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Originally published as Genetics Published Articles Ahead of Print on February 1, 2006.
Genetics, Vol. 172, 1243-1250, February 2006, Copyright © 2006
doi:10.1534/genetics.105.047290
Unique Evolutionary Mechanism in R-Genes Under the Presence/Absence Polymorphism in Arabidopsis thaliana
Jingdan Shen*,1,
Hitoshi Araki
,1,
Lingling Chen*,
Jian-Qun Chen* and
Dacheng Tian*,2
* State Key Laboratory of Pharmaceutical Biotechnology, Department of Biology, Nanjing University, Nanjing 210093, China and Department of Zoology, Oregon State University, Corvallis, Oregon 97331
2 Corresponding author: Department of Biology, Nanjing University, 22 Hankou Rd., Nanjing 210093, China.
E-mail: dtian{at}nju.edu.cn
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 the 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 (two to nine, 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 a high Ka/Ks ratio in A. thaliana, nucleotide sequences of this region in the R-P/A showed a 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 were constantly high between presence and absence accessions for the R-genes (Dxy = 0.031–0.103). 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.
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