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Functional divergence of duplicated genes results in a novel blast resistance gene Pi50 at the Pi2/9 locus

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Abstract

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We characterized a novel blast resistance gene Pi50 at the Pi2/9 locus; Pi50 is derived from functional divergence of duplicated genes. The unique features of Pi50 should facilitate its use in rice breeding and improve our understanding of the evolution of resistance specificities.

Abstract

Rice blast disease, caused by the fungal pathogen Magnaporthe oryzae, poses constant, major threats to stable rice production worldwide. The deployment of broad-spectrum resistance (R) genes provides the most effective and economical means for disease control. In this study, we characterize the broad-spectrum R gene Pi50 at the Pi2/9 locus, which is embedded within a tandem cluster of 12 genes encoding proteins with nucleotide-binding site and leucine-rich repeat (NBS–LRR) domains. In contrast with other Pi2/9 locus, the Pi50 cluster contains four duplicated genes (Pi50_NBS4_1 to 4) with extremely high nucleotide sequence similarity. Moreover, these duplicated genes encode two kinds of proteins (Pi50_NBS4_1/2 and Pi50_NBS4_3/4) that differ by four amino acids. Complementation tests and resistance spectrum analyses revealed that Pi50_NBS4_1/2, not Pi50_NBS4_3/4, control the novel resistance specificity as observed in the Pi50 near isogenic line, NIL-e1. Pi50 shares greater than 96 % amino acid sequence identity with each of three other R proteins, i.e., Pi9, Piz-t, and Pi2, and has amino acid changes predominantly within the LRR region. The identification of Pi50 with its novel resistance specificity will facilitate the dissection of mechanisms behind the divergence and evolution of different resistance specificities at the Pi2/9 locus.

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Acknowledgments

We thank Y. L. Peng and S. Q. Wu for providing rice blast isolates. This research is supported by grants from the National Transgenic Research Projects (2014ZX0800904B), the National Natural Science Foundation (31301304, 31461143019), the Guangzhou sciences and technology project (2012J2200066, 2012J4300059), Earmarked Fund for Modern Agro-Industry Technology Research System (CARS-01-24).

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  1. Jingluan Han

    Present address: College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China

Authors and Affiliations

  1. Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, China

    Jing Su, Wenjuan Wang, Jingluan Han, Shen Chen, Congying Wang, Liexian Zeng, Aiqing Feng, Jianyuan Yang & Xiaoyuan Zhu

  2. Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, 1031, Metro Manila, Philippines

    Bo Zhou

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Communicated by M. Thomson.

J. Su and W. Wang contributed equally to this work.

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122_2015_2579_MOESM1_ESM.pdf

Supplementary Fig. S1 Pairwise comparison of Pi50_NBS4_1 respectively with Pi50_NBS4_3 (top panel) and Pi50_NBS2 (lower panel). The sequence alignment was conducted using BLAST2 (http://www.ncbi.nlm.nih.gov) and the graphic summary was captured in scale. The sequence of Pi50_NBS4_1 was used as the subject for each comparison. The promoter/exon/intron are indicated corresponding to their positions

122_2015_2579_MOESM2_ESM.pdf

Supplementary Fig. S2 Overall good synteny with respect to gene order and composition between the Pi2 and Pi50 loci. The X-axis displays the genomic context of NBS–LRR genes at the Pi50 locus and the Y-axis displays the one at the Pi2 locus. The pseudomolecule of the Pi50 locus is composed of three fragments, i.e., the NIP side (GenBank accession no. KP985759), the central genomic block (GenBank accession no. KP985761), and the PK side (GenBank accession no. KP985760) was compared to the sequence of the Pi2 locus (GenBank accession no. DQ352453) using BLAST2. Nine orthologous groups (Pi50_NBS1-4, Pi50_NBS8-12) each indicated in different colors are named only for the Pi50 locus as an example. (PDF 54 kb)

122_2015_2579_MOESM3_ESM.pdf

Supplementary Fig. S3 Phylogenetic analysis of different NBS–LRR genes at the Pi2/9 locus. Pi2_NBS4, Pi9_NBS3, and Piz-t_NBS4 correspond to functional genes Pi2, Pi9, and Piz-t respectively. The Pi2/9 homologues in Nipponbare were named with the clone name AP005659. The tree was constructed using a neighbor-joining algorithm based on the predicted full-length sequence of proteins. Numbers on the branches indicate the percentage of 1000 bootstrap replicates. The unit branch length is equivalent to 0.1 amino acid substitutions per site, as indicated by the bar at the upper left corner. (PDF 24 kb) (PDF 13 kb)

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Su, J., Wang, W., Han, J. et al. Functional divergence of duplicated genes results in a novel blast resistance gene Pi50 at the Pi2/9 locus. Theor Appl Genet 128, 2213–2225 (2015). https://doi.org/10.1007/s00122-015-2579-9

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