Functional and Evolutionary Analysis of the Pi2/9 Locus in Rice
The Pi2/9 locus has been extensively used for effective resistance to the devastating rice blast disease caused by the fungus Magnaporthe oryza in rice breeding program for long time. This locus has been found to harbor at least 6 resistance genes [Pi9, Pi2, Piz-t, Piz, Pigm(t), and Pi40(t)], which confer broad-spectrum resistance against different sets of M. oryzae isolates. We have successfully characterized three of them (Pi9, Pi2, and Piz-t) using multi-faceted approaches. All the three genes encode proteins with a nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domain and belong to a member of a gene cluster comprising of multiple gene members in each resistant cultivar. All the three resistance genes share extreme sequence similarity to each other while the LRR domains possess most of their sequence variants. Strikingly, the total eight amino acid differences that distinguish the Pi2 from the Piz-t were exclusively confined within three consecutive LRRs, indicating that the LRR domain plays a major role in determination of their resistance specificities. Intra- and inter-haplotype analysis of the Pi2/9 locus from 5 different rice haplotypes revealed that an obvious orthologous relationship had been maintained at the Pi2/9 locus among haplotypes. The paralogues, contrariwise, show significant sequence divergence within each haplotype. However, the finding that all the NBS-LRR homologues at the Pi2/9 locus utilize the same intron phase 2 suggested that the Pi2/9 locus might be evolved from a progenitor locus that was consisted of a single NBS-LRR gene with the same intron phase. The cloning of the three resistance genes and evolutionary analysis of the Pi2/9 locus provided insight into the understanding of the mechanism underlying the broad-spectrum resistance and its evolution.
KeywordsResistance genes Evolution Oryza sativa Gene cluster
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