Evolutionary dynamics and impacts of chromosome regions carrying R-gene clusters in rice.

Mizuno H, Katagiri S, Kanamori H, Mukai Y, Sasaki T, Matsumoto T, Wu J.

Sci Rep. 2020 Jan 21;10(1):872. doi: 10.1038/s41598-020-57729-w.

Abstract

To elucidate R-gene evolution, we compared the genomic compositions and structures of chromosome regions carrying R-gene clusters among cultivated and wild rice species. Map-based sequencing and gene annotation of orthologous genomic regions (1.2 to 1.9 Mb) close to the terminal end of the long arm of rice chromosome 11 revealed R-gene clusters within six cultivated and ancestral wild rice accessions. NBS-LRR R-genes were much more abundant in Asian cultivated rice (O. sativa L.) than in its ancestors, indicating that homologs of functional genes involved in the same pathway likely increase in number because of tandem duplication of chromosomal segments and were selected during cultivation. Phylogenetic analysis using amino acid sequences indicated that homologs of paired Pikm1-Pikm2 (NBS-LRR) genes conferring rice-blast resistance were likely conserved among all cultivated and wild rice species we examined, and the homolog of Xa3/Xa26 (LRR-RLK) conferring bacterial blight resistance was lacking only in Kasalath.

See: https://www.nature.com/articles/s41598-020-57729-w

Figure 2:

Detection of location and distribution pattern of R-genes. On the basis of the positions of DNA markers, the whole R-gene cluster region examined is divided into four subregions, A to D. Arrowheads indicate intact or pseudo NBS-LRR and LRR-RLK genes. Subregion C contains the Pik/Pikm locus responsible for rice blast resistance and subregion D contains the Xa3/Xa26 locus responsible for bacterial blight disease resistance indicated by red arrows. The black arrows grouped by “dup” indicates the unit of segmental duplication. The duplicated gene pairs in opposite directions were circled.