Cytoplasmic male sterility (CMS) has been extensively used for hybrid seed production in many major crops. Honglian CMS (HL-CMS) is one of the three major types of CMS in rice and has contributed greatly to food security worldwide. The HL-CMS trait is associated with an aberrant chimeric mitochondrial transcript, atp6-orfH79, which causes pollen sterility and can be rescued by two nonallelic restorer-offertility (Rf) genes, Rf5 or Rf6. Here, we report the identification of Rf6, which encodes a novel pentatricopeptide repeat (PPR) family protein with a characteristic duplication of PPR motifs 3-5. RF6 is targeted to mitochondria, where it physically associates with hexokinase 6 (OsHXK6) and promotes the processing of the aberrant CMSassociated transcript atp6-orfH79 at nucleotide 1238, which ensures normal pollen development and restores fertility. The duplicated motif 3 of RF6 is essential for RF6-OsHXK6 interactions, processing of the aberrant transcript, and restoration of fertility. Furthermore, reductions in the level of OsHXK6 result in atp6-orfH79 transcript accumulation and male sterility. Together these results reveal a novel mechanism for CMS restoration by which RF6 functions with OsHXK6 to restore HL-CMS fertility. The present study also provides insight into the function of hexokinase 6 in regulating mitochondrial RNA metabolism and may facilitate further exploitation of heterosis in rice.cytoplasmic male sterility | pentatricopeptide repeat | restorer-of-fertility | RF6 | hexokinase 6 P lant cytoplasmic male sterility (CMS) is a trait characterized by a lack of functional pollen grains in plants, although female gametes are still viable (1). CMS has been widely used to produce hybrid seeds to improve plant yield, improve resistance to diseases or stresses, or enhance taste (2). Plant CMS results from genomic incompatibility between mitochondria and nuclei and is typically associated with an aberrant chimeric gene in the mitochondria (3-6). A specific set of nuclear genes called restorer-of-fertility (Rf) genes, which primarily belong to the pentatricopeptide repeat (PPR) family, repress CMS through the promotion of the cleavage, degradation, or editing of CMS-associated aberrant transcripts or the inhibition of the translation of these genes (7-9). PPR proteins regulate RNA metabolism at multiple levels, from RNA editing, stability, processing, and splicing to translation (10, 11). PPR proteins can be classified into PLS and P families based on the structure of PPR motifs (11). PLS family members generally exhibit direct RNA binding (12)(13)(14) or editing activity (15-17), whereas P-family proteins often lack sites for binding to RNA, particularly mitochondrial CMS-related RNA (18,19). Most of the known PPR proteins implicated in restoration of fertility (RF) are P-family members. Thus, RF-related PPR proteins may require additional partners, such as RNA-binding or splicing factors to process CMSrelated transcripts.Rice CMS is categorized into three major types: Wild Abortive (WA), originating from...

BackgroundMost agronomic traits in rice are complex and polygenic. The identification of quantitative trait loci (QTL) for grain length is an important objective of rice genetic research and breeding programs.ResultsHerein, we identified 99 QTL for grain length by GWAS based on approximately 10 million single nucleotide polymorphisms from 504 cultivated rice accessions (Oryza sativa L.), 13 of which were validated by four linkage populations and 92 were new loci for grain length. We scanned the Ho (observed heterozygosity per locus) index of coupled-parents of crosses mapping the same QTL, based on linkage and association mapping, and identified two new genes for grain length. We named this approach as Ho-LAMap. A simulation study of six known genes showed that Ho-LAMap could mine genes rapidly across a wide range of experimental variables using deep-sequencing data. We used Ho-LAMap to clone a new gene, OsLG3, as a positive regulator of grain length, which could improve rice yield without influencing grain quality. Sequencing of the promoter region in 283 rice accessions from a wide geographic range identified four haplotypes that seem to be associated with grain length. Further analysis showed that OsLG3 alleles in the indica and japonica evolved independently from distinct ancestors and low nucleotide diversity of OsLG3 in indica indicated artificial selection. Phylogenetic analysis showed that OsLG3 might have much potential value for improvement of grain length in japonica breeding.ConclusionsThe results demonstrated that Ho-LAMap is a potential approach for gene discovery and OsLG3 is a promising gene to be utilized in genomic assisted breeding for rice cultivar improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12915-017-0365-7) contains supplementary material, which is available to authorized users.

Gnp4/LAX2 interferes with the OsIAA3–OsARF25 interaction to activate the expression of OsERF142/SMOS1, and hence regulates grain length in rice.

The pentatricopeptide repeat (PPR) protein family is a large family characterized by tandem arrays of a degenerate 35-amino-acid motif whose members function as important regulators of organelle gene expression at the post-transcriptional level. Despite the roles of PPRs in RNA editing in organelles, their editing activities and the underlying mechanism remain obscure. Here, we show that a novel DYW motif-containing PPR protein, PPS1, is associated with five conserved RNA-editing sites of nad3 located in close proximity to each other in mitochondria, all of which involve conversion from proline to leucine in rice. Both pps1 RNAi and heterozygous plants are characterized by delayed development and partial pollen sterility at vegetative stages and reproductive stage. RNA electrophoresis mobility shift assays (REMSAs) and reciprocal competition assays using different versions of nad3 probes confirm that PPS1 can bind to cis-elements near the five affected sites, which is distinct from the existing mode of PPR-RNA binding because of the continuity of the editing sites. Loss of editing at nad3 in pps1 reduces the activity of several complexes in the mitochondrial electron transport chain and affects mitochondrial morphology. Taken together, our results indicate that PPS1 is required for specific editing sites in nad3 in rice.