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1.
Plant Physiol ; 192(1): 307-325, 2023 05 02.
Artigo em Inglês | MEDLINE | ID: mdl-36755501

RESUMO

Y900 is one of the top hybrid rice (Oryza sativa) varieties, with its yield exceeding 15 t·hm-2. To dissect the mechanism of heterosis, we sequenced the male parent line R900 and female parent line Y58S using long-read and Hi-C technology. High-quality reference genomes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 single-nucleotide polymorphisms, 299,149 insertions/deletions, and 4,757 structural variations. The level of variation between Y58S and R900 was the lowest among the comparisons of Y58S with other rice genomes. More than 75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the portion of Geng/japonica (GJ)-type genetic components from different male parents increased with yield increasing in their corresponding hybrids. Transcriptome analysis revealed that the partial dominance effect was the main genetic effect that constituted the heterosis of Y900. In the hybrid, both alleles from the two parents were expressed, and their expression patterns were dynamically regulated in different tissues. The cis-regulation was dominant for young panicle tissues, while trans-regulation was more common in leaf tissues. Overdominance was surprisingly prevalent in stems and more likely regulated by the trans-regulation mechanism. Additionally, R900 contained many excellent GJ haplotypes, such as NARROW LEAF1, Oryza sativa SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13, and Grain number, plant height, and heading date8, making it a good complement to Y58S. The fine-tuned mechanism of heterosis involves genome-wide variation, GJ introgression, key functional genes, and dynamic gene/allele expression and regulation pattern changes in different tissues and growth stages.


Assuntos
Vigor Híbrido , Oryza , Vigor Híbrido/genética , Oryza/genética , Perfilação da Expressão Gênica , Hibridização Genética
2.
Proc Natl Acad Sci U S A ; 118(29)2021 07 20.
Artigo em Inglês | MEDLINE | ID: mdl-34266944

RESUMO

Plant architecture is an important agronomic trait that affects crop yield. Here, we report that a gene involved in programmed cell death, OsPDCD5, negatively regulates plant architecture and grain yield in rice. We used the CRISPR/Cas9 system to introduce loss-of-function mutations into OsPDCD5 in 11 rice cultivars. Targeted mutagenesis of OsPDCD5 enhanced grain yield and improved plant architecture by increasing plant height and optimizing panicle type and grain shape. Transcriptome analysis showed that OsPDCD5 knockout affected auxin biosynthesis, as well as the gibberellin and cytokinin biosynthesis and signaling pathways. OsPDCD5 interacted directly with OsAGAP, and OsAGAP positively regulated plant architecture and grain yield in rice. Collectively, these findings demonstrate that OsPDCD5 is a promising candidate gene for breeding super rice cultivars with increased yield potential and superior quality.


Assuntos
Proteínas Reguladoras de Apoptose/metabolismo , Grão Comestível/crescimento & desenvolvimento , Proteínas de Plantas/metabolismo , Estruturas Vegetais/crescimento & desenvolvimento , Proteínas Reguladoras de Apoptose/genética , Citocininas/metabolismo , Grão Comestível/genética , Regulação da Expressão Gênica de Plantas , Giberelinas/metabolismo , Ácidos Indolacéticos/metabolismo , Mutagênese , Oryza/genética , Oryza/crescimento & desenvolvimento , Melhoramento Vegetal , Proteínas de Plantas/genética , Estruturas Vegetais/genética , Plantas Geneticamente Modificadas , Ligação Proteica , Transdução de Sinais/genética
3.
J Integr Plant Biol ; 63(10): 1695-1711, 2021 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-34302720

RESUMO

Interactions and co-evolution between plants and herbivorous insects are critically important in agriculture. Brown planthopper (BPH) is the most severe insect of rice, and the biotypes adapt to feed on different rice genotypes. Here, we present genomics analyses on 1,520 global rice germplasms for resistance to three BPH biotypes. Genome-wide association studies identified 3,502 single nucleotide polymorphisms (SNPs) and 59 loci associated with BPH resistance in rice. We cloned a previously unidentified gene Bph37 that confers resistance to BPH. The associated loci showed high nucleotide diversity. Genome-wide scans for trans-species polymorphisms revealed ancient balancing selection at the loci. The secondarily evolved insect biotypes II and III exhibited significantly higher virulence and overcame more rice varieties than the primary biotype I. In response, more SNPs and loci evolved in rice for resistance to biotypes II and III. Notably, three exceptional large regions with high SNP density and resistance-associated loci on chromosomes 4 and 6 appear distinct between the resistant and susceptible rice varieties. Surprisingly, these regions in resistant rice might have been retained from wild species Oryza nivara. Our findings expand the understanding of long-term interactions between rice and BPH and provide resistance genes and germplasm resources for breeding durable BPH-resistant rice varieties.


Assuntos
Evolução Biológica , Hemípteros , Herbivoria , Oryza/genética , Seleção Genética , Animais , Cromossomos de Plantas , Pool Gênico , Especificidade da Espécie
4.
Plant Biotechnol J ; 19(7): 1443-1455, 2021 07.
Artigo em Inglês | MEDLINE | ID: mdl-33544956

RESUMO

The development of embryo sacs is crucial for seed production in plants, but the genetic basis regulating the meiotic crossover formation in the macrospore and microspore mother cells remains largely unclear. Here, we report the characterization of a spontaneous rice female sterile variation 1 mutant (fsv1) that showed severe embryo sacs abortion with low seed-setting rate. Through map-based cloning and functional analyses, we isolated the causal gene of fsv1, OsMLH3 encoding a MutL-homolog 3 protein, an ortholog of HvMLH3 in barley and AtMLH3 in Arabidopsis. OsMLH3 and OsMLH1 (MutL-homolog 1) interact to form a heterodimer (MutLγ) to promote crossover formation in the macrospore and microspore mother cells and development of functional megaspore during meiosis, defective OsMLH3 or OsMLH1 in fsv1 and CRISPR/Cas9-based knockout lines results in reduced type I crossover and bivalent frequency. The fsv1 and OsMLH3-knockout lines are valuable germplasms for development of female sterile restorer lines for mechanized seed production of hybrid rice.


Assuntos
Troca Genética , Oryza , Fertilidade , Meiose/genética , Proteínas MutL/genética , Oryza/genética
5.
Plant Biotechnol J ; 19(2): 251-260, 2021 02.
Artigo em Inglês | MEDLINE | ID: mdl-32741081

RESUMO

Heterosis utilization is the most effective way to improve rice yields. The cytoplasmic male-sterility (CMS) and photoperiod/thermosensitive genic male-sterility (PTGMS) systems have been widely used in rice production. However, the rate of resource utilization for the CMS system hybrid rice is low, and the hybrid seed production for the PTGMS system is affected by the environment. The technical limitations of these two breeding methods restrict the rapid development of hybrid rice. The advantages of the genic male-sterility (GMS) rice, such as stable sterility and free combination, can fill the gaps of the first two generations of hybrid rice technology. At present, the third-generation hybrid rice breeding technology is being used to realize the application of GMS materials in hybrid rice. This study aimed to use an artificial CMS gene as a pollen killer to create a smart sterile line for hybrid rice production. The clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9) technology was used to successfully obtain a CYP703A3-deficient male-sterile mutant containing no genetically modified component in the genetic background of indica 9311. Through young ear callus transformation, this mutant was transformed with three sets of element-linked expression vectors, including pollen fertility restoration gene CYP703A3, pollen-lethality gene orfH79 and selection marker gene DsRed2. The maintainer 9311-3B with stable inheritance was obtained, which could realize the batch breeding of GMS materials. Further, the sterile line 9311-3A and restorer lines were used for hybridization, and a batch of superior combinations of hybrid rice was obtained.


Assuntos
Oryza , Infertilidade das Plantas/genética , Oryza/genética , Melhoramento Vegetal , Tecnologia
6.
Sci China Life Sci ; 64(9): 1502-1521, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-33165813

RESUMO

The brown planthopper (BPH) (Nilaparvata lugens Stål) is a highly destructive pest that seriously damages rice (Oryza sativa L.) and causes severe yield losses. To better understand the physiological and metabolic mechanisms through which BPHs respond to resistant rice, we combined mass-spectrometry-based lipidomics with transcriptomic analysis and gene knockdown techniques to compare the lipidomes of BPHs feeding on either of the two resistant (NIL-Bph6 and NIL-Bph9) plants or a wild-type, BPH susceptible (9311) plant. Insects that were fed on resistant rice transformed triglyceride (TG) to phosphatidylcholine (PC) and digalactosyldiacylglycerol (DGDG), with these lipid classes showing significant alterations in fatty acid composition. Moreover, the insects that were fed on resistant rice were characterized by prominent expression changes in genes involved in lipid metabolism processes. Knockdown of the NlBmm gene, which encodes a lipase that regulates the mobilization of lipid reserves, significantly increased TG content and feeding performance of BPHs on resistant plants relative to dsGFP-injected BPHs. Our study provides the first detailed description of lipid changes in BPHs fed on resistant and susceptible rice genotypes. Results from BPHs fed on resistant rice plants reveal that these insects can accelerate TG mobilization to provide energy for cell proliferation, body maintenance, growth and oviposition.


Assuntos
Hemípteros/genética , Hemípteros/metabolismo , Herbivoria , Lipidômica , Lipólise , Oryza/genética , Oryza/metabolismo , Animais
7.
Front Plant Sci ; 11: 571280, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32973857

RESUMO

The brown planthopper (BPH), Nilaparvata lugens Stål, is one of the major pests of rice. It uses its stylet to penetrate rice phloem, feeding on rice sap and causing direct damage to rice or even plant death. During the feeding process, BPHs secrete saliva into plant tissues, which plays crucial roles in the plant-insect interactions. However, little is known about how the salivary proteins secreted by BPH affect feeding ability and how they induce plant immune responses. Here, we identified an N. lugens Salivary Protein 1 (NlSP1) by screening salivary proteome and characterized its functions in BPH and plants. NlSP1 induces cell death, H2O2 accumulation, the expression of defense-related genes, and callose deposition in planta. The active region of NlSP1 that induces plant cell death is located in its N-terminal region. Inhibition of NlSP1 expression in BPHs reduced their feeding ability and had a lethal effect on them. Most importantly, we demonstrated that NlSP1 was able to be secreted into rice plant during feeding process and form a complex with certain interacting partner of rice. These results provide a detailed characterization of a salivary protein from BPHs and offers new insights into our understanding of rice-BPH interaction.

8.
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
9.
Proc Natl Acad Sci U S A ; 117(38): 23499-23509, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32907946

RESUMO

Understanding the molecular basis of male sterility and developing practical male-sterility systems are essential for heterosis utilization and commercial hybrid seed production in crops. Here, we report molecular regulation by genic male-sterility gene maize male sterility 7 (ZmMs7) and its application for developing a dominant male-sterility system in multiple species. ZmMs7 is specifically expressed in maize anthers, encodes a plant homeodomain (PHD) finger protein that functions as a transcriptional activator, and plays a key role in tapetal development and pollen exine formation. ZmMs7 can interact with maize nuclear factor Y (NF-Y) subunits to form ZmMs7-NF-YA6-YB2-YC9/12/15 protein complexes that activate target genes by directly binding to CCAAT box in their promoter regions. Premature expression of ZmMs7 in maize by an anther-specific promoter p5126 results in dominant and complete male sterility but normal vegetative growth and female fertility. Early expression of ZmMs7 downstream genes induced by prematurely expressed ZmMs7 leads to abnormal tapetal development and pollen exine formation in p5126-ZmMs7 maize lines. The p5126-ZmMs7 transgenic rice and Arabidopsis plants display similar dominant male sterility. Meanwhile, the mCherry gene coupled with p5126-ZmMs7 facilitates the sorting of dominant sterility seeds based on fluorescent selection. In addition, both the ms7-6007 recessive male-sterility line and p5126-ZmMs7M dominant male-sterility line are highly stable under different genetic germplasms and thus applicable for hybrid maize breeding. Together, our work provides insight into the mechanisms of anther and pollen development and a promising technology for hybrid seed production in crops.


Assuntos
Regulação da Expressão Gênica de Plantas/genética , Infertilidade das Plantas/genética , Proteínas de Plantas/genética , Regiões Promotoras Genéticas/genética , Zea mays/genética , Arabidopsis/genética , Produtos Agrícolas , Oryza/genética , Plantas Geneticamente Modificadas/genética , Plantas Geneticamente Modificadas/crescimento & desenvolvimento , Pólen/genética , Zea mays/crescimento & desenvolvimento
10.
Proc Natl Acad Sci U S A ; 117(1): 271-277, 2020 01 07.
Artigo em Inglês | MEDLINE | ID: mdl-31848246

RESUMO

Brown planthopper (BPH) is one of the most destructive insects affecting rice (Oryza sativa L.) production. Phenylalanine ammonia-lyase (PAL) is a key enzyme involved in plant defense against pathogens, but the role of PAL in insect resistance is still poorly understood. Here we show that expression of the majority of PALs in rice is significantly induced by BPH feeding. Knockdown of OsPALs significantly reduces BPH resistance, whereas overexpression of OsPAL8 in a susceptible rice cultivar significantly enhances its BPH resistance. We found that OsPALs mediate resistance to BPH by regulating the biosynthesis and accumulation of salicylic acid and lignin. Furthermore, we show that expression of OsPAL6 and OsPAL8 in response to BPH attack is directly up-regulated by OsMYB30, an R2R3 MYB transcription factor. Taken together, our results demonstrate that the phenylpropanoid pathway plays an important role in BPH resistance response, and provide valuable targets for genetic improvement of BPH resistance in rice.


Assuntos
Hemípteros/efeitos dos fármacos , Oryza/enzimologia , Oryza/metabolismo , Fenilalanina Amônia-Liase/metabolismo , Fenilalanina Amônia-Liase/farmacologia , Doenças das Plantas/imunologia , Fatores de Transcrição/metabolismo , Animais , DNA de Plantas/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Técnicas de Silenciamento de Genes , Genes de Plantas , Interações Hospedeiro-Parasita/genética , Interações Hospedeiro-Parasita/fisiologia , Lignina/metabolismo , Oryza/genética , Oryza/imunologia , Fenilalanina Amônia-Liase/genética , Doenças das Plantas/genética , Doenças das Plantas/parasitologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Plantas Geneticamente Modificadas/genética , Ácido Salicílico/metabolismo
11.
Rice (N Y) ; 12(1): 39, 2019 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-31140005

RESUMO

BACKGROUND: The breeding and large-scale adoption of hybrid rice is an important achievement in modern agriculture. Mechanized seed production is urgently needed for widespread adoption of hybrid rice because it can compensate for the shortage of manual labor to meet the growing food demands in China. RESULTS: Here, we report the development of a mechanized hybrid rice seed production method using a female sterile rice. In this method, three closely linked gene expression cassettes were introduced into female sterile rice. The three expression cassettes are: 1) a rice female fertility gene expression cassette; 2) a pollen-lethal gene expression cassette; and 3) a red fluorescence protein gene expression cassette. During the self-fertilization process of a heterozygous transgenic rice plant, pollen grains carrying the transgene die off and cannot participate in fertilization; pollen grains not carrying a transgene can normally fertilize the female gamete, leading to fructification. By means of fluorescence-assisted sorting, homogeneous female sterile rice seeds are sorted out from other seeds carrying the transgene and are used for mechanized hybrid rice seed production; heterozygous seeds carrying the transgene can then be used in the multiplication of female sterile rice. CONCLUSIONS: This technology solves the difficulty of multiplying female-sterile rice, allows for mechanized production of hybrid rice seed, and will prove especially valuable in systems using a mixed-planting, mixed-harvesting approach. Moreover, it uses transgenic technology that has not yet been employed in a seed production process in which the output is non-transgenic seeds.

12.
Proc Natl Acad Sci U S A ; 116(9): 3494-3501, 2019 02 26.
Artigo em Inglês | MEDLINE | ID: mdl-30808744

RESUMO

Rice (Oryza sativa L.) is a chilling-sensitive staple crop that originated in subtropical regions of Asia. Introduction of the chilling tolerance trait enables the expansion of rice cultivation to temperate regions. Here we report the cloning and characterization of HAN1, a quantitative trait locus (QTL) that confers chilling tolerance on temperate japonica rice. HAN1 encodes an oxidase that catalyzes the conversion of biologically active jasmonoyl-L-isoleucine (JA-Ile) to the inactive form 12-hydroxy-JA-Ile (12OH-JA-Ile) and fine-tunes the JA-mediated chilling response. Natural variants in HAN1 diverged between indica and japonica rice during domestication. A specific allele from temperate japonica rice, which gained a putative MYB cis-element in the promoter of HAN1 during the divergence of the two japonica ecotypes, enhances the chilling tolerance of temperate japonica rice and allows it to adapt to a temperate climate. The results of this study extend our understanding of the northward expansion of rice cultivation and provide a target gene for the improvement of chilling tolerance in rice.


Assuntos
Adaptação Fisiológica/genética , Oryza/genética , Proteínas de Plantas/genética , Estresse Fisiológico/genética , Clima , Ciclopentanos/metabolismo , Variação Genética , Isoleucina/análogos & derivados , Isoleucina/genética , Isoleucina/metabolismo , Oryza/crescimento & desenvolvimento , Locos de Características Quantitativas/genética
13.
Rice (N Y) ; 10(1): 43, 2017 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-28936774

RESUMO

BACKGROUND: Increasing rice yield with fewer external inputs is critical to ensuring food security, reducing environmental costs, and improving returns. Use of hybrid rice has expanded greatly in China due to its higher yield potential. Meanwhile, large and increasing amounts of nitrogen (N) fertilizers have been used for expanding rice production in China. It is not clear to what extent the success of hybrid rice in China is associated with N fertilizer inputs. FINDINGS: We observed that the higher grain yield with N fertilizer in hybrid rice was driven more by a higher yield without N fertilizer than by increases in grain yield with N fertilizer under moderate to high soil fertility conditions. CONCLUSIONS: Our results suggest that greater application of N fertilizers is not needed to benefit from hybrid rice production under moderate to high soil fertility conditions, and that improving and maintaining soil fertility should be a focus for sustaining hybrid rice production. Moreover, our study also indicates that zero-N testing may be a potentially useful tool to develop hybrid rice with high yield and without requirement of greater external N inputs under moderate to high soil fertility conditions.

14.
Proc Natl Acad Sci U S A ; 113(41): E6026-E6035, 2016 10 11.
Artigo em Inglês | MEDLINE | ID: mdl-27663737

RESUMO

Hybrid rice is the dominant form of rice planted in China, and its use has extended worldwide since the 1970s. It offers great yield advantages and has contributed greatly to the world's food security. However, the molecular mechanisms underlying heterosis have remained a mystery. In this study we integrated genetics and omics analyses to determine the candidate genes for yield heterosis in a model two-line rice hybrid system, Liang-you-pei 9 (LYP9) and its parents. Phenomics study revealed that the better parent heterosis (BPH) of yield in hybrid is not ascribed to BPH of all the yield components but is specific to the BPH of spikelet number per panicle (SPP) and paternal parent heterosis (PPH) of effective panicle number (EPN). Genetic analyses then identified multiple quantitative trait loci (QTLs) for these two components. Moreover, a number of differentially expressed genes and alleles in the hybrid were mapped by transcriptome profiling to the QTL regions as possible candidate genes. In parallel, a major QTL for yield heterosis, rice heterosis 8 (RH8), was found to be the DTH8/Ghd8/LHD1 gene. Based on the shared allelic heterozygosity of RH8 in many hybrid rice cultivars, a common mechanism for yield heterosis in the present commercial hybrid rice is proposed.


Assuntos
Genoma de Planta , Vigor Híbrido/genética , Hibridização Genética , Oryza/genética , Oryza/metabolismo , Fenótipo , Locos de Características Quantitativas , Transcriptoma , Alelos , Mapeamento Cromossômico , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genes de Plantas , Ligação Genética , Genômica/métodos , Genótipo , Polimorfismo de Nucleotídeo Único , Característica Quantitativa Herdável
15.
J Integr Plant Biol ; 58(10): 836-847, 2016 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-26936408

RESUMO

Traits such as grain shape, panicle length and seed shattering, play important roles in grain yield and harvest. In this study, the cloning and functional analysis of PANICLE TRAITS 2 (PT2), a novel gene from the Indica rice Chuandali (CDL), is reported. PT2 is synonymous with Growth-Regulating Factor 4 (OsGRF4), which encodes a growth-regulating factor that positively regulates grain shape and panicle length and negatively regulates seed shattering. Higher expression of OsGRF4 is correlated with larger grain, longer panicle and lower seed shattering. A unique OsGRF4 mutation, which occurs at the OsmiRNA396 target site of OsGRF4, seems to be associated with high levels of OsGRF4 expression, and results in phenotypic difference. Further research showed that OsGRF4 regulated two cytokinin dehydrogenase precursor genes (CKX5 and CKX1) resulting in increased cytokinin levels, which might affect the panicle traits. High storage capacity and moderate seed shattering of OsGRF4 may be useful in high-yield breeding and mechanized harvesting of rice. Our findings provide additional insight into the molecular basis of panicle growth.


Assuntos
Grão Comestível/crescimento & desenvolvimento , Grão Comestível/metabolismo , Oryza/crescimento & desenvolvimento , Oryza/genética , Proteínas de Plantas/metabolismo , Citocininas/metabolismo , Grão Comestível/genética , Regulação da Expressão Gênica de Plantas , Oxirredutases/genética , Oxirredutases/metabolismo , Proteínas de Plantas/genética , Sementes/genética , Sementes/crescimento & desenvolvimento , Sementes/metabolismo
16.
Mol Genet Genomics ; 291(1): 297-307, 2016 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-26334612

RESUMO

The future of rice breeding will likely be built on the basis of the further utilization of heterosis between elite cultivars and genetic resources from distant subspecies of rice. Previous studies have proved that exogenous genomic DNA transformation methods can be used to transfer genetic information from distant relatives (donor) into cultivated rice (recipient). However, the mechanism underlying this form of genetic transfer is poorly characterized, and the genes that cause the phenotypic changes in these variants are typically difficult to identify. This study examined YVB, a stable variant line with greatly improved grain quality traits that was derived from an indica variety (V20B) by transferring genomic DNA of O.minuta through the "spike-stalk injection method (SIM)". We used restriction-site associated DNA sequencing technology (RAD-seq) to evaluate a population of BC1F5 backcross lines (YVB × V20B); the RAD-seq data were used to construct a genetic linkage map with high-density SNPs for use in association analysis exploring genotype-phenotype relationships at the whole-genome level. A total of 17 quantitative trait loci (QTLs) for rice quality traits were mapped to chromosomes 3, 5, 6, 8, and 9. 8 major QTLs controlling different phenotypic variations were mapped to the same region of chromosome 5. This region contained the GS5 gene for grain weight and the qSW5/GW5 gene for grain width. This study provides new resources and insights into the molecular mechanisms of grain trait phenotypic variation and the transmission of genetic information via the introduction of genomic DNA to a distantly related crop relative species.


Assuntos
Grão Comestível/genética , Oryza/genética , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Cruzamento/métodos , Mapeamento Cromossômico/métodos , Cromossomos de Plantas/genética , Testes Genéticos/métodos , Genótipo , Endogamia/métodos , Fenótipo , Análise de Sequência de DNA/métodos
17.
Planta ; 241(1): 157-66, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25236969

RESUMO

MAIN CONCLUSION: In this study, we reported that a F-box protein, OsADF, as one of the direct targets of TDR , plays a critical role in rice tapetum cell development and pollen formation. The tapetum, the innermost sporophytic tissue of anther, plays an important supportive role in male reproduction in flowering plants. After meiosis, tapetal cells undergo programmed cell death (PCD) and provide nutrients for pollen development. Previously we showed that tapetum degeneration retardation (TDR), a basic helix-loop-helix transcription factor, can trigger tapetal PCD and control pollen wall development during anther development. However, the comprehensive regulatory network of TDR remains to be investigated. In this study, we cloned and characterized a panicle-specific expression F-box protein, anther development F-box (OsADF). By qRT-PCR and RNA in situ hybridization, we further confirmed that OsADF expressed specially in tapetal cells from stage 9 to stage 12 during anther development. In consistent with this specific expression pattern, the RNAi transgenic lines of OsADF exhibited abnormal tapetal degeneration and aborted microspores development, which eventually grew pollens with reduced fertility. Furthermore, we demonstrated that the TDR, a key regulator in controlling rice anther development, could regulate directly the expression of OsADF by binding to E-box motifs of its promoter. Therefore, this work highlighted the possible regulatory role of TDR, which regulates tapetal cell development and pollen formation via triggering the possible ADF-mediated proteolysis pathway.


Assuntos
Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Proteínas F-Box/genética , Flores/genética , Oryza/genética , Proteínas de Plantas/genética , Sequência de Aminoácidos , Sequência de Bases , Fatores de Transcrição Hélice-Alça-Hélice Básicos/metabolismo , Membrana Celular/metabolismo , Proteínas F-Box/classificação , Proteínas F-Box/metabolismo , Flores/crescimento & desenvolvimento , Flores/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Regulação da Expressão Gênica de Plantas , Hibridização In Situ , Microscopia de Fluorescência , Modelos Genéticos , Dados de Sequência Molecular , Cebolas/genética , Cebolas/metabolismo , Oryza/crescimento & desenvolvimento , Oryza/metabolismo , Filogenia , Epiderme Vegetal/citologia , Epiderme Vegetal/metabolismo , Proteínas de Plantas/classificação , Proteínas de Plantas/metabolismo , Interferência de RNA , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Fatores de Tempo
18.
Proc Natl Acad Sci U S A ; 111(46): 16337-42, 2014 Nov 18.
Artigo em Inglês | MEDLINE | ID: mdl-25378698

RESUMO

Success of modern agriculture relies heavily on breeding of crops with maximal regional adaptability and yield potentials. A major limiting factor for crop cultivation is their flowering time, which is strongly regulated by day length (photoperiod) and temperature. Here we report identification and characterization of Days to heading 7 (DTH7), a major genetic locus underlying photoperiod sensitivity and grain yield in rice. Map-based cloning reveals that DTH7 encodes a pseudo-response regulator protein and its expression is regulated by photoperiod. We show that in long days DTH7 acts downstream of the photoreceptor phytochrome B to repress the expression of Ehd1, an up-regulator of the "florigen" genes (Hd3a and RFT1), leading to delayed flowering. Further, we find that haplotype combinations of DTH7 with Grain number, plant height, and heading date 7 (Ghd7) and DTH8 correlate well with the heading date and grain yield of rice under different photoperiod conditions. Our data provide not only a macroscopic view of the genetic control of photoperiod sensitivity in rice but also a foundation for breeding of rice cultivars better adapted to the target environments using rational design.


Assuntos
Genes de Plantas , Oryza/genética , Fotoperíodo , Proteínas de Plantas/fisiologia , Locos de Características Quantitativas , Adaptação Fisiológica , Agrobacterium tumefaciens/genética , Biomassa , Clonagem Molecular , Cruzamentos Genéticos , Regulação da Expressão Gênica de Plantas , Vetores Genéticos/genética , Haplótipos/genética , Oryza/crescimento & desenvolvimento , Oryza/efeitos da radiação , Reguladores de Crescimento de Plantas/genética , Proteínas de Plantas/genética , Proteínas Recombinantes de Fusão/metabolismo , Fatores de Tempo
19.
Nat Commun ; 5: 4768, 2014 Sep 09.
Artigo em Inglês | MEDLINE | ID: mdl-25203424

RESUMO

Rice stripe virus (RSV) causes one of the most serious viral diseases of rice (Oryza sativa L.), but the molecular basis of RSV resistance has remained elusive. Here we show that the resistant allele of rice STV11 (STV11-R) encodes a sulfotransferase (OsSOT1) catalysing the conversion of salicylic acid (SA) into sulphonated SA (SSA), whereas the gene product encoded by the susceptible allele STV11-S loses this activity. Sequence analyses suggest that the STV11-R and STV11-S alleles were predifferentiated in different geographic populations of wild rice, Oryza rufipogon, and remained prevalent in cultivated indica and japonica rice varieties, respectively. Introgression of the STV11-R allele into susceptible cultivars or heterologous transfer of STV11-R into tobacco plants confers effective resistance against RSV. Our results shed new insights into plant viral defense mechanisms and suggest effective means of breeding RSV-resistant crops using molecular marker-assisted selection or genetic engineering.


Assuntos
Resistência à Doença/genética , Oryza/genética , Proteínas de Plantas/genética , Sulfotransferases/genética , Tenuivirus , Alelos , Cruzamento , Produtos Agrícolas/genética , Engenharia Genética , Oryza/virologia , Doenças das Plantas/genética , Ácido Salicílico/metabolismo , Sulfotransferases/metabolismo , Viroses/genética
20.
Mol Genet Genomics ; 289(3): 303-15, 2014 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-24414128

RESUMO

Genetic diversity within parental lines of hybrid rice is the foundation of heterosis utilization and yield improvement. Previous studies have suggested that genetic diversity was narrow in cytoplasmic male sterile (CMS/A line) and restorer lines (R line) for Three-line hybrid rice. However, the genetic diversity within maintainer lines (B line), especially at a genome-wide scale, remains largely unknown. In the present study, we performed deep re-sequencing of the elite maintainer line V20B (Oryza sativa L. ssp. indica). We then compared the V20B sequence with the 93-11 (Oryza sativa L. ssp. indica) genome sequence. 112.1 × 106 paired-end reads (PE reads) were generated with approximately 30-fold sequencing depth. The V20B PE reads uniquely covered 87.6 % of the 93-11 genome sequence. Overall, a total of 660,778 single-nucleotide polymorphism (SNPs) and 266,301 insertions and deletions (InDels) were identified, yielding an average of 2.1 SNPs/kb and 0.8 InDels/kb. Genome-wide distribution of the SNPs and InDels was non-random, and variation-rich and variation-poor regions were identified in all chromosomes. A total of 20,562 non-synonymous SNPs spanning 8,854 genes were annotated. Our results identified DNA polymorphisms at the genome-wide scale and uncovered the high level of genetic diversity between V20B and 93-11. Our results proved that next-generation sequencing technologies can be powerful tools to study genome-wide DNA polymorphisms, to query genetic diversity, and to enable molecular improvement efforts with Three-line hybrid rice. Further, our results also indicated that 93-11 could be used as core germplasm for the improvement of wild-abortive CMS lines and the maintainer lines.


Assuntos
Evolução Molecular , Oryza/genética , Polimorfismo Genético , Mapeamento Cromossômico , DNA de Plantas , Genoma de Planta , Genótipo , Sequenciamento de Nucleotídeos em Larga Escala , Hibridização Genética , Mutação INDEL , Anotação de Sequência Molecular , Fenótipo , Plantas Geneticamente Modificadas
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