Over-expression of the rice LRK1 gene improves quantitative yield components

Alternative splicing of lncRNA LAIR fine-tunes the regulation of neighboring yield-related gene LRK1 expression in rice

The diversity in alternative splicing of long noncoding RNAs (lncRNAs) poses a challenge for functional annotation of lncRNAs. Moreover, little is known on the effects of alternatively spliced lncRNAs on crop yield. In this study, we cloned nine isoforms resulting from the alternative splicing of the lncRNA LAIR in rice. The LAIR isoforms are generated via alternative 5'/3' splice sites and different combinations of specific introns. All LAIR isoforms activate the expression of the neighboring LRK1 gene and enhance yield-related rice traits. In addition, there are slight differences in the binding ability of LAIR isoforms to the epigenetic modification-related proteins OsMOF and OsWDR5, which affect the enrichment of H4K16ac and H3K4me3 at the LRK1 locus, and consequently fine-tune the regulation of LRK1 expression and yield-related traits. These differences in binding may be caused by polymorphic changes to the RNA secondary structure resulting from alternative splicing. It was also observed that the composition of LAIR isoforms was sensitive to abiotic stress. These findings suggest that the alternative splicing of LAIR leads to the formation of a functional transcript population that precisely regulates yield-related gene expression, which may be relevant for phenotypic polymorphism-based crop breeding under changing environmental conditions.

GWAS in a Collection of Bulgarian Old and Modern Bread Wheat Accessions Uncovers Novel Genomic Loci for Grain Protein Content and Thousand Kernel Weight

Genetic enhancement of grain production and quality is a priority in wheat breeding projects. In this study, we assessed two key agronomic traits-grain protein content (GPC) and thousand kernel weight (TKW)-across 179 Bulgarian contemporary and historic varieties and landraces across three growing seasons. Significant phenotypic variation existed for both traits among genotypes and seasons, and no discernible difference was evident between the old and modern accessions. To understand the genetic basis of the traits, we conducted a genome-wide association study with MLM using phenotypic data from the crop seasons, best linear unbiased estimators, and genotypic data from the 25K Infinium iSelect array. As a result, we detected 16 quantitative trait nucleotides (QTNs) associated with GPC and 15 associated with TKW, all of which passed the false discovery rate threshold. Seven loci favorably influenced GPC, resulting in an increase of 1.4% to 8.1%, while four loci had a positive impact on TKW with increases ranging from 1.9% to 8.4%. While some loci confirmed previously published associations, four QTNs linked to GPC on chromosomes 2A, 7A, and 7B, as well as two QTNs related to TKW on chromosomes 1B and 6A, may represent novel associations. Annotations for proteins involved in the senescence-associated nutrient remobilization and in the following buildup of resources required for seed germination have been found for selected putative candidate genes. These include genes coding for storage proteins, cysteine proteases, cellulose-synthase, alpha-amylase, transcriptional regulators, and F-box and RWP-RK family proteins. Our findings highlight promising genomic regions for targeted breeding programs aimed at improving grain yield and protein content.

Eukaryotic Translation Elongation Factor OsEF1A Positively Regulates Drought Tolerance and Yield in Rice

Drought is one of the most serious stresses affecting rice growth. Drought stress causes accelerated senescence, reduced fertility, and subsequent reductions in crop yield. Eukaryotic translation elongation factor EF1A is an important multifunctional protein that plays an essential role in the translation of eukaryotic proteins. In this study, we localized and cloned the OsEF1A gene in rice (Oryza sativa) in order to clarify its role in drought tolerance and yield. Subcellular localization revealed that it was mainly localized to the cell membrane, cytoskeleton and nucleus. Compared with the wild-type, OsEF1A overexpressing transgenic plants had significantly more tillers and grains per plant, resulting in a significantly higher yield. Increases in the relative water content and proline content were also observed in the transgenic seedlings under drought stress, with a decrease in the malondialdehyde content, all of which are representative of drought tolerance. Taken together, these findings suggest that OsEF1A plays a positive regulatory role in rice nutritional development under drought stress. These findings will help support future studies aimed at improving yield and stress tolerance in rice at the molecular level, paving the way for a new green revolution.

Over-Expression of Dehydroascorbate Reductase Improves Salt Tolerance, Environmental Adaptability and Productivity in Oryza sativa

Abiotic stress induces reactive oxygen species (ROS) generation in plants, and high ROS levels can cause partial or severe oxidative damage to cellular components that regulate the redox status. Here, we developed salt-tolerant transgenic rice plants that overexpressed the dehydroascorbate reductase gene (OsDHAR1) under the control of a stress-inducible sweet potato promoter (SWPA2). OsDHAR1-expressing transgenic plants exhibited improved environmental adaptability compared to wild-type plants, owing to enhanced ascorbate levels, redox homeostasis, photosynthetic ability, and membrane stability through cross-activation of ascorbate-glutathione cycle enzymes under paddy-field conditions, which enhanced various agronomic traits, including root development, panicle number, spikelet number per panicle, and total grain yield. dhar2-knockdown plants were susceptible to salt stress, and owing to poor seed maturation, exhibited reduced biomass (root growth) and grain yield under paddy field conditions. Microarray revealed that transgenic plants highly expressed genes associated with cell growth, plant growth, leaf senescence, root development, ROS and heavy metal detoxification systems, lipid metabolism, isoflavone and ascorbate recycling, and photosynthesis. We identified the genetic source of functional genomics‒based molecular breeding in crop plants and provided new insights into the physiological processes underlying environmental adaptability, which will enable improvement of stress tolerance and crop species productivity in response to climate change.

Genome-wide analysis of polymorphisms identified domestication-associated long low-diversity region carrying important rice grain size/weight quantitative trait loci

Rice grain size and weight are major determinants of grain quality and yield and so have been under rigorous selection since domestication. However, the genetic basis for contrasting grain size/weight trait among Indian germplasms and their association with domestication-driven evolution is not well understood. In this study, two long (LGG) and two short grain (SGG) genotypes were resequenced. LGG (LGR and PB 1121) differentiated from SGG (Sonasal and Bindli) by 504 439 single nucleotide polymorphisms (SNPs) and 78 166 insertion-and-deletion polymorphisms. The LRK gene cluster was different and a truncation mutation in the LRK8 kinase domain was associated with LGG. Phylogeny with 3000 diverse rice accessions revealed that the four sequenced genotypes belonged to the japonica group and were at the edge of the clades indicating them to be the potential source of genetic diversity available in Indian rice germplasm. Six SNPs were significantly associated with grain size/weight and the top four of these could be validated in mapping a population, suggesting this study as a valuable resource for high-throughput genotyping. A contiguous long low-diversity region (LDR) of approximately 6 Mb carrying a major grain weight quantitative trait loci (harbouring OsTOR gene) was identified on Chromosome 5. This LDR was identified as an evolutionary important site with significant positive selection and multiple selection sweeps, and showed association with many domestication-related traits, including grain size/weight. The aus population retained more allelic variations in the LDR than the japonica and indica populations, suggesting it to be one of the divergence loci. All the data and analyses can be accessed from the RiceSzWtBase database.

Genome-Wide Association Study Unravels LRK1 as a Dark Respiration Regulator in Rice (Oryza sativa L.)

Respiration is a major plant physiological process that generates adenosine triphosphate (ATP) to support the various pathways involved in the plant growth and development. After decades of focused research on basic mechanisms of respiration, the processes and major proteins involved in respiration are well elucidated. However, much less is known about the natural variation of respiration. Here we conducted a survey on the natural variation of leaf dark respiration (Rd) in a global rice minicore diversity panel and applied a genome-wide association study (GWAS) in rice (Oryza sativa L.) to determine candidate loci associated with Rd. This rice minicore diversity panel consists of 206 accessions, which were grown under both growth room (GR) and field conditions. We found that Rd shows high single-nucleotide polymorphism (SNP) heritability under GR and it is significantly affected by genotype-environment interactions. Rd also exhibits strong positive correlation to the leaf thickness and chlorophyll content. GWAS results of Rd collected under GR and field show an overlapped genomic region in the chromosome 3 (Chr.3), which contains a lead SNP (3m29440628). There are 12 candidate genes within this region; among them, three genes show significantly higher expression levels in accessions with high Rd. Particularly, we observed that the LRK1 gene, annotated as leucine rich repeat receptor kinase, was up-regulated four times. We further found that a single significantly associated SNPs at the promoter region of LRK1, was strongly correlated with the mean annual temperature of the regions from where minicore accessions were collected. A rice lrk1 mutant shows only ~37% Rd of that of WT and retarded growth following exposure to 35 °C for 30 days, but only 24% reduction in growth was recorded under normal temperature (25 °C). This study demonstrates a substantial natural variation of Rd in rice and that the LRK1 gene can regulate leaf dark respiratory fluxes, especially under high temperature.

Lectin Receptor-Like Kinases: The Sensor and Mediator at the Plant Cell Surface

Lectin receptor-like kinases (LecRLKs), a plant-specific receptor-like kinase (RLK) sub-family, have been recently found to play crucial roles in plant development and responses to abiotic and biotic stresses. In this review, we first describe the classification and structures of Lectin RLKs. Then we focus on the analysis of functions of LecRLKs in various biological processes and discuss the status of LecRLKs from the ligands they recognize, substrate they target, signaling pathways they are involved in, to the overall regulation of growth-defense tradeoffs. LecRLKs and the signaling components they interact with constitute recognition and protection systems at the plant cell surface contributing to the detection of environmental changes monitoring plant fitness.

Short Panicle 3 controls panicle architecture by upregulating APO2/RFL and increasing cytokinin content in rice

Inflorescence architecture is a major determinant of spikelet numbers per panicle, a key component of grain yield in rice. In this study, Short Panicle 3 (SP3) was identified from a short panicle 3 (sp3) mutant in which T-DNA was inserted in the promoter of SP3, resulting in a knockdown mutation. SP3 encodes a DNA binding with one finger (Dof) transcriptional activator. Quantitative real time (qRT)-PCR and RNA in situ hybridization assays confirmed that SP3 is preferentially expressed in the young rice inflorescence, specifically in the branch primordial regions. SP3 acts as a negative regulator of inflorescence meristem abortion by upregulating APO2/RFL. SP3 both up- and downregulates expression of genes involved in cytokinin biosynthesis and catabolism, respectively. Consequently, cytokinin concentrations are decreased in young sp3 panicles, thereby leading to small panicles having fewer branches and spikelets. Our findings support a model in which SP3 regulates panicle architecture by modulating cytokinin homeostasis. Potential applications to rice breeding, through gene-editing of the SP3 promoter are assessed.

Computational approach towards understanding structural and functional role of cytokinin oxidase/dehydrogenase 2 (CKX2) in enhancing grain yield in rice plant

Cytokinin oxidase/dehydrogenase (CKX) is the only known enzyme associated with irreversible degradation of cytokinins in plants. CKX2 contains flavin adenine dinucleotide (FAD) domain. Earlier studies utilising antisense & hpRNAi suppression techniques in mutant/transgenic rice plants revealed that when CKX2 binds with FAD, CKX2 expression reduces, which in turn causes cytokinin aggregation in inflorescence meristem that subsequently enhances both branches and grain number resulting in increased grain yield. Owing to the non-existence of complete three-dimensional structure of CKX2, insight into the structure and function of CKX2 and its relationship with its cofactor FAD is still a topic of debate. In the present study, computational approach was employed to estimate the three-dimensional structure of CKX2 through comparative modelling approach. Later, CKX2 and FAD interaction study was performed to understand the underlying mechanism involved with reduced expression of CKX2. Molecular dynamic simulation studies of both CKX2 and CKX-FAD complex revealed that after binding with FAD, CKX2 experienced increased pressure and reduced RMSD, potential energy and free energy landscape energy, which in turn lessen anti-correlation between almost all α and β strands and random motion of C-α, subsequently reducing CKX2 expression. In near future, these information can be utilised for increasing rice yield under irrigated field condition by introgression of Gn1a gene through marker assisted back-crossing breeding. AbbreviationsGROMACSGROningen MAchine for Chemical SimulationsNPTConstant Number of Particles, Volume and TemperatureRMSDRoot Mean Square DeviationRMSFRoot Mean Square FluctuationsQTLquantitative trait lociFADflavin adenine dinucleotideNVTConstant Number of Particles, Pressure and TemperatureLINCSLinear Constraint SolverCKX2Cytokinin oxidase/dehydrogenase 2MM/PBSAMolecular Mechanics/Poisson-Boltzmann surface areaSDFStructure Data FileCommunicated by Ramaswamy H. Sarma.

Systems model-guided rice yield improvements based on genes controlling source, sink, and flow

A large number of genes related to source, sink, and flow have been identified after decades of research in plant genetics. Unfortunately, these genes have not been effectively utilized in modern crop breeding. This perspective paper aims to examine the reasons behind such a phenomenon and propose a strategy to resolve this situation. Specifically, we first systematically survey the currently cloned genes related to source, sink, and flow; then we discuss three factors hindering effective application of these identified genes, which include the lack of effective methods to identify limiting or critical steps in a signaling network, the misplacement of emphasis on properties, at the leaf, instead of the whole canopy level, and the non-linear complex interaction between source, sink, and flow. Finally, we propose the development of systems models of source, sink and flow, together with a detailed simulation of interactions between them and their surrounding environments, to guide effective use of the identified elements in modern rice breeding. These systems models will contribute directly to the definition of crop ideotype and also identification of critical features and parameters that limit the yield potential in current cultivars.

Genome-wide association study of agronomic traits in rice cultivated in temperate regions

BACKGROUND

Rice plants are sensitive to the agro-climate conditions, being photoperiod one of main factor contributing to their adaptation to the region where they are grown. Dissecting the genetic bases underlying diversity in rice populations adapted to specific environmental conditions is a fundamental resource for breeding. In this study we have analysed a collection of japonica varieties adapted to temperate regions to perform association studies with traits of high agronomical interest such as heading date, plant height, number of panicles, panicle length and number of grains per panicle.

RESULTS

We have performed a genome wide association study using a panel of 1713 SNPs that, based on previous linkage disequilibrium estimations, provides a full coverage of the whole genome. We have found a total of 43 SNPs associated with variations in the different traits. The identified SNPs were distributed across the genome except in chromosome 12, where no associated SNPs were found. The inspection of the vicinity of these markers also revealed a set of genes associated with physiological functions strongly linked to agronomic traits. Of special relevance are two genes involved in gibberellin homeostasis that are associated with plant height and panicle length. We also detected novel associated sites with heading date, panicle length and number of grain per panicle.

CONCLUSION

We have identified loci associated with important agronomic traits among cultivars adapted to temperate conditions. Some of these markers co-localized with already known genes or QTLs, but the association also provided novel molecular markers that can be of help to elucidate the complicated genetic mechanism controlling important agronomic traits, as flowering regulation in the non-dependent photoperiod pathway. The detected associated markers may provide important tools for the genetic improvement of rice cultivars in temperate regions.

Overexpressing lncRNA LAIR increases grain yield and regulates neighbouring gene cluster expression in rice

Long noncoding RNAs (lncRNAs) are essential regulators of gene expression in eukaryotes. Despite increasing knowledge on the function of lncRNAs, little is known about their effects on crop yield. Here, we identify a lncRNA transcribed from the antisense strand of neighbouring gene LRK (leucine-rich repeat receptor kinase) cluster named LAIR (LRK Antisense Intergenic RNA). LAIR overexpression increases rice grain yield and upregulates the expression of several LRK genes. Additionally, chromatin immunoprecipitation assay results indicate H3K4me3 and H4K16ac are significantly enriched at the activated LRK1 genomic region. LAIR binds histone modification proteins OsMOF and OsWDR5 in rice cells, which are enriched in LRK1 gene region. Moreover, LAIR is demonstrated to bind 5' and 3' untranslated regions of LRK1 gene. Overall, this study reveals the role of lncRNA LAIR in regulating rice grain yield and lncRNAs may be useful targets for crop breeding.

A Pathogen-Responsive Leucine Rich Receptor Like Kinase Contributes to Fusarium Resistance in Cereals

Receptor-like kinases form the largest family of receptors in plants and play an important role in recognizing pathogen-associated molecular patterns and modulating the plant immune responses to invasive fungi, including cereal defenses against fungal diseases. But hitherto, none have been shown to modulate the wheat response to the economically important Fusarium head blight (FHB) disease of small-grain cereals. Homologous genes were identified on barley chromosome 6H (HvLRRK-6H) and wheat chromosome 6DL (TaLRRK-6D), which encode the characteristic domains of surface-localized receptor like kinases. Gene expression studies validated that the wheat TaLRRK-6D is highly induced in heads as an early response to both the causal pathogen of FHB disease, Fusarium graminearum, and its' mycotoxic virulence factor deoxynivalenol. The transcription of other wheat homeologs of this gene, located on chromosomes 6A and 6B, was also up-regulated in response to F. graminearum. Virus-induced gene silencing (VIGS) of the barley HvLRRK-6H compromised leaf defense against F. graminearum. VIGS of TaLRRK-6D in two wheat cultivars, CM82036 (resistant to FHB disease) and cv. Remus (susceptible to FHB), confirmed that TaLRRK-6D contributes to basal resistance to FHB disease in both genotypes. Although the effect of VIGS did not generally reduce grain losses due to FHB, this experiment did reveal that TaLRRK-6D positively contributes to grain development. Further gene expression studies in wheat cv. Remus indicated that VIGS of TaLRRK-6D suppressed the expression of genes involved in salicylic acid signaling, which is a key hormonal pathway involved in defense. Thus, this study provides the first evidence of receptor like kinases as an important component of cereal defense against Fusarium and highlights this gene as a target for enhancing cereal resistance to FHB disease.

Duplication of an upstream silencer of FZP increases grain yield in rice

Transcriptional silencer and copy number variants (CNVs) are associated with gene expression. However, their roles in generating phenotypes have not been well studied. Here we identified a rice quantitative trait locus, SGDP7 (Small Grain and Dense Panicle 7). SGDP7 is identical to FZP (FRIZZY PANICLE), which represses the formation of axillary meristems. The causal mutation of SGDP7 is an 18-bp fragment, named CNV-18bp, which was inserted ~5.3 kb upstream of FZP and resulted in a tandem duplication in the cultivar Chuan 7. The CNV-18bp duplication repressed FZP expression, prolonged the panicle branching period and increased grain yield by more than 15% through substantially increasing the number of spikelets per panicle (SPP) and slightly decreasing the 1,000-grain weight (TGW). The transcription repressor OsBZR1 binds the CGTG motifs in CNV-18bp and thereby represses FZP expression, indicating that CNV-18bp is the upstream silencer of FZP. These findings showed that the silencer CNVs coordinate a trade-off between SPP and TGW by fine-tuning FZP expression, and balancing the trade-off could enhance yield potential.

Overexpression of the leucine-rich receptor-like kinase gene LRK2 increases drought tolerance and tiller number in rice

Drought represents a key limiting factor of global crop distribution. Receptor-like kinases play major roles in plant development and defence responses against stresses such as drought. In this study, LRK2, which encodes a leucine-rich receptor-like kinase, was cloned and characterized and found to be localized on the plasma membrane in rice. Promoter-GUS analysis revealed strong expression in tiller buds, roots, nodes and anthers. Transgenic plants overexpressing LRK2 exhibited enhanced tolerance to drought stress due to an increased number of lateral roots compared with the wild type at the vegetative stage. Moreover, ectopic expression of LRK2 seedlings resulted in increased tiller development. Yeast two-hybrid screening and bimolecular fluorescence complementation (BiFC) indicated a possible interaction between LRK2 and elongation factor 1 alpha (OsEF1A) in vitro. These results suggest that LRK2 functions as a positive regulator of the drought stress response and tiller development via increased branch development in rice. These findings will aid our understanding of branch regulation in other grasses and support improvements in rice genetics.

Ectopic expression of Arabidopsis FD and FD PARALOGUE in rice results in dwarfism with size reduction of spikelets

Key flowering genes, FD and FD PARALOGUE (FDP) encoding bZIP transcription factors that interact with a FLOWERING LOCUS T (FT) in Arabidopsis were ectopically expressed in rice since we found AtFD and AtFDP also interact with HEADING DATE 3a (Hd3a) and RICE FLOWERING LOCUS T 1 (RFT1). Transgenic rice plants overexpressing AtFD and AtFDP caused reduction in plant height and spikelet size with decreased expression of genes involved in cell elongation without significant flowering time alteration in spite of increased expression of OsMADS14 and OsMADS15, rice homologues of APETALA1 (AP1) in the leaves. Simultaneous overexpression of AtFD and AtFDP enhanced phenotypes seen with overexpression of either single gene while transgenic rice plants expressing AtFD or AtFDP under the control of phloem-specific Hd3a promoter were indistinguishable from wild-type rice. Candidate genes responsible for the phenotypes were identified by comparison of microarray hybridization and their expression pattern was also examined in WT and transgenic rice plants. It has so far not been reported that AtFD and AtFDP affect cell elongation in plants, and our findings provide novel insight into the possible roles of AtFD and AtFDP in the mesophyll cells of plants, and potential genetic tools for manipulation of crop architecture.

Genome-wide analysis of Dongxiang wild rice (Oryza rufipogon Griff.) to investigate lost/acquired genes during rice domestication

BACKGROUND

It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetically elucidate the substantially phenotypic and physiological changes from wild rice to cultivated rice at the whole genome level.

RESULTS

Instead of comparing two assembled genomes, this study directly compared the Dongxiang wild rice (DXWR) Illumina sequencing reads with the Nipponbare (O. sativa) complete genome without assembly of the DXWR genome. Based on the results from the comparative genomics analysis, structural variations (SVs) between DXWR and Nipponbare were determined to locate deleted genes which could have been acquired by Nipponbare during rice domestication. To overcome the limit of the SV detection, the DXWR transcriptome was also sequenced and compared with the Nipponbare transcriptome to discover the genes which could have been lost in DXWR during domestication. Both 1591 Nipponbare-acquired genes and 206 DXWR-lost transcripts were further analyzed using annotations from multiple sources. The NGS data are available in the NCBI SRA database with ID SRP070627.

CONCLUSIONS

These results help better understanding the domestication from wild rice to cultivated rice at the whole genome level and provide a genomic data resource for rice genetic research or breeding. One finding confirmed transposable elements contribute greatly to the genome evolution from wild rice to cultivated rice. Another finding suggested the photophosphorylation and oxidative phosphorylation system in cultivated rice could have adapted to environmental changes simultaneously during domestication.

Development and application of a novel genome-wide SNP array reveals domestication history in soybean

Domestication of soybeans occurred under the intense human-directed selections aimed at developing high-yielding lines. Tracing the domestication history and identifying the genes underlying soybean domestication require further exploration. Here, we developed a high-throughput NJAU 355 K SoySNP array and used this array to study the genetic variation patterns in 367 soybean accessions, including 105 wild soybeans and 262 cultivated soybeans. The population genetic analysis suggests that cultivated soybeans have tended to originate from northern and central China, from where they spread to other regions, accompanied with a gradual increase in seed weight. Genome-wide scanning for evidence of artificial selection revealed signs of selective sweeps involving genes controlling domestication-related agronomic traits including seed weight. To further identify genomic regions related to seed weight, a genome-wide association study (GWAS) was conducted across multiple environments in wild and cultivated soybeans. As a result, a strong linkage disequilibrium region on chromosome 20 was found to be significantly correlated with seed weight in cultivated soybeans. Collectively, these findings should provide an important basis for genomic-enabled breeding and advance the study of functional genomics in soybean.

The phenome analysis of mutant alleles in Leucine-Rich Repeat Receptor-Like Kinase genes in rice reveals new potential targets for stress tolerant cereals

Plants are constantly exposed to a variety of biotic and abiotic stresses that reduce their fitness and performance. At the molecular level, the perception of extracellular stimuli and the subsequent activation of defense responses require a complex interplay of signaling cascades, in which protein phosphorylation plays a central role. Several studies have shown that some members of the Leucine-Rich Repeat Receptor-Like Kinase (LRR-RLK) family are involved in stress and developmental pathways. We report here a systematic analysis of the role of the members of this gene family by mutant phenotyping in the monocotyledon model plant rice, Oryza sativa. We have then targeted 176 of the ∼320 LRR-RLK genes (55.7%) and genotyped 288 mutant lines. Position of the insertion was confirmed in 128 lines corresponding to 100 LRR-RLK genes (31.6% of the entire family). All mutant lines harboring homozygous insertions have been screened for phenotypes under normal conditions and under various abiotic stresses. Mutant plants have been observed at several stages of growth, from seedlings in Petri dishes to flowering and grain filling under greenhouse conditions. Our results show that 37 of the LRR-RLK rice genes are potential targets for improvement especially in the generation of abiotic stress tolerant cereals.

Over-expression of an S-domain receptor-like kinase extracellular domain improves panicle architecture and grain yield in rice

The S-domain receptor kinase (SRK) comprises a highly polymorphic subfamily of receptor-like kinases (RLKs) originally found to be involved in the self-incompatibility response in Brassica. Although several members have been identified to play roles in developmental control and disease responses, the correlation between SRKs and yield components in rice is still unclear. The utility of transgenic expression of a dominant negative form of SRK, OsLSK1 (Large spike S-domain receptor like Kinase 1), is reported here for the improvement of grain yield components in rice. OsLSK1 was highly expressed in nodes of rice and is a plasma membrane protein. The expression of OsLSK1 responded to the exogenous application of growth hormones, to abiotic stresses, and its extracellular domain could form homodimers or heterodimers with other related SRKs. Over-expression of a truncated version of OsLSK1 (including the extracellular and transmembrane domain of OsLSK1 without the intracellular kinase domain) increased plant height and improve yield components, including primary branches per panicle and grains per primary branch, resulting in about a 55.8% increase of the total grain yield per plot (10 plants). Transcriptional analysis indicated that several key genes involved in the GA biosynthetic and signalling pathway were up-regulated in transgenic plants. However, full-length cDNA over-expression and RNAi of OsLSK1 transgenic plants did not exhibit a detectable visual phenotype and possible reasons for this were discussed. These results indicate that OsLSK1 may act redundantly with its homologues to affect yield traits in rice and manipulation of OsLSK1 by the dominant negative method is a practicable strategy to improve grain yield in rice and other crops.

The genetic basis of natural variation in seed size and seed number and their trade-off using Arabidopsis thaliana MAGIC lines

Offspring number and size are key traits determining an individual's fitness and a crop's yield. Yet, extensive natural variation within species is observed for these traits. Such variation is typically explained by trade-offs between fecundity and quality, for which an optimal solution is environmentally dependent. Understanding the genetic basis of seed size and number, as well as any possible genetic constraints preventing the maximization of both, is crucial from both an evolutionary and applied perspective. We investigated the genetic basis of natural variation in seed size and number using a set of Arabidopsis thaliana multiparent advanced generation intercross (MAGIC) lines. We also tested whether life history affects seed size, number, and their trade-off. We found that both seed size and seed number are affected by a large number of mostly nonoverlapping QTL, suggesting that seed size and seed number can evolve independently. The allele that increases seed size at most identified QTL is from the same natural accession, indicating past occurrence of directional selection for seed size. Although a significant trade-off between seed size and number is observed, its expression depends on life-history characteristics, and generally explains little variance. We conclude that the trade-off between seed size and number might have a minor role in explaining the maintenance of variation in seed size and number, and that seed size could be a valid target for selection.

Whole-genome quantitative trait locus mapping reveals major role of epistasis on yield of rice

Although rice yield has been doubled in most parts of the world since 1960s, thanks to the advancements in breeding technologies, the biological mechanisms controlling yield are largely unknown. To understand the genetic basis of rice yield, a number of quantitative trait locus (QTL) mapping studies have been carried out, but whole-genome QTL mapping incorporating all interaction effects is still lacking. In this paper, we exploited whole-genome markers of an immortalized F2 population derived from an elite rice hybrid to perform QTL mapping for rice yield characterized by yield per plant and three yield component traits. Our QTL model includes additive and dominance main effects of 1,619 markers and all pair-wise interactions, with a total of more than 5 million possible effects. The QTL mapping identified 54, 5, 28 and 4 significant effects involving 103, 9, 52 and 7 QTLs for the four traits, namely the number of panicles per plant, the number of grains per panicle, grain weight, and yield per plant. Most identified QTLs are involved in digenic interactions. An extensive literature survey of experimentally characterized genes related to crop yield shows that 19 of 54 effects, 4 of 5 effects, 12 of 28 effects and 2 of 4 effects for the four traits, respectively, involve at least one QTL that locates within 2 cM distance to at least one yield-related gene. This study not only reveals the major role of epistasis influencing rice yield, but also provides a set of candidate genetic loci for further experimental investigation.

Identification and characterization of OsEBS, a gene involved in enhanced plant biomass and spikelet number in rice

Common wild rice (Oryza rufipogon Griff.) is an important genetic reservoir for rice improvement. We investigated a quantitative trait locus (QTL), qGP5-1, which is related to plant height, leaf size and panicle architecture, using a set of introgression lines of O. rufipogon in the background of the Indica cultivar Guichao2 (Oryza sativa L.). We cloned and characterized qGP5-1 and confirmed that the newly identified gene OsEBS (enhancing biomass and spikelet number) increased plant height, leaf size and spikelet number per panicle, leading to an increase in total grain yield per plant. Our results showed that the increased size of vegetative organs in OsEBS-expressed plants was enormously caused by increasing cell number. Sequence alignment showed that OsEBS protein contains a region with high similarity to the N-terminal conserved ATPase domain of Hsp70, but it lacks the C-terminal regions of the peptide-binding domain and the C-terminal lid. More results indicated that OsEBS gene did not have typical characteristics of Hsp70 in this study. Furthermore, Arabidopsis (Arabidopsis thaliana) transformed with OsEBS showed a similar phenotype to OsEBS-transgenic rice, indicating a conserved function of OsEBS among plant species. Together, we report the cloning and characterization of OsEBS, a new QTL that controls rice biomass and spikelet number, through map-based cloning, and it may have utility in improving grain yield in rice.

Narrowing down the targets for yield improvement in rice under normal and abiotic stress conditions via expression profiling of yield-related genes

BACKGROUND

Crop improvement targeting high yield and tolerance to environmental stresses has become the need of the hour. Yield improvement via breeding or gene pyramiding aiming comprehensive incorporation of the agronomically favored traits requires an in-depth understanding of the molecular basis of these traits. The present study describes expression profiling of yield-related genes in rice with respect to different developmental stages and various abiotic stress conditions.

RESULTS

Our analysis indicates developmental regulation of the yield-related genes pertaining to the genetic reprogramming involved at the corresponding developmental stage. The gene expression data can be utilized to specifically select particular genes which can potentially function synergistically for enhancing the yield while maintaining the source-sink balance. Furthermore, to gain some insights into the molecular basis of yield penalty during various abiotic stresses, the expression of selected yield-related genes has also been analyzed by qRT-PCR under such stress conditions. Our analysis clearly showed a tight transcriptional regulation of a few of these yield-related genes by abiotic stresses. The stress-responsive expression patterns of these genes could explain some of the most important stress-related physiological manifestations such as reduced tillering, smaller panicles and early completion of the life cycle owing to reduced duration of vegetative and reproductive phases.

CONCLUSIONS

Development of high yielding rice varieties which maintain their yield even under stress conditions may be achieved by simultaneous genetic manipulation of certain combination of genes such as LRK1 and LOG, based on their function and expression profile obtained in the present study. Our study would aid in investigating in future, whether over-expressing or knocking down such yield-related genes can improve the grain yield potential in rice.

Molecular characterization and comparative sequence analysis of defense-related gene, Oryza rufipogon receptor-like protein kinase 1

Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structural prediction of extra cellular domains, cluster analysis and comparative gene expression.

Yield-related QTLs and their applications in rice genetic improvement

Grain yield is one of the most important indexes in rice breeding, which is governed by quantitative trait loci (QTLs). Different mapping populations have been used to explore the QTLs controlling yield related traits. Primary populations such as F(2) and recombinant inbred line populations have been widely used to discover QTLs in rice genome-wide, with hundreds of yield-related QTLs detected. Advanced populations such as near isogenic lines (NILs) are efficient to further fine-map and clone target QTLs. NILs for primarily identified QTLs have been proposed and confirmed to be the ideal population for map-based cloning. To date, 20 QTLs directly affecting rice grain yield and its components have been cloned with NIL-F(2) populations, and 14 new grain yield QTLs have been validated in the NILs. The molecular mechanisms of a continuously increasing number of genes are being unveiled, which aids in the understanding of the formation of grain yield. Favorable alleles for rice breeding have been 'mined' from natural cultivars and wild rice by association analysis of known functional genes with target trait performance. Reasonable combination of favorable alleles has the potential to increase grain yield via use of functional marker assisted selection.

Rice ethylene-response AP2/ERF factor OsEATB restricts internode elongation by down-regulating a gibberellin biosynthetic gene

Plant height is a decisive factor in plant architecture. Rice (Oryza sativa) plants have the potential for rapid internodal elongation, which determines plant height. A large body of physiological research has shown that ethylene and gibberellin are involved in this process. The APETALA2 (AP2)/Ethylene-Responsive Element Binding Factor (ERF) family of transcriptional factors is only present in the plant kingdom. This family has various developmental and physiological functions. A rice AP2/ERF gene, OsEATB (for ERF protein associated with tillering and panicle branching) was cloned from indica rice variety 9311. Bioinformatic analysis suggested that this ERF has a potential new function. Ectopic expression of OsEATB showed that the cross talk between ethylene and gibberellin, which is mediated by OsEATB, might underlie differences in rice internode elongation. Analyses of gene expression demonstrated that OsEATB restricts ethylene-induced enhancement of gibberellin responsiveness during the internode elongation process by down-regulating the gibberellin biosynthetic gene, ent-kaurene synthase A. Plant height is negatively correlated with tiller number, and higher yields are typically obtained from dwarf crops. OsEATB reduces rice plant height and panicle length at maturity, promoting the branching potential of both tillers and spikelets. These are useful traits for breeding high-yielding crops.

Rice functional genomics research: progress and implications for crop genetic improvement

Rice is a staple food crop and has become a reference of monocot plant for functional genomic research. With the availability of high quality rice genome sequence, there has been rapid accumulation of functional genomic resources, including: large mutant libraries by T-DNA insertion, transposon tagging, and chemical mutagenesis; global expression profiles of the genes in the entire life cycle of rice growth and development; full-length cDNAs for both indica and japonica rice; sequences from resequencing large numbers of diverse germplasm accessions. Such resource development has greatly accelerated gene cloning. By the end of 2010, over 600 genes had been cloned using various methods. Many of the genes control agriculturally useful traits such as yield, grain quality, resistances to biotic and abiotic stresses, and nutrient-use efficiency, thus have potential utility in crop genetic improvement. This review was aimed to provide a comprehensive summary of such progress. We also presented our perspective for future studies.

Identification of heterotic loci associated with yield-related traits in Chinese common wild rice (Oryza rufipogon Griff.)

Many rice breeding programs have currently reached yield plateaus as a result of limited genetic variability in parental strains. Dongxiang common wild rice (Oryza rufipogon Griff.) is the progenitor of cultivated rice (Oryza sativa L.) and serves as an important gene pool for the genetic improvement of rice cultivars. In this study, heterotic loci (HLs) associated with six yield-related traits were identified in wild and cultivated rice and investigated using a set of 265 introgression lines (ILs) of O. rufipogon Griff. in the background of the Indica high-yielding cultivar Guichao 2 (O. sativa L.). Forty-two HLs were detected by a single point analysis of mid-parent heterosis values from test cross F(1) offspring, and 30 (71.5%) of these HLs showed significantly positive effects, consistent with the superiority shown by the F(1) test cross population in the six yield-related traits under study. Genetic mapping of hsp11, a locus responsible for the number of spikelets per panicle, confirmed the utility of these HLs. The results indicate that favorable HLs capable of improving agronomic traits are available. The identification of HLs between wild rice and cultivated rice could lead to a new strategy for the application of heterosis in rice breeding.