Unique evolutionary mechanism in R-genes under the presence/absence polymorphism in Arabidopsis thaliana

While the presence/absence polymorphism is commonly observed in disease resistance (R-) genes in Arabidopsis, only a few R-genes under the presence/absence polymorphism (R-P/A) have been investigated. To understand the mechanism of molecular evolution of R-P/A, we investigated genetic variation of nine R-P/A in A. thaliana from worldwide populations. The number of possessed R-genes varied widely among accessions (2-9, on average 4.3±1.6/accession). No pair of accessions shared the same haplotype, and no clear geographic differentiation was observed with respect to the pattern of presence/absence of the R-genes investigated. Presence allele frequencies also varied among loci (25-70%), and no linkage disequilibrium was detected among them. Although the LRR region in regular R-genes is known to be highly polymorphic and has high Ka/Ks ratio in A. thaliana, nucleotide sequences of this region in the R-P/A showed relatively low level of genetic variation = 0.0002-0.016), and low Ka/Ks (0.03-0.70, <1). In contrast, the nucleotide diversities around the deletion junction of R-P/A was constantly high between presence and absence accessions for the R-genes (0.031-0.103, average Dxy = 0.050). Our results suggest that R-P/A loci evolved differently from other R-gene loci, and that balancing selection plays an important role in molecular evolution of R-P/A.

Key Words: Arabidopsis, balancing selection, disease resistance gene, population genetics, presence/absence polymorphism

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