Mining Rice Disease Resistance Genes Using Gramene

Disease pathogens severely impact rice production and pose an increasing threat as climate change impacts pest range. Breeding for natural resistance is a proven strategy but limited by sources of variation. Wild relatives of rice, collected from around the world, provide an untapped reservoir of resistance genes. Taking advantage of an 11-species genome set in Gramene (www.gramene.org) that spans the Oryzeae tribe, we discovered over 4500 NLR (nucleotide-binding domain and leucine-rich repeat containing) genes in 28 families. Rapid diversification of complex haplotypes by gene expansion and loss is typical of NLR genes, contributing to disease adaptation. Summing over the 28 NLR families in the Compara database, we found a 10-fold increase in duplication rates in lineages leading to both Asian and African cultivated rice, consistent with selection for resistance traits prior to domestication. Most NLR were positionally clustered, often forming complex arrangements of distantly related genes. Yet, clear orthologous relationships and evidence of conserved underlying haplotype structures could be drawn, even among more distantly related species. Adjacent heterogeneous pairs, with head-to-head arrangement, showed a disproportionate prevalence, conservation, and association with putative integrated decoy domains, suggesting function as coupled NLR gene pairs. Striking variation in domain structure suggests that swapping of various decoy domains contributes to the evolution of haplotype diversity and resistance specificity. This study has opened a treasure trove of potentially novel resistance functions that may help in the future development and sustainability of rice. Funded by NSF awards #1026200 and #1127112.