RESUMEN
Crown roots are the main components of root systems in cereals. Elucidating the mechanisms of crown root formation is instrumental for improving nutrient absorption, stress tolerance, and yield in cereal crops. Several members of the WUSCHEL-related homeobox (WOX) and lateral organ boundaries domain (LBD) transcription factor families play essential roles in controlling crown root development in rice (Oryza sativa). However, the functional relationships among these transcription factors in regulating genes involved in crown root development remain unclear. Here, we identified LBD16 as an additional regulator of rice crown root development. We showed that LBD16 is a direct downstream target of WOX11, a key crown root development regulator in rice. Our results indicated that WOX11 enhances LBD16 transcription by binding to its promoter and recruiting its interaction partner JMJ706, a demethylase that removes histone H3 lysine 9 dimethylation (H3K9me2) from the LBD16 locus. In addition, we established that LBD16 interacts with WOX11, thereby impairing JMJ706-WOX11 complex formation and repressing its own transcriptional activity. Together, our results reveal a feedback system regulating genes that orchestrate crown root development in rice, in which LBD16 acts as a molecular rheostat.
Asunto(s)
Regulación de la Expresión Génica de las Plantas , Oryza , Proteínas de Plantas , Raíces de Plantas , Factores de Transcripción , Oryza/genética , Oryza/crecimiento & desarrollo , Oryza/metabolismo , Raíces de Plantas/crecimiento & desarrollo , Raíces de Plantas/genética , Raíces de Plantas/metabolismo , Proteínas de Plantas/metabolismo , Proteínas de Plantas/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Histona Demetilasas/metabolismo , Histona Demetilasas/genética , Regiones Promotoras Genéticas/genéticaRESUMEN
Grain chalkiness reduces the quality of rice (Oryza sativa) and is a highly undesirable trait for breeding and marketing. However, the underlying molecular cause of chalkiness remains largely unknown. Here, we cloned the F-box gene WHITE-CORE RATE 1 (WCR1), which negatively regulates grain chalkiness and improves grain quality in rice. A functional A/G variation in the promoter region of WCR1 generates the alleles WCR1A and WCR1G, which originated from tropical japonica and wild rice Oryza ruï¬pogon, respectively. OsDOF17 is a transcriptional activator that binds to the AAAAG cis-element in the WCR1A promoter. WCR1 positively affects the transcription of the metallothionein gene MT2b and interacts with MT2b to inhibit its 26S proteasome-mediated degradation, leading to decreased reactive oxygen species production and delayed programmed cell death in rice endosperm. This, in turn, leads to reduced chalkiness. Our findings uncover a molecular mechanism underlying rice chalkiness and identify the promising natural variant WCR1A, with application potential for rice breeding.
Asunto(s)
Endospermo , Oryza , Grano Comestible/genética , Endospermo/genética , Regulación de la Expresión Génica de las Plantas/genética , Homeostasis/genética , Oryza/genética , Oryza/metabolismo , Oxidación-ReducciónRESUMEN
The concentration, chemical speciation, and spatial distribution of essential and toxic mineral elements in cereal seeds have important implications for human health. To identify genes responsible for element uptake, translocation, and storage, high-throughput phenotyping methods are needed to visualize element distribution and concentration in seeds. Here, we used X-ray fluorescence microscopy (µ-XRF) as a method for rapid and high-throughput phenotyping of seed libraries and developed an ImageJ-based pipeline to analyze the spatial distribution of elements. Using this method, we nondestructively scanned 4,190 ethyl methanesulfonate (EMS)-mutagenized M1 rice (Oryza sativa) seeds and 533 diverse rice accessions in a genome-wide association study (GWAS) panel to simultaneously measure concentrations and spatial distribution of elements in the embryo, endosperm, and aleurone layer. A total of 692 putative mutants and 65 loci associated with the spatial distribution of elements in rice seed were identified. This powerful method provides a basis for investigating the genetics and molecular mechanisms controlling the accumulation and spatial variations of mineral elements in plant seeds.
Asunto(s)
Estudio de Asociación del Genoma Completo , Oryza , Humanos , Rayos X , Semillas/genética , Minerales , Microscopía Fluorescente , Oryza/genéticaRESUMEN
Zinc (Zn) is an essential micronutrient for most organisms including humans, and Zn deficiency is widespread in human populations, particularly in underdeveloped regions. Cereals such as rice (Oryza sativa) are the major dietary source of Zn for most people. However, the molecular mechanism underlying Zn uptake in rice is still not fully understood. Here, we report that a member of the ZIP (ZRT, IRT-like protein) family, OsZIP9, contributes to Zn uptake in rice. It was expressed in the epidermal and exodermal cells of lateral roots, localized in the plasma membrane and induced during Zn deficiency. Yeast-expressed OsZIP9 showed much higher Zn influx transport activity than other rice ZIP proteins in a wide range of Zn concentrations. OsZIP9 knockout rice plants showed a significant reduction in growth at low Zn concentrations, but could be rescued by a high Zn supply. Compared with the wild type, accumulation of Zn in root, shoot and grain was much lower in knockout lines, particularly with a low supply of Zn under both hydroponic and paddy soil conditions. OsZIP9 also showed Co uptake activity. Natural variation of OsZIP9 expression level is highly associated with Zn content in milled grain among rice varieties in the germplasm collection. Taken together, these results show that OsZIP9 is an important influx transporter responsible for the take up of Zn and Co from external media into root cells.
Asunto(s)
Proteínas Portadoras/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Zinc/metabolismo , Proteínas Portadoras/genética , Cobalto/metabolismo , Regulación de la Expresión Génica de las Plantas , Genes de Plantas/genética , Oryza/genéticaRESUMEN
The ubiquitin 26S proteasome system (UPS) is critical for enabling plants to alter their proteomes to integrate internal and external signals for the photoperiodic induction of flowering. We previously demonstrated that HAF1, a C3HC4 RING domain-containing E3 ubiquitin ligase, is essential to precisely modulate the timing of Heading Date1 accumulation and to ensure appropriate photoperiodic responses under short-day conditions in rice (Oryza sativa). However, how HAF1 mediates flowering under long-day conditions remains unknown. In this study, we show that OsELF3 (EARLY FLOWERING3) is the direct substrate of HAF1 for ubiquitination in vitro and in vivo. HAF1 is required for maintaining the circadian rhythm of OsELF3 accumulation during photoperiodic responses in rice. In addition, the haf1 oself3 double mutant headed as late as oself3 plants under long-day conditions. An amino acid variation (L558S) within the interaction domain of OsELF3 with HAF1 greatly contributes to the variation in heading date among japonica rice accessions. The japonica accessions carrying the OsELF3(L)-type allele are found at higher latitudes, while varieties carrying the OsELF3(S)-type allele are found at lower latitudes. Taken together, our findings suggest that HAF1 precisely modulates the diurnal rhythm of OsELF3 accumulation to ensure the appropriate heading date in rice.
Asunto(s)
Oryza/fisiología , Proteínas de Plantas/metabolismo , Ubiquitina-Proteína Ligasas/metabolismo , Ritmo Circadiano , Epistasis Genética , Flores/metabolismo , Flores/fisiología , Regulación de la Expresión Génica de las Plantas , Luz , Mutación , Fotoperiodo , Proteínas de Plantas/genética , Plantas Modificadas Genéticamente , Complejo de la Endopetidasa Proteasomal/metabolismo , Dominios Proteicos , Nicotiana/genética , Ubiquitina-Proteína Ligasas/genética , UbiquitinaciónRESUMEN
Rice (Oryza sativa) is an important dietary source of both essential micronutrients and toxic trace elements for humans. The genetic basis underlying the variations in the mineral composition, the ionome, in rice remains largely unknown. Here, we describe a comprehensive study of the genetic architecture of the variation in the rice ionome performed using genome-wide association studies (GWAS) of the concentrations of 17 mineral elements in rice grain from a diverse panel of 529 accessions, each genotyped at â¼6.4 million single nucleotide polymorphism loci. We identified 72 loci associated with natural ionomic variations, 32 that are common across locations and 40 that are common within a single location. We identified candidate genes for 42 loci and provide evidence for the causal nature of three genes, the sodium transporter gene Os-HKT1;5 for sodium, Os-MOLYBDATE TRANSPORTER1;1 for molybdenum, and Grain number, plant height, and heading date7 for nitrogen. Comparison of GWAS data from rice versus Arabidopsis (Arabidopsis thaliana) also identified well-known as well as new candidates with potential for further characterization. Our study provides crucial insights into the genetic basis of ionomic variations in rice and serves as an important foundation for further studies on the genetic and molecular mechanisms controlling the rice ionome.
Asunto(s)
Estudio de Asociación del Genoma Completo/métodos , Oryza/genética , Variación Genética/genética , Genotipo , Desequilibrio de Ligamiento/genética , Polimorfismo de Nucleótido Simple/genética , Sitios de Carácter Cuantitativo/genéticaRESUMEN
Appearance and taste are important factors in rice (Oryza sativa) grain quality. Here, we investigated the taste scores and related eating-quality traits of 533 diverse cultivars to assess the relationships between-and genetic basis of-rice taste and eating-quality. A genome-wide association study highlighted the Wx gene as the major factor underlying variation in taste and eating quality. Notably, a novel waxy (Wx) allele, Wxla , which combined two mutations from Wxb and Wxin , exhibited a unique phenotype. Reduced GBSSI activity conferred Wxla rice with both a transparent appearance and good eating quality. Haplotype analysis revealed that Wxla was derived from intragenic recombination. In fact, the recombination rate at the Wx locus was estimated to be 3.34 kb/cM, which was about 75-fold higher than the genome-wide mean, indicating that intragenic recombination is a major force driving diversity at the Wx locus. Based on our results, we propose a new network for Wx evolution, noting that new Wx alleles could easily be generated by crossing genotypes with different Wx alleles. This study thus provides insights into the evolution of the Wx locus and facilitates molecular breeding for quality in rice.
Asunto(s)
Oryza/genética , Proteínas de Plantas/metabolismo , Alelos , Regulación de la Expresión Génica de las Plantas/genética , Regulación de la Expresión Génica de las Plantas/fisiología , Estudio de Asociación del Genoma Completo , Proteínas de Plantas/genéticaRESUMEN
Combining ability is a measure for selecting elite parents and predicting hybrid performance in plant breeding. However, the genetic basis of combining ability remains unclear and a global view of combining ability from diverse mating designs is lacking. We developed a North Carolina II (NCII) population of 96 Oryza sativa and four male sterile lines to identify parents of greatest value for hybrid rice production. Statistical analyses indicated that general combining ability (GCA) and specific combining ability (SCA) contributed variously to different agronomic traits. In a genome-wide association study (GWAS) of agronomic traits, GCA and SCA, we identified 34 significant associations (P < 2.39 × 10-7 ). The superior alleles of GCA loci (Ghd8, GS3 and qSSR4) accumulated in parental lines with high GCA and explained 30.03% of GCA variance in grain yield, indicating that molecular breeding of high GCA parental lines is feasible. The distinct distributions of these QTLs contributed to the differentiation of parental GCA in subpopulations. GWAS of SCA identified 12 more loci that showed dominance on corresponding agronomic traits. We conclude that the accumulation of superior GCA and SCA alleles is an important contributor to heterosis and QTLs that greatly contributed to combining ability in our study would accelerate the identification of elite inbred lines and breeding of super hybrids.
Asunto(s)
Vigor Híbrido , Oryza/genética , Fitomejoramiento , Sitios de Carácter Cuantitativo , Estudios de Asociación Genética , FenotipoRESUMEN
Copper (Cu) is an essential micronutrient for plant growth. However, the molecular mechanisms underlying Cu trafficking and distribution to different organs in rice (Oryza sativa) are poorly understood. Here, we report the function and role of Antioxidant Protein1 (OsATX1), a Cu chaperone in rice. Knocking out OsATX1 resulted in increased Cu concentrations in roots, whereas OsATX1 overexpression reduced root Cu concentrations but increased Cu accumulation in the shoots. At the reproductive stage, the concentrations of Cu in developing tissues, including panicles, upper nodes and internodes, younger leaf blades, and leaf sheaths of the main tiller, were increased significantly in OsATX1-overexpressing plants and decreased in osatx1 mutants compared with the wild type. The osatx1 mutants also showed a higher Cu concentration in older leaves. Yeast two-hybrid and bimolecular fluorescence complementation assays showed that OsATX1 interacts with the rice heavy metal P1B-ATPases HMA4, HMA5, HMA6, and HMA9. These results suggest that OsATX1 may function to deliver Cu to heavy metal P1B-ATPases for Cu trafficking and distribution in order to maintain Cu homeostasis in different rice tissues. In addition, heterologous expression of OsATX1 in the yeast (Saccharomyces cerevisiae) cadmium-sensitive mutant Δycf1 increased the tolerance to Cu and cadmium by decreasing their respective concentrations in the transformed yeast cells. Taken together, our results indicate that OsATX1 plays an important role in facilitating root-to-shoot Cu translocation and the redistribution of Cu from old leaves to developing tissues and seeds in rice.
Asunto(s)
Adenosina Trifosfatasas/metabolismo , Cobre/metabolismo , Metales Pesados/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Adenosina Trifosfatasas/genética , Transporte Biológico , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Mutación , Oryza/genética , Oryza/crecimiento & desarrollo , Hojas de la Planta/genética , Hojas de la Planta/crecimiento & desarrollo , Hojas de la Planta/metabolismo , Proteínas de Plantas/genética , Plantas Modificadas Genéticamente , Unión ProteicaRESUMEN
Excessive cadmium (Cd) accumulation in rice poses a potential threat to human health. Rice varieties vary in their Cd content, which depends mainly on root-to-shoot translocation of Cd. However, cultivars accumulating high Cd in the natural population have not been completely investigated. In this study, we analyzed the variation in Cd accumulation in a diverse panel of 529 rice cultivars. Only a small proportion (11 of 529) showed extremely high root-to-shoot Cd transfer rates, and in seven of these cultivars this was caused by two known OsHMA3 alleles. Using quantitative trait loci mapping, we identified a new OsHMA3 allele that was associated with high Cd accumulation in three of the remaining cultivars. Using heterologous expression in yeast and comparative analysis among different rice cultivars, we observed that this new allele was weak at both the transcriptional and protein levels compared with the functional OsHMA3 genotypes. The weak Cd transport activity was further demonstrated to be caused by a Gly to Arg substitution at position 512. Our study comprehensively analyzed the variation in root-to-shoot Cd translocation rates in cultivated rice and identified a new OsHMA3 allele that caused high Cd accumulation in a few rice cultivars.
Asunto(s)
Alelos , Cadmio/metabolismo , Oryza/genética , Oryza/metabolismo , Proteínas de Plantas/genética , Secuencia de Aminoácidos , Transporte Biológico , Segregación Cromosómica , Regulación de la Expresión Génica de las Plantas , Ligamiento Genético , Haplotipos/genética , Mapeo Físico de Cromosoma , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Raíces de Plantas/metabolismo , Brotes de la Planta/metabolismo , Sitios de Carácter Cuantitativo/genéticaRESUMEN
Cellular pH homeostasis is fundamental for life, and all cells adapt to maintain this balance. In plants, the chemical form of nitrogen supply, nitrate and ammonium, is one of the cellular pH dominators. We report that the rice nitrate transporter OsNRT2.3 is transcribed into two spliced isoforms with a natural variation in expression ratio. One splice form, OsNRT2.3b is located on the plasma membrane, is expressed mainly in the phloem, and has a regulatory motif on the cytosolic side that acts to switch nitrate transport activity on or off by a pH-sensing mechanism. High OsNRT2.3b expression in rice enhances the pH-buffering capacity of the plant, increasing N, Fe, and P uptake. In field trials, increased expression of OsNRT2.3b improved grain yield and nitrogen use efficiency (NUE) by 40%. These results indicate that pH sensing by the rice nitrate transporter OsNRT2.3b is important for plant adaption to varied N supply forms and can provide a target for improving NUE.
Asunto(s)
Proteínas de Transporte de Anión/metabolismo , Oryza/genética , Proteínas de Plantas/metabolismo , Compuestos de Amonio/metabolismo , Proteínas de Transporte de Anión/química , Proteínas de Transporte de Anión/genética , Citosol/química , Citosol/metabolismo , Regulación de la Expresión Génica de las Plantas , Concentración de Iones de Hidrógeno , Transportadores de Nitrato , Nitratos/metabolismo , Nitrógeno/metabolismo , Oryza/química , Oryza/crecimiento & desarrollo , Oryza/metabolismo , Proteínas de Plantas/química , Proteínas de Plantas/genéticaRESUMEN
Intensive rice breeding over the past 50 y has dramatically increased productivity especially in the indica subspecies, but our knowledge of the genomic changes associated with such improvement has been limited. In this study, we analyzed low-coverage sequencing data of 1,479 rice accessions from 73 countries, including landraces and modern cultivars. We identified two major subpopulations, indica I (IndI) and indica II (IndII), in the indica subspecies, which corresponded to the two putative heterotic groups resulting from independent breeding efforts. We detected 200 regions spanning 7.8% of the rice genome that had been differentially selected between IndI and IndII, and thus referred to as breeding signatures. These regions included large numbers of known functional genes and loci associated with important agronomic traits revealed by genome-wide association studies. Grain yield was positively correlated with the number of breeding signatures in a variety, suggesting that the number of breeding signatures in a line may be useful for predicting agronomic potential and the selected loci may provide targets for rice improvement.
Asunto(s)
Marcadores Genéticos/genética , Variación Genética , Genoma de Planta/genética , Oryza/crecimiento & desarrollo , Oryza/genética , Fitomejoramiento/historia , Fitomejoramiento/métodos , Biología Computacional , Estudio de Asociación del Genoma Completo , Historia del Siglo XX , Historia del Siglo XXI , Análisis de Regresión , Selección GenéticaRESUMEN
Rice Variation Map (RiceVarMap, http:/ricevarmap.ncpgr.cn) is a database of rice genomic variations. The database provides comprehensive information of 6,551,358 single nucleotide polymorphisms (SNPs) and 1,214,627 insertions/deletions (INDELs) identified from sequencing data of 1479 rice accessions. The SNP genotypes of all accessions were imputed and evaluated, resulting in an overall missing data rate of 0.42% and an estimated accuracy greater than 99%. The SNP/INDEL genotypes of all accessions are available for online query and download. Users can search SNPs/INDELs by identifiers of the SNPs/INDELs, genomic regions, gene identifiers and keywords of gene annotation. Allele frequencies within various subpopulations and the effects of the variation that may alter the protein sequence of a gene are also listed for each SNP/INDEL. The database also provides geographical details and phenotype images for various rice accessions. In particular, the database provides tools to construct haplotype networks and design PCR-primers by taking into account surrounding known genomic variations. These data and tools are highly useful for exploring genetic variations and evolution studies of rice and other species.
Asunto(s)
Bases de Datos de Ácidos Nucleicos , Variación Genética , Genoma de Planta , Oryza/genética , Genotipo , Haplotipos , Mutación INDEL , Polimorfismo de Nucleótido SimpleRESUMEN
Excessive cadmium (Cd) accumulation in rice poses a risk to food safety. OsHMA3 plays an important role in restricting Cd translocation from roots to shoots. A non-functional allele of OsHMA3 has been reported in some Indica rice cultivars with high Cd accumulation, but it is not known if OsHMA3 allelic variation is associated with Cd accumulation in Japonica cultivars. In this study, we identified a Japonica cultivar with consistently high Cd accumulation in shoots and grain in both field and greenhouse experiments. The cultivar possesses an OsHMA3 allele with a predicted amino acid mutation at the 380(th) position from Ser to Arg. The haplotype had no Cd transport activity when the gene was expressed in yeast, and the allele did not complement a known nonfunctional allele of OsHMA3 in F1 test. The allele is present only in temperate Japonica cultivars among diversity panels of 1483 rice cultivars. Different cultivars possessing this allele showed greatly increased root-to-shoot Cd translocation and a shift in root Cd speciation from Cd-S to Cd-O bonding determined by synchrotron X-ray absorption spectroscopy. Our study has identified a new loss-of-function allele of OsHMA3 in Japonica rice cultivars leading to high Cd accumulation in shoots and grain.
Asunto(s)
Adenosina Trifosfatasas/genética , Cadmio/metabolismo , Grano Comestible/metabolismo , Oryza/genética , Proteínas de Plantas/genética , Adenosina Trifosfatasas/metabolismo , Alelos , Prueba de Complementación Genética , Oryza/metabolismo , Fenotipo , Proteínas de Plantas/metabolismo , Brotes de la Planta/metabolismo , Polimorfismo Genético , Espectroscopía de Absorción de Rayos X , LevadurasRESUMEN
BACKGROUND: Mechanized dry seeded rice can save both labour and water resources. Rice seedling establishment is sensitive to sowing depth while mesocotyl elongation facilitates the emergence of deeply sown seeds. RESULTS: A set of 270 rice accessions, including 170 from the mini-core collection of Chinese rice germplasm (C Collection) and 100 varieties used in a breeding program for drought resistance (D Collection), was screened for mesocotyl lengths of seedlings grown in water (MLw) in darkness and in 5 cm sand culture (MLs). Twenty six accessions (10.53 %) have MLw longer than 1.0 cm. Eleven accessions had the highest mesocotyl lengths, i.e. 1.4 - 5.05 cm of MLw and 3.0 - 6.4 cm in 10 cm sand culture, including 7 upland landraces or varieties. The genotypic data of 1,019,883 SNPs were developed by re-sequencing of those accessions. A whole-genome SNP array (Rice SNP50) was used to genotype 24 accessions as a validation panel, giving 98.41 % of consistent SNPs with the re-sequencing data in average. GWAS based on compressed mixed linear model was conducted using GAPIT. Based on a threshold of -log(P) ≥8.0, 13 loci were associated to MLw on rice chromosome 1, 3, 4, 5, 6 and 9, respectively. Three associated loci, on chromosome 3, 6, and 10, were detected for MLs. A set of 99 associated SNPs for MLw, based on a compromised threshold (-log(P) ≥7.0), located in intergenic regions or different positions of 36 annotated genes, including one cullin and one growth regulating factor gene. CONCLUSIONS: Higher proportion and extension of elongated mesocotyls were observed in the mini-core collection of rice germplasm and upland rice landraces or varieties, possibly causing the correlation between mesocotyl elongation and drought resistance. GWAS found 13 loci for mesocotyl length measured in dark germination that confirmed the previously reported co-location of two QTLs across populations and experiments. Associated SNPs hit 36 annotated genes including function-matching candidates like cullin and GRF. The germplasm with elongated mesocotyl, especially upland landraces or varieties, and the associated SNPs could be useful in further studies and breeding of mechanized dry seeded rice.
Asunto(s)
Estudio de Asociación del Genoma Completo , Oryza/genética , Polimorfismo de Nucleótido Simple , Oryza/crecimiento & desarrollo , Brotes de la Planta/genética , Brotes de la Planta/crecimiento & desarrollo , Plantones/genética , Plantones/crecimiento & desarrollo , Análisis de Secuencia de ADNRESUMEN
Manganese (Mn) is an essential micronutrient for plants playing an important role in many physiological functions. OsNRAMP5 is a major transporter responsible for Mn and cadmium uptake in rice, but whether it is involved in the root-to-shoot translocation and distribution of these metals is unknown. In this work, OsNRAMP5 was found to be highly expressed in hulls. It was also expressed in leaves but the expression level decreased with leaf age. High-magnification observations revealed that OsNRAMP5 was enriched in the vascular bundles of roots and shoots especially in the parenchyma cells surrounding the xylem. The osnramp5 mutant accumulated significantly less Mn in shoots than the wild-type plants even at high levels of Mn supply. Furthermore, a high supply of Mn could compensate for the loss in the root uptake ability in the mutant, but not in the root-to-shoot translocation of Mn, suggesting that the absence of OsNRAMP5 reduces the transport of Mn from roots to shoots. The results suggest that OsNRAMP5 plays an important role in the translocation and distribution of Mn in rice plants in addition to its role in Mn uptake.
Asunto(s)
Regulación de la Expresión Génica de las Plantas , Manganeso/metabolismo , Proteínas de Transporte de Membrana/genética , Oryza/genética , Proteínas de Plantas/genética , Transporte Biológico , Proteínas de Transporte de Membrana/metabolismo , Oryza/metabolismo , Proteínas de Plantas/metabolismo , Brotes de la Planta/metabolismo , Reacción en Cadena en Tiempo Real de la PolimerasaRESUMEN
Phosphate (Pi) homeostasis in plants is required for plant growth and development, and is achieved by the coordination of Pi acquisition, translocation from roots to shoots, and remobilization within plants. Previous reports have demonstrated that over-expression of OsPHR2 (the homolog of AtPHR1) and knockdown of OsSPX1 result in accumulation of excessive shoot Pi in rice. Here we report that OsPHR2 positively regulates the low-affinity Pi transporter gene OsPT2 by physical interaction and upstream regulation of OsPHO2 in roots. OsPT2 is responsible for most of the OsPHR2-mediated accumulation of excess shoot Pi. OsSPX1 suppresses the regulation on expression of OsPT2 by OsPHR2 and the accumulation of excess shoot Pi, but it does not suppress induction of OsPT2 or the accumulation of excessive shoot Pi in the Ospho2 mutant. Our data also show that OsSPX1 is a negative regulator of OsPHR2 and is involved in the feedback of Pi-signaling network in roots that is defined by OsPHR2 and OsPHO2. This finding provides new insight into the regulatory mechanism of Pi uptake, translocation, allocation and homeostasis in plants.
Asunto(s)
Oryza/genética , Fosfatos/metabolismo , Proteínas de Plantas/metabolismo , Brotes de la Planta/metabolismo , ADN Bacteriano/genética , Regulación de la Expresión Génica de las Plantas , Homeostasis , Mutagénesis Insercional , Mutación , Oryza/metabolismo , Proteínas de Plantas/genética , Raíces de Plantas/metabolismo , Plantas Modificadas Genéticamente/genética , Plantas Modificadas Genéticamente/metabolismo , ARN de Planta/genéticaRESUMEN
Since domestication, rice has cultivated in a wide range of latitudes with different day lengths. Selection of diverse natural variations in heading date and photoperiod sensitivity is critical for adaptation of rice to different geographical environments. To unravel the genetic architecture underlying natural variation of rice flowering time, we conducted a genome wide association study (GWAS) using several association analysis strategies with a diverse worldwide collection of 529 O. sativa accessions. Heading date was investigated in three environments under long-day or short-day conditions, and photosensitivity was evaluated. By dividing the whole association panel into subpopulations and performing GWAS with both linear mixed models and multi-locus mixed-models, we revealed hundreds of significant loci harboring novel candidate genes as well as most of the known flowering time genes. In total, 127 hotspots were detected in at least two GWAS. Universal genetic heterogeneity was found across subpopulations. We further detected abundant interactions between GWAS loci, especially in indica. Functional gene families were revealed from enrichment analysis of the 127 hotspots. The results demonstrated a rich of genetic interactions in rice flowering time genes and such epistatic interactions contributed to the large portions of missing heritability in GWAS. It suggests the increased complexity of genetic heterogeneity might discount the power of increasing the sample sizes in GWAS.
Asunto(s)
Epistasis Genética/fisiología , Flores , Regulación de la Expresión Génica de las Plantas/fisiología , Genes de Plantas/fisiología , Oryza , Flores/genética , Flores/crecimiento & desarrollo , Estudio de Asociación del Genoma Completo , Oryza/genética , Oryza/crecimiento & desarrolloRESUMEN
Cloning quantitative trait locus (QTL) is time consuming and laborious, which hinders the understanding of natural variation and genetic diversity. Here, we introduce RapMap, a method for rapid multi-QTL mapping by employing F2 gradient populations (F2GPs) constructed by minor-phenotypic-difference accessions. The co-segregation standard of the single-locus genetic models ensures simultaneous integration of a three-in-one framework in RapMap i.e. detecting a real QTL, confirming its effect, and obtaining its near-isogenic line-like line (NIL-LL). We demonstrate the feasibility of RapMap by cloning eight rice grain-size genes using 15 F2GPs in three years. These genes explain a total of 75% of grain shape variation. Allele frequency analysis of these genes using a large germplasm collection reveals directional selection of the slender and long grains in indica rice domestication. In addition, major grain-size genes have been strongly selected during rice domestication. We think application of RapMap in crops will accelerate gene discovery and genomic breeding.
Asunto(s)
Biología Computacional/métodos , Grano Comestible/genética , Oryza/genética , Sitios de Carácter Cuantitativo/genética , Selección Genética , Mapeo Cromosómico/métodos , Cromosomas de las Plantas/genética , Productos Agrícolas/genética , Domesticación , Estudio de Asociación del Genoma Completo/métodos , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Oryza/clasificación , Fenotipo , Filogenia , Fitomejoramiento/métodos , Semillas/genética , Especificidad de la EspecieRESUMEN
Rice grain oil is a valuable nutrient source. However, the genetic basis of oil biosynthesis in rice grains remains unclear. In this study, we performed a genome-wide association study on oil composition and oil concentration in a diverse panel of 533 cultivated rice accessions. High variation for 11 oil-related traits was observed, and the oil composition of rice grains showed differentiation among the subpopulations. We identified 46 loci that are significantly associated with grain oil concentration or composition, 16 of which were detected in three recombinant inbred line populations. Twenty-six candidate genes encoding enzymes involved in oil metabolism were identified from these 46 loci, four of which (PAL6, LIN6, MYR2, and ARA6) were found to contribute to natural variation in oil composition and to show differentiation among the subpopulations. Interestingly, population genetic analyses revealed that specific haplotypes of PAL6 and LIN6 have been selected in japonica rice. Based on these results, we propose a possible oil biosynthetic pathway in rice grains. Collectively, our results provide new insights into the genetic basis of oil biosynthesis in rice grains and can facilitate marker-based breeding of rice varieties with enhanced oil and grain quality.