Identification of neutral genes at pollen sterility loci Sd and Se of cultivated rice (Oryza sativa) with wild rice (O. rufipogon) origin

A natural gene drive system confers reproductive isolation in rice

Hybrid sterility restricts the utilization of superior heterosis of indica-japonica inter-subspecific hybrids. In this study, we report the identification of RHS12, a major locus controlling male gamete sterility in indica-japonica hybrid rice. We show that RHS12 consists of two genes (iORF3/DUYAO and iORF4/JIEYAO) that confer preferential transmission of the RHS12-i type male gamete into the progeny, thereby forming a natural gene drive. DUYAO encodes a mitochondrion-targeted protein that interacts with OsCOX11 to trigger cytotoxicity and cell death, whereas JIEYAO encodes a protein that reroutes DUYAO to the autophagosome for degradation via direct physical interaction, thereby detoxifying DUYAO. Evolutionary trajectory analysis reveals that this system likely formed de novo in the AA genome Oryza clade and contributed to reproductive isolation (RI) between different lineages of rice. Our combined results provide mechanistic insights into the genetic basis of RI as well as insights for strategic designs of hybrid rice breeding.

APOK3, a pollen killer antidote in Arabidopsis thaliana

The principles of heredity state that the two alleles carried by a heterozygote are equally transmitted to the progeny. However, genomic regions that escape this rule have been reported in many organisms. It is notably the case of genetic loci referred to as gamete killers, where one allele enhances its transmission by causing the death of the gametes that do not carry it. Gamete killers are of great interest, particularly to understand mechanisms of evolution and speciation. Although being common in plants, only a few, all in rice, have so far been deciphered to the causal genes. Here, we studied a pollen killer found in hybrids between two accessions of Arabidopsis thaliana. Exploring natural variation, we observed this pollen killer in many crosses within the species. Genetic analyses revealed that three genetically linked elements are necessary for pollen killer activity. Using mutants, we showed that this pollen killer works according to a poison-antidote model, where the poison kills pollen grains not producing the antidote. We identified the gene encoding the antidote, a chimeric protein addressed to mitochondria. De novo genomic sequencing in twelve natural variants with different behaviors regarding the pollen killer revealed a hyper variable locus, with important structural variations particularly in killer genotypes, where the antidote gene recently underwent duplications. Our results strongly suggest that the gene has newly evolved within A. thaliana. Finally, we identified in the protein sequence polymorphisms related to its antidote activity.

Comparative study on cytogenetics and transcriptome between diploid and autotetraploid rice hybrids harboring double neutral genes

Double pollen fertility neutral genes, San and Sbn, can control pollen sterility in intersubspecific (indica × japonica) rice hybrids, which has excellent potential to increase rice yield. Previous studies showed that polyploidy could increase the interaction of three pollen sterility loci, i.e. Sa, Sb and Sc, which cause pollen sterility in autotetraploid rice hybrids, and hybrid fertility could be improved by double neutral genes, San and Sbn, in autotetraploid rice hybrids. We compared cytological and transcriptome data between autotetraploid and diploid rice hybrid during meiosis and single microspore stages to understand the molecular mechanism of neutral genes for overcoming pollen sterility in autotetraploid rice hybrids, which harbored double neutral genes. Cytological results revealed that the double neutral genes resulted in higher pollen fertility (76.74%) and lower chromosomal abnormalities in autotetraploid hybrid than in parents during metaphase I, metaphase II, anaphase I and anaphase II. Moreover, autotetraploid rice hybrid displayed stronger heterosis than a diploid hybrid. Compared with diploid rice hybrid, a total of 904 and 68 differently expressed genes (DEGs) were identified explicitly in autotetraploid hybrid at meiosis and single microspore stages, respectively. Of these, 133 and 41 genes were detected in higher-parent dominance and transgressive up-regulation dominance, respectively, which were considered autotetraploid potential heterosis genes, including a meiosis-related gene (Os01g0917500, MSP1) and two meiosis specific-genes (Os07g0624900 and Os04g0208600). Gene Ontology (GO) and Kyoto Encyclopedia of Gene and Genomes pathway (KEGG) analysis revealed that DEGs significantly enriched in amino acid metabolism and photosynthesis metabolism. These results indicated that meiosis-specific and meiosis-related genes, and amino acids and photosynthesis metabolism-related genes contribute to higher yield and pollen fertility in autotetraploid rice hybrid. This study provides a theoretical basis for molecular mechanisms of heterosis in autotetraploid rice harboring double neutral genes for pollen fertility.

Neutral alleles at hybrid sterility loci of Oryza glaberrima from AA genome relatives in Genus Oryza

Hybrid sterility between Oryza sativa and O. glaberrima is a main reproduction barrier when transferring the favorable alleles from O. glaberrima to O. sativa and it happens due to allelic interaction at sterility loci. Neutral alleles at each locus have the potential to overcome the sterility between the two cultivated rice species. In this study, an O. sativa cultivar Dianjingyou 1 (DJY1) and its near-isogenic lines (NILs) harboring the single sterility allele S1-glab, S19-glab, S20-glab, S37-glab, S38-glab and S39-glab as the tested lines were crossed with O. glaberrima, O. rufipogon, O. nivara, O. glumaepatula, O. barthii, O. meridionalis and O. sativa so as to detect the neutral alleles of these loci. Pollen fertility was investigated in the paired F₁s based on two seasons' result and genotypic segregation was also analyzed in some F₂ populations to confirm the results of pollen fertility investigation. The neutral alleles of S38-n and S39-n were identified based upon the pollen fertility and genotypic segregation analysis for the first time. The neutral alleles of sterility loci detected from present report have the potential to know of the nature of interspecific hybrid sterility, and to overcome the interspecific hybrid sterility between O. sativa and O. glaberrima.

Pollen Killer Gene S35 Function Requires Interaction with an Activator That Maps Close to S24, Another Pollen Killer Gene in Rice

Pollen killer genes disable noncarrier pollens, and are responsible for male sterility and segregation distortion in hybrid populations of distantly related plant species. The genetic networks and the molecular mechanisms underlying the pollen killer system remain largely unknown. Two pollen killer genes, S24 and S35, have been found in an intersubspecific cross of Oryza sativa ssp. indica and japonica The effect of S24 is counteracted by an unlinked locus EFS Additionally, S35 has been proposed to interact with S24 to induce pollen sterility. These genetic interactions are suggestive of a single S24-centric genetic pathway (EFS-S24-S35) for the pollen killer system. To examine this hypothetical genetic pathway, the S35 and the S24 regions were further characterized and genetically dissected in this study. Our results indicated that S35 causes pollen sterility independently of both the EFS and S24 genes, but is dependent on a novel gene close to the S24 locus, named incentive for killing pollen (INK). We confirmed the phenotypic effect of the INK gene separately from the S24 gene, and identified the INK locus within an interval of less than 0.6 Mb on rice chromosome 5. This study characterized the genetic effect of the two independent genetic pathways of INK-S35 and EFS-S24 in indica-japonica hybrid progeny. Our results provide clear evidence that hybrid male sterility in rice is caused by several pollen killer networks with multiple factors positively and negatively regulating pollen killer genes.