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1.
Plant Genome ; 13(1): e20001, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-33016624

RESUMO

African wild rice Oryza longistaminata, one of the eight AA- genome species in the genus Oryza, possesses highly valued traits, such as the rhizomatousness for perennial rice breeding, strong tolerance to biotic and abiotic stresses, and high biomass production on poor soils. To obtain the high-quality reference genome for O. longistaminata we employed a hybrid assembly approach through incorporating Illumina and PacBio sequencing datasets. The final genome assembly comprised only 107 scaffolds and was approximately ∼363.5 Mb, representing ∼92.7% of the estimated African wild rice genome (∼392 Mb). The N50 lengths of the assembled contigs and scaffolds were ∼46.49 Kb and ∼6.83 Mb, indicating ∼3.72-fold and ∼18.8-fold improvement in length compared to the earlier released assembly (∼12.5 Kb and 364 Kb, respectively). Aided with Hi-C data and syntenic relationship with O. sativa, these assembled scaffolds were anchored into 12 pseudo-chromosomes. Genome annotation and comparative genomic analysis reveal that lineage-specific expansion of gene families that respond to biotic- and abiotic stresses are of great potential for mining novel alleles to overcome major diseases and abiotic adaptation in rice breeding programs. This reference genome of African wild rice will greatly enlarge the existing database of rice genome resources and unquestionably form a solid base to understand genomic basis underlying highly valued phenotypic traits and search for novel gene sources in O. longistaminata for the future rice breeding programs.


Assuntos
Oryza , Genoma , Genômica , Oryza/genética , Análise de Sequência de DNA
2.
Plant Genome ; 13(1): e20005, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-33016626

RESUMO

A genome-wide association study (GWAS) needs to have a suitable population. The factors that affect a GWAS (e.g. population structure, sample size, and sequence analysis and field testing costs) need to be considered. Mixed populations containing subpopulations of different genetic backgrounds may be suitable populations. We conducted simulation experiments to see if a population with high genetic diversity, such as a diversity panel, should be added to a target population, especially when the target population harbors small genetic diversity. The target population was 112 accessions of Oryza sativa L. subsp. japonica, mainly developed in Japan. We combined the target population with three populations that had higher genetic diversity. These were 100 indica accessions, 100 japonica accessions, and 100 accessions with various genetic backgrounds. The results showed that the GWAS's power with a mixed population was generally higher than with a separate population. Also, the optimal GWAS populations varied depending on the fixation index (FST ) of the quantitative trait nucleotides (QTNs) and the polymorphism of QTNs in each population. When a QTN was polymorphic in a target population, a target population combined with a higher diversity population improved the QTN's detection power. By investigating FST and the expected heterozygosity (He ) as factors influencing the detection power, we showed that single nucleotide polymorphisms with high FST or low He are less likely to be detected by GWAS with mixed populations. Sequenced or genotyped germplasm collections can improve the GWAS's detection power by using a subset of the collections with a target population.


Assuntos
Oryza , Estudo de Associação Genômica Ampla , Genótipo , Japão , Oryza/genética , Polimorfismo de Nucleotídeo Único
3.
Pestic Biochem Physiol ; 170: 104681, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32980063

RESUMO

Chitosan oligosaccharides (COS) can elicit plant immunity and defence responses in rice plants, but exactly how this promotes plant growth remains largely unknown. Herein, we explored the effects of 0.5 mg/L COS on plant growth promotion in rice seedlings by measuring root and stem length, investigating biochemical factors in whole plants via proteomic analysis, and confirming upregulated and downregulated genes by real-time quantitative PCR. Pathway enrichment results showed that COS promoted root and stem growth, and stimulated metabolic (biosynthetic and catabolic processes) and photosynthesis in rice plants during the seedling stage. Expression levels of genes related to chlorophyll a-b binding, RNA binding, catabolic processes and calcium ion binding were upregulated following COS treatment. Furthermore, comparative analysis indicated that numerous proteins involved in the biosynthesis, metabolic (catabolic) processes and photosynthesis pathways were upregulated. The findings indicate that COS may upregulate calcium ion binding, photosynthesis, RNA binding, and catabolism proteins associated with plant growth during the rice seedling stage.


Assuntos
Quitosana , Oryza/genética , Clorofila A , Regulação da Expressão Gênica de Plantas , Oligossacarídeos , Proteínas de Plantas/genética , Proteômica , Plântula/genética
4.
PLoS Pathog ; 16(8): e1008801, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32866183

RESUMO

Rice stripe virus (RSV) is one of the most destructive viral diseases affecting rice production. However, so far, only one RSV resistance gene has been cloned, the molecular mechanisms underlying host-RSV interaction are still poorly understood. Here, we show that increasing levels or signaling of brassinosteroids (BR) and jasmonic acid (JA) can significantly enhance the resistance against RSV. On the contrary, plants impaired in BR or JA signaling are more susceptible to RSV. Moreover, the enhancement of RSV resistance conferred by BR is impaired in OsMYC2 (a key positive regulator of JA response) knockout plants, suggesting that BR-mediated RSV resistance requires active JA pathway. In addition, we found that RSV infection suppresses the endogenous BR levels to increase the accumulation of OsGSK2, a key negative regulator of BR signaling. OsGSK2 physically interacts with OsMYC2, resulting in the degradation of OsMYC2 by phosphorylation and reduces JA-mediated defense to facilitate virus infection. These findings not only reveal a novel molecular mechanism mediating the crosstalk between BR and JA in response to virus infection and deepen our understanding about the interaction of virus and plants, but also suggest new effective means of breeding RSV resistant crops using genetic engineering.


Assuntos
Brassinosteroides/metabolismo , Ciclopentanos/metabolismo , Oryza , Oxilipinas/metabolismo , Plantas Geneticamente Modificadas , Transdução de Sinais , Tenuivirus , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/genética , Fatores de Transcrição de Zíper de Leucina e Hélice-Alça-Hélix Básicos/metabolismo , Oryza/genética , Oryza/metabolismo , Oryza/virologia , Doenças das Plantas/genética , Doenças das Plantas/virologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/metabolismo , Plantas Geneticamente Modificadas/virologia , Tenuivirus/genética , Tenuivirus/metabolismo
5.
Nat Commun ; 11(1): 4778, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32963241

RESUMO

Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders.


Assuntos
Variação Genética , Vigor Híbrido/genética , Oryza/genética , Cruzamento , Proteínas de Transporte de Cátions/genética , China , Cruzamentos Genéticos , Deleção de Genes , Genes de Plantas , Hibridização Genética , Oryza/classificação , Filogenia , Proteínas de Plantas/genética , Polimorfismo de Nucleotídeo Único
6.
PLoS One ; 15(7): e0236943, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32735612

RESUMO

Halophyte Lobularia maritima LmSAP encodes an A20AN1 zinc-finger stress-associated protein which expression is up-regulated by abiotic stresses and heavy metals in transgenic tobacco. To deepen our understanding of LmSAP function, we isolated a 1,147 bp genomic fragment upstream of LmSAP coding sequence designated as PrLmSAP. In silico analyses of PrLmSAP revealed the presence of consensus CAAT and TATA boxes and cis-regulatory elements required for abiotic stress, phytohormones, pathogen, and wound responses, and also for tissue-specific expression. The PrLmSAP sequence was fused to the ß-glucuronidase (gusA) reporter gene and transferred to rice. Histochemical GUS staining showed a pattern of tissue-specific expression in transgenic rice, with staining observed in roots, coleoptiles, leaves, stems and floral organs but not in seeds or in the root elongation zone. Wounding strongly stimulated GUS accumulation in leaves and stems. Interestingly, we observed a high stimulation of the promoter activity when rice seedlings were exposed to NaCl, PEG, ABA, MeJA, GA, cold, and heavy metals (Al3+, Cd2+, Cu2+ and Zn2+). These results suggest that the LmSAP promoter can be a convenient tool for stress-inducible gene expression and is a potential candidate for crop genetic engineering.


Assuntos
Regulação da Expressão Gênica de Plantas/genética , Regiões Promotoras Genéticas , Plantas Tolerantes a Sal/genética , Estresse Fisiológico/genética , Dedos de Zinco/genética , Produtos Agrícolas/genética , Engenharia Genética , Glucuronidase/metabolismo , Metais Pesados/metabolismo , Especificidade de Órgãos , Oryza/genética , Folhas de Planta/metabolismo , Raízes de Plantas/metabolismo , Caules de Planta/metabolismo , Plantas Geneticamente Modificadas/metabolismo , Tabaco/genética
7.
PLoS One ; 15(8): e0237774, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32797075

RESUMO

The source-sink relationship determines the ultimate grain yield of rice. In this study, we used a set of reciprocal introgression lines (ILs) derived from Xuishui09 × IR2061 to map quantitative trait loci (QTLs) that were associated with sink-, source-, and grain yield-related traits. A total of 95 QTLs influencing eight measured traits were identified using 6181 high-quality single nucleotide polymorphism markers. Nine background-independent QTLs were consistently detected in seven chromosomal regions in different genetic backgrounds. Seven QTLs clusters simultaneously affected sink-, source-, and grain yield-related traits, probably due to the genetic basis of significant correlations of grain yield with source and sink traits. We selected 15 candidate genes in the four QTLs consistently identified in the two populations by performing gene-based association and haplotype analyses using 2288 accessions from the 3K project. Among these, LOC_Os03g48970 for qTSN3b, LOC_Os06g04710 for qFLL6a, and LOC_Os07g32510 for qTGW7 were considered as the most likely candidate genes based on functional annotations. These results provide a basis for further study of candidate genes and for the development of high-yield rice varieties by balancing source-sink relationships using marker-assisted selection.


Assuntos
Grão Comestível/genética , Oryza/genética , Locos de Características Quantitativas , Cromossomos de Plantas/genética , Grão Comestível/crescimento & desenvolvimento , Genes de Plantas , Oryza/crescimento & desenvolvimento , Polimorfismo de Nucleotídeo Único
8.
PLoS Pathog ; 16(8): e1008326, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32804988

RESUMO

CRISPR/Cas has become the state-of-the-art technology for genetic manipulation in diverse organisms, enabling targeted genetic changes to be performed with unprecedented efficiency. Here we report on the first establishment of robust CRISPR/Cas editing in the important necrotrophic plant pathogen Botrytis cinerea based on the introduction of optimized Cas9-sgRNA ribonucleoprotein complexes (RNPs) into protoplasts. Editing yields were further improved by development of a novel strategy that combines RNP delivery with cotransformation of transiently stable vectors containing telomeres, which allowed temporary selection and convenient screening for marker-free editing events. We demonstrate that this approach provides superior editing rates compared to existing CRISPR/Cas-based methods in filamentous fungi, including the model plant pathogen Magnaporthe oryzae. Genome sequencing of edited strains revealed very few additional mutations and no evidence for RNP-mediated off-targeting. The high performance of telomere vector-mediated editing was demonstrated by random mutagenesis of codon 272 of the sdhB gene, a major determinant of resistance to succinate dehydrogenase inhibitor (SDHI) fungicides by in bulk replacement of the codon 272 with codons encoding all 20 amino acids. All exchanges were found at similar frequencies in the absence of selection but SDHI selection allowed the identification of novel amino acid substitutions which conferred differential resistance levels towards different SDHI fungicides. The increased efficiency and easy handling of RNP-based cotransformation is expected to accelerate molecular research in B. cinerea and other fungi.


Assuntos
Botrytis/fisiologia , Sistemas CRISPR-Cas , Edição de Genes , Oryza/microbiologia , Doenças das Plantas/microbiologia , Ribonucleoproteínas/antagonistas & inibidores , Telômero/genética , Vetores Genéticos/administração & dosagem , Vetores Genéticos/genética , Oryza/genética , Doenças das Plantas/genética , Ribonucleoproteínas/genética
9.
Nat Commun ; 11(1): 4079, 2020 08 14.
Artigo em Inglês | MEDLINE | ID: mdl-32796936

RESUMO

DNA methylation is an epigenetic modification that specifies the basic state of pluripotent stem cells and regulates the developmental transition from stem cells to various cell types. In flowering plants, the shoot apical meristem (SAM) contains a pluripotent stem cell population which generates the aerial part of plants including the germ cells. Under appropriate conditions, the SAM undergoes a developmental transition from a leaf-forming vegetative SAM to an inflorescence- and flower-forming reproductive SAM. While SAM characteristics are largely altered in this transition, the complete picture of DNA methylation remains elusive. Here, by analyzing whole-genome DNA methylation of isolated rice SAMs in the vegetative and reproductive stages, we show that methylation at CHH sites is kept high, particularly at transposable elements (TEs), in the vegetative SAM relative to the differentiated leaf, and increases in the reproductive SAM via the RNA-dependent DNA methylation pathway. We also show that half of the TEs that were highly methylated in gametes had already undergone CHH hypermethylation in the SAM. Our results indicate that changes in DNA methylation begin in the SAM long before germ cell differentiation to protect the genome from harmful TEs.


Assuntos
Metilação de DNA , Meristema/crescimento & desenvolvimento , Meristema/genética , Oryza/genética , Brotos de Planta/crescimento & desenvolvimento , Brotos de Planta/genética , Elementos de DNA Transponíveis , Biologia do Desenvolvimento , Epigenômica , Flores , Regulação da Expressão Gênica de Plantas , Inflorescência , Folhas de Planta/metabolismo , Proteínas de Plantas/genética
10.
PLoS One ; 15(8): e0237018, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32785241

RESUMO

Fragrance in rice grains is a key quality trait determining its acceptability and marketability. Intensive research on rice aroma identified mutations in betaine aldehyde dehydrogenase (OsBADH2) leading to production of aroma in rice. Gene editing technologies like CRISPR/Cas9 system has opened new avenues for accelerated improvement of rice grain quality through targeted mutagenesis. In this study, we have employed CRISPR/Cas9 tool to create novel alleles of OsBADH2 leading to introduction of aroma into an elite non-aromatic rice variety ASD16. PCR analysis of putative transformants using primers targeting the flanking regions of sgRNA in the 7th exon of OsBADH2 identified 37.5% potential multi-allelic mutations in T0 generation. Sensory evaluation test in the leaves of T0 lines identified thirteen lines belonging to five independent events producing aroma. Sequence analysis of these aromatic T0 lines identified 22 different types of mutations located within -17 bp to +15bp of sgRNA region. The -1/-2 bp deletion in the line # 8-19 and -8/-5 bp deletion in the line # 2-16 produced strong aroma and the phenotype was stably inherited in the T1 generation. Comparative volatile profiling detected novel aromatic compounds viz., pyrrolidine, pyridine, pyrazine, pyradazine and pyrozole in the grains of T1 progenies of line # 8-19. This study has demonstrated the use of CRISPR/Cas9 in creating novel alleles of OsBADH2 to introduce aroma into any non-aromatic rice varieties.


Assuntos
Betaína-Aldeído Desidrogenase/genética , Oryza/genética , Alelos , Betaína-Aldeído Desidrogenase/metabolismo , Sistemas CRISPR-Cas/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Edição de Genes/métodos , Genes de Plantas/genética , Genoma de Planta/genética , Mutação/genética , Odorantes/análise , Fenótipo , Plantas Geneticamente Modificadas/genética
11.
Ecotoxicol Environ Saf ; 204: 111063, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32791358

RESUMO

The lipocalins genes have been assigned for involving in the responses of organisms to various stress factors. The function of lipocalins under PCB18 stress was addressed by pathway complementation in the Oryza sativa L. OsTIL-silenced mutant. The growth of wild type (WT) and OsTIL-silenced mutant (MT) callus were suppressed by PCB18, and MT varieties were inhibited more seriously than WT varieties. Meanwhile, only WT varieties showed "Hormesis" effect. Compared with WT (3 day > 90.0%, 6 day ≤45.5%), MT varieties kept high removing efficiency by HPLC analysis. Varied gene transcription after OsTIL silencing was demonstrated between two varieties, especially obvious under PCB stress. Silenced OsTIL induced more protective gene transcriptions by qPCR analysis, OsVDE at 3 day, OsCHL, OsZEP1, OsZEP2 and OsUN at 6 day and OsZEP2 at 9 day. PCB18 stress further irritated these genes transcription in MT varieties. The defense stagy in WT varieties was that the transcriptions of lipocalins were inhibited to reduce PCB18 accumulation and toxicity. OsTIL could effectively limit PCB18 accumulation and toxicity. After TIL lacking, OsCHL, OsZEP1, OsZEP2 and OsUN in mutant were strongly evoked to against PCB stress. Remarkably, OsUN and OsZEP2 gene expressions were responded to PCB18 stress in both two varieties.


Assuntos
Poluentes Ambientais/toxicidade , Lipocalinas/genética , Oryza/efeitos dos fármacos , Estresse Oxidativo/efeitos dos fármacos , Bifenilos Policlorados/toxicidade , Ativação Transcricional/efeitos dos fármacos , Regulação da Expressão Gênica de Plantas , Inativação Gênica , Genes de Plantas , Oryza/genética , Oryza/crescimento & desenvolvimento , Estresse Oxidativo/genética
12.
Gene ; 761: 145043, 2020 Nov 30.
Artigo em Inglês | MEDLINE | ID: mdl-32777530

RESUMO

Tonoplast Intrinsic Proteins (TIPs) constitute a significant class of the aquaporins. The TIPs control water trade among cytosolic and vacuolar compartments and can also transport glycerol, ammonia, urea, hydrogen peroxide, metals/metalloids, and so forth. Additionally, TIPs are engaged with different abiotic stress responses and developmental processes like leaf expansion, root elongation and seed germination. In this study, ten TIP genes in the rice genome were identified from Oryza sativa ssp indica. Among these, representative groups of TIP genes were cloned and sequenced whilst some TIP sequences showed stop codons in the coding region. The secondary structure analysis represented six conserved transmembrane helices along with the inter-helical regions having conserved motifs. The representative three-dimensional tetrameric design of protein sequence of TIP1;1 displayed key features like NPA motifs, aromatic/arginine (ar/R) selectivity filters, and Froger's residues. The vacuolar localization, transmembrane topological properties, and conserved motif analysis of the cloned genes altogether supported their identity as TIPs. An unrooted phylogenetic tree delineated the relatedness of TIPs from Oryza with different species and bunched them into five clades. The promoter analysis uncovered key regulons associated with administering abiotic stress responses. Gene expression studies showed thatTIPsare differentially regulated under salt and drought stress at various time points in shoots and roots of rice. Also, the pattern of expression was found to be significantly variable in five different rice tissues. The heat-map based tissue and stress- specific expression analysis supported the experimental findings. In conclusion, the identification and transcript-level expression studies of TIPs significantly contribute towards the comprehension of their utilitarian significance in the abiotic stress response.


Assuntos
Proteínas de Membrana/genética , Proteínas de Membrana/metabolismo , Oryza/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Aquaporinas/genética , Aquaporinas/metabolismo , Clonagem Molecular/métodos , Secas , Perfilação da Expressão Gênica/métodos , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Oryza/metabolismo , Filogenia , Folhas de Planta/metabolismo , Cloreto de Sódio/metabolismo , Estresse Fisiológico/genética , Vacúolos/genética , Água/metabolismo
13.
Plant Mol Biol ; 104(3): 249-261, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32715397

RESUMO

Secondary cell wall not only provides rigidity and mechanical resistance to plants, but also has a large impact on plant growth and adaptation to environments. Biosynthesis of secondary cell wall is regulated by a complicated signaling transduction network; however, it is still unclear how the transcriptional regulation of secondary cell wall biosynthesis works at the molecular level. Here, we report in rice that OVATE family proteins 6 (OsOFP6) is a positive regulator in modulating expression of the genes related to biosynthesis of the secondary cell wall. Transgenic plants with knock-down of OsOFP6 by RNA interference showed increased leaf angle, which resulted from the thinner secondary cell wall with reduced amounts of cellulose and lignin, whilst overexpression of OsOFP6 in rice led to the thinker secondary cell wall with increased lignin content. Protein-protein interaction analysis revealed that OsOFP6 interacts with Oryza sativa homeobox 15 (OSH15), a class I KNOX protein. The interaction of OsOFP6 and OSH15 enhanced the transcriptional activity of OSH15 which binds to the promoter of OsIRX9 (Oryza sativa IRREGULAR XYLEM 9). Taken together, our study provides insights into the function of OsOFP6 in regulating leaf angle and the control of biosynthesis of secondary cell wall.


Assuntos
Parede Celular/metabolismo , Oryza/metabolismo , Folhas de Planta/metabolismo , Proteínas de Plantas/metabolismo , Proteínas Repressoras/metabolismo , Fatores de Transcrição/metabolismo , Arabidopsis/genética , Proteínas de Arabidopsis/genética , Parede Celular/ultraestrutura , Celulose/metabolismo , Regulação da Expressão Gênica de Plantas , Proteínas de Homeodomínio/metabolismo , Lignina/metabolismo , Oryza/genética , Folhas de Planta/anatomia & histologia , Folhas de Planta/citologia , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas/genética , Regiões Promotoras Genéticas , Domínios e Motivos de Interação entre Proteínas , Interferência de RNA , Proteínas Repressoras/genética , Fatores de Transcrição/genética , Xilema/metabolismo
14.
Mol Cell ; 79(5): 728-740.e6, 2020 09 03.
Artigo em Inglês | MEDLINE | ID: mdl-32721385

RESUMO

Cytosine base editors (CBEs) generate C-to-T nucleotide substitutions in genomic target sites without inducing double-strand breaks. However, CBEs such as BE3 can cause genome-wide off-target changes via sgRNA-independent DNA deamination. By leveraging the orthogonal R-loops generated by SaCas9 nickase to mimic actively transcribed genomic loci that are more susceptible to cytidine deaminase, we set up a high-throughput assay for assessing sgRNA-independent off-target effects of CBEs in rice protoplasts. The reliability of this assay was confirmed by the whole-genome sequencing (WGS) of 10 base editors in regenerated rice plants. The R-loop assay was used to screen a series of rationally designed A3Bctd-BE3 variants for improved specificity. We obtained 2 efficient CBE variants, A3Bctd-VHM-BE3 and A3Bctd-KKR-BE3, and the WGS analysis revealed that these new CBEs eliminated sgRNA-independent DNA off-target edits in rice plants. Moreover, these 2 base editor variants were more precise at their target sites by producing fewer multiple C edits.


Assuntos
Citidina Desaminase/genética , Citosina , Edição de Genes/métodos , Antígenos de Histocompatibilidade Menor/genética , Oryza/genética , Citosina/química , Genes de Plantas , Humanos , Mutação , RNA Guia/química , RNA de Plantas/química , Reprodutibilidade dos Testes
15.
Nature ; 584(7819): 109-114, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32669710

RESUMO

The size of plants is largely determined by growth of the stem. Stem elongation is stimulated by gibberellic acid1-3. Here we show that internode stem elongation in rice is regulated antagonistically by an 'accelerator' and a 'decelerator' in concert with gibberellic acid. Expression of a gene we name ACCELERATOR OF INTERNODE ELONGATION 1 (ACE1), which encodes a protein of unknown function, confers cells of the intercalary meristematic region with the competence for cell division, leading to internode elongation in the presence of gibberellic acid. By contrast, upregulation of DECELERATOR OF INTERNODE ELONGATION 1 (DEC1), which encodes a zinc-finger transcription factor, suppresses internode elongation, whereas downregulation of DEC1 allows internode elongation. We also show that the mechanism of internode elongation that is mediated by ACE1 and DEC1 is conserved in the Gramineae family. Furthermore, an analysis of genetic diversity suggests that mutations in ACE1 and DEC1 have historically contributed to the selection of shorter plants in domesticated populations of rice to increase their resistance to lodging, and of taller plants in wild species of rice for adaptation to growth in deep water. Our identification of these antagonistic regulatory factors enhances our understanding of the gibberellic acid response as an additional mechanism that regulates internode elongation and environmental fitness, beyond biosynthesis and gibberellic acid signal transduction.


Assuntos
Giberelinas/metabolismo , Oryza/crescimento & desenvolvimento , Oryza/metabolismo , Caules de Planta/crescimento & desenvolvimento , Caules de Planta/metabolismo , Aclimatação , Mutação , Oryza/genética , Reguladores de Crescimento de Planta/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Caules de Planta/genética , Locos de Características Quantitativas , Transdução de Sinais
16.
PLoS One ; 15(7): e0236139, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32667944

RESUMO

In this study, we suggested a hypothesis test method that was robust to different genotype encodings in a genome-wide association analysis of continuous traits. When the population stratification is corrected for using a method based on principal component analysis, ordinally (or categorically) encoded genotypes are adjusted and turn into continuous values. Due to the adjustment of the encoded genotype, the association test result using conventional methods, such as the test of Pearson's correlation coefficient, was shown to be dependent on how genotypes were encoded. To overcome this shortcoming, we proposed a non-parametric test based on Kendall's tau. Because Kendall's tau deals with rank, rather than value, associations between adjusted genotype and phenotype values, Kendall's test can be more robust than Pearson's test under different genotype encodings. We assessed the robustness of Kendall's test and compared with that of Pearson's test in terms of the difference in p-values obtained by using different genotype encodings. With simulated as well as real data set, we demonstrated that Kendall's test was more robust than Pearson's test under different genotype encodings. The proposed method can be applicable to the broad topics of interest in population genetics and comparative genomics, in which novel genetic variants are associated with traits. This study may also bring about a cautious approach to the genotype encoding in the numerical analysis.


Assuntos
Algoritmos , Genoma de Planta , Genótipo , Oryza/genética , Fenótipo , Proteínas de Plantas/genética , Estudos de Associação Genética , Estudo de Associação Genômica Ampla
17.
PLoS One ; 15(7): e0227785, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32673318

RESUMO

A panel of 60 genotypes comprising New Plant Types (NPTs) along with indica, tropical and temperate japonica genotypes was phenotypically evaluated for four seasons in irrigated situation for grain yield per se and component traits. Twenty NPT genotypes were found promising with an average grain yield varying from 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 8% within genotypes, 68% among the genotypes within the population and 24% among the populations were observed (AMOVA). This information may help in identification of potential parents for development of transgressive segregants with very high yield. The association analysis using GLM and MLM models led to the identification of 30 and 10 SSR markers associated with 70 and 16 QTLs, respectively. Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely tiller number (qTL-6.1, qTL-11.1, qTL-4.1), panicle length (qPL-1.1, qPL-5.1, qPL-7.1, qPL-8.1), flag leaf length (qFLL-8.1, qFLL-9.1), flag leaf width (qFLW-6.2, qFLW-5.1, qFLW-8.1, qFLW-7.1), total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight (qTGW-a1.1, qTGW-a9.2, qTGW-5.1, qTGW-8.1), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se (qYLD-5.1, qYLD-6.1a, qYLD-11.1).Some of the SSRs were co-localized with more than two traits. The highest co-localization was identified with RM5709 linked to nine traits, followed by RM297 with five traits. Similarly, RM5575, RM204, RM168, RM112, RM26499 and RM22899 were also recorded to be co-localized with more than one trait and could be rated as important for marker-assisted backcross breeding programs, for pyramiding of these QTLs for important yield traits, to produce new-generation rice for prospective increment in yield potentiality and breaking yield ceiling.


Assuntos
Oryza/genética , Locos de Características Quantitativas , Grão Comestível/genética , Variação Genética , Genótipo , Repetições de Microssatélites/genética , Oryza/fisiologia , Fenótipo , Folhas de Planta/genética , Folhas de Planta/fisiologia , Análise de Componente Principal
18.
Plant Mol Biol ; 104(1-2): 137-150, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32623622

RESUMO

KEY MESSAGE: OsGhd7 gene was discovered by screening our rice activation tagging population. CRISPR-Cas9 created knockouts of OsGhd7 conferred early flowering and early maturity in rice varieties across multiple geographical locations in China. Our research shows that OsGhd7 is a good target for breeding early maturity rice varieties, and an excellent example of the advantages of applying the CRISPR-Cas9 technology for trait improvement. Flowering time (heading date) is an important trait for crop cultivation and yield. In this study, we discovered a late flowering gene OsGhd7 by screening our rice activation tagging population, and demonstrated that overexpression of OsGhd7 delayed flowering time in rice, and the delay in flowering time depended on the transgene expression level. OsGhd7 is a functional allele of the Ghd7 gene family; knockouts of OsGhd7 generated by CRISPR-Cas9 significantly accelerated flowering time and the earliness of the flowering time depended on field location. The homozygous OsGhd7 knockout lines showed approximately 8, 10, and 20 days earlier flowering than controls at three different locations in China (Changsha City, Sanya City, and Beijing City, respectively) that varied from 18.25° N to 39.90° N. Furthermore, knockouts of OsGhd7 also showed an early flowering phenotype in different rice varieties, indicating OsGhd7 can be used as a common target gene for using the CRISPR technology to modulate rice flowering time. The importance of OsGhd7 and CRISPR technology for breeding early maturity rice varieties are discussed.


Assuntos
Sistemas CRISPR-Cas/genética , Flores/genética , Oryza/genética , Proteínas de Plantas/genética , Alelos , Sequência de Bases , Clonagem Molecular , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Flores/metabolismo , Regulação da Expressão Gênica de Plantas , Técnicas de Inativação de Genes , Oryza/metabolismo , Fenótipo , Desenvolvimento Vegetal/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas/genética , Reprodução , Alinhamento de Sequência
19.
Plant Mol Biol ; 104(1-2): 97-112, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32643113

RESUMO

KEY MESSAGE: By integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars. Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, α-Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences from Arabidopsis heat-shock genes also suggest that OsBIP2 may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars.


Assuntos
Resposta ao Choque Térmico/genética , Oryza/genética , Oryza/metabolismo , Locos de Características Quantitativas/genética , Locos de Características Quantitativas/fisiologia , Bases de Dados Genéticas , Regulação da Expressão Gênica de Plantas , Genes de Plantas/genética , Genômica , Temperatura Alta , Oryza/crescimento & desenvolvimento , Fenótipo , Desenvolvimento Vegetal/genética , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Regiões Promotoras Genéticas , Reprodução , Estresse Fisiológico/genética , Termotolerância
20.
PLoS One ; 15(7): e0236349, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32701993

RESUMO

Peptide signalling is an integral part of cell-to-cell communication which helps to relay the information responsible for coordinating cell proliferation and differentiation. Phytosulfokine Receptor (PSKR) is a transmembrane LRR-RLK family protein with a binding site for small signalling peptide, phytosulfokine (PSK). PSK signalling through PSKR promotes normal growth and development and also plays a role in defense responses. Like other RLKs, these PSKRs might have a role in signal transduction pathways related to abiotic stress responses. Genome-wide analysis of phytosulfokine receptor gene family has led to the identification of fifteen putative members in the Oryza sativa genome. The expression analysis of OsPSKR genes done using RNA-seq data, showed that these genes were differentially expressed in different tissues and responded specifically to heat, salt, drought and cold stress. Furthermore, the real-time quantitative PCR for fifteen OsPSKR genes revealed temporally and spatially regulated gene expression corresponding to salinity and drought stress. Our results provide useful information for a better understanding of OsPSKR genes and provide the foundation for additional functional exploration of the rice PSKR gene family in development and stress response.


Assuntos
Genoma de Planta/genética , Oryza/genética , Hormônios Peptídicos/genética , Peptídeos/genética , Proteínas de Plantas/genética , Secas , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/genética , Peptídeos/classificação , Filogenia , Salinidade , Transdução de Sinais/genética , Cloreto de Sódio/metabolismo , Estresse Fisiológico/genética
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