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1.
Nat Commun ; 11(1): 5539, 2020 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-33139747

RESUMO

DNA methylation is a ubiquitous chromatin feature, present in 25% of cytosines in the maize genome, but variation and evolution of the methylation landscape during maize domestication remain largely unknown. Here, we leverage whole-genome sequencing (WGS) and whole-genome bisulfite sequencing (WGBS) data on populations of modern maize, landrace, and teosinte (Zea mays ssp. parviglumis) to estimate epimutation rates and selection coefficients. We find weak evidence for direct selection on DNA methylation in any context, but thousands of differentially methylated regions (DMRs) are identified population-wide that are correlated with recent selection. For two trait-associated DMRs, vgt1-DMR and tb1-DMR, HiChIP data indicate that the interactive loops between DMRs and respective downstream genes are present in B73, a modern maize line, but absent in teosinte. Our results enable a better understanding of the evolutionary forces acting on patterns of DNA methylation and suggest a role of methylation variation in adaptive evolution.


Assuntos
Domesticação , Grão Comestível/genética , Evolução Molecular , Regulação da Expressão Gênica de Plantas , Zea mays/genética , Sequenciamento de Cromatina por Imunoprecipitação , Metilação de DNA , DNA de Plantas/genética , DNA de Plantas/isolamento & purificação , Epigênese Genética , Genoma de Planta , México , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único , Seleção Genética
2.
J Plant Res ; 133(6): 827-839, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-33090298

RESUMO

Sagittaria is a genus of ca. 40 species in the aquatic plant family Alismataceae with a nearly global distribution, and a center of diversity in the New World. Two thirds of the known species are native to the Americas, while only a few species are distributed in Africa, Asia and Europe. A previous biogeographic analysis of the genus suggested an African origin for the genus with subsequent dispersal to North America and then to East Asia. Here we expanded the taxon sampling with a focus on the New World taxa and applied species delimitation and biogeographic analyses to revise the knowledge of the phylogeny and evolution of the genus. We obtained largely similar topologies from the chloroplast DNA and nuclear DNA (ITS) data sets. The 74 accessions sampled for our analyses were delimited into 29 species and several cryptic taxa were revealed in widely distributed species. Biogeographic analysis supported basal diversification in South America and subsequent colonization to North America and Asia.


Assuntos
Evolução Biológica , Filogenia , Sagittaria/classificação , África , Ásia , Teorema de Bayes , DNA de Cloroplastos/genética , DNA de Plantas/genética , DNA Espaçador Ribossômico/genética , Europa (Continente) , Extremo Oriente , América do Norte , Análise de Sequência de DNA , América do Sul
3.
Nucleic Acids Res ; 48(17): 9637-9648, 2020 09 25.
Artigo em Inglês | MEDLINE | ID: mdl-32890394

RESUMO

The MADS transcription factors (TF), SEPALLATA3 (SEP3) and AGAMOUS (AG) are required for floral organ identity and floral meristem determinacy. While dimerization is obligatory for DNA binding, SEP3 and SEP3-AG also form tetrameric complexes. How homo and hetero-dimerization and tetramerization of MADS TFs affect genome-wide DNA-binding and gene regulation is not known. Using sequential DNA affinity purification sequencing (seq-DAP-seq), we determined genome-wide binding of SEP3 homomeric and SEP3-AG heteromeric complexes, including SEP3Δtet-AG, a complex with a SEP3 splice variant, SEP3Δtet, which is largely dimeric and SEP3-AG tetramer. SEP3 and SEP3-AG share numerous bound regions, however each complex bound unique sites, demonstrating that protein identity plays a role in DNA-binding. SEP3-AG and SEP3Δtet-AG share a similar genome-wide binding pattern; however the tetrameric form could access new sites and demonstrated a global increase in DNA-binding affinity. Tetramerization exhibited significant cooperative binding with preferential distances between two sites, allowing efficient binding to regions that are poorly recognized by dimeric SEP3Δtet-AG. By intersecting seq-DAP-seq with ChIP-seq and expression data, we identified unique target genes bound either in SEP3-AG seq-DAP-seq or in SEP3/AG ChIP-seq. Seq-DAP-seq is a versatile genome-wide technique and complements in vivo methods to identify putative direct regulatory targets.


Assuntos
Proteína AGAMOUS de Arabidopsis/metabolismo , Proteínas de Arabidopsis/metabolismo , Proteínas de Homeodomínio/metabolismo , Análise de Sequência de DNA/métodos , Fatores de Transcrição/metabolismo , Proteína AGAMOUS de Arabidopsis/genética , Proteínas de Arabidopsis/genética , Sítios de Ligação , Proteínas de Transporte/genética , DNA de Plantas/genética , DNA de Plantas/metabolismo , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Proteínas de Homeodomínio/genética , Complexos Multiproteicos/genética , Complexos Multiproteicos/metabolismo , Multimerização Proteica , Fatores de Transcrição/genética
4.
Proc Natl Acad Sci U S A ; 117(38): 23991-24000, 2020 09 22.
Artigo em Inglês | MEDLINE | ID: mdl-32879011

RESUMO

The genomic sequences of crops continue to be produced at a frenetic pace. It remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Chromatin accessibility assays enable discovery of functional elements; however, to uncover the full portfolio of cis-elements would require profiling of many combinations of cell types, tissues, developmental stages, and environments. Here, we explore the potential to use DNA methylation profiles to develop more complete annotations. Using leaf tissue in maize, we define ∼100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs are found greater than 2 kb from genes. UMRs are highly stable in multiple vegetative tissues, and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf, and these represent regions with potential to become accessible in specific cell types or developmental stages. These UMRs often occur near genes that are expressed in other tissues and are enriched for binding sites of transcription factors. The leaf-inaccessible UMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMR space in four additional monocots ranges from 80 to 120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures provide powerful filters to distill large genomes down to the small fraction of putative functional genes and regulatory elements.


Assuntos
Metilação de DNA/genética , Regulação da Expressão Gênica de Plantas/genética , Genoma de Planta/genética , Sequências Reguladoras de Ácido Nucleico/genética , Cromatina/química , Cromatina/genética , Cromatina/metabolismo , DNA de Plantas/genética , Folhas de Planta/genética , Folhas de Planta/metabolismo , Zea mays/genética
5.
PLoS One ; 15(9): e0227397, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32925921

RESUMO

The continuous and sole dependence on imidazolinone (IMI) herbicides for weedy rice control has led to the evolution of herbicide resistance in weedy rice populations across various countries growing IMI herbicide-resistant rice (IMI-rice), including Malaysia. A comprehensive study was conducted to elucidate occurrence, level, and mechanisms endowing resistance to IMI herbicides in putative resistant (R) weedy rice populations collected from three local Malaysian IMI-rice fields. Seed bioassay and whole-plant dose-response experiments were conducted using commercial IMI herbicides. Based on the resistance index (RI) quantification in both experiments, the cross-resistance pattern of R and susceptible (S) weedy rice populations and control rice varieties (IMI-rice variety MR220CL2 and non-IMI-rice variety MR219) to imazapic and imazapyr was determined. A molecular investigation was carried out by comparing the acetohydroxyacid synthase (AHAS) gene sequences of the R and S populations and the MR220CL2 and MR219 varieties. The AHAS gene sequences of R weedy rice were identical to those of MR220CL2, exhibiting a Ser-653-Asn substitution, which was absent in MR219 and S plants. In vitro assays were conducted using analytical grade IMI herbicides of imazapic (99.3%) and imazapyr (99.6%) at seven different concentrations. The results demonstrated that the AHAS enzyme extracted from the R populations and MR220CL2 was less sensitive to IMI herbicides than that from S and MR219, further supporting that IMI herbicide resistance was conferred by target-site mutation. In conclusion, IMI resistance in the selected populations of Malaysian weedy rice could be attributed to a Ser-653-Asn mutation that reduced the sensitivity of the target site to IMI herbicides. To our knowledge, this study is the first to show the resistance mechanism in weedy rice from Malaysian rice fields.


Assuntos
Acetolactato Sintase/genética , Resistência a Herbicidas/genética , Oryza/efeitos dos fármacos , Proteínas de Plantas/genética , Plantas Daninhas/efeitos dos fármacos , Acetoína/análise , Acetoína/metabolismo , Acetolactato Sintase/metabolismo , Substituição de Aminoácidos , Asparagina/genética , Bioensaio , Análise Mutacional de DNA , DNA de Plantas/genética , DNA de Plantas/isolamento & purificação , Ensaios Enzimáticos , Herbicidas/farmacologia , Imidazóis/farmacologia , Lactatos/metabolismo , Malásia , Mutação , Niacina/análogos & derivados , Niacina/farmacologia , Ácidos Nicotínicos/farmacologia , Oryza/genética , Proteínas de Plantas/metabolismo , Plantas Daninhas/genética , Sementes/efeitos dos fármacos , Serina/análise , Serina/genética , Serina/metabolismo , Controle de Plantas Daninhas/métodos
6.
PLoS One ; 15(9): e0239123, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32925982

RESUMO

Cultivated diversity is considered an insurance against major climatic variability. However, since the 1980s, several studies have shown that climate variability and agricultural changes may already have locally eroded crop genetic diversity. We studied pearl millet diversity in Senegal through a comparison of pearl millet landraces collected 40 years apart. We found that more than 20% of villages visited in 1976 had stopped growing pearl millet. Despite this, its overall genetic diversity has been maintained but differentiation between early- and late-flowering accessions has been reduced. We also found stronger crop-to-wild gene flow than wild-to-crop gene flow and that wild-to-crop gene flow was weaker in 2016 than in 1976. In conclusion, our results highlight genetic homogenization in Senegal. This homogenization within cultivated pearl millet and between wild and cultivated forms is a key factor in genetic erosion and it is often overlooked. Improved assessment and conservation strategies are needed to promote and conserve both wild and cultivated pearl millet diversity.


Assuntos
Produção Agrícola/tendências , Produtos Agrícolas/genética , Evolução Molecular , Variação Genética , Pennisetum/genética , Conservação dos Recursos Naturais , Produção Agrícola/história , Produção Agrícola/estatística & dados numéricos , DNA de Plantas/genética , DNA de Plantas/isolamento & purificação , Flores/crescimento & desenvolvimento , Fluxo Gênico , História do Século XX , História do Século XXI , Senegal
7.
J Plant Res ; 133(6): 765-782, 2020 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-32815044

RESUMO

Scrophularia takesimensis is a critically endangered endemic species of Ulleung Island, Korea. A previous molecular phylogenetic study based on nuclear ribosomal DNA (nrDNA) internal transcribed spacer (ITS) sequences with very limited sampling suggested that it is most closely related to the clade comprising S. alata and S. grayanoides. To determine the origin of S. takesimensis, we sampled a total of 171 accessions including S. takesimensis (9 populations and 63 individuals) and two closely related species, S. alata (11 populations and 68 individuals) and S. grayanoides (5 populations and 40 individuals) from eastern Asia and sequenced ITS and two chloroplast DNA (cpDNA) non-coding regions. Previously sequenced representative species of Scrophularia (109 taxa for ITS and 80 taxa for cpDNA) were combined with our data set and analyzed. While the global scale ITS phylogenetic tree suggests monophyly for each of the three eastern Asian species, S. takesimensis appears to be more closely related (albeit weakly) to a clade containing eastern North American/Caribbean species than to either S. alata or S. grayanoides. By contrast, the global scale cpDNA phylogenetic tree demonstrates that the eastern North America/Caribbean clade is sister to a clade comprising the three eastern Asian species. In addition, the monophyletic S. takesimensis is deeply embedded within paraphyletic S. alata, sharing its most recent common ancestor with populations from Japan/Sakhalin. Two divergent, geographically structured cp haplotype groups within S. takesimensis suggest at least two independent introductions from different source areas. A new and accurate chromosome number of S. takesimensis (2n = 94) is reported and some conservation strategies are discussed.


Assuntos
Conservação dos Recursos Naturais , Espécies em Perigo de Extinção , Filogenia , Scrophularia/classificação , DNA de Cloroplastos/genética , DNA de Plantas/genética , DNA Espaçador Ribossômico/genética , Evolução Molecular , Ilhas , República da Coreia , Análise de Sequência de DNA
8.
PLoS One ; 15(8): e0237538, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32804981

RESUMO

Dearth of genomic resources particularly, microsatellite markers in nutritionally and commercially important fruit crop, guava necessitate the development of the novel genomic SSR markers through the library enrichment techniques. Three types of 3' -biotinylated oligonucleotide probes [(CT)14, (GT)12, and (AAC)8] were used to develop microsatellite enriched libraries. A total of 153 transformed colonies were screened of which 111 positive colonies were subjected for Sanger sequencing. The clones having more than five motif repeats were selected for primer designing and a total of 38 novel genomic simple sequence repeats could be identified. The g-SSRs had the motif groups ranging from monomer to pentamer out of which dimer group occurred the most (89.47%). Out of 38 g-SSRs markers developed, 26 were found polymorphic, which showed substantial genetic diversity among the guava genotypes including wild species. The average number of alleles per locus, major allele frequency, gene diversity, expected heterozygosity and polymorphic information content of 26 SSRs were 3.46, 0.56, 0.53, 0.29 and 0.46, respectively. The rate of cross-species transferability of the developed g-SSR loci varied from 38.46 to 80.77% among the studied wild Psidium species. Generation of N-J tree based on 26 SSRs grouped the 40 guava genotypes into six clades with two out-groups, the wild guava species showed genetic distinctness from cultivated genotypes. Furthermore, population structure analysis grouped the guava genotypes into three genetic groups, which were partly supported by PCoA and N-J tree. Further, AMOVA and PCoA deciphered high genetic diversity among the present set of guava genotypes including wild species. Thus, the developed novel g-SSRs were found efficient and informative for diversity and population structure analyses of the guava genotypes. These developed novel g-SSR loci would add to the new genomic resource in guava, which may be utilized in genomic-assisted guava breeding.


Assuntos
Repetições de Microssatélites , Psidium/classificação , Análise de Sequência de DNA/métodos , DNA de Plantas/genética , Evolução Molecular , Frequência do Gene , Variação Genética , Genética Populacional , Biblioteca Genômica , Psidium/genética , Especificidade da Espécie
9.
PLoS One ; 15(6): e0235073, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32584862

RESUMO

The 'Fuji' line includes many varieties with a similar genetic background and consistent inducement factors with epigenetic occurrence, thus it may be considered an ideal candidate for epigenetic research. In this study, 91 bud mutations of 'Fuji' apple were used as the test materials. Using the genetic variation within 'Fuji' as the control, the characteristics of epigenetic variation at different levels in both varieties and mutant groups were examined. The results showed that: (1) the global genomic DNA methylation level of the 91 bud mutants of 'Fuji' ranged from 29.120%-45.084%, with an average of 35.910%. Internal cytosine methylation was the main DNA methylation pattern. Regarding the variation of methylation patterns of 'Fuji' mutants, the vast majority of loci maintained the original methylation pattern existed in 'Fuji'. CHG methylation variation was the main type of variation; (2) the variation in methylation patterns between the mutant groups was greater than that of methylation levels. Among these patterns, the variation in CHG methylation patterns (including CHG hypermethylation and CHG demethylation) was expected to be dominant. The observed variation in methylation levels was more important in the Color mutant group; however, the variation in methylation patterns was more obvious in both the early maturation and Spur mutant groups. Moreover, the range of variation in the Early-maturation group was much wider than that in the Spur mutant group; (3) epigenetic diversity and genetic diversity were both low between the mutant groups. In the 'Fuji' mutant groups, there was few correlation between genetic and epigenetic variation, and epigenetic differentiation resulted in more loci with moderate or greater differentiation; (4) the purifying selection seemed to play a major role in the differentiation of different groups of 'Fuji' mutants (65.618%), but epigenetic diversity selection still occurred at nearly 35% of loci. Sixteen epigenetic outlier loci were detected.


Assuntos
Metilação de DNA , DNA de Plantas , Epigênese Genética , Loci Gênicos , Malus , Mutação , DNA de Plantas/genética , DNA de Plantas/metabolismo , Malus/genética , Malus/metabolismo
10.
Artigo em Inglês | MEDLINE | ID: mdl-32378983

RESUMO

Ionizing radiation in environment comes from various natural and anthropogenic sources. The effect of radioactivity released after the CNPP (Chernobyl Nuclear Power Plant) on plant systems remains of great interest. Even now, more than three decades after the nuclear accident, the long-lived radionuclides represent a strong stress factor. Herein, the emphasis has been placed on analysis of genetic variability represented by activation of LTR (Long Terminal Repeat)-retrotransposons. Polymorphism in LTR-retrotransposon insertions has been investigated throughout the genome of two flax varieties, Kyivskyi and Bethune. For this purpose, two retrotransposon-based marker techniques, IRAP (Inter-Retrotransposon Amplified Polymorphism) and iPBS (inter-Primer Binding Site), have been employed. The hypothesis that chronic radioactive stress may induce mechanism of retransposition has been supported by the activation of FL9, FL11 and FL12 LTR-retrotransposons in flax seeds harvested from radioactive environment. Out of two retrotransposon-based approaches, IRAP appears to be more suitable for identification of LTR-retrotransposon polymorphism. Even though the LTR-retrotransposon polymorphism was identified, the results suggest the high level of plant adaptation in the radioactive Chernobyl area. However, it is not really surprising that plants developed an effective strategy to survive in radio-contaminated environment over the past 30 years.


Assuntos
Acidente Nuclear de Chernobyl , Linho/genética , Genoma de Planta , Polimorfismo Genético , Retroelementos/genética , Sequências Repetidas Terminais , Sítios de Ligação , DNA de Plantas/genética , Linho/crescimento & desenvolvimento , Linho/efeitos da radiação , Marcadores Genéticos , Modelos Teóricos , Radiação Ionizante , Ucrânia
11.
PLoS One ; 15(5): e0232471, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32379780

RESUMO

Many studies on Heracleum have shown poor correspondence between observed molecular clusters and established taxonomic classification amongst closely related species. This might reflect both unresolved taxonomy but perhaps also a lack of good genetic markers. This lack of appropriate and cost effective species-specific genetic markers hinders a resolved relationship for the species complex, and this in turn causes profound management challenges for a genus that contains both endemic species, with important ecological roles, and species with an invasive potential. Microsatellites are traditionally considered markers of choice for comprehensive, yet inexpensive, analyses of genetic variation, including examination of population structure, species identity, linkage map construction and cryptic speciation. In this study, we have used double digest restriction site associated DNA sequencing (ddRADseq) to develop microsatellite markers in Heracleum rechingeri. Genomic DNA from three individuals were digested with Sbf1 and Nde1 and size selected for library construction. The size-selected fragments were sequenced on an Ion Torrent sequencer and a total of 54 microsatellite sequences were bioinformatically confirmed. Twenty five loci were then tested for amplification, resulting in 19 of these being successfully amplified across eight species, comprising both the so-called thick-stemmed species (H. persicum, H. rechingeri, H. gorganicum and H. lasiopetalum), and thin-stemmed species (H. anisactis, H. pastinasifolium and H. transcaucasicum). Both Bayesian and distance-based clustering, and principal coordinate analyses clearly separated these into two groups. Surprisingly, three H. pastinacifolium populations were not separated from populations of the morphologically similar endemic species, H. anisactis, suggesting lack of genetic differentiation. Likewise, high genetic similarity was found between H. persicum and H. rechingeri populations, questioning taxonomic separation at the species level between these taxa. Further analyses are needed to re-evaluate the taxonomic significance of observed morphological variability currently applied to distinguish these sister taxa. Nevertheless, our results represent progress in the effort to develop cost-efficient molecular tools for species discrimination in this genus.


Assuntos
Heracleum/classificação , Heracleum/genética , Sequência de Bases , Teorema de Bayes , Análise por Conglomerados , DNA de Plantas/genética , Repetições de Dinucleotídeos , Marcadores Genéticos , Genética Populacional , Sequenciamento de Nucleotídeos em Larga Escala , Irã (Geográfico) , Repetições de Microssatélites , Filogenia , Análise de Sequência de DNA , Especificidade da Espécie
12.
PLoS One ; 15(5): e0233056, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32396546

RESUMO

The content and composition of seed storage proteins is largely responsible for wheat end-use quality. They mainly consist of polymeric glutenins and monomeric gliadins. According to their electrophoretic mobility, gliadins and glutenins are subdivided into several fractions. Glutenins are classified as high molecular weight or low molecular weight glutenin subunits (HMW-GSs and LMW-GSs, respectively). LMW-GSs are encoded by multigene families located at the orthologous Glu-3 loci. We designed a set of 16 single-nucleotide polymorphism (SNP) markers that are able to detect SDS-PAGE alleles at the Glu-A3 and Glu-B3 loci. The SNP markers captured the diversity of alleles in 88 international reference lines and 27 Mexican cultivars, when compared to SDS-PAGE and STS markers, however, showed a slightly larger percent of multiple alleles, mainly for Glu-B3. SNP markers were then used to determine the Glu-1 and Glu-3 allele composition in 54 CIMMYT historical lines and demonstrated to be useful tool for breeding programs to improve wheat end product properties.


Assuntos
Glutens/genética , Triticum/genética , Alelos , Sequência de Bases , Pão , DNA de Plantas/genética , Genes de Plantas , Marcadores Genéticos , Glutens/química , Peso Molecular , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único , Subunidades Proteicas , Sitios de Sequências Rotuladas
13.
PLoS One ; 15(5): e0232479, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32407369

RESUMO

Single nucleotide polymorphisms (SNPs) are highly abundant, amendable to high-throughput genotyping, and useful for a number of breeding and genetics applications in crops. SNP frequencies vary depending on the species and populations under study, and therefore target SNPs need to be carefully selected to be informative for each application. While multiple SNP genotyping systems are available for rice (Oryza sativa L. and its relatives), they vary in their informativeness, cost, marker density, speed, flexibility, and data quality. In this study, we report the development and performance of the Cornell-IR LD Rice Array (C7AIR), a second-generation SNP array containing 7,098 markers that improves upon the previously released C6AIR. The C7AIR is designed to detect genome-wide polymorphisms within and between subpopulations of O. sativa, as well as O. glaberrima, O. rufipogon and O. nivara. The C7AIR combines top-performing SNPs from several previous rice arrays, including 4,007 SNPs from the C6AIR, 2,056 SNPs from the High Density Rice Array (HDRA), 910 SNPs from the 384-SNP GoldenGate sets, 189 SNPs from the 44K array selected to add information content for elite U.S. tropical japonica rice varieties, and 8 trait-specific SNPs. To demonstrate its utility, we carried out a genome-wide association analysis for plant height, employing the C7AIR across a diversity panel of 189 rice accessions and identified 20 QTLs contributing to plant height. The C7AIR SNP chip has so far been used for genotyping >10,000 rice samples. It successfully differentiates the five subpopulations of Oryza sativa, identifies introgressions from wild and exotic relatives, and is useful for quantitative trait loci (QTL) and association mapping in diverse materials. Moreover, data from the C7AIR provides valuable information that can be used to select informative and reliable SNP markers for conversion to lower-cost genotyping platforms for genomic selection and other downstream applications in breeding.


Assuntos
DNA de Plantas/genética , Análise de Sequência com Séries de Oligonucleotídeos , Oryza/genética , Polimorfismo de Nucleotídeo Único , Marcadores Genéticos , Genoma de Planta , Estudo de Associação Genômica Ampla , Oryza/classificação , Filogenia , Melhoramento Vegetal , Locos de Características Quantitativas , Especificidade da Espécie
14.
Gene ; 753: 144800, 2020 Aug 30.
Artigo em Inglês | MEDLINE | ID: mdl-32454179

RESUMO

Sugarcane is one among the most important commercial crops used to produce sugar, ethanol, and other byproducts, which significantly contributes in the GDP of India and many other countries around the world. Genetic diversity is a platform for any breeding program of a plant species. Estimation of the genetic variability and population structure play a vital role for conservation planning and management of plant genetic resources. Genetic variability serves as a source of noble alleles responsible for key agronomic and quality traits, which ultimately form basis for identification and selection of promising parents for breeding programs. In the present study genetic diversity and population structure of 139 accessions of the genus Saccharum, allied genera of family Poaceae and cultivars were assessed using informative microsatellite (SSR) markers. A sum of 427 alleles was produced using 61 polymorphic primers and number of alleles generated was ranged from 2 to 13 with an average of 7 alleles per locus. PIC values were ranged from 0.35 to 0.90, with a mean value of 0.66 for all the markers evaluated. Cluster analysis based on UPGMA method revealed three major clusters which were further subdivided into nine subclusters. Population structure analysis also established three subpopulations of used accession set, however there were no correlation of sub-groupings with that of place of origin. AMOVA analysis also confirmed that 83% and 17% of total variations were attributed to the within- and between-populations, correspondingly, demonstrating greater exchange of gene pool across places of origin. The principal component analysis (PCA) demonstrated the distribution of accessions in the scatter-plot was substantially dispersed, revealing rich genetic diversity among accessions of different species. The findings from this study will be useful in breeding programs for introgression of noble alleles into modern cultivars by exploiting natural genetic variation existing in sugarcane genetic resources.


Assuntos
Variação Genética/genética , Repetições de Microssatélites/genética , Saccharum/genética , Alelos , Análise por Conglomerados , DNA de Plantas/genética , Frequência do Gene/genética , Genótipo , Índia , Fenótipo , Filogenia , Melhoramento Vegetal/métodos
15.
Proc Natl Acad Sci U S A ; 117(21): 11836-11842, 2020 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-32398372

RESUMO

Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.


Assuntos
Fases de Leitura Aberta/genética , Oryza/genética , Mapeamento de Interação de Proteínas/métodos , Mapas de Interação de Proteínas/genética , Análise de Sequência de DNA/métodos , Biologia Computacional/métodos , DNA de Plantas/genética , Bases de Dados Genéticas , Genoma de Planta/genética , Sequenciamento de Nucleotídeos em Larga Escala/métodos
16.
Biol Res ; 53(1): 21, 2020 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-32410692

RESUMO

BACKGROUND: Liriodendron chinense ranges widely in subtropical China and northern Vietnam; however, it inhabits several small, isolated populations and is now an endangered species due to its limited seed production. The objective of this study was to develop a set of nuclear SSR (simple sequence repeats) and multiple chloroplast genome markers for genetic studies in L. chinense and their characterization in diverse germplasm. RESULTS: We performed low-coverage whole genome sequencing of the L. chinense from four genotypes, assembled the chloroplast genome and identified nuclear SSR loci by searching in contigs for SSR motifs. Comparative analysis of the four chloroplast genomes of L. chinense revealed 45 SNPs, 17 indels, 49 polymorphic SSR loci, and five small inversions. Most chloroplast intraspecific polymorphisms were located in the interspaces of single-copy regions. In total, 6147 SSR markers were isolated from low-coverage whole genome sequences. The most common SSR motifs were dinucleotide (70.09%), followed by trinucleotide motifs (23.10%). The motif AG/TC (33.51%) was the most abundant, followed by TC/AG (25.53%). A set of 13 SSR primer combinations were tested for amplification and their ability to detect polymorphisms in a set of 109 L. chinense individuals, representing distinct varieties or germplasm. The number of alleles per locus ranged from 8 to 28 with an average of 21 alleles. The expected heterozygosity (He) varied from 0.19 to 0.93 and the observed heterozygosity (Ho) ranged from 0.11 to 0.79. CONCLUSIONS: The genetic resources characterized and tested in this study provide a valuable tool to detect polymorphisms in L. chinense for future genetic studies and breeding programs.


Assuntos
Genoma de Cloroplastos/genética , Genoma de Planta/genética , Liriodendron/genética , Polimorfismo Genético/genética , Alelos , Primers do DNA/genética , DNA de Plantas/genética , Genótipo , Repetições de Microssatélites , Sequenciamento Completo do Genoma
17.
J Food Sci ; 85(6): 1629-1634, 2020 Jun.
Artigo em Inglês | MEDLINE | ID: mdl-32468625

RESUMO

Tea, a popular aromatic infusion and food supplement, prepared from Camellia sinensis (L.) Kuntze leaves, is often subjected to adulteration with various undeclared inorganic and plant-derived materials. Cashew (Anacardium occidentale L.) nut husk is one of the most common plant tea adulterants. To date, there are limited DNA-based technologies for tea authentication and quantitative detection of adulterants. Herein, we used a universal plant DNA barcoding marker coupled with High Resolution Melting (Bar-HRM) analysis to authenticate tea products from cashew ground nut. Additionally, cashew-specific markers coupled with HRM technology were used to detect and quantify adulteration of tea with cashew DNA. This methodology can reliably detect admixtures as low as 1% v/v cashew in commercial tea products. Overall, our results demonstrate that the HRM technology is a strong molecular approach in tea authentication, capable of detecting very low adulterations in DNA admixtures. PRACTICAL APPLICATION: In this study, we established the use of high-resolution DNA-based technologies for the detection of cashew adulteration in tea, even in very low quantities. The technology could be applied to a greater range of plant-based tea adulterants. This work is expected to facilitate the traceability and authenticity of tea products and form the basis for the development of strategies against fraudulent practices.


Assuntos
Anacardium/genética , Camellia sinensis/genética , Contaminação de Alimentos/análise , Chá/química , Anacardium/química , Camellia sinensis/química , Código de Barras de DNA Taxonômico/métodos , DNA de Plantas/química , DNA de Plantas/genética , Contaminação de Alimentos/economia , Marcadores Genéticos , Chá/economia , Temperatura de Transição
18.
Food Chem ; 326: 126986, 2020 Oct 01.
Artigo em Inglês | MEDLINE | ID: mdl-32407998

RESUMO

In the present work, a barcode-DNA analysis method is described for the detection of plant oil adulteration in milk and dairy products. The method relies on the fact that plant DNA should not be present in readily detectable amounts in a dairy product unless it contains undeclared plant material. Thus, a universal plant barcode is chosen as the target to be amplified from dairy samples. Accordingly, barcode PCR-CE (PCR-capillary electrophoresis) assays are described, which do not require preliminary information on the species source of the adulterant oil type. Two PCR-CE assays, one operating on the plastid trnL (UAA) intron and the other targeting its inner P6 loop in nested format, were shown to detect corn, soybean, rapeseed and sunflower oils in clarified butter, milk and yogurt. Both barcodes are robustly amplified with extremely conserved primers. While the intron provides the species discrimination ability, the P6 loop provides superior detection sensitivity.


Assuntos
DNA de Plantas/análise , Laticínios/análise , Eletroforese Capilar/métodos , Leite/química , Óleos Vegetais/química , Animais , Código de Barras de DNA Taxonômico , DNA de Plantas/genética , DNA de Plantas/metabolismo , Óleos Vegetais/metabolismo , Plastídeos/genética , Reação em Cadeia da Polimerase , Soja/genética , Iogurte/análise , Zea mays/genética
19.
PLoS One ; 15(5): e0233503, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32442184

RESUMO

Recently-emerged base editing technologies could create single base mutations at precise genomic positions without generation DNA double strand breaks. Herbicide resistant mutations have been successfully introduced to different plant species, including Arabidopsis, watermelon, wheat, potato and tomato via C to T (or G to A on the complementary strand) base editors (CBE) at the P197 position of endogenous acetolactate synthase (ALS) genes. Additionally, G to A conversion to another conserved amino acid S653 on ALS gene could confer tolerance to imidazolinone herbicides. However, no such mutation was successfully generated via CBE, likely due to the target C base is outside of the classic base editing window. Since CBE driven by egg cell (EC) specific promoter would re-edit the wild type alleles in egg cells and early embryos, we hypothesized the diversity of base editing outcomes could be largely increased at later generations to allow selection of desired herbicide resistant mutants. To test this hypothesis, we aimed to introduce C to T conversion to the complement strand of S653 codon at ALS gene, hosting a C at the 10th position within the 20-nt spacer sequence outside of the classic base editing window. While we did not detect base-edited T1 plants, efficient and diverse base edits emerged at later generations. Herbicide resistant mutants with different editing outcomes were recovered when T3 and T4 seeds were subject to herbicide selection. As expected, most herbicide resistant plants contained S653N mutation as a result of G10 to A10. Our results showed that CBE could create imidazolinone herbicide resistant trait in Arabidopsis and be potentially applied to crops to facilitate weed control.


Assuntos
Arabidopsis/efeitos dos fármacos , Arabidopsis/genética , Resistência a Herbicidas/genética , Acetolactato Sintase/genética , Substituição de Aminoácidos , Proteínas de Arabidopsis/genética , Sequência de Bases , Sistemas CRISPR-Cas , DNA de Plantas/genética , Edição de Genes , Genes de Plantas , Herbicidas/farmacologia , Imidazolinas/farmacologia , Mutagênese Sítio-Dirigida , Melhoramento Vegetal , Plantas Geneticamente Modificadas/efeitos dos fármacos , Plantas Geneticamente Modificadas/genética , Seleção Genética , Controle de Plantas Daninhas
20.
Nat Commun ; 11(1): 1675, 2020 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-32245969

RESUMO

The laurel family within the Magnoliids has attracted attentions owing to its scents, variable inflorescences, and controversial phylogenetic position. Here, we present a chromosome-level assembly of the Litsea cubeba genome, together with low-coverage genomic and transcriptomic data for many other Lauraceae. Phylogenomic analyses show phylogenetic discordance at the position of Magnoliids, suggesting incomplete lineage sorting during the divergence of monocots, eudicots, and Magnoliids. An ancient whole-genome duplication (WGD) event occurred just before the divergence of Laurales and Magnoliales; subsequently, independent WGDs occurred almost simultaneously in the three Lauralean lineages. The phylogenetic relationships within Lauraceae correspond to the divergence of inflorescences, as evidenced by the phylogeny of FUWA, a conserved gene involved in determining panicle architecture in Lauraceae. Monoterpene synthases responsible for production of specific volatile compounds in Lauraceae are functionally verified. Our work sheds light on the evolution of the Lauraceae, the genetic basis for floral evolution and specific scents.


Assuntos
Cromossomos de Plantas/genética , Evolução Molecular , Especiação Genética , Genoma de Planta , Litsea/genética , Vias Biossintéticas/genética , DNA de Plantas/genética , DNA de Plantas/isolamento & purificação , Duplicação Gênica , Perfilação da Expressão Gênica , Genômica , Inflorescência/genética , Litsea/metabolismo , Anotação de Sequência Molecular , Odorantes , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Análise de Sequência de DNA
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