Liu Yaoguang

Mapping of the rice (Oryza sativa L.) thermo-sensitive genic male sterile gene tms5 with EST and SSR markers

With the cDNA suppression subtraction hybridization method, a spikelet-specific cDNA library was constructed that expressed at meiosis stage in rice. A total of 121 cDNA fragments were selected from the library and used as EST (expressed sequence tags) markers to detect the polymorphism between Annong N, a normal fertile Indica rice line and Annong S-1, its spontaneous mutant with thermo-sensitive genic male sterility, using the RFLP (restriction fragment length polymorphism) technique. HN57, one of the EST probes, could detect polymorphism between them. The results of segregation analysis with the F2 population developed from Annong S-1 and Annong N indicate that HN57 co-segregates with the thermo-sensitive genic male-sterility controlled by tms5, the recessive gene in Annong S-1. This marker is located on the 31.2-cM region of the chromosome 2 of RGP (rice genome research program) genetic map. To further determine the location of tms5, 80 SSR (simple sequence repeat) markers around this region were developed, and 12 of them were polymorphic. And finally, the tms5 was mapped within region of 181 kb by using these new markers.

Discovery, utilization and molecular mechanisms of CMS-WA in rice

The discovery and exploitation of the Wild Abortive type cytoplasmic male sterility (CMS-WA) is a key issue in hybrid rice breeding for utilization of heterosis, which is the best successful case for exploitation of wild plant resources in agriculture. In this review, we traced the history of discovery and research of CMS-WA, and introduced the latest progresses on study of the molecular basis of CMS-WA and its restoration as well as the evolution of the related genes. The Chinese scientist Yuan LongPing pioneered the study of male sterility in rice since 1964. In 1970s, Yuan’s group discovered a male sterile wild rice ( Oryza rufipogon Griff.) plant in Hainan Island of China, and designated this material as “Wild Abortive (WA)”. Genetic study showed that this male sterility is conferred by the cytoplasm, thus is called CMS-WA. Chinese breeders made great efforts to breed CMS lines by introgression of the CMS-WA cytoplasm into a number of rice cultivars via backcrossing. Accordingly, related maintainer lines and restorer lines were bred to successfully develop the “three-line” system for hybrid rice production. The commercial hybrid rice was released in 1976 in China, and has occupied about 50% of the total rice planting area since the late 1980s, which increased grain yield by 20%–30%. In recent years, scientists have made great progress on the molecular studies of CMS-WA and its restoration, and the evolution of the genes for this system. As representative in this field, LIU YaoGuang’s group isolated the CMS-WA gene WA352 from the mitochondrial genome, which is a new gene consisting of multiple mitochondrial genomic segments of unknown function. WA352 is expressed constitutively into three transcripts, but the WA352 protein accumulates specifically in the anther tapetal cells at the microspore mother cell stage, and interacts directly with a nucleus-encoded protein COX11, which is the assembly factor for cytochrome c oxidase and also has a role in scavenge of reactive oxygen species (ROS) and inhibition of programmed cell death (PCD). When WA352 arrests COX11 by the interaction, the metabolism of ROS is affected, leading to ROS burst and cytochrome c release to the cytosol and triggering premature PCD in the tapetum. This abnormal tapetal degeneration eventually causes pollen abortion. Two loci, Rf3 and Rf4 , were mapped on chromosome 1 and 10, respectively, as the restorer genes for CMS-WA. Rf4 was firstly cloned recently by Liu’s group. Rf4 encodes a pentatricopeptide repeat (PPR) protein (PPR9-782-M) possessing a mitochondrial transit signal and 18 PPR motifs, with high similarity to PPR3-791-M encoded by Rf1a of the CMS-BT system. The Rf4 protein decreases the mRNA level of WA352 , thereby restoring WA352 -mediated male sterility probably in a post-transcriptional mechanism. However, Rf3 does not affect the WA352 transcript abundance but impairs the production of WA352 protein. Thus, the studies indicate that plant CMS/restoration systems comprises multiple layers of cytoplasmic-nuclear gene interactions in the molecular level. Recently, LIU’s group further studied the evolutionary trajectory of WA352 by identification and characterization of a number of mitochondrial genomic recombinant structures related to WA352 in the wild rice. These structures originated and evolved through complex evolutionary routes by multiple rearrangements in the mitochondrial genome of O. rufipogon. The study revealed that functional CMS genes originated from non-CMS protogenes by sequence variation-based functionalization as well as substoichiometric shifting (i.e., copy number variation). Finally, this review discussed the key issues and future directions of the hybrid rice breeding programs.

A protocol for CRISPR/Cas9-based multi-gene editing and sequence decoding of mutant sites in plants

Genome editing with CRISPR/Cas9 has become an effective tool for gene functionality dissection and crop improvement. Accordingly, we have developed a CRISPR/Cas9 vector system for robust multi-gene editing in plants. Our inventory includes six versatile binary vectors and 12 intermediary sgRNA vectors with different U3 and U6 promoters, to achieve high efficient multi-gene editing, under specific antibiotic selections in both monocot and dicot plants. Additionally, we also have developed an integrated web-based software toolkit, CRISPR-GE, to facilitate the utilization CRISPR/Cas9 in plants. In this protocol, we provide detailed procedures for using the CRISPR/Cas9 system, including target site selection, construction of CRISPR/Cas9 binary vectors, Sanger-sequencing-based genotyping of mutant sites, and troubleshooting for common problems.