Theor Appl Genet (2011) 122:385–394 DOI 10.1007/s00122-010-1454-y 123 ORIGINAL PAPER Independent evolution of a new allele of F 1 pollen sterility gene S27 encoding mitochondrial ribosomal protein L27 in Oryza nivara Khin Thanda Win · Yoshiyuki Yamagata · Yuta Miyazaki · Kazuyuki Doi · Hideshi Yasui · Atsushi Yoshimura Received: 12 June 2010 / Accepted: 8 September 2010 / Published online: 28 September 2010  Springer-Verlag 2010 Abstract Loss of function of duplicated genes plays an important role in the evolution of postzygotic reproductive isolation. The widespread occurrence of gene duplication followed by rapid loss of function of some of the duplicate gene copies suggests the independent evolution of loss-of- function alleles of duplicate genes in divergent lineages of speciation. Here, we found a novel loss-of-function allele of S27 in the Asian annual wild species Oryza nivara, des- ignated S27-niv s , that leads to F 1 pollen sterility in a cross between O. sativa and O. nivara. Genetic linkage analysis and complementation analysis demonstrated that S27-niv s lies at the same locus as the previously identiWed S27 locus and S27-niv s is a loss-of-function allele of S27. S27-niv s is composed of two tandem mitochondrial ribosomal protein L27 genes (mtRPL27a and mtRPL27b), both of which are inactive. The coding and promoter regions of S27-niv s showed a number of nucleotide diVerences from the functional S27-T65 + allele. The structure of S27-niv s is diVerent from that of a previously identi Wed null S27 allele, S27-glum s , in the South American wild rice species O. glumaepatula, in which mtRPL27a and mtRPL27b are absent. These results show that the mechanisms for loss-of-function of S27-niv s and S27-glum s are diVerent. Our results provide experimental evidence that diVerent types of loss-of-function alleles are distributed in geographically and phylogenetically isolated species and represent a potential mechanism for postzygotic isolation in divergent species. Introduction Gene duplication provides opportunities to increase gene diversity during evolution. Because the original function supplied from one gene copy allows the other copy to escape elimination through selection, duplicate genes allow the accumulation of mutations that introduce a new func- tion (neo-functionalization), divide the original function (sub-functionalization), or cause loss of function (non-func- tionalization) (Lynch and Force 2000). Recent studies have demonstrated that duplicate genes contribute to reproduc- tive isolation, which generally prevents gene Xow between species, and they play an important role in plant speciation (Rieseberg and Willis 2007). For example, the neo-func- tionalized duplicate gene Odysseus-site Homeobox (OdsH) causes postzygotic reproductive isolation in Drosophila (Sun et al. 2004). Similarly, non-functionalization has con- tributed to a passive type of postzygotic reproductive isola- tion through reciprocal loss of duplicate genes between two divergent species; when this occurs, selection against hybrids may occur in either a sporophytic (zygotic) or gametophytic (gametic) manner (Bikard et al. 2009; Yamagata et al. 2010). Genome-wide analysis has shown a very high rate of gene duplication and a rapid loss of most duplicate genes within a few million years (Lynch and Communicated by E. Guiderdoni. Electronic supplementary material The online version of this article (doi:10.1007/s00122-010-1454-y) contains supplementary material, which is available to authorized users. K. T. Win · Y. Yamagata · Y. Miyazaki · K. Doi · H. Yasui · A. Yoshimura (&) Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka 812-8581, Japan e-mail: ayoshi@agr.kyushu-u.ac.jp Present Address: K. Doi Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya 464-8601, Japan