Long-read sequencing reveals the allelic diversity of the self-incompatibility gene across natural populations inPetunia(Solanaceae)

Abstract

AbstractSelf-incompatibility (SI) is a genetic mechanism to prevent self-fertilization and thereby promote outcrossing in hermaphroditic plant species through discrimination of self and non-self pollen by pistils. In many SI systems, recognition between pollen and pistils is controlled by a single multiallelic locus (calledS-locus), in which numbers of alleles (calledS-alleles) are segregating. Because of the extreme level of polymorphism of theS-locus, identifications ofS-alleles have been a major issue in many SI studies for decades. Here we report an RNA-seq-based method to explore allelic diversity of theS-locus by employing the long-read sequencing technology of the Oxford Nanopore MinION, and applied it for the gametophytic SI system ofPetunia(Solanaceae), in which the female determinant is a secreted ribonuclease called S-RNase that inhibits the elongation of self-pollen tubes by degrading RNA. We developed a method to identifyS-alleles by the search ofS-RNasesequences, using the previously reported sequences as queries, and found in total 62 types ofS-RNaseincluding 45 novel types. We validated this method through Sanger sequencing and crossing experiments, confirming the sequencing accuracy and SI phenotypes corresponding to genotypes. Then, using the obtained sequence data together with PCR-based genotyping in a larger sample set of 187 plants, we investigated the diversity, frequency, and the level of shared polymorphism ofS-alleles across populations and species. The method as well as the dataset obtained inPetuniawill be an important basis for further studying the evolution of S-RNase-based gametophytic SI systems in natural populations.Significance statementFlowering plants have evolved molecular mechanisms called self-incompatibility (SI) for discriminating self and non-self pollen at pistils to prevent self-fertilization, which is often deleterious due to inbreeding depression. The specificity of SI is usually determined by numbers of highly divergent alleles (calledS-alleles) segregating at a single locus, and identifications ofS-alleles have been a major issue in many SI systems. Here we report a new method to identifyS-alleles by employing a long-read sequencing technology and applied it for the gametophytic SI system ofPetunia, identifying 62 types ofS-alleles including 45 novel types. The method as well as the dataset obtained in this study will be an important basis for the research of SI evolution.