Genetic and Geographic Patterns of Duplicate DPL Genes Causing Genetic Incompatibility Within Rice: Implications for Multiple Domestication Events in Rice

摘要

Strong genetic incompatibilities exist between two primary rice subspecies,indicaandjaponica. However, the wild ancestors of rice,O. nivaraSharma et Shastry andO. rufipogonGriff., are genetically compatible. How this genetic incompatibility became established has not been clearly elucidated. To provide insights into the process, we analyzed a pair of hybrid sterility genes in rice,DOPPELGANGER 1(DPL1) andDOPPELGANGER 2(DPL2). Either of the two loci can have one defective allele (DPL1-andDPL2-). Hybrid pollen carrying bothDPL1-andDPL2-alleles is sterile. To explore the origination ofDPL1-andDPL2-, we sequenced theDPL1andDPL2genes of 811 individual plants, includingOryza sativa(132),O. nivara(296) andO. rufipogon(383). We then obtained 20DPL1and 34DPL2sequences ofO. sativafrom online databases. Using these sequences, we analyzed the genetic and geographic distribution patterns ofDPLgenes in modern rice and its wild ancestors. Compared with the ancestral populations,DPL1-andDPL2-showed reduced diversity but increased frequency in modern rice. We speculated that the diversity reduction was due to a historic genetic bottleneck, and the frequency had likely increased because the defective alleles were preferred following this artificial selection. Such results indicated that standing variances in ancestral lines can lead to severe incompatibilities among descendants. Haplotype analysis indicated that theDPL1-haplotype of rice emerged from anO. nivarapopulation in India, whereas theDPL2-haplotype emerged fromO. rufipogonin South China. Hence, the evolutionary history of DPLs conforms to the presumed multiple domestication events of modern rice.