and in controlled conditions.

Leaf scald in barley ( Hordeum vulgare ) is a foliar disease caused by Rhynchosporium commune . This disease causes leaf necrosis and decreased grain yield and quality. Disease control consists in adapting management practices, using fungicides and resistant varieties. Knowledge of avirulence and resistance genes is crucial to develop resistant varieties and reduce the use of fungicides. This study aimed at characterizing the genetic diversity of NIP genes in R. commune isolates present in France and identifying genomic regions associated to leaf scald resistance. 103 isolates of R. commune from different locations and varieties were sampled. Characterization of NIP diversity for 81 isolates showed 15 haplotypes for NIP1 but only three for NIP2 and two for NIP3 . A panel of 289 winter barley varieties genotyped using the iSelect 50K SNP array was tested in 14 field trials under natural inoculation and against three isolates in controlled conditions. Single environment and GWAS meta-analysis across trials showed 19 QTLs associated to leaf scald resistance. Some regions corresponded to known resistance genes ( Rrs1, Rrs2, Rrs12, Rrs14, Rrs17 ), others colocalized with previously identified QTLs while a few could be new sources of resistance. Most of the regions were largely present in this germplasm although three remained underrepresented. There was a high correlation between the average resistance level and the number of favourable alleles present in the varieties and a genomic prediction model showed good predictive ability for leaf scald resistance.