Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 3.920
Filtrar
1.
PLoS One ; 15(8): e0230404, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32866150

RESUMO

High-throughput SNP genotyping has become a precondition to move to higher precision and wider genome coverage genetic analysis of natural and breeding populations of non-model species. We developed a 44,318 annotated SNP catalog for Araucaria angustifolia, a grandiose subtropical conifer tree, one of the only two native Brazilian gymnosperms, critically endangered due to its valuable wood and seeds. Following transcriptome assembly and annotation, SNPs were discovered from RNA-seq and pooled RAD-seq data. From the SNP catalog, an Axiom® SNP array with 3,038 validated SNPs was developed and used to provide a comprehensive look at the genetic diversity and structure of 15 populations across the natural range of the species. RNA-seq was a far superior source of SNPs when compared to RAD-seq in terms of conversion rate to polymorphic markers on the array, likely due to the more efficient complexity reduction of the huge conifer genome. By matching microsatellite and SNP data on the same set of A. angustifolia individuals, we show that SNPs reflect more precisely the actual genome-wide patterns of genetic diversity and structure, challenging previous microsatellite-based assessments. Moreover, SNPs corroborated the known major north-south genetic cline, but allowed a more accurate attribution to regional versus among-population differentiation, indicating the potential to select ancestry-informative markers. The availability of a public, user-friendly 3K SNP array for A. angustifolia and a catalog of 44,318 SNPs predicted to provide ~29,000 informative SNPs across ~20,000 loci across the genome, will allow tackling still unsettled questions on its evolutionary history, toward a more comprehensive picture of the origin, past dynamics and future trend of the species' genetic resources. Additionally, but not less importantly, the SNP array described, unlocks the potential to adopt genomic prediction methods to accelerate the still very timid efforts of systematic tree breeding of A. angustifolia.


Assuntos
Araucaria/genética , Brasil , Genoma de Planta/genética , Genômica/métodos , Genótipo , Repetições de Microssatélites/genética , Polimorfismo de Nucleotídeo Único/genética , Traqueófitas/genética , Transcriptoma/genética , Árvores/genética
2.
Nat Commun ; 11(1): 4447, 2020 09 07.
Artigo em Inglês | MEDLINE | ID: mdl-32895382

RESUMO

Tea is an economically important plant characterized by a large genome, high heterozygosity, and high species diversity. In this study, we assemble a 3.26-Gb high-quality chromosome-scale genome for the 'Longjing 43' cultivar of Camellia sinensis var. sinensis. Genomic resequencing of 139 tea accessions from around the world is used to investigate the evolution and phylogenetic relationships of tea accessions. We find that hybridization has increased the heterozygosity and wide-ranging gene flow among tea populations with the spread of tea cultivation. Population genetic and transcriptomic analyses reveal that during domestication, selection for disease resistance and flavor in C. sinensis var. sinensis populations has been stronger than that in C. sinensis var. assamica populations. This study provides resources for marker-assisted breeding of tea and sets the foundation for further research on tea genetics and evolution.


Assuntos
Camellia sinensis/genética , Resistência à Doença/genética , Evolução Molecular , Genoma de Planta/genética , Melhoramento Vegetal , Domesticação , Perfilação da Expressão Gênica , Genômica , Filogenia , Polimorfismo de Nucleotídeo Único
3.
Nat Commun ; 11(1): 3795, 2020 07 30.
Artigo em Inglês | MEDLINE | ID: mdl-32732942

RESUMO

Angiosperms have become the dominant terrestrial plant group by diversifying for ~145 million years into a broad range of environments. During the course of evolution, numerous morphological innovations arose, often preceded by whole genome duplications (WGD). The mustard family (Brassicaceae), a successful angiosperm clade with ~4000 species, has been diversifying into many evolutionary lineages for more than 30 million years. Here we develop a species inventory, analyze morphological variation, and present a maternal, plastome-based genus-level phylogeny. We show that increased morphological disparity, despite an apparent absence of clade-specific morphological innovations, is found in tribes with WGDs or diversification rate shifts. Both are important processes in Brassicaceae, resulting in an overall high net diversification rate. Character states show frequent and independent gain and loss, and form varying combinations. Therefore, Brassicaceae pave the way to concepts of phylogenetic genome-wide association studies to analyze the evolution of morphological form and function.


Assuntos
Evolução Biológica , Brassicaceae/classificação , Brassicaceae/genética , Evolução Molecular , Genoma de Planta/genética , Variação Genética/genética , Estudo de Associação Genômica Ampla , Filogenia
4.
Nat Commun ; 11(1): 4058, 2020 08 13.
Artigo em Inglês | MEDLINE | ID: mdl-32792480

RESUMO

Tomatoes come in a multitude of shapes and flavors despite a narrow genetic pool. Here, we leverage whole-genome resequencing data available for 602 cultivated and wild accessions to determine the contribution of transposable elements (TEs) to tomato diversity. We identify 6,906 TE insertions polymorphisms (TIPs), which result from the mobilization of 337 distinct TE families. Most TIPs are low frequency variants and TIPs are disproportionately located within or adjacent to genes involved in environmental responses. In addition, genic TE insertions tend to have strong transcriptional effects and they can notably lead to the generation of multiple transcript isoforms. Using genome-wide association studies (GWAS), we identify at least 40 TIPs robustly associated with extreme variation in major agronomic traits or secondary metabolites and in most cases, no SNP tags the TE insertion allele. Collectively, these findings highlight the unique role of TE mobilization in tomato diversification, with important implications for breeding.


Assuntos
Elementos de DNA Transponíveis/genética , Lycopersicon esculentum/genética , Evolução Molecular , Genoma de Planta/genética , Estudo de Associação Genômica Ampla , Polimorfismo Genético/genética
6.
PLoS One ; 15(8): e0238383, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32845934

RESUMO

A robust Genotyping-By-Sequencing (GBS) pipeline platform was examined to provide accurate discovery of Single Nucleotide Polymorphisms (SNPs) in a cape gooseberry (Physalis peruviana L.) and related taxa germplasm collection. A total of 176 accessions representing, wild, weedy, and commercial cultivars as well as related taxa from the Colombian germplasm bank and other world repositories were screened using GBS. The pipeline parameters mnLCov of 0.5 and a mnScov of 0.7, tomato and potato genomes, and cape gooseberry transcriptome for read alignments, were selected to better assess diversity and population structure in cape gooseberry and related taxa. A total of 7,425 SNPs, derived from P. peruviana common tags (unique 64 bp sequences shared between selected species), were used. Within P. peruviana, five subpopulations with a high genetic diversity and allele fixation (HE: 0.35 to 0.36 and FIS: -0.11 to -0.01, respectively) were detected. Conversely, low genetic differentiation (FST: 0.01 to 0.05) was also observed, indicating a high gene flow among subpopulations. These results contribute to the establishment of adequate conservation and breeding strategies for Cape gooseberry and closely related Physalis species.


Assuntos
Genoma de Planta/genética , Lycopersicon esculentum/genética , Physalis/classificação , Physalis/genética , Solanum tuberosum/genética , Marcadores Genéticos/genética , Técnicas de Genotipagem , Polimorfismo de Nucleotídeo Único/genética , Análise de Componente Principal
7.
Plant Mol Biol ; 104(3): 297-307, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32748081

RESUMO

KEY MESSAGE: We have developed multiplex genome editing toolkits for citrus that significantly improve citrus genome editing efficacy. CRISPR/Cas systems have been engineered for genome editing in many organisms, including plants. However, the gene editing efficiency in citrus via CRISPR technology remains too low to be implemented for genetic improvement in practice. Moreover, it is very difficult to obtain homozygous or biallelic knockout mutants in citrus. Here, we have developed multiplex genome editing toolkits for citrus including PEG-mediated protoplast transformation, a GFP reporter system that allows the rapid assessment of CRISPR constructs, citrus U6 promoters with improved efficacy, and tRNA-mediated or Csy4-mediated multiplex genome editing. Using the toolkits, we successfully conducted genome modification of embryogenic protoplast cells and epicotyl tissues. We have achieved a biallelic mutation rate of 44.4% and a homozygous mutation rate of 11.1%, representing a significant improvement in citrus genome editing efficacy. In addition, our study lays the foundation for nontransgenic genome editing of citrus.


Assuntos
Citrus/genética , Edição de Genes/métodos , Genoma de Planta/genética , Homozigoto , Mutação , Sistemas CRISPR-Cas , Técnicas de Inativação de Genes , Genes de Plantas/genética , Plantas Geneticamente Modificadas , Regiões Promotoras Genéticas , Protoplastos , RNA Guia/genética , RNA de Transferência/genética
8.
Am J Bot ; 107(8): 1148-1164, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32830865

RESUMO

PREMISE: Whole-genome duplications (WGDs) are prevalent throughout the evolutionary history of plants. For example, dozens of WGDs have been phylogenetically localized across the order Brassicales, specifically, within the family Brassicaceae. A WGD event has also been identified in the Cleomaceae, the sister family to Brassicaceae, yet its placement, as well as that of WGDs in other families in the order, remains unclear. METHODS: Phylo-transcriptomic data were generated and used to infer a nuclear phylogeny for 74 Brassicales taxa. Genome survey sequencing was also performed on 66 of those taxa to infer a chloroplast phylogeny. These phylogenies were used to assess and confirm relationships among the major families of the Brassicales and within Brassicaceae. Multiple WGD inference methods were then used to assess the placement of WGDs on the nuclear phylogeny. RESULTS: Well-supported chloroplast and nuclear phylogenies for the Brassicales and the putative placement of the Cleomaceae-specific WGD event Th-ɑ are presented. This work also provides evidence for previously hypothesized WGDs, including a well-supported event shared by at least two members of the Resedaceae family, and a possible event within the Capparaceae. CONCLUSIONS: Phylogenetics and the placement of WGDs within highly polyploid lineages continues to be a major challenge. This study adds to the conversation on WGD inference difficulties by demonstrating that sampling is especially important for WGD identification and phylogenetic placement. Given its economic importance and genomic resources, the Brassicales continues to be an ideal group for assessing WGD inference methods.


Assuntos
Duplicação Gênica , Magnoliopsida/genética , Evolução Molecular , Genoma , Genoma de Planta/genética , Humanos , Filogenia , Poliploidia
9.
PLoS One ; 15(8): e0237018, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32785241

RESUMO

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


Assuntos
Betaína-Aldeído Desidrogenase/genética , Oryza/genética , Alelos , Betaína-Aldeído Desidrogenase/metabolismo , Sistemas CRISPR-Cas/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Edição de Genes/métodos , Genes de Plantas/genética , Genoma de Planta/genética , Mutação/genética , Odorantes/análise , Fenótipo , Plantas Geneticamente Modificadas/genética
10.
PLoS One ; 15(7): e0235434, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32649700

RESUMO

The genetic diversity of North American soybean cultivars has been largely influenced by a small number of ancestors. High yielding breeding lines that possess exotic pedigrees have been developed, but identifying beneficial exotic alleles has been difficult as a result of complex interactions of yield alleles with genetic backgrounds and environments as well as the highly quantitative nature of yield. PI 416937 has been utilized in the development of many high yielding lines that have been entered into the USDA Southern States Uniform Tests over the past ~20 years. The primary goal of this research was to identify genomic regions under breeding selection from PI 416937 and introduce a methodology for identifying and potentially utilizing beneficial diversity from lines prevalent in the ancestry of elite cultivars. Utilizing SoySNP50K Infinium BeadChips, 52 high yielding PI 416937-derived lines as well as their parents were genotyped to identify PI 416937 alleles under breeding selection. Nine genomic regions across three chromosomes and 17 genomic regions across seven chromosomes were identified where PI 416937 alleles were under positive or negative selection. Minimal significant associations between PI 416937 alleles and yield were observed in replicated yield trials of five RIL populations, highlighting the difficulty of consistently detecting yield associations.


Assuntos
Cruzamento , Variação Genética/genética , Soja/genética , Alelos , Mapeamento Cromossômico , Cromossomos de Plantas , Genoma de Planta/genética , Genômica , Genótipo , Humanos , Locos de Características Quantitativas/genética , Sementes/genética , Sementes/crescimento & desenvolvimento , Soja/crescimento & desenvolvimento , Estados Unidos
11.
Gene ; 758: 144961, 2020 Oct 20.
Artigo em Inglês | MEDLINE | ID: mdl-32693148

RESUMO

Ginkgo biloba L. is regarded as the most ancient living tree, and its kernel has been used as a traditional Chinese medicine for more than 2,000 years. The leaf extracts of this tree have been among the bestselling herbal remedies in Western countries since the last century. To understand the biosynthesis of the pharmacologically active ingredients in G. biloba, flavonoids and terpenoid trilactones (TTLs), we sequenced the transcriptomes of G. biloba leaves, kernels and testae with Iso-Seq and RNA-Seq technologies and obtained 152,524 clean consensus reads. When these reads were used to improve the annotation of the G. biloba genome, 4,856 novel genes, 25,583 new isoforms of previously annotated genes and 4,363 lncRNAs were discovered. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that genes involved in growth, regulation and response to stress were more likely to be regulated by alternative splicing (AS) or alternative polyadenylation (APA), which represent the two most important posttranscriptional regulation mechanisms. It was found that some of the characterized genes involved in the biosynthesis of flavonoids and TTLs were also possibly regulated by AS and APA. Using phylogenetic and gene expression pattern analyses, some candidate genes for the biosynthesis of flavonoids and TTLs were screened. After qRT-PCR validation, the final candidate genes for flavonoid biosynthesis included three UDP-glycosyltransferases and one MYB transcription factor, while the candidate genes for TTL biosynthesis included two cytochrome P450 and one WRKY transcription factor. Our study suggested that Iso-Seq may play an important role in improving genome annotation, elucidating AS and APA mechanisms and discovering candidate genes involved in the biosynthesis of some secondary metabolites.


Assuntos
Flavonoides/biossíntese , Regulação da Expressão Gênica de Plantas/genética , Ginkgo biloba/genética , Ginkgo biloba/metabolismo , Lactonas/metabolismo , Terpenos/metabolismo , Processamento Alternativo/genética , Sistema Enzimático do Citocromo P-450/genética , Perfilação da Expressão Gênica , Genoma de Planta/genética , Extratos Vegetais , Transcriptoma , Sequenciamento Completo do Genoma
12.
PLoS Genet ; 16(7): e1008964, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32716939

RESUMO

Chromatin regulation of eukaryotic genomes depends on the formation of nucleosome complexes between histone proteins and DNA. Histone variants, which are diversified by sequence or expression pattern, can profoundly alter chromatin properties. While variants in histone H2A and H3 families are well characterized, the extent of diversification of histone H2B proteins is less understood. Here, we report a systematic analysis of the histone H2B family in plants, which have undergone substantial divergence during the evolution of each major group in the plant kingdom. By characterising Arabidopsis H2Bs, we substantiate this diversification and reveal potential functional specialization that parallels the phylogenetic structure of emergent clades in eudicots. In addition, we identify a new class of highly divergent H2B variants, H2B.S, that specifically accumulate during chromatin compaction of dry seed embryos in multiple species of flowering plants. Our findings thus identify unsuspected diverse properties among histone H2B proteins in plants that has manifested into potentially novel groups of histone variants.


Assuntos
Arabidopsis/genética , Cromatina/genética , Evolução Molecular , Histonas/genética , Arabidopsis/classificação , Eucariotos , Genoma de Planta/genética , Histonas/classificação , Família Multigênica/genética
13.
Nat Commun ; 11(1): 3375, 2020 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-32632155

RESUMO

Hybridization can drive speciation. We examine the hypothesis that Castanea henryi var. omeiensis is an evolutionary lineage that originated from hybridization between two near-sympatric diploid taxa, C. henryi var. henryi and C. mollissima. We produce a high-quality genome assembly for mollissima and characterize evolutionary relationships among related chestnut taxa. Our results show that C. henryi var. omeiensis has a mosaic genome but has accumulated divergence in all 12 chromosomes. We observe positive correlation between admixture proportions and recombination rates across the genome. Candidate barrier genomic regions, which isolate var. henryi and mollissima, are re-assorted in the hybrid lineage. We further find that the putative barrier segments concentrate in genomic regions with less recombination, suggesting that interaction between natural selection and recombination shapes the evolution of hybrid genomes during hybrid speciation. This study highlights that reassortment of parental barriers is an important mechanism in generating biodiversity.


Assuntos
Diploide , Fagaceae/genética , Genoma de Planta/genética , Hibridização Genética , Mosaicismo , Ploidias , Algoritmos , Evolução Molecular , Fagaceae/classificação , Especiação Genética , Modelos Genéticos , Recombinação Genética , Seleção Genética , Especificidade da Espécie , Sequenciamento Completo do Genoma/métodos
14.
Curr Opin Plant Biol ; 56: 118-126, 2020 08.
Artigo em Inglês | MEDLINE | ID: mdl-32604025

RESUMO

Banana production is severely constrained by many pathogens and pests, particularly where a number of them are co-existing. The use of disease-resistant banana varieties is one of the most effective ways to mitigate the negative impacts of pathogens on banana production. Recent advances in new breeding techniques have the potential to accelerate breeding of banana for disease resistance. The CRISPR/Cas9 based genome editing has emerged as the most powerful tool for crop improvement due to its capability of creating precise alterations in plant genome and trait stacking through multiplexing. Recently, the robust CRISPR/Cas9-based genome editing of banana has been established, which can be applied for developing disease-resistant varieties. This article presents a synopsis of recent advancements and perspectives on the application of genome editing for generating disease-resistant banana varieties. It also summarizes the current status of regulatory requirements for the release of genome-edited crop varieties among different countries.


Assuntos
Edição de Genes , Musa , Sistemas CRISPR-Cas/genética , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Resistência à Doença/genética , Genoma de Planta/genética , Humanos , Musa/genética
15.
Cytogenet Genome Res ; 160(6): 329-334, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32683370

RESUMO

Rubus yellow net virus (RYNV) infects Rubus spp., causing a severe decline when present in mixed infections with other viruses. RYNV belongs to the family Caulimoviridae, also known as plant pararetroviruses, which can exist as episomal or integrated elements (endogenous). Most of integrated pararetroviruses are noninfectious; however, a few cases have been reported where they excised from the plant genome and formed infectious particles. Graft transmission onto indicator plants R. occidentalis "Munger" has been the standard test method for RYNV detection in certification programs. Previously, it was noticed that some RYNV PCR-positive plants did not induce symptoms on "Munger", suggesting an integration event. In this study, bio-indexing and different molecular techniques were employed to differentiate between integrated and episomal RYNV sequences. Reverse transcription-PCR using RYNV-specific oligonucleotides after DNase treatment generated positive results for the virus in graft transmissible isolates (episomal) only. To confirm these results, rolling circle amplification on DNA preparations from the same samples resulted in amplicons identified as RYNV only from plants with graft transmissible RYNV. High-throughput sequencing was used to identify the RYNV-like sequences present in the host DNA. These results indicate the integration of RYNV into the red raspberry genome and highlight the necessity to recognize this phenomenon (integration) in future Rubus quarantine and certification programs.


Assuntos
Caulimoviridae/genética , Genoma de Planta/genética , Vírus de Plantas/genética , Rubus/genética , Rubus/virologia , Integração Viral/genética , Caulimoviridae/isolamento & purificação , Doenças das Plantas/genética , Doenças das Plantas/prevenção & controle , Doenças das Plantas/virologia , Vírus de Plantas/isolamento & purificação , Plasmídeos/genética
16.
PLoS One ; 15(7): e0236349, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32701993

RESUMO

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


Assuntos
Genoma de Planta/genética , Oryza/genética , Hormônios Peptídicos/genética , Peptídeos/genética , Proteínas de Plantas/genética , Secas , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/genética , Peptídeos/classificação , Filogenia , Salinidade , Transdução de Sinais/genética , Cloreto de Sódio/metabolismo , Estresse Fisiológico/genética
17.
PLoS One ; 15(7): e0236454, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32702710

RESUMO

Flax (Linum usitatissimum) is a member of family linaceae with annual growth habit. It is included among those crops which were domesticated very early and has been used in development related studies as a model plant. In plants, Calmodulin-binding transcription activators (CAMTAs) comprise a unique set of Calmodulin-binding proteins. To elucidate the transport mechanism of secondary metabolites in flax, a genome-based study on these transporters was performed. The current investigation identified nine CAMTAs proteins, classified into three categories during phylogenetic analysis. Each group had significant evolutionary role as illustrated by the conservation of gene structures, protein domains and motif organizations over the distinctive phylogenetic classes. GO annotation suggested a link to sequence-specific DNA and protein binding, response to low temperature and transcription regulation by RNA polymerase II. The existence of different hormonal and stress responsive cis-regulatory elements in promotor region may directly correlate with the variation of their transcripts. MicroRNA target analysis revealed that various groups of miRNA families targeted the LuCAMTAs genes. Identification of CAMTA genes, miRNA studies and phylogenetic analysis may open avenues to uncover the underlying functional mechanism of this important family of genes in flax.


Assuntos
Proteínas de Ligação a Calmodulina/genética , Evolução Molecular , Linho/genética , Família Multigênica/genética , Proteínas de Ligação a Calmodulina/classificação , Genoma de Planta/genética , Filogenia , Ligação Proteica
18.
Plant Mol Biol ; 104(1-2): 113-136, 2020 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-32627097

RESUMO

KEY MESSAGE: Present study revealed a complex relationship among histone H3 methylation (examined using H3K4/K27me3 marks), cytosine DNA methylation and differential gene expression during Lr28 mediated leaf rust resistance in wheat. During the present study, genome-wide histone modifications were examined in a pair of near isogenic lines (NILs) (with and without Lr28 in the background of cv. HD2329). The two histone marks used included H3K4me3 (an activation mark) and H3K27me3 (a repression mark). The results were compared with levels of expression (using RNA-seq) and DNA methylation (MeDIP) data obtained using the same pair of NILs. Some of the salient features of the present study include the following: (i) large scale differential binding sites (DBS) were available for only H3K4me3 in the susceptible cultivar, but for both H3K4me3 and H3K27me3 in its resistant NIL; (ii) DBSs for H3K27me3 mark were more abundant (> 80%) in intergenic regions, whereas DBSs for H3K4me3 were distributed in all genomic regions including exons, introns, intergenic, TTS (transcription termination sites) and promoters; (iii) fourteen (14) genes associated with DBSs showed co-localization for both the marks; (iv) only a small fraction (7% for H3K4me3 and 12% for H3K27me3) of genes associated with DBSs matched with the levels of gene expression inferred from RNA-seq data; (v) validation studies using qRT-PCR were conducted on 26 selected representative genes; results for only 11 genes could be validated. The proteins encoded by important genes involved in promoting infection included domains generally carried by R gene proteins such as Mlo like protein, protein kinases and purple acid phosphatase. Similarly, proteins encoded by genes involved in resistance included those carrying domains for lectin kinase, R gene, aspartyl protease, etc. Overall, the results suggest a very complex network of downstream genes that are expressed during compatible and incompatible interactions; some of the genes identified during the present study may be used in future validation studies involving RNAi/overexpression approaches.


Assuntos
Basidiomycota/metabolismo , Resistência à Doença/genética , Genes de Plantas/genética , Genoma de Planta/genética , Histonas/genética , Doenças das Plantas/genética , Triticum/genética , Triticum/metabolismo , Imunoprecipitação da Cromatina , Metilação de DNA , Regulação da Expressão Gênica de Plantas , Ligação Genética , Histonas/metabolismo , Anotação de Sequência Molecular , Doenças das Plantas/microbiologia , Folhas de Planta/genética , Folhas de Planta/microbiologia , Regiões Promotoras Genéticas , Reprodutibilidade dos Testes , Alinhamento de Sequência , Análise de Sequência , Análise de Sequência de RNA , Transcrição Genética , Triticum/microbiologia
19.
PLoS One ; 15(6): e0234863, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32574201

RESUMO

Durum wheat (Triticum turgidum L. ssp. durum) is one of the top crops in Kazakhstan, where it is cultivated in different ecological niches, mainly at higher latitudes in the steppe zone of the northern region. Therefore, local breeding programs for durum wheat are primarily focused on selection for high productivity in Northern Kazakhstan based on the introduction of promising foreign germplasm and the adoption of marker-assisted selection. In this study, a world tetraploid wheat collection consisted of 184 primitive and domesticated accessions, which were previously genotyped using 16,425 polymorphic SNP markers, was field-tested in Northern and South-eastern Kazakhstan. The field tests have allowed the identification of 80 durum wheat promising lines in Northern Kazakhstan in comparison with a local standard cultivar. Also, GGE (Genotype and Genotype by Environment) biplot analyses for yield performance revealed that accessions of T. dicoccum, T. carthlicum, and T. turanicum also have potential to improve durum wheat yield in the region. The genome-wide association study (GWAS) has allowed the identification of 83 MTAs (marker-trait associations) for heading date, seed maturation time, plant height, spike length, number of fertile spikes, number of kernels per spike, and thousand kernel weight. The comparison of the 83 identified MTAs with those previously reported in GWAS for durum wheat suggests that 38 MTAs are presumably novel, while the co-localization of a large number of MTAs with those previously published confirms the validity of the results of this study. The MTAs reported herewith will provide the opportunity to implement marker-assisted selection in ongoing durum wheat breeding projects targeting higher productivity in the region.


Assuntos
Genoma de Planta/genética , Melhoramento Vegetal , Locos de Características Quantitativas , Seleção Genética , Triticum/genética , Estudo de Associação Genômica Ampla , Pradaria , Cazaquistão , Desequilíbrio de Ligação , Polimorfismo de Nucleotídeo Único , Tetraploidia
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA