Viruses are responsible for some of the most important crop diseases. However, few resistance genes from major crops are cloned and the knowledge about virus resistance mechanisms is insufficient. One of the most important pathogens of rice in Africa is the Rice yellow mottle virus (RYMV), while in Europe, Barley yellow dwarf virus (BYDV), transmitted by aphids, and soil-borne Barley yellow mosaic virus (BaYMV) and Barley mild mosaic virus (BaMMV), transmitted by Polymyxa graminis, are of prime importance in barley.
In the Asian rice species Oryza sativa, resistance to RYMV is utterly rare. Combining gene mapping, allele mapping, and GWAS in the African species Oryza glaberrima, we uncovered three major resistance genes, totalizing ten different resistance alleles, as well as partial resistance QTLs.
In barley, to date, only two genes providing resistance to BaYMV/BaMMV, and none to BYDV, have been cloned. Crop wild relatives broaden the genetic basis of resistance and can allow to find additional resistance genes and get closer to achieve durable protection of the crop. We mapped two dominant resistance genes to BaMMV/BaYMV and BYDV from the barley wild relative Hordeum bulbosum. Recombination in crosses between barley and H. bulbosum are scarce. However, using recent high-throughput genotyping methods, screening of very large populations is now possible. Rym14Hb confers resistance against BaMMV/BaYMV. Using GBS genotyping of 427 F5 plant and fine mapping in a population of 8,000 F2 plants, we achieved to set its interval to 2 Mb, despite its location in a telomeric region. The second gene, Ryd4Hb, provides resistance to BYDV. We screened around 16,000 F2 plants, and fine-mapped the gene in a 67 kb interval on the barley reference genome. The analysis of the orthologous interval in the ten accessions part of barley pangenome, as well as the genome assembly of the Ryd4Hb donor introgression line, showed a very large variability of this interval, including duplication of NLR genes. Ongoing work includes CRISPR-Cas9 knock-out of the four candidate NLR genes in the Ryd4Hb donor introgression line, as well as the study of genetic variation at this locus in Triticeae diversity.