Genetic analysis of GEFs and GDIs in rice reveals the roles of OsGEF5,OsGDI1,and OsGEF3 in the regulation of grain size and plant height

Guanine nucleotide exchange factors(GEFs)and guanine nucleotide-dissociation inhibitors(GDIs)regulate small GTPase proteins,which function as molecular switches in various signaling pathways,but their identification and functions in plants are not well understood.Using in-silico analysis and transgenic approaches,respectively,we dissected the evolutionary relationships and functions of all GEF and GDI genes in rice.Intron-exon distribution and phylogenetic analyses identified 30 GEF and 10 GDI genes in rice that shared close evolutionary relationships with other eukaryotes.Tissue-specific expression and co-expression analyses revealed that phylogenetically related genes had similar expression patterns.GEF and GDI genes were highly expressed in panicles,hulls,and stamens.Co-expression network analysis identified panicle and stamen-specific modules of co-expressed genes in both families.Mapping of these genes in known protein interactomes further identified two and one small G-protein sub-networks.A mutant library of GEF and GDI families was constructed by CRISPR knockout of each gene,and their genotypes and phenotypes were confirmed.Phenotype changes occurred with the mutation of only three genes(OsGEF5,OsGDI1,and OsGEF3).OsGEF5 and OsGDI1 single mutants exhibited significantly reduced height and longer and thinner grains,whereas OsGEF3 mutants had reduced grain length compared to the wild type.Haplotype and eGWAS analyses showed that natural variations in the three genes affected gene expression in reproductive tissues that were significantly associated with the phenotypic variation.BiFC assays demonstrated that GDI1 and GEF3 interacted with grain-size protein GS3,pointing to a role of these genes in the regulation of grain size and plant architecture connected to heterotrimeric G-proteins in rice.

Improving the resistance of the rice PTGMS line Feng39S by pyramiding blast,bacterial blight,and brown planthopper resistance genes

Knowledge of rice(Oryza sativa L.)genes and various DNA markers can be used in genomic breeding programs aimed at developing improved elite rice cultivars.We used an efficient genomic breeding approach to pyramid four resistance genes(Pi2,Xa23,Bph14,and Bph15)in the popular photoperiod-and thermosensitive genic male sterile(PTGMS)rice line Feng39S.We performed foreground selection for the target genes,followed by recombinant selection and background selection.This process reduced the sizes of the genomic segments harboring the target genes(566.8 kb for Pi2,1143.9 kb for Xa23,774.7 kb for Bph14,and 1574.9 kb for Bph15)and accelerated the recovery of the recurrent parent genome to proportions ranging from 98.77%to 99.16%,thus resulting in four near-isogenic lines.To assemble the four resistance genes in Feng39S,we performed a double-way cross combined with foreground and background selection to generate two improved lines of Feng39S(Pi2+Xa23+Bph14+Bph15)with a recurrent parent genome recovery of 98.98%.The two lines showed agronomic performance,grain quality,and fertility–sterility transition characteristics similar to those of the original Feng39S line.The newly developed PTGMS lines and corresponding hybrid combinations were resistant to various field blast isolates and seven representative isolates of bacterial blight.At the seedling stage,the lines also showed resistance against brown planthopper.This study provides an efficient and accurate genomic breeding approach for introducing desirable traits into PTGMS lines.

Genetic architecture and key genes controlling the diversity of oil composition in rice grains

Rice grain oil is a valuable nutrient source.However,the genetic basis of oil biosynthesis in rice grains remains unclear.In this study,we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice accessions.High variation for 11 oil-related traits was observed,and the oil composition of rice grains showed differentiation among the subpopulations.We identified 46 loci that are significantly associated with grain oil concentration or composition,16 of which were detected in three recombinant inbred line populations.Twenty-six candidate genes encoding enzymes involved in oil metabolism were identified from these 46 loci,four of which(PAL6,LIN6,MYR2,and ARA6)were found to contribute to natural variation in oil composition and to show differentiation among the subpopulations.Interestingly,population genetic analyses revealed that specific haplotypes of PAL6 and LIN6 have been selected in japonica rice.Based on these results,we propose a possible oil biosynthetic pathway in rice grains.Collectively,our results provide new insights into the genetic basis of oil biosynthesis in rice grains and can facilitate marker-based breeding of rice varieties with enhanced oil and grain quality.

Understanding the genetic and molecular constitutions of heterosis for developing hybrid rice

The wide adoption of hybrid rice has greatly increased rice yield in the last several decades.The utilization of heterosis facilitated by male sterility has been a common strategy for hybrid rice development.Here,we summarize our efforts in the genetic and molecular understanding of heterosis and male sterility together with the related progress from other research groups.Analyses of F1 diallel crosses show that strong heterosis widely exists in hybrids of diverse germplasms,and inter-subspecific hybrids often display higher heterosis.Using the elite hybrid Shanyou 63 as a model,an immortalized F2 population design is conducted for systematic characterization of the biological mechanism of heterosis,with identification of loci controlling heterosis of yield and yield component traits.Dominance,overdominance,and epistasis all play important roles in the genetic basis of heterosis;quantitative assessment of these components well addressed the three classical genetic hypotheses for heterosis.Environment-sensitive genic male sterility(EGMS)enables the development of two-line hybrids,and long noncoding RNAs often function as regulators of EGMS.Inter-subspecific hybrids show greatly reduced fertility;the identification and molecular characterization of hybrid sterility genes offer strategies for overcoming inter-subspecific hybrid sterility.These developments have significant implications for future hybrid rice improvement using genomic breeding.

Genome-wide Association Analyses Reveal the Genetic Basis of Stigma Exsertion in Rice

Stigma exsertion, a key determinant of the rice mating system, greatly contributes to the application of heterosis in rice. Although a few quantitative trait loci associated with stigma exsertion have been fine map- ped or cloned, the underlying genetic architecture remains unclear. We performed a genome-wide associ- ation study on stigma exsertion and related floral traits using 6.5 million SNPs characterized in 533 diverse accessions of Oryza sativa. We identified 23 genomic loci that are significantly associated with stigma exsertion and related traits, three of which are co-localized with three major grain size genes GS3, GW5, and GW2. Further analyses indicated that these three genes affected the stigma exsertion by controlling the size and shape of the spikelet and stigma. Combinations of GS3 and GW5 largely defined the levels of stigma exsertion and related traits. Selections of these two genes resulted in specific distributions of floral traits among subpopulations of O. sativa. The low stigma exsertion combination gw5GS3 existed in half of the cultivated rice varieties; therefore, introducing the GW5gs3 combination into male sterile lines is of high potential for improving the seed production of hybrid rice.

The molecular and evolutionary basis of reproductive isolation in plants

Reproductive isolation is defined as processes that prevent individuals of different populations from mating, survival or producing fertile offspring. Reproductive isolation is critical for driving speciation and maintaining species identity, which has been a fundamental concern in evolutionary biology. In plants,reproductive isolation can be divided into prezygotic and postzygotic reproductive barriers, according to its occurrence at different developmental stages. Postzygotic reproductive isolation caused by reduced fitness in hybrids is frequently observed in plants, which hinders gene flow between divergent populations and has substantial effects on genetic differentiation and speciation, and thus is a major obstacle for utilization of heterosis in hybrid crops. During the past decade, China has made tremendous progress in molecular and evolutionary basis of prezygotic and postzygotic reproductive barriers in plants. Present understandings in reproductive isolation especially with new data in the last several years well support three evolutionary genetic models, which represent a general mechanism underlying genomic differentiation and speciation. The updated understanding will offer new approaches for the development of wide-compatibility or neutral varieties, which facilitate breeding of hybrid rice as well as other hybrid crops.

Advances in the understanding of inter-subspecific hybrid sterility and wide-compatibility in rice

Hybrid sterility is a major form of postzygotic reproductive isolation and frequently occurs in hybrids between divergent populations, such as the indica and japonica subspecies of Asian cultivated rice (Oryza sativa L.). It has been a major barrier for utilization of the strong heterosis expressed in hybrids between indica and japonica. A large number of loci for rice inter-subspecific hybrid sterility have been identified by genetic analysis. Cytological studies revealed that male and female gamete abortions and reduced affinity between the uniting gametes all occurred in indica-japonica hybrids, suggesting the complexity of the causes for inter-subspecific hybrid sterility. Two genes conditioning embryo-sac and pollen sterility respectively in indica-japonica hybrids have been cloned recently, providing opportunities for molecular characterization of the indica-japonica hybrid sterility and wide-compatibility. Future studies should aim at cloning more genes for indica-japonica hybrid sterility, characterizing the underlying molecular mechanism, and utilization of the findings for the development of inter-subspecific hybrids to increase rice productivity.

The origin of Wx^(la) provides new insights into the improvement of grain quality in rice

Appearance and taste are important factors in rice(Oryza sativa) grain quality. Here, we investigated the taste scores and related eating-quality traits of533 diverse cultivars to assess the relationships between—and genetic basis of—rice taste and eating-quality. A genome-wide association study highlighted the Wx gene as the major factor underlying variation in taste and eating quality. Notably, a novel waxy(Wx) allele, Wx^(la), which combined two mutations from Wx^(b) and Wx^(in), exhibited a unique phenotype. Reduced GBSSI activity conferred Wx^(la) rice with both a transparent appearance and good eating quality. Haplotype analysis revealed that Wx^(la) was derived from intragenic recombination. In fact,the recombination rate at the Wx locus was estimated to be 3.34 kb/c M, which was about 75-fold higher than the genome-wide mean, indicating that intragenic recombination is a major force driving diversity at the Wx locus. Based on our results, we propose a new network for Wx evolution, noting that new Wx alleles could easily be generated by crossing genotypes with different Wx alleles. This study thus provides insights into the evolution of the Wx locus and facilitates molecular breeding for quality in rice.

Recurrent breakdown and rebalance of segregation distortion in the genomes: battle for the transmission advantage

Mendel’s laws state that each of the two alleles would segregate during gamete formation and show the same transmission ratio in the next generation.However,an unexpected biased allele transmission was first detected in Drosophila a century ago,and was subsequently observed in other animals,plants,and microorganisms.Such segregation distortion(SD)shows substantial effects in population structure and fitness of the progenies,which would ultimately lead to reproductive isolation and speciation.Here,we trace the early investigations on the violation of Mendelian genetic principle,which appears as a wideexistence phenomenon rather than a case of exception.The occurence of SD in the whole genome was observed in a number of plant species at the single-and multi-locus level.Biased transmission ratio might occur at meiosis stage due to asymmetric movement of the chromosome;transmission ratio advantage is also caused by interaction and battle between the alleles from respective genomes at the genetic and molecular level.The origin of a SD system is likely to be determined by coevolution of the killer and protector via recurrent breakdown or rebalance loop.These updated understandings also promote genetic improvement of hybrid crops.

Origination and Establishment of a Trigenic Reproductive Isolation System in Rice

Dear Editor,Reproductive isolation is both the indicator and a primary force of speciation, and plays a key role in maintaining species identity. Understanding the origin and mechanisms of reproductive isola- tion is of fundamental importance in evolutionary biology. In recent years, a number of genes that induce reproductive barriers have been identified in several model organisms such as Drosophila, rodents, yeast, Arabidopsis.

Genome-wide dissection of segregation distortion using multiple inter-subspecific crosses in rice

Mendelian inheritance can ensure equal segregation of alleles from parents to offspring, which provides fundamental basis for genetics and molecular biology. Segregation distortion(SD) leads to preferential transmission of certain alleles from generation to generation. Such violation of Mendelian genetic principle is often accompanied by reproductive isolation and eventually speciation. Although SD is observed in a wide range of species from plants to animals, genome-wide dissection of such biased transmission of gametes is rare. Using nine inter-subspecific rice crosses, a genome-wide screen for SD loci is performed, which reveals 61 single-locus quantitative trait loci and 194 digenic interactions showing distorted transmission ratio, among which 24 new SD loci are identified. Biased transmission of alleles is observed in all nine crosses, suggesting that SD exists extensively in rice populations. 72.13% distorted regions are repeatedly detected in multiple populations, and the most prevalent SD hotspot that observed in eight populations is mapped to chromosome 3. Xian alleles are transmitted at higher frequencies than geng alleles in inter-subspecific crosses, which change the genetic composition of the rice populations. Epistatic interaction contributes significantly to the deviation of Mendelian segregation at the whole-genome level in rice, which is distinct from that in animals. These results provide an extensive archive for investigating the genetic basis of SD in rice, which have significant implications in understanding the reproductive isolation and formation of inter-subspecific barriers during the evolution.

Engineering Introns to Express RNA Guides for Cas9- and Cpfl-Mediated Multiplex Genome Editing

The clustered regularly interspaced short palindromic repeat （CRISPR） system has emerged as the revolu- tionary platform for DNA targeting. This system uses a site-specific RNA guide to direct a CRISPR effector （e.g., Cas9 and Cpfl） to a DNA target. Here, we elaborate a general strategy to simultaneously express multiple guide RNAs （gRNA） and CRISPR RNAs （crRNA） from introns of Cas9 and Cpfl. This method utilizes the endogenous tRNA processing system or crRNA processing activity of Cpfl to cleave the spliced intron that contains tRNA-gRNA polycistron or crRNA-crRNA array. We demonstrated that the tRNA-gRNA intron is able to fuse with Cas9 as one gene. Such a hybrid gene could be expressed using one polymerase II promoter, and exhibited high efficiency and robustness in simultaneously targeting multiple sites. We also implemented this strategy in Cpfl-mediated genome editing using intronic tRNA-crRNA and crRNA-crRNA arrays. Interestingly, hybrid genes containing Cpfl and intronic crRNA array exhibited remarkably increased efficiency compared with the conventional Cpfl vectors. Taken together, this study presents a method to express CRISPR reagents from one hybrid gene to increase genome-editing efficiency and capacity. Owing to its simplicity and versatility, this method could be broadly used to develop sophisticated CRISPR tools in eukaryotes.

Artificial Selection in Domestication and Breeding Prevents Speciation in Rice

Speciation has long been regarded as an irreversible process once the reproductive barriers had been established.However,unlike in natural populations,artificial selection might either accelerate or prevent speciation processes in domesticated species.Asian cultivated rice is a target crop for both domestication and artificial breeding;it contains two subspecies of indica and japonica,which usually produce sterile inter-subspecific hybrids due to reproductive barriers.In this study,we constructed the evolutionary trajectory of a reproductive isolation system S5,which regulates fertility in indica-japonica hybrids via three adjacent genes,based on the data of 606 accessions including two cultivated and 11 wild rice species.Although hybrid sterility haplotypes at S5 lead to establishment of a killer-protector reproductive barrier,origin of wide-compatibility haplotypes by complex hybridization and recombination provides an opposing force to reproductive isolation and thus prevents speciation during domestication.Analysis in a diallel set of 209 crosses involving 21 parents showed that the wide-compatibility genotypes largely rescued fertility of indica-japonica hybrids,indicating that the wide-compatibility gene would enable gene flow to maintain species coherence.This counteracting system indicates that combined effects of natural evolution and artificial selection may result in reversible processes of speciation in rice,which may also have implications for genetic improvement of rice.

Understanding and breaking down the reproductive barrier between Asian and African cultivated rice: a new start for hybrid rice breeding

Oryza sativa and O.glaberrima,commonly known as Asian and African cultivated rice,are two domesticated rice species in Oryza genus.Asian cultivated rice may produce higher yields with better quality,whereas African cultivated rice shows a wide range of tolerance to abiotic and biotic stresses.Interspecific hybrids between O.sativa and O.glaberrima would show strong heterosis and thus increasing production because of their distant genetic diversity and complementary agronomic traits.However,reduced fertility is observed in hybrids from interspecific crosses;this hinders further utilization of rice heterosis in agriculture production.Such severe abnormal development of gametophytes in hybrids is caused by reproductive isolation,a process that prevents individuals of genetically diverged groups from mating,survival or producing fertile offspring.

minimal genome design to maximally guarantee fertile inter-subspecific hybrid rice

Hybrid rice has made considerable contributions to achieve the ambitious goal of food security for the world's population.Hybrid rice from indica/xian and japonica/geng subspecies shows much higher heter-osis and is thereby an important innovation in promoting rice production in the next decade.However,such inter-subspecific hybrid rice has long suffered from serious hybrid sterility,which is a major challenge that needs to be addressed.In this study,we performed a genome design strategy to produce fertile inter-subspecific hybrid by creation of wide compatibility varieties that are able to overcome hybrid sterility.Based on combined genetic analyses in two indica-japonica crosses,we determined that four hybrid ste-rility loci,S5,f5,pf12 and Sc,are the major QTLs controlling inter-subspecific hybrid sterility and thus the minimal targets that can be manipulated for breeding sub-specific hybrid rice.We then cloned the pf12 lo-cus,one of the most effective loci for hybrid male sterility,by map-based cloning,and showed that artificial disruption of pf12A gene at this locus could successfully rescue hybrid fertility.We further dissected the genetic basis of wide compatibility using three pairwise crosses from a wide-compatibility variety Dular and representative indica and japonica varieties.On this basis,we constructed and assembled different combinations of naturally compatible alleles of four loci,S5,Sc,pf12,and f5,and found that the improved lines could fully recover pollen and embryo sac fertility in test-crossed F,s,thereby completely fulfilling the demands of inter-subspecific hybrid spikelet fertility in agricultural production.This breeding scheme would facilitate redesign of future inter-subspecific hybrid rice with a higher yield potential.

The Os14-3-3 family genes regulate grain size in rice

Rice is one of the most important cereal crops in the world,providing food for more than half of the global population;therefore,increasing grain yield is a major goal of rice breeding.Rice grain yield is largely dependent on grain size,which is specified by its three dimensions(grain length,width,and thickness)and by the degree of grain filling(Xing and Zhang,2010;Fan and Li,2019).Grain size is an important agronomic trait for stable yield,appearance,milling quality,and domestication in rice that is controlled by multiple genes.Thus,discovering more genes regulating grain size for understanding the regulatory mechanisms underlying natural variations is important in crop molecular breeding(Zuo and Li,2014).

RNA-Directed DNA Methylation Is Involved in Regulating Photoperiod-Sensitive Male Sterility in Rice

Photoperiod-sensitive male sterility （PSMS） is a valuable germplasm for hybrid rice breeding. Recently, we cloned pros3, a locus controlling PSMS, which encodes a long non-coding RNA called LDMAR required for normal male fertility of the rice plant under long-day conditions. Increased methylation in the promoter of LDMAR in the PSMS rice （Nongken 58S） relative to the wild-type （Nongken 58） reduced expression of LDMAR leading to male sterility under long-day conditions. In this study, we identified a siRNA named Psi-LDMAR in the LDMAR promoter region that was more abundant in Nongken 58S than in Nongken 58. We showed that Psi-LDMAR was likely derived from AKl11270, a transcript obtained from the sense strand of the LDMAR promoter with its 3＇-end having a 110-base overlap with the 5＇-end of LDMAR. Overexpressing AKl11270 in Nongken 58S greatly enriched Psi-LDMAR, which induced RNA-directed DNA methylation in the LDMAR promoter and repressed the expression of LDMAR. Reduction of LDMAR in Nongken 58S changed the critical day length for fertility recovery and delayed the fertility recovery under short-day conditions. This result added to our understanding of the molecular mechanism for PSMS.

The RING E3 ligase CLG1 targets GS3 for degradation via the endosome pathway to determine grain size in rice

G-protein signaling and ubiquitin-dependent degradation are both involved in grain development in rice,but how these pathways are coordinated in regulating this process is unknown.Here,we show that Chang Li Geng 1(CLG1),which encodes an E3 ligase,regulates grain size by targeting the Gγprotein GS3,a negative regulator of grain length,for degradation.Overexpression of CLG1 led to increased grain length,while overexpression of mutated CLG1 with changes in three conserved amino acids decreased grain length.We found that CLG1 physically interacts with and ubiquitinats GS3which is subsequently degraded through the endosome degradation pathway,leading to increased grain size.Furthermore,we identified a critical SNP in the exon 3 of CLG1 that is significantly associated with grain size variation in a core collection of cultivated rice.This SNP results in an amino acid substitution from Arg to Ser at position 163 of CLG1 that enhances the E3 ligase activity of CLG1 and thus increases rice grain size.Both the expression level of CLG1 and the SNP CLG1163S may be useful variations for manipulating grain size in rice.

Mapping quantitative trait loci using binned genotypes

Precise mapping of quantitative trait loci(QTLs)is critical for assessing genetic effects and identifying candidate genes for quantitative traits.Interval and composite interval mappings have been the methods of choice for several decades,which have provided tools for identifying genomic regions harboring causal genes for quantitative traits.Historically,the concept was developed on the basis of sparse marker maps where genotypes of loci within intervals could not be observed.Currently,genomes of many organisms have been saturated with markers due to the new sequencing technologies.Genotyping by sequencing usually generates hundreds of thousands of single nucleotide polymorphisms(SNPs),which often include the causal polymorphisms.The concept of interval no longer exists,prompting the necessity of a norm change in QTL mapping technology to make use of the high-volume genomic data.Here we developed a statistical method and a software package to map QTLs by binning markers into haplotype blocks,called bins.The new method detects associations of bins with quantitative traits.It borrows the mixed model methodology with a polygenic control from genome-wide association studies(GWAS)and can handle all kinds of experimental populations under the linear mixed model(LMM)framework.We tested the method using both simulated data and data from populations of rice.The results showed that this method has higher power than the current methods.An R package named binQTL is available from GitHub.