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1.
BMC Plant Biol ; 24(1): 194, 2024 Mar 16.
Artículo en Inglés | MEDLINE | ID: mdl-38493116

RESUMEN

BACKGROUND: In soybeans, faster canopy coverage (CC) is a highly desirable trait but a fully covered canopy is unfavorable to light interception at lower levels in the canopy with most of the incident radiation intercepted at the top of the canopy. Shoot architecture that influences CC is well studied in crops such as maize and wheat, and altering architectural traits has resulted in enhanced yield. However, in soybeans the study of shoot architecture has not been as extensive. RESULTS: This study revealed significant differences in CC among the selected soybean accessions. The rate of CC was found to decrease at the beginning of the reproductive stage (R1) followed by an increase during the R2-R3 stages. Most of the accessions in the study achieved maximum rate of CC between R2-R3 stages. We measured Light interception (LI), defined here as the ratio of Photosynthetically Active Radiation (PAR) transmitted through the canopy to the incoming PAR or the radiation above the canopy. LI was found to be significantly correlated with CC parameters, highlighting the relationship between canopy structure and light interception. The study also explored the impact of plant shape on LI and CO2 assimilation. Plant shape was characterized into distinct quantifiable parameters and by modeling the impact of plant shape on LI and CO2 assimilation, we found that plants with broad and flat shapes at the top maybe more photosynthetically efficient at low light levels, while conical shapes were likely more advantageous when light was abundant. Shoot architecture of plants in this study was described in terms of whole plant, branching and leaf-related traits. There was significant variation for the shoot architecture traits between different accessions, displaying high reliability. We found that that several shoot architecture traits such as plant height, and leaf and internode-related traits strongly influenced CC and LI. CONCLUSION: In conclusion, this study provides insight into the relationship between soybean shoot architecture, canopy coverage, and light interception. It demonstrates that novel shoot architecture traits we have defined here are genetically variable, impact CC and LI and contribute to our understanding of soybean morphology. Correlations between different architecture traits, CC and LI suggest that it is possible to optimize soybean growth without compromising on light transmission within the soybean canopy. In addition, the study underscores the utility of integrating low-cost 2D phenotyping as a practical and cost-effective alternative to more time-intensive 3D or high-tech low-throughput methods. This approach offers a feasible means of studying basic shoot architecture traits at the field level, facilitating a broader and efficient assessment of plant morphology.


Asunto(s)
Glycine max , Fotosíntesis , Dióxido de Carbono , Reproducibilidad de los Resultados , Productos Agrícolas , Hojas de la Planta , Luz
2.
Plant Physiol ; 193(4): 2691-2710, 2023 Nov 22.
Artículo en Inglés | MEDLINE | ID: mdl-37610244

RESUMEN

Fusarium head blight (FHB) of barley (Hordeum vulgare) causes yield losses and accumulation of trichothecene mycotoxins (e.g. deoxynivalenol [DON]) in grains. Glucosylation of DON to the nontoxic DON-3-O-glucoside (D3G) is catalyzed by UDP-glucosyltransferases (UGTs), such as barley UGT13248. We explored the natural diversity of UGT13248 in 496 barley accessions and showed that all carried potential functional alleles of UGT13248, as no genotypes showed strongly increased seedling sensitivity to DON. From a TILLING population, we identified 2 mutant alleles (T368I and H369Y) that, based on protein modeling, likely affect the UDP-glucose binding of UGT13248. In DON feeding experiments, DON-to-D3G conversion was strongly reduced in spikes of these mutants compared to controls, and plants overexpressing UGT13248 showed increased resistance to DON and increased DON-to-D3G conversion. Moreover, field-grown plants carrying the T368I or H369Y mutations inoculated with Fusarium graminearum showed increased FHB disease severity and reduced D3G production. Barley is generally considered to have type II resistance that limits the spread of F. graminearum from the infected spikelet to adjacent spikelets. Point inoculation experiments with F. graminearum showed increased infection spread in T368I and H369Y across the spike compared to wild type, while overexpression plants showed decreased spread of FHB symptoms. Confocal microscopy revealed that F. graminearum spread to distant rachis nodes in T368I and H369Y mutants but was arrested at the rachis node of the inoculated spikelet in wild-type plants. Taken together, our data reveal that UGT13248 confers type II resistance to FHB in barley via conjugation of DON to D3G.


Asunto(s)
Fusarium , Hordeum , Hordeum/genética , Hordeum/metabolismo , Glucosiltransferasas/genética , Glucosiltransferasas/metabolismo , Uridina Difosfato/metabolismo , Enfermedades de las Plantas/genética
3.
Plant J ; 111(4): 1183-1202, 2022 08.
Artículo en Inglés | MEDLINE | ID: mdl-35704392

RESUMEN

Accurate characterisation of splice junctions (SJs) as well as transcription start and end sites in reference transcriptomes allows precise quantification of transcripts from RNA-seq data, and enables detailed investigations of transcriptional and post-transcriptional regulation. Using novel computational methods and a combination of PacBio Iso-seq and Illumina short-read sequences from 20 diverse tissues and conditions, we generated a comprehensive and highly resolved barley reference transcript dataset from the European 2-row spring barley cultivar Barke (BaRTv2.18). Stringent and thorough filtering was carried out to maintain the quality and accuracy of the SJs and transcript start and end sites. BaRTv2.18 shows increased transcript diversity and completeness compared with an earlier version, BaRTv1.0. The accuracy of transcript level quantification, SJs and transcript start and end sites have been validated extensively using parallel technologies and analysis, including high-resolution reverse transcriptase-polymerase chain reaction and 5'-RACE. BaRTv2.18 contains 39 434 genes and 148 260 transcripts, representing the most comprehensive and resolved reference transcriptome in barley to date. It provides an important and high-quality resource for advanced transcriptomic analyses, including both transcriptional and post-transcriptional regulation, with exceptional resolution and precision.


Asunto(s)
Hordeum , Transcriptoma , Perfilación de la Expresión Génica/métodos , Hordeum/genética , RNA-Seq , Análisis de Secuencia de ARN/métodos , Transcriptoma/genética
4.
Plant J ; 111(6): 1580-1594, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35834607

RESUMEN

The distribution of recombination events along large cereal chromosomes is uneven and is generally restricted to gene-rich telomeric ends. To understand how the lack of recombination affects diversity in the large pericentromeric regions, we analysed deep exome capture data from a final panel of 815 Hordeum vulgare (barley) cultivars, landraces and wild barleys, sampled from across their eco-geographical ranges. We defined and compared variant data across the pericentromeric and non-pericentromeric regions, observing a clear partitioning of diversity both within and between chromosomes and germplasm groups. Dramatically reduced diversity was found in the pericentromeres of both cultivars and landraces when compared with wild barley. We observed a mixture of completely and partially differentiated single-nucleotide polymorphisms (SNPs) between domesticated and wild gene pools, suggesting that domesticated gene pools were derived from multiple wild ancestors. Patterns of genome-wide linkage disequilibrium, haplotype block size and number, and variant frequency within blocks showed clear contrasts among individual chromosomes and between cultivars and wild barleys. Although most cultivar chromosomes shared a single major pericentromeric haplotype, chromosome 7H clearly differentiated the two-row and six-row types associated with different geographical origins. Within the pericentromeric regions we identified 22 387 non-synonymous SNPs, 92 of which were fixed for alternative alleles in cultivar versus wild accessions. Surprisingly, only 29 SNPs found exclusively in the cultivars were predicted to be 'highly deleterious'. Overall, our data reveal an unconventional pericentromeric genetic landscape among distinct barley gene pools, with different evolutionary processes driving domestication and diversification.


Asunto(s)
Hordeum , Cromosomas , Domesticación , Hordeum/genética , Desequilibrio de Ligamiento/genética
5.
Theor Appl Genet ; 136(8): 174, 2023 Jul 21.
Artículo en Inglés | MEDLINE | ID: mdl-37477711

RESUMEN

KEY MESSAGE: Selection over 70 years has led to almost complete fixation of a haplotype spanning ~ 250 Mbp of chomosome 5H in European two-rowed spring barleys, possibly originating from North Africa. Plant breeding and selection have shaped the genetic composition of modern crops over the past decades and centuries and have led to great improvements in agronomic and quality traits. Knowledge of the genetic composition of breeding germplasm is essential to make informed decisions in breeding programs. In this study, we characterized the structure and composition of 209 barley cultivars representative of the European two-rowed spring barley germplasm of the past 190 years. Utilizing high-density SNP marker data, we identified a distinct centromeric haplotype spanning a ~ 250 Mbp large region on chromosome 5H which likely was first introduced into the European breeding germplasm in the early to mid-twentieth century and has been non-recombining and under strong positive selection over the past 70 years. Almost all cultivars in our panel that were released after 2000 carry this new haplotype, suggesting that this region carries one or several genes conferring highly beneficial traits. Using the global barley collection of the German Federal ex situ gene bank at IPK Gatersleben, we found the new haplotype at high frequencies in six-rowed spring-type landraces from Northern Africa, from which it may have been introduced into modern European barley germplasm via southern European landraces. The presence of a 250 Mbp genomic region characterized by lack of recombination and high levels of fixation in modern barley germplasm has substantial implications for the genetic diversity of the modern barley germplasm and for barley breeding.


Asunto(s)
Hordeum , Haplotipos , Hordeum/genética , Fitomejoramiento , Fenotipo , Cromosomas
6.
Theor Appl Genet ; 136(7): 154, 2023 Jun 15.
Artículo en Inglés | MEDLINE | ID: mdl-37318664

RESUMEN

KEY MESSAGE: Two QTL were identified using linkage mapping approaches, one on hop linkage group 3 (qHl_Chr3.PMR1) associated with powdery mildew resistance and a second on linkage group 10 (cqHl_ChrX.SDR1) associated with sex determination. Hop (Humulus lupulus L.) is a dioecious species cultivated for use in beer. Hop powdery mildew, caused by Podosphaera macularis, is a constraint in many growing regions. Thus, identifying markers associated with powdery mildew resistance and sex provides the opportunity to pyramid R-genes and select female plants as seedlings, respectively. Our objectives were to characterize the genetic basis of R1-mediated resistance in the cultivar Zenith which provides resistance to pathogen races in the US, identify quantitative trait loci (QTL) associated with R1 and sex, and develop markers for molecular breeding-based approaches. Phenotypic evaluation of the population indicated that R1-based resistance and sex are inherited monogenically. We constructed a genetic map using 1339 single nucleotide polymorphisms (SNPs) based upon genotype-by-sequencing of 128 F1 progeny derived from a Zenith × USDA 21058M biparental population. SNPs were assigned to 10 linkage groups comprising a map length of 1204.97 cM with an average density of 0.94 cM/marker. Quantitative trait locus mapping identified qHl_Chr3.PMR1, associated with R1 on linkage group 3 (LOD = 23.57, R2 = 57.2%), and cqHl_ChrX.SDR1, associated with sex on linkage group 10 (LOD = 5.42, R2 = 25.0%). Kompetitive allele-specific PCR (KASP) assays were developed for both QTL and assessed against diverse germplasm. Our results indicate that KASP markers associated with R1 may be limited to materials that are pedigree-related to Zenith, whereas markers associated with sex may be transferable across populations. The high-density map, QTL, and associated KASP markers will enable selecting for sex and R1-mediated resistance in hop.


Asunto(s)
Humulus , Sitios de Carácter Cuantitativo , Humulus/genética , Enfermedades de las Plantas/genética , Mapeo Cromosómico/métodos , Genotipo , Resistencia a la Enfermedad/genética
7.
Genome Res ; 29(12): 1962-1973, 2019 12.
Artículo en Inglés | MEDLINE | ID: mdl-31744902

RESUMEN

The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic shoot growth. Meristems show a striking diversity in shape and size. How this morphological diversity relates to variation in plant architecture and the molecular circuitries driving it are unclear. By generating a high-resolution gene expression atlas of the vegetative maize shoot apex, we show here that distinct sets of genes govern the regulation and identity of stem cells in maize versus Arabidopsis. Cell identities in the maize SAM reflect the combinatorial activity of transcription factors (TFs) that drive the preferential, differential expression of individual members within gene families functioning in a plethora of cellular processes. Subfunctionalization thus emerges as a fundamental feature underlying cell identity. Moreover, we show that adult plant characters are, to a significant degree, regulated by gene circuitries acting in the SAM, with natural variation modulating agronomically important architectural traits enriched specifically near dynamically expressed SAM genes and the TFs that regulate them. Besides unique mechanisms of maize stem cell regulation, our atlas thus identifies key new targets for crop improvement.


Asunto(s)
Arabidopsis/genética , Bases de Datos de Ácidos Nucleicos , Regulación de la Expresión Génica de las Plantas/fisiología , Genes de Plantas , Meristema/genética , Arabidopsis/metabolismo , Meristema/metabolismo
8.
Plant Cell Physiol ; 62(1): 8-27, 2021 Mar 25.
Artículo en Inglés | MEDLINE | ID: mdl-33244607

RESUMEN

Bread wheat is a major crop that has long been the focus of basic and breeding research. Assembly of its genome has been difficult because of its large size and allohexaploid nature (AABBDD genome). Following the first reported assembly of the genome of the experimental strain Chinese Spring (CS), the 10+ Wheat Genomes Project was launched to produce multiple assemblies of worldwide modern cultivars. The only Asian cultivar in the project is Norin 61, a representative Japanese cultivar adapted to grow across a broad latitudinal range, mostly characterized by a wet climate and a short growing season. Here, we characterize the key aspects of its chromosome-scale genome assembly spanning 15 Gb with a raw scaffold N50 of 22 Mb. Analysis of the repetitive elements identified chromosomal regions unique to Norin 61 that encompass a tandem array of the pathogenesis-related 13 family. We report novel copy-number variations in the B homeolog of the florigen gene FT1/VRN3, pseudogenization of its D homeolog and the association of its A homeologous alleles with the spring/winter growth habit. Furthermore, the Norin 61 genome carries typical East Asian functional variants different from CS, ranging from a single nucleotide to multi-Mb scale. Examples of such variation are the Fhb1 locus, which confers Fusarium head-blight resistance, Ppd-D1a, which confers early flowering, Glu-D1f for Asian noodle quality and Rht-D1b, which introduced semi-dwarfism during the green revolution. The adoption of Norin 61 as a reference assembly for functional and evolutionary studies will enable comprehensive characterization of the underexploited Asian bread wheat diversity.


Asunto(s)
Resistencia a la Enfermedad/genética , Flores/crecimiento & desarrollo , Genes de Plantas/genética , Genoma de Planta/genética , Triticum/genética , Mapeo Cromosómico , Cromosomas de las Plantas/genética , Citogenética , Asia Oriental , Flores/genética , Fusarium , Genes de Plantas/fisiología , Estudios de Asociación Genética , Variación Genética/genética , Variación Genética/fisiología , Genoma de Planta/fisiología , Genotipo , Filogenia , Alineación de Secuencia , Análisis de Secuencia de ADN , Triticum/crecimiento & desarrollo , Triticum/inmunología , Triticum/fisiología
9.
Theor Appl Genet ; 134(12): 3963-3981, 2021 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-34455452

RESUMEN

KEY MESSAGE: Fine mapping of barley 6H pericentromeric region identified FHB QTL with opposite effects, and high grain protein content was associated with increased FHB severity. Resistance to Fusarium head blight (FHB), kernel discoloration (KD), deoxynivalenol (DON) accumulation and grain protein content (GPC) are important traits for breeding malting barley varieties. Previous work mapped a Chevron-derived FHB QTL to the pericentromeric region of 6H, coinciding with QTL for KD resistance and GPC. The Chevron allele reduced FHB and KD, but unfavorably increased GPC. To determine whether the correlations are caused by linkage or pleiotropy, a fine mapping approach was used to dissect the QTL underlying these quality and disease traits. Two populations, referred to as Gen10 and Gen10/Lacey, derived from a recombinant near-isogenic line (rNIL) were developed. Recombinants were phenotyped for FHB, KD, DON, GPC and other agronomic traits. Three FHB, two DON and two KD QTLs were identified. One of the three FHB QTLs, one DON QTL and one KD QTL were coincident with the GPC QTL, which contains the Hv-NAM1 locus affecting grain protein accumulation. The Chevron allele at the GPC QTL increased GPC and FHB and decreased DON and KD. The other two FHB QTL and the other DON and KD QTL were identified in the regions flanking the Hv-NAM1 locus, and the Chevron alleles decreased FHB, DON and KD. Our results suggested that the QTL associated with FHB, KD, DON and GPC in the pericentromeric region of 6H was controlled by both pleiotropy and tightly linked loci. The rNILs identified in this study with low FHB severity and moderate GPC may be used for breeding malting barley cultivars.


Asunto(s)
Resistencia a la Enfermedad/genética , Fusarium/patogenicidad , Proteínas de Granos/análisis , Hordeum/genética , Enfermedades de las Plantas/genética , Alelos , Mapeo Cromosómico , Cromosomas de las Plantas/genética , Pleiotropía Genética , Genotipo , Fenotipo , Enfermedades de las Plantas/microbiología , Sitios de Carácter Cuantitativo
10.
Theor Appl Genet ; 134(2): 529-542, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33184704

RESUMEN

KEY MESSAGE: The first cytological characterization of the 2NvS segment in hexaploid wheat; complete de novo assembly and annotation of 2NvS segment; 2NvS frequency is increasing 2NvS and is associated with higher yield. The Aegilops ventricosa 2NvS translocation segment has been utilized in breeding disease-resistant wheat crops since the early 1990s. This segment is known to possess several important resistance genes against multiple wheat diseases including root knot nematode, stripe rust, leaf rust and stem rust. More recently, this segment has been associated with resistance to wheat blast, an emerging and devastating wheat disease in South America and Asia. To date, full characterization of the segment including its size, gene content and its association with grain yield is lacking. Here, we present a complete cytological and physical characterization of this agronomically important translocation in bread wheat. We de novo assembled the 2NvS segment in two wheat varieties, 'Jagger' and 'CDC Stanley,' and delineated the segment to be approximately 33 Mb. A total of 535 high-confidence genes were annotated within the 2NvS region, with > 10% belonging to the nucleotide-binding leucine-rich repeat (NLR) gene families. Identification of groups of NLR genes that are potentially N genome-specific and expressed in specific tissues can fast-track testing of candidate genes playing roles in various disease resistances. We also show the increasing frequency of 2NvS among spring and winter wheat breeding programs over two and a half decades, and the positive impact of 2NvS on wheat grain yield based on historical datasets. The significance of the 2NvS segment in wheat breeding due to resistance to multiple diseases and a positive impact on yield highlights the importance of understanding and characterizing the wheat pan-genome for better insights into molecular breeding for wheat improvement.


Asunto(s)
Aegilops/crecimiento & desarrollo , Basidiomycota/fisiología , Regulación de la Expresión Génica de las Plantas , Fitomejoramiento , Enfermedades de las Plantas/genética , Proteínas de Plantas/metabolismo , Triticum/crecimiento & desarrollo , Aegilops/genética , Aegilops/microbiología , Pan , Mapeo Cromosómico , Cromosomas de las Plantas/genética , Marcadores Genéticos , Enfermedades de las Plantas/microbiología , Proteínas de Plantas/genética , Triticum/genética , Triticum/microbiología
12.
Plant Biotechnol J ; 18(12): 2456-2465, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-32452105

RESUMEN

Effective evaluation of millions of crop genetic stocks is an essential component of exploiting genetic diversity to achieve global food security. By leveraging genomics and data analytics, genomic prediction is a promising strategy to efficiently explore the potential of these gene banks by starting with phenotyping a small designed subset. Reliable genomic predictions have enhanced selection of many macroscopic phenotypes in plants and animals. However, the use of genomicprediction strategies for analysis of microscopic phenotypes is limited. Here, we exploited the power of genomic prediction for eight maize traits related to the shoot apical meristem (SAM), the microscopic stem cell niche that generates all the above-ground organs of the plant. With 435 713 genomewide single-nucleotide polymorphisms (SNPs), we predicted SAM morphology traits for 2687 diverse maize inbreds based on a model trained from 369 inbreds. An empirical validation experiment with 488 inbreds obtained a prediction accuracy of 0.37-0.57 across eight traits. In addition, we show that a significantly higher prediction accuracy was achieved by leveraging the U value (upper bound for reliability) that quantifies the genomic relationships of the validation set with the training set. Our findings suggest that double selection considering both prediction and reliability can be implemented in choosing selection candidates for phenotyping when exploring new diversity is desired. In this case, individuals with less extreme predicted values and moderate reliability values can be considered. Our study expands the turbocharging gene banks via genomic prediction from the macrophenotypes into the microphenotypic space.


Asunto(s)
Genómica , Zea mays , Animales , Genotipo , Modelos Genéticos , Fenotipo , Polimorfismo de Nucleótido Simple , Reproducibilidad de los Resultados , Selección Genética
13.
Plant Cell Environ ; 43(8): 1844-1861, 2020 08.
Artículo en Inglés | MEDLINE | ID: mdl-32459028

RESUMEN

Despite representing a sizeable fraction of the canopy, very little is known about leaf sheath gas exchange in grasses. Specifically, estimates of sheath stomatal conductance, transpiration and photosynthesis along with their responses to light, CO2 and vapour pressure deficit (VPD) are unknown. Furthermore, the anatomical basis of these responses is poorly documented. Here, using barley as a model system, and combining leaf-level gas exchange, whole-plant gravimetric measurements, transpiration inhibitors, anatomical observations, and biophysical modelling, we found that sheath and blade stomatal conductance and transpiration were similar, especially at low light, in addition to being genotypically variable. Thanks to high abaxial stomata densities and surface areas nearly half those of the blades, sheaths accounted for up to 17% of the daily whole-plant water use, which -surprisingly- increased to 45% during the nighttime. Sheath photosynthesis was on average 17-25% that of the blade and was associated with lower water use efficiency. Finally, sheaths responded differently to the environment, exhibiting a lack of response to CO2 but a strong sensitivity to VPD. Overall, these results suggest a key involvement of sheaths in feedback loops between canopy architecture and gas exchange with potentially significant implications on adaptation to current and future climates in grasses.


Asunto(s)
Dióxido de Carbono/metabolismo , Hordeum/anatomía & histología , Hordeum/fisiología , Productos Agrícolas/fisiología , Genotipo , Hordeum/genética , Minnesota , Modelos Biológicos , Fotosíntesis/fisiología , Hojas de la Planta/anatomía & histología , Hojas de la Planta/fisiología , Estomas de Plantas/fisiología , Transpiración de Plantas/fisiología , Presión de Vapor , Agua/metabolismo
14.
Plant Physiol ; 176(4): 2750-2760, 2018 04.
Artículo en Inglés | MEDLINE | ID: mdl-29440592

RESUMEN

The shoot apical and axillary meristems control shoot development, effectively influencing lateral branch and leaf formation. The barley (Hordeum vulgare) uniculm2 (cul2) mutation blocks axillary meristem development, and mutant plants lack lateral branches (tillers) that normally develop from the crown. A genetic screen for cul2 suppressors recovered two recessive alleles of ELIGULUM-A (ELI-A) that partially rescued the cul2 tillering phenotype. Mutations in ELI-A produce shorter plants with fewer tillers and disrupt the leaf blade-sheath boundary, producing liguleless leaves and reduced secondary cell wall development in stems and leaves. ELI-A is predicted to encode an unannotated protein containing an RNaseH-like domain that is conserved in land plants. ELI-A transcripts accumulate at the preligule boundary, the developing ligule, leaf margins, cells destined to develop secondary cell walls, and cells surrounding leaf vascular bundles. Recent studies have identified regulatory similarities between boundary development in leaves and lateral organs. Interestingly, we observed ELI-A transcripts at the preligule boundary, suggesting that ELI-A contributes to boundary formation between the blade and sheath. However, we did not observe ELI-A transcripts at the axillary meristem boundary in leaf axils, suggesting that ELI-A is not involved in boundary development for axillary meristem development. Our results show that ELI-A contributes to leaf and lateral branch development by acting as a boundary gene during ligule development but not during lateral branch development.


Asunto(s)
Hordeum/genética , Meristema/genética , Hojas de la Planta/genética , Proteínas de Plantas/genética , Flores/genética , Flores/crecimiento & desarrollo , Flores/metabolismo , Regulación del Desarrollo de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Hordeum/crecimiento & desarrollo , Hordeum/metabolismo , Meristema/crecimiento & desarrollo , Meristema/metabolismo , Mutación , Filogenia , Hojas de la Planta/crecimiento & desarrollo , Hojas de la Planta/metabolismo , Proteínas de Plantas/clasificación , Proteínas de Plantas/metabolismo , Tallos de la Planta/crecimiento & desarrollo , Tallos de la Planta/metabolismo
15.
New Phytol ; 217(3): 1292-1306, 2018 02.
Artículo en Inglés | MEDLINE | ID: mdl-29155438

RESUMEN

Circular RNAs (circRNAs) are covalently closed RNA molecules. Recent studies have shown that circRNAs can arise from the transcripts of transposons. Given the prevalence of transposons in the maize genome and dramatic genomic variation driven by transposons, we hypothesize that transposons in maize may be involved in the formation of circRNAs and further modulate phenotypic variation. We performed circRNA-Seq on B73 seedling leaves and uncovered 2804 high-confidence maize circRNAs, which show distinct genomic features. Comprehensive analyses demonstrated that sequences related to LINE1-like elements (LLEs) and their Reverse Complementary Pairs (LLERCPs) are significantly enriched in the flanking regions of circRNAs. Interestingly, as the number of LLERCPs increase, the accumulation of circRNAs varies, whereas that of linear transcripts decreases. Furthermore, genes with LLERCP-mediated circRNAs are enriched among loci that are associated with phenotypic variation. These results suggest that circRNAs are likely to be involved in the modulation of phenotypic variation by LLERCPs. Further, we showed that the presence/absence variation of LLERCPs was associated with expression variation of circRNA-circ1690 and was related to ear height, potentially through the interplay between circRNAs and functional linear transcripts. Our first study of maize circRNAs uncovers a potential new way for transposons to modulate transcriptomic and phenotypic variations.


Asunto(s)
Elementos Transponibles de ADN/genética , ARN/genética , Transcriptoma/genética , Zea mays/genética , Secuencia de Bases , Genes de Plantas , Sitios Genéticos , Fenotipo , ARN/metabolismo , ARN Circular , ARN de Planta/genética , ARN de Planta/metabolismo , Retroelementos/genética
16.
Nature ; 491(7426): 711-6, 2012 Nov 29.
Artículo en Inglés | MEDLINE | ID: mdl-23075845

RESUMEN

Barley (Hordeum vulgare L.) is among the world's earliest domesticated and most important crop plants. It is diploid with a large haploid genome of 5.1 gigabases (Gb). Here we present an integrated and ordered physical, genetic and functional sequence resource that describes the barley gene-space in a structured whole-genome context. We developed a physical map of 4.98 Gb, with more than 3.90 Gb anchored to a high-resolution genetic map. Projecting a deep whole-genome shotgun assembly, complementary DNA and deep RNA sequence data onto this framework supports 79,379 transcript clusters, including 26,159 'high-confidence' genes with homology support from other plant genomes. Abundant alternative splicing, premature termination codons and novel transcriptionally active regions suggest that post-transcriptional processing forms an important regulatory layer. Survey sequences from diverse accessions reveal a landscape of extensive single-nucleotide variation. Our data provide a platform for both genome-assisted research and enabling contemporary crop improvement.


Asunto(s)
Genoma de Planta/genética , Hordeum/genética , Análisis de Secuencia de ADN , Empalme Alternativo/genética , Codón sin Sentido/genética , Productos Agrícolas/genética , Evolución Molecular , Regulación de la Expresión Génica de las Plantas , Genes de Plantas/genética , Genómica , Hordeum/clasificación , Anotación de Secuencia Molecular , Mapeo Físico de Cromosoma , Polimorfismo de Nucleótido Simple/genética , Secuencias Repetitivas de Ácidos Nucleicos/genética , Transcriptoma/genética
17.
J Exp Bot ; 68(9): 2187-2197, 2017 04 01.
Artículo en Inglés | MEDLINE | ID: mdl-28407119

RESUMEN

Fusarium Head Blight is a disease of cereal crops that causes severe yield losses and mycotoxin contamination of grain. The main causal pathogen, Fusarium graminearum, produces the trichothecene toxins deoxynivalenol or nivalenol as virulence factors. Nivalenol-producing isolates are most prevalent in Asia but co-exist with deoxynivalenol producers in lower frequency in North America and Europe. Previous studies identified a barley UDP-glucosyltransferase, HvUGT13248, that efficiently detoxifies deoxynivalenol, and when expressed in transgenic wheat results in high levels of type II resistance against deoxynivalenol-producing F. graminearum. Here we show that HvUGT13248 is also capable of converting nivalenol into the non-toxic nivalenol-3-O-ß-d-glucoside. We describe the enzymatic preparation of a nivalenol-glucoside standard and its use in development of an analytical method to detect the nivalenol-glucoside conjugate. Recombinant Escherichia coli expressing HvUGT13248 glycosylates nivalenol more efficiently than deoxynivalenol. Overexpression in yeast, Arabidopsis thaliana, and wheat leads to increased nivalenol resistance. Increased ability to convert nivalenol to nivalenol-glucoside was observed in transgenic wheat, which also exhibits type II resistance to a nivalenol-producing F. graminearum strain. Our results demonstrate the HvUGT13248 can act to detoxify deoxynivalenol and nivalenol and provide resistance to deoxynivalenol- and nivalenol-producing Fusarium.


Asunto(s)
Fusarium/metabolismo , Glucosiltransferasas/genética , Hordeum/genética , Enfermedades de las Plantas/genética , Proteínas de Plantas/genética , Tricotecenos/metabolismo , Resistencia a la Enfermedad/genética , Glucosiltransferasas/metabolismo , Hordeum/enzimología , Hordeum/microbiología , Interacciones Huésped-Patógeno , Enfermedades de las Plantas/microbiología , Proteínas de Plantas/metabolismo , Plantas Modificadas Genéticamente/genética , Plantas Modificadas Genéticamente/metabolismo , Plantas Modificadas Genéticamente/microbiología , Triticum/genética , Triticum/metabolismo , Triticum/microbiología
18.
Plant J ; 84(1): 216-27, 2015 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-26252423

RESUMEN

Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.


Asunto(s)
Cromosomas Artificiales Bacterianos/genética , Genoma de Planta/genética , Hordeum/genética , Datos de Secuencia Molecular
19.
BMC Genomics ; 17: 387, 2016 05 21.
Artículo en Inglés | MEDLINE | ID: mdl-27206761

RESUMEN

BACKGROUND: Fusarium graminearum causes Fusarium head blight (FHB), a major disease problem worldwide. Resistance to FHB is controlled by quantitative trait loci (QTL) of which two are located on barley chromosomes 2H bin8 and 6H bin7. The mechanisms of resistance mediated by FHB QTL are poorly defined. RESULTS: Near-isogenic lines (NILs) carrying Chevron-derived resistant alleles for the two QTL were developed and exhibited FHB resistance in field trials. To understand the molecular responses associated with resistance, transcriptomes of the NILs and recurrent parents (M69 and Lacey) were investigated with RNA sequencing (RNA-Seq) after F. graminearum or mock inoculation. A total of 2083 FHB-responsive transcripts were detected and provide a gene expression atlas for the barley-F. graminearum interaction. Comparative analysis of the 2Hb8 resistant (R) NIL and M69 revealed that the 2Hb8 R NIL exhibited an elevated defense response in the absence of fungal infection and responded quicker than M69 upon fungal infection. The 6Hb7 R NIL displayed a more rapid induction of a set of defense genes than Lacey during the early stage of fungal infection. Overlap of differentially accumulated genes were identified between the two R NILs, suggesting that certain responses may represent basal resistance to F. graminearum and/or general biotic stress response and were expressed by both resistant genotypes. Long noncoding RNAs (lncRNAs) have emerged as potential key regulators of transcription. A total of 12,366 lncRNAs were identified, of which 604 were FHB responsive. CONCLUSIONS: The current transcriptomic analysis revealed differential responses conferred by two QTL during F. graminearum infection and identified genes and lncRNAs that were associated with FHB resistance.


Asunto(s)
Resistencia a la Enfermedad/genética , Fusarium , Hordeum/genética , Hordeum/microbiología , Enfermedades de las Plantas/genética , Enfermedades de las Plantas/microbiología , Sitios de Carácter Cuantitativo , Transcriptoma , Alelos , Cromosomas de las Plantas , Análisis por Conglomerados , Perfilación de la Expresión Génica , Regulación de la Expresión Génica de las Plantas , Genotipo , Interacciones Huésped-Patógeno/genética , Fenotipo , ARN de Planta
20.
BMC Genomics ; 17(1): 875, 2016 11 04.
Artículo en Inglés | MEDLINE | ID: mdl-27814670

RESUMEN

BACKGROUND: Gene duplication is prevalent in many species and can result in coding and regulatory divergence. Gene duplications can be classified as whole genome duplication (WGD), tandem and inserted (non-syntenic). In maize, WGD resulted in the subgenomes maize1 and maize2, of which maize1 is considered the dominant subgenome. However, the landscape of co-expression network divergence of duplicate genes in maize is still largely uncharacterized. RESULTS: To address the consequence of gene duplication on co-expression network divergence, we developed a gene co-expression network from RNA-seq data derived from 64 different tissues/stages of the maize reference inbred-B73. WGD, tandem and inserted gene duplications exhibited distinct regulatory divergence. Inserted duplicate genes were more likely to be singletons in the co-expression networks, while WGD duplicate genes were likely to be co-expressed with other genes. Tandem duplicate genes were enriched in the co-expression pattern where co-expressed genes were nearly identical for the duplicates in the network. Older gene duplications exhibit more extensive co-expression variation than younger duplications. Overall, non-syntenic genes primarily from inserted duplications show more co-expression divergence. Also, such enlarged co-expression divergence is significantly related to duplication age. Moreover, subgenome dominance was not observed in the co-expression networks - maize1 and maize2 exhibit similar levels of intra subgenome correlations. Intriguingly, the level of inter subgenome co-expression was similar to the level of intra subgenome correlations, and genes from specific subgenomes were not likely to be the enriched in co-expression network modules and the hub genes were not predominantly from any specific subgenomes in maize. CONCLUSIONS: Our work provides a comprehensive analysis of maize co-expression network divergence for three different types of gene duplications and identifies potential relationships between duplication types, duplication ages and co-expression consequences.


Asunto(s)
Duplicación de Gen , Regulación de la Expresión Génica de las Plantas , Redes Reguladoras de Genes , Genoma de Planta , Zea mays/genética , Perfilación de la Expresión Génica , Genes de Plantas
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