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1.
Nat Commun ; 12(1): 4141, 2021 07 06.
Artigo em Inglês | MEDLINE | ID: mdl-34230471

RESUMO

Genetic gain in potato is hampered by the heterozygous tetraploid genome of cultivated potato. Converting potato into a diploid inbred-line based F1-hybrid crop provides a promising route towards increased genetic gain. The introduction of a dominant S-locus inhibitor (Sli) gene into diploid potato germplasm allows efficient generation of self-fertilized seeds and thus the development of potato inbred lines. Little is known about the structure and function of the Sli locus. Here we describe the mapping of Sli to a 12.6 kb interval on chromosome 12 using a recombinant screen approach. One of two candidate genes present in this interval shows a unique sequence that is exclusively present in self-compatible lines. We describe an expression vector that converts self-incompatible genotypes into self-compatible and a CRISPR-Cas9 vector that converts SC genotypes into SI. The Sli gene encodes an F-box protein that is specifically expressed in pollen from self-compatible plants. A 533 bp insertion in the promotor of that gene leads to a gain of function mutation, which overcomes self-pollen rejection.


Assuntos
Genes de Plantas/genética , Melhoramento Vegetal , Proteínas de Plantas/genética , Solanum tuberosum/genética , Sistemas CRISPR-Cas , Mapeamento Cromossômico , Cromossomos de Plantas , Diploide , Genótipo , Heterozigoto , Magnoliopsida , Pólen/genética , Sementes/metabolismo , Autoincompatibilidade em Angiospermas/genética
2.
Int J Mol Sci ; 22(11)2021 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-34063853

RESUMO

Plant diseases are responsible for substantial crop losses each year and affect food security and agricultural sustainability. The improvement of crop resistance to pathogens through breeding represents an environmentally sound method for managing disease and minimizing these losses. The challenge is to breed varieties with a stable and broad-spectrum resistance. Different approaches, from markers to recent genomic and 'post-genomic era' technologies, will be reviewed in order to contribute to a better understanding of the complexity of host-pathogen interactions and genes, including those with small phenotypic effects and mechanisms that underlie resistance. An efficient combination of these approaches is herein proposed as the basis to develop a successful breeding strategy to obtain resistant crop varieties that yield higher in increasing disease scenarios.


Assuntos
Produtos Agrícolas/genética , Resistência à Doença/genética , Genoma de Planta/genética , Doenças das Plantas/genética , Agricultura/métodos , Animais , Genes de Plantas/genética , Genômica/métodos , Interações Hospedeiro-Patógeno/genética , Humanos , Melhoramento Vegetal/métodos
3.
Int J Mol Sci ; 22(10)2021 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-34069840

RESUMO

The biosynthesis and storage of lipids in oil crop seeds involve many gene families, such as nonspecific lipid-transfer proteins (nsLTPs). nsLTPs are cysteine-rich small basic proteins essential for plant development and survival. However, in sesame, information related to nsLTPs was limited. Thus, the objectives of this study were to identify the Sesamum indicum nsLTPs (SiLTPs) and reveal their potential role in oil accumulation in sesame seeds. Genome-wide analysis revealed 52 SiLTPs, nonrandomly distributed on 10 chromosomes in the sesame variety Zhongzhi 13. Following recent classification methods, the SiLTPs were divided into nine types, among which types I and XI were the dominants. We found that the SiLTPs could interact with several transcription factors, including APETALA2 (AP2), DNA binding with one finger (Dof), etc. Transcriptome analysis showed a tissue-specific expression of some SiLTP genes. By integrating the SiLTPs expression profiles and the weighted gene co-expression network analysis (WGCNA) results of two contrasting oil content sesame varieties, we identified SiLTPI.23 and SiLTPI.28 as the candidate genes for high oil content in sesame seeds. The presumed functions of the candidate gene were validated through overexpression of SiLTPI.23 in Arabidopsis thaliana. These findings expand our knowledge on nsLTPs in sesame and provide resources for functional studies and genetic improvement of oil content in sesame seeds.


Assuntos
Proteínas de Transferência de Fosfolipídeos/genética , Proteínas de Transferência de Fosfolipídeos/metabolismo , Sesamum/genética , Proteínas de Transporte/metabolismo , Etiquetas de Sequências Expressas , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Óleos Vegetais/metabolismo , Sementes/genética , Sesamum/metabolismo , Fatores de Transcrição/metabolismo
4.
Int J Mol Sci ; 22(10)2021 May 18.
Artigo em Inglês | MEDLINE | ID: mdl-34069912

RESUMO

Cell wall invertase (CWIN) activity and the expression of the corresponding gene were previously observed to be significantly elevated in a Cu-tolerant population of Elsholtzia haichowensis relative to a non-tolerant population under copper stress. To understand the differences in CWIN gene regulation between the two populations, their CWIN promoter ß-glucuronidase (GUS) reporter vectors were constructed. GUS activity was measured in transgenic Arabidopsis in response to copper, sugar, and phytohormone treatments. Under the copper treatment, only the activity of the CWIN promoter from the Cu-tolerant population was slightly increased. Glucose and fructose significantly induced the activity of CWIN promoters from both populations. Among the phytohormone treatments, only salicylic acid induced significantly higher (p < 0.05) activity of the Cu-tolerant CWIN promoter relative to the non-tolerant promoters. Analysis of 5'-deletion constructs revealed that a 270-bp promoter fragment was required for SA induction of the promoter from the Cu-tolerant population. Comparison of this region in the two CWIN promoters revealed that it had 10 mutation sites and contained CAAT-box and W-box cis-elements in the Cu-tolerant promoter only. This work provides insights into the regulatory role of SA in CWIN gene expression and offers an explanation for differences in CWIN expression between E. haichowensis populations.


Assuntos
Parede Celular/genética , Lamiaceae/genética , beta-Frutofuranosidase/genética , Arabidopsis/genética , Parede Celular/metabolismo , Cobre/metabolismo , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Lamiaceae/metabolismo , Proteínas de Plantas/genética , Plantas Geneticamente Modificadas/genética , Regiões Promotoras Genéticas/genética , Ácido Salicílico/metabolismo , beta-Frutofuranosidase/metabolismo
5.
Nat Commun ; 12(1): 3498, 2021 06 09.
Artigo em Inglês | MEDLINE | ID: mdl-34108452

RESUMO

Plant genomes vary greatly in size, organization, and architecture. Such structural differences may be highly relevant for inference of genome evolution dynamics and phylogeny. Indeed, microsynteny-the conservation of local gene content and order-is recognized as a valuable source of phylogenetic information, but its use for the inference of large phylogenies has been limited. Here, by combining synteny network analysis, matrix representation, and maximum likelihood phylogenetic inference, we provide a way to reconstruct phylogenies based on microsynteny information. Both simulations and use of empirical data sets show our method to be accurate, consistent, and widely applicable. As an example, we focus on the analysis of a large-scale whole-genome data set for angiosperms, including more than 120 available high-quality genomes, representing more than 50 different plant families and 30 orders. Our 'microsynteny-based' tree is largely congruent with phylogenies proposed based on more traditional sequence alignment-based methods and current phylogenetic classifications but differs for some long-contested and controversial relationships. For instance, our synteny-based tree finds Vitales as early diverging eudicots, Saxifragales within superasterids, and magnoliids as sister to monocots. We discuss how synteny-based phylogenetic inference can complement traditional methods and could provide additional insights into some long-standing controversial phylogenetic relationships.


Assuntos
Genoma de Planta/genética , Magnoliopsida/genética , Filogenia , Sintenia , Evolução Molecular , Genes de Plantas/genética , Magnoliopsida/classificação , Modelos Genéticos , Família Multigênica/genética
6.
Nat Commun ; 12(1): 3604, 2021 06 14.
Artigo em Inglês | MEDLINE | ID: mdl-34127667

RESUMO

A narrow genetic basis in modern cultivars and strong linkage disequilibrium in peach (Prunus persica) has restricted resolution power for association studies in this model fruit species, thereby limiting our understanding of economically important quality traits including fruit flavor. Here, we present a high-quality genome assembly for a Chinese landrace, Longhua Shui Mi (LHSM), a representative of the Chinese Cling peaches that have been central in global peach genetic improvement. We also map the resequencing data for 564 peach accessions to this LHSM assembly at an average depth of 26.34× per accession. Population genomic analyses reveal a fascinating history of convergent selection for sweetness yet divergent selection for acidity in eastern vs. western modern cultivars. Molecular-genetics and biochemical analyses establish that PpALMT1 (aluminum-activated malate transporter 1) contributes to their difference of malate content and that increases fructose content accounts for the increased sweetness of modern peach fruits, as regulated by PpERDL16 (early response to dehydration 6-like 16). Our study illustrates the strong utility of the genomics resources for both basic and applied efforts to understand and exploit the genetic basis of fruit quality in peach.


Assuntos
Frutas/genética , Genoma de Planta , Metagenômica , Prunus persica/genética , Frutas/metabolismo , Regulação da Expressão Gênica de Plantas , Genes de Plantas/genética , Loci Gênicos , Variação Genética , Tamanho do Genoma , Genômica , Desequilíbrio de Ligação , Filogenia , Melhoramento Vegetal , Polimorfismo de Nucleotídeo Único , Prunus persica/classificação , Prunus persica/metabolismo , Análise de Sequência de DNA , Açúcares
7.
Int J Mol Sci ; 22(11)2021 May 28.
Artigo em Inglês | MEDLINE | ID: mdl-34071242

RESUMO

Organic acids are key components that determine the taste and flavor of fruits and play a vital role in maintaining fruit quality and nutritive value. In this study, the fruits of two cultivars of passion fruit Yellow (Passiflora edulis f. flavicarpa) and purple (Passiflora edulis f. edulis) were harvested at five different developmental stages (i.e., fruitlet, green, veraison, near-mature and mature stage) from an orchard located in subtropical region of Fujian Province, China. The contents of six organic acids were quantified using ultra-performance liquid chromatography (UPLC), activities of citric acid related enzymes were determined, and expression levels of genes involved in citric acid metabolism were measured by quantitative real-time PCR (qRT-PCR). The results revealed that citric acid was the predominant organic acid in both cultivars during fruit development. The highest citric acid contents were observed in both cultivars at green stage, which were reduced with fruit maturity. Correlation analysis showed that citrate synthase (CS), cytosolic aconitase (Cyt-ACO) and cytosolic isocitrate dehydrogenase (Cyt-IDH) may be involved in regulating citric acid biosynthesis. Meanwhile, the PeCS2, PeACO4, PeACO5 and PeIDH1 genes may play an important role in regulating the accumulation of citric acid. This study provides new insights for future elucidation of key mechanisms regulating organic acid biosynthesis in passion fruit.


Assuntos
Ácido Cítrico/análise , Frutas/química , Frutas/genética , Compostos Orgânicos/análise , Passiflora/química , Passiflora/genética , China , Frutas/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Genes de Plantas/genética , Isocitrato Desidrogenase , Valor Nutritivo , Passiflora/crescimento & desenvolvimento , Extratos Vegetais
8.
BMC Plant Biol ; 21(1): 283, 2021 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-34157965

RESUMO

BACKGROUND: Sesame is a rare example of non-model and minor crop for which numerous genetic loci and candidate genes underlying features of interest have been disclosed at relatively high resolution. These progresses have been achieved thanks to the applications of the genome-wide association study (GWAS) approach. GWAS has benefited from the availability of high-quality genomes, re-sequencing data from thousands of genotypes, extensive transcriptome sequencing, development of haplotype map and web-based functional databases in sesame. RESULTS: In this paper, we reviewed the GWAS methods, the underlying statistical models and the applications for genetic discovery of important traits in sesame. A novel online database SiGeDiD ( http://sigedid.ucad.sn/ ) has been developed to provide access to all genetic and genomic discoveries through GWAS in sesame. We also tested for the first time, applications of various new GWAS multi-locus models in sesame. CONCLUSIONS: Collectively, this work portrays steps and provides guidelines for efficient GWAS implementation in sesame, a non-model crop.


Assuntos
Produtos Agrícolas/genética , Estudo de Associação Genômica Ampla/métodos , Sesamum/genética , Genes de Plantas/genética , Genoma de Planta/genética , Modelos Genéticos
9.
BMC Plant Biol ; 21(1): 286, 2021 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-34157966

RESUMO

BACKGROUND: Brassica napus is an essential crop for oil and livestock feed. Eventually, this crop's economic interest is at the most risk due to anthropogenic climate change. DELLA proteins constitute a significant repressor of plant growth to facilitate survival under constant stress conditions. DELLA proteins lack DNA binding domain but can interact with various transcription factors or transcription regulators of different hormonal families. Significant progress has been made on Arabidopsis and cereal plants. However, no comprehensive study regarding DELLA proteins has been delineated in rapeseed. RESULTS: In our study, we have identified 10 BnaDELLA genes. All of the BnaDELLA genes are closely related to five AtDELLA genes, suggesting a relative function and structure. Gene duplication and synteny relationship among Brassica. napus, Arabidopsis. thaliana, Brassica rapa, Brassica oleracea, and Brassica nigra genomes were also predicted to provide valuable insights into the BnaDELLA gene family evolutionary characteristics. Chromosomal mapping revealed the uneven distribution of BnaDELLA genes on eight chromosomes, and site-specific selection assessment proposes BnaDELLA genes purifying selection. The motifs composition in all BnaDELLA genes is inconsistent; however, every BnaDELLA gene contains 12 highly conserved motifs, encoding DELLA and GRAS domains. The two known miRNAs (bna-miR6029 and bna-miR603) targets BnaC07RGA and BnaA09GAI, were also predicted. Furthermore, quantitative real-time PCR (qRT-PCR) analysis has exhibited the BnaDELLA genes diverse expression patterns in the root, mature-silique, leaf, flower, flower-bud, stem, shoot-apex, and seed. Additionally, cis-acting element prediction shows that all BnaDELLA genes contain light, stress, and hormone-responsive elements on their promoters. The gene ontology (GO) enrichment report indicated that the BnaDELLA gene family might regulate stress responses. Combine with transcriptomic data used in this study, we detected the distinct expression patterns of BnaDELLA genes under biotic and abiotic stresses. CONCLUSION: In this study, we investigate evolution feature, genomic structure, miRNAs targets, and expression pattern of the BnaDELLA gene family in B. napus, which enrich our understanding of BnaDELLA genes in B. napus and suggests modulating individual BnaDELLA expression is a promising way to intensify rapeseed stress tolerance and harvest index.


Assuntos
Brassica napus/genética , Genes de Plantas/genética , Brassica napus/fisiologia , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Evolução Molecular , Genes de Plantas/fisiologia , Estudo de Associação Genômica Ampla , MicroRNAs/genética , Filogenia , Proteínas de Plantas/genética , Proteínas de Plantas/fisiologia , RNA de Plantas/genética , Alinhamento de Sequência , Estresse Fisiológico , Transcriptoma
10.
BMC Plant Biol ; 21(1): 284, 2021 Jun 22.
Artigo em Inglês | MEDLINE | ID: mdl-34157974

RESUMO

BACKGROUND: Identifying genes involved in salt tolerance in the recretohalophyte Limonium bicolor could facilitate the breeding of crops with enhanced salt tolerance. Here we cloned the previously uncharacterized gene LbHLH and explored its role in salt tolerance. RESULTS: The 2,067-bp open reading frame of LbHLH encodes a 688-amino-acid protein with a typical helix-loop-helix (HLH) domain. In situ hybridization showed that LbHLH is expressed in salt glands of L. bicolor. LbHLH localizes to the nucleus, and LbHLH is highly expressed during salt gland development and in response to NaCl treatment. To further explore its function, we heterologously expressed LbHLH in Arabidopsis thaliana under the 35S promoter. The overexpression lines showed significantly increased trichome number and reduced root hair number. LbHLH might interact with GLABRA1 to influence trichome and root hair development, as revealed by yeast two-hybrid analysis. The transgenic lines showed higher germination percentages and longer roots than the wild type under NaCl treatment. Analysis of seedlings grown on medium containing sorbitol with the same osmotic pressure as 100 mM NaCl demonstrated that overexpressing LbHLH enhanced osmotic resistance. CONCLUSION: These results indicate that LbHLH enhances salt tolerance by reducing root hair development and enhancing osmotic resistance under NaCl stress.


Assuntos
Fatores de Transcrição Hélice-Alça-Hélice Básicos/genética , Genes de Plantas/genética , Proteínas de Plantas/genética , Raízes de Plantas/crescimento & desenvolvimento , Plumbaginaceae/genética , Plantas Tolerantes a Sal/genética , Fatores de Transcrição Hélice-Alça-Hélice Básicos/fisiologia , Clonagem Molecular , Genes de Plantas/fisiologia , Hibridização In Situ , Pressão Osmótica , Proteínas de Plantas/fisiologia , Plumbaginaceae/metabolismo , Plumbaginaceae/fisiologia , Reação em Cadeia da Polimerase , Estresse Salino , Tolerância ao Sal/genética , Plantas Tolerantes a Sal/metabolismo , Plantas Tolerantes a Sal/fisiologia , Técnicas do Sistema de Duplo-Híbrido
11.
BMC Plant Biol ; 21(1): 291, 2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-34167462

RESUMO

Brassinosteroids (BRs) play important roles in plant growth and development. Although BR receptors have been intensively studied in Arabidopsis, those in foxtail millet remain largely unknown. Here, we show that the BR signaling function of BRASSINOSTEROID INSENSITIVE 1 (BRI1) is conserved between Arabidopsis and foxtail millet, a new model species for C4 and Panicoideae grasses. We identified four putative BR receptor genes in the foxtail millet genome: SiBRI1, SiBRI1-LIKE RECEPTOR KINASE 1 (SiBRL1), SiBRL2 and SiBRL3. Phylogenetic analysis was used to classify the BR receptors in dicots and monocots into three branches. Analysis of their expression patterns by quantitative real-time PCR (qRT-PCR) showed that these receptors were ubiquitously expressed in leaves, stems, dark-grown seedlings, roots and non-flowering spikelets. GFP fusion experiments verified that SiBRI1 localized to the cell membrane. We also explored the SiBRI1 function in Arabidopsis through complementation experiments. Ectopic overexpression of SiBRI1 in an Arabidopsis BR receptor loss-of-function mutant, bri1-116, mostly reversed the developmental defects of the mutant. When SiBRI1 was overexpressed in foxtail millet, the plants showed a drooping leaf phenotype and root development inhibition, lateral root initiation inhibition, and the expression of BR synthesis genes was inhibited. We further identified BRI1-interacting proteins by immunoprecipitation (IP)-mass spectrometry (MS). Our results not only demonstrate that SiBRI1 plays a conserved role in BR signaling in foxtail millet but also provide insight into the molecular mechanism of SiBRI1.


Assuntos
Brassinosteroides/metabolismo , Genes de Plantas/genética , Proteínas de Plantas/genética , Receptores de Superfície Celular/genética , Setaria (Planta)/genética , Arabidopsis/genética , Arabidopsis/fisiologia , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/fisiologia , Evolução Molecular , Filogenia , Proteínas de Plantas/metabolismo , Proteínas de Plantas/fisiologia , Raízes de Plantas/crescimento & desenvolvimento , Proteínas Quinases/genética , Proteínas Quinases/fisiologia , Receptores de Superfície Celular/metabolismo , Receptores de Superfície Celular/fisiologia , Setaria (Planta)/metabolismo
12.
BMC Plant Biol ; 21(1): 288, 2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-34167468

RESUMO

BACKGROUND: B-box (BBX) genes play important roles in plant growth regulation and responses to abiotic stresses. The plant growth and yield production of allotetraploid rapeseed is usually hindered by diverse nutrient stresses. However, no systematic analysis of Brassicaceae BBXs and the roles of BBXs in the regulation of nutrient stress responses have not been identified and characterized previously. RESULTS: In this study, a total of 536 BBXs were identified from nine brassicaceae species, including 32 AtBBXs, 66 BnaBBXs, 41 BoBBXs, 43 BrBBXs, 26 CrBBXs, 81 CsBBXs, 52 BnBBXs, 93 BjBBXs, and 102 BcBBXs. Syntenic analysis showed that great differences in the gene number of Brassicaceae BBXs might be caused by genome duplication. The BBXs were respectively divided into five subclasses according to their phylogenetic relationships and conserved domains, indicating their diversified functions. Promoter cis-element analysis showed that BBXs probably participated in diverse stress responses. Protein-protein interactions between BnaBBXs indicated their functions in flower induction. The expression profiles of BnaBBXs were investigated in rapeseed plants under boron deficiency, boron toxicity, nitrate limitation, phosphate shortage, potassium starvation, ammonium excess, cadmium toxicity, and salt stress conditions using RNA-seq data. The results showed that different BnaBBXs showed differential transcriptional responses to nutrient stresses, and some of them were simultaneously responsive to diverse nutrient stresses. CONCLUSIONS: Taken together, the findings investigated in this study provided rich resources for studying Brassicaceae BBX gene family and enriched potential clues in the genetic improvement of crop stress resistance.


Assuntos
Brassica napus/genética , Brassicaceae/genética , Genes de Plantas/genética , Fatores de Transcrição/genética , Brassica napus/fisiologia , Sequência Conservada , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/fisiologia , Estudo de Associação Genômica Ampla , Filogenia , Mapas de Interação de Proteínas , Estresse Fisiológico , Sintenia , Tetraploidia , Fatores de Transcrição/fisiologia
13.
BMC Plant Biol ; 21(1): 292, 2021 Jun 24.
Artigo em Inglês | MEDLINE | ID: mdl-34167472

RESUMO

BACKGROUND: Parthenocarpy results in traits attractive to both consumers and breeders, and it overcomes the obstacle of self-incompatibility in the fruit set of horticultural crops, including pear (Pyrus bretshneider). However, there is limited knowledge regarding the genetic and molecular mechanisms that regulate parthenogenesis. RESULTS: Here, in a transcriptional comparison between pollination-dependent fruit and GA4-induced parthenocarpy, PbCYP78A6 was identified and proposed as a candidate gene involved in parthenocarpy. PbCYP78A6 is similar to Arabidopsis thaliana CYP78A6 and highly expressed in pear hypanthia. The increased PbCYP78A6 expression, as assessed by RT-qPCR, was induced by pollination and GA4 exposure. The ectopic overexpression of PbCYP78A6 contributed to parthenocarpic fruit production in tomato. The PbCYP78A6 expression coincided with fertilized and parthenocarpic fruitlets development and the expression of fruit development-related genes as assessed by cytological observations and RT-qPCR, respectively. PbCYP78A6 RNA interference and overexpression in pear calli revealed that the gene is an upstream regulator of specific fruit development-related genes in pear. CONCLUSIONS: Our findings indicate that PbCYP78A6 plays a critical role in fruit formation and provide insights into controlling parthenocarpy.


Assuntos
Ciclo Celular , Sistema Enzimático do Citocromo P-450/genética , Genes de Plantas/genética , Partenogênese , Proteínas de Plantas/genética , Pyrus/metabolismo , Ciclo Celular/genética , Ciclo Celular/fisiologia , Sistema Enzimático do Citocromo P-450/fisiologia , Perfilação da Expressão Gênica , Genes de Plantas/fisiologia , Partenogênese/genética , Partenogênese/fisiologia , Filogenia , Proteínas de Plantas/fisiologia , Polinização , Pyrus/genética , Pyrus/crescimento & desenvolvimento , Pyrus/fisiologia
14.
BMC Plant Biol ; 21(1): 295, 2021 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-34174836

RESUMO

BACKGROUND: Drought is a common phenomenon worldwide. It is also one of the main abiotic factors that affect the growth and quality of strawberry. The dehydration-responsive element binding protein (DREB) members that belong to the APETALA2/ethylene-responsive element binding protein (AP2/EREBP) superfamily are unique transcription factors in plants that play important roles in the abiotic stress response. RESULTS: Here, a total of 119 AP2/EREBP genes were identified in Fragaria vesca, and the AP2/EREBP superfamily was divided into AP2, RAV, ERF, DREB, and soloist subfamilies, containing 18, 7, 61, 32, and one member(s), respectively. The DREB subfamily was further divided into six subgroups (A-1 to A-6) based on phylogenetic analysis. Gene structure, conserved motifs, chromosomal location, and synteny analysis were conducted to comprehensively investigate the characteristics of FvDREBs. Furthermore, transcriptome analysis revealed distinctive expression patterns among the FvDREB genes in strawberry plants exposed to drought stress. The expression of FvDREB6 of the A-2 subgroup was down-regulated in old leaves and up-regulated in young leaves in response to drought. Furthermore, qRT-PCR analysis found that FvDREB8 from the A-2 subgroup had the highest expression level under drought stress. Together, analyses with the expression pattern, phylogenetic relationship, motif, and promoter suggest that FvDREB18 may play a critical role in the regulation of FvDREB1 and FvDREB2 expression. CONCLUSIONS: Our findings provide new insights into the characteristics and potential functions of FvDREBs. These FvDREB genes should be further studied as they appear to be excellent candidates for drought tolerance improvement of strawberry.


Assuntos
Fragaria/genética , Regulação da Expressão Gênica de Plantas/genética , Genes de Plantas/genética , Proteínas de Plantas/genética , Fatores de Transcrição/genética , Transcriptoma , Sequência Conservada , Desidratação , Fragaria/metabolismo , Fragaria/fisiologia , Regulação da Expressão Gênica de Plantas/fisiologia , Genes de Plantas/fisiologia , Estudo de Associação Genômica Ampla , Proteínas de Plantas/fisiologia , Reação em Cadeia da Polimerase em Tempo Real , Fatores de Transcrição/fisiologia
15.
BMC Plant Biol ; 21(1): 296, 2021 Jun 28.
Artigo em Inglês | MEDLINE | ID: mdl-34182934

RESUMO

BACKGROUND: Moso bamboo, the fastest growing plant on earth, is an important source for income in large areas of Asia, mainly cultivated in China. Lateral organ boundaries domain (LBD) proteins, a family of transcription factors unique to plants, are involved in multiple transcriptional regulatory pathways and play important roles in lateral organ development, pathogen response, secondary growth, and hormone response. The LBD gene family has not previously been characterized in moso bamboo (Phyllostachys edulis). RESULTS: In this study, we identified 55 members of the LBD gene family from moso bamboo and found that they were distributed non-uniformly across its 18 chromosomes. Phylogenetic analysis showed that the moso bamboo LBD genes could be divided into two classes. LBDs from the same class share relatively conserved gene structures and sequences encoding similar amino acids. A large number of hormone response-associated cis-regulatory elements were identified in the LBD upstream promoter sequences. Synteny analysis indicated that LBDs in the moso bamboo genome showed greater collinearity with those of O. sativa (rice) and Zea mays (maize) than with those of Arabidopsis and Capsicum annuum (pepper). Numerous segmental duplicates were found in the moso bamboo LBD gene family. Gene expression profiles in four tissues showed that the LBD genes had different spatial expression patterns. qRT-PCR assays with the Short Time-series Expression Miner (STEM) temporal expression analysis demonstrated that six genes (PeLBD20, PeLBD29, PeLBD46, PeLBD10, PeLBD38, and PeLBD06) were consistently up-regulated during the rapid growth and development of bamboo shoots. In addition, 248 candidate target genes that function in a variety of pathways were identified based on consensus LBD binding motifs. CONCLUSIONS: In the current study, we identified 55 members of the moso bamboo transcription factor LBD and characterized for the first time. Based on the short-time sequence expression software and RNA-seq data, the PeLBD gene expression was analyzed. We also investigated the functional annotation of all PeLBDs, including PPI network, GO, and KEGG enrichment based on String database. These results provide a theoretical basis and candidate genes for studying the molecular breeding mechanism of rapid growth of moso bamboo.


Assuntos
Genes de Plantas/genética , Poaceae/genética , Fatores de Transcrição/genética , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Sequência Conservada , Evolução Molecular , Regulação da Expressão Gênica de Plantas/genética , Estudo de Associação Genômica Ampla , Filogenia , Alinhamento de Sequência , Transcriptoma
16.
BMC Plant Biol ; 21(1): 298, 2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34187351

RESUMO

BACKGROUND: Awn of rice is an important domestication trait closely associated with yield traits. Therefore, the identification of genes for awn development is of great significance for the elucidation of molecular mechanism of awn development and the genetic improvement of yield traits in rice. RESULTS: In this study, using chromosome segment substitution lines (CSSLs) derived from a long-awned Guangxi common wild rice (GXCWR, Oryza rufipogon Griff.) and a short-awned indica cultivar 9311, we identified An-4, a potential quantitative trait locus (QTL) for awn development. Then, An-4 was fine mapped into a 56-kb region of chromosome 2, which contained four annotated genes. Among these four annotated genes, Os02g0594800 was concluded to be the potential candidate gene for An-4. An-4 exhibited pleiotropic effects on awn development and several yield traits. Scanning electron microscopy (SEM) analysis showed that An-4 significantly promoted awn development at Sp7 and Sp8 stage of spikelet development. Transcriptome analysis suggested that An-4 might influence the development of awn by regulating the expression of genes related to growth, developmental process, channel regulation and extracellular region. By contrast to those of 9311, the expression level of OsRR5 in CSSL128 was significantly down-regulated, whereas the expression levels of OsCKX2 and OsGA2ox5 in CSSL128 were significantly up-regulated. In addition, our study showed that An-4 had additive effects with other genes for awn development, such as An-1, An-2/LABA1 and An-3/GAD1/RAE2. CONCLUSIONS: The identification of An-4 lays a foundation for cloning of An-4 and further elucidation of the molecular mechanism of awn development. Moreover, the identification of favorable allelic variation of An-4 from 9311 will be useful to improve rice yield traits.


Assuntos
Genes de Plantas/genética , Oryza/crescimento & desenvolvimento , Componentes Aéreos da Planta/crescimento & desenvolvimento , Locos de Características Quantitativas/genética , Mapeamento Cromossômico , Cromossomos de Plantas/genética , Perfilação da Expressão Gênica , Genes de Plantas/fisiologia , Microscopia Eletrônica de Varredura , Oryza/genética , Componentes Aéreos da Planta/genética , Característica Quantitativa Herdável
17.
BMC Plant Biol ; 21(1): 297, 2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34187352

RESUMO

Here we respond to the paper entitled "Contribution of anthocyanin pathways to fruit flesh coloration in pitayas" (Fan et al., BMC Plant Biol 20:361, 2020). In this paper Fan et al. 2020 propose that the anthocyanins can be detected in the betalain-pigmented genus Hylocereus, and suggest they are responsible for the colouration of the fruit flesh. We are open to the idea that, given the evolutionary maintenance of fully functional anthocyanin synthesis genes in betalain-pigmented species, anthocyanin pigmentation might co-occur with betalain pigments, as yet undetected, in some species. However, in absence of the LC-MS/MS spectra and co-elution/fragmentation of the authentic standard comparison, the findings of Fan et al. 2020 are not credible. Furthermore, our close examination of the paper, and re-analysis of datasets that have been made available, indicate numerous additional problems. Namely, the failure to detect betalains in an untargeted metabolite analysis, accumulation of reported anthocyanins that does not correlate with the colour of the fruit, absence of key anthocyanin synthesis genes from qPCR data, likely mis-identification of key anthocyanin genes, unreproducible patterns of correlated RNAseq data, lack of gene expression correlation with pigmentation accumulation, and putative transcription factors that are weak candidates for transcriptional up-regulation of the anthocyanin pathway.


Assuntos
Antocianinas/metabolismo , Betalaínas/metabolismo , Cactaceae/metabolismo , Vias Biossintéticas , Cactaceae/genética , Frutas/metabolismo , Cromatografia Gasosa-Espectrometria de Massas , Genes de Plantas/genética , Reação em Cadeia da Polimerase , Transcriptoma
18.
BMC Plant Biol ; 21(1): 302, 2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34187359

RESUMO

BACKGROUND: Understanding the determinants of free asparagine concentration in wheat grain is necessary to reduce levels of the processing contaminant acrylamide in baked and toasted wheat products. Although crop management strategies can help reduce asparagine concentrations, breeders have limited options to select for genetic variation underlying this trait. Asparagine synthetase enzymes catalyse a critical step in asparagine biosynthesis in plants and, in wheat, are encoded by five homeologous gene triads that exhibit distinct expression profiles. Within this family, TaASN2 genes are highly expressed during grain development but TaASN-B2 is absent in some varieties. RESULTS: Natural genetic diversity in the asparagine synthetase gene family was assessed in different wheat varieties revealing instances of presence/absence variation and other polymorphisms, including some predicted to affect the function of the encoded protein. The presence and absence of TaASN-B2 was determined across a range of UK and global common wheat varieties and related species, showing that the deletion encompassing this gene was already present in some wild emmer wheat genotypes. Expression profiling confirmed that TaASN2 transcripts were only detectable in the grain, while TaASN3.1 genes were highly expressed during the early stages of grain development. TaASN-A2 was the most highly expressed TaASN2 homeologue in most assayed wheat varieties. TaASN-B2 and TaASN-D2 were expressed at similar, lower levels in varieties possessing TaASN-B2. Expression of TaASN-A2 and TaASN-D2 did not increase to compensate for the absence of TaASN-B2, so total TaASN2 expression was lower in varieties lacking TaASN-B2. Consequently, free asparagine concentrations in field-produced grain were, on average, lower in varieties lacking TaASN-B2, although the effect was lost when free asparagine accumulated to very high concentrations as a result of sulphur deficiency. CONCLUSIONS: Selecting wheat genotypes lacking the TaASN-B2 gene may be a simple and rapid way for breeders to reduce free asparagine concentrations in commercial wheat grain.


Assuntos
Asparagina/metabolismo , Aspartato-Amônia Ligase/genética , Deleção de Genes , Triticum/genética , Aspartato-Amônia Ligase/metabolismo , Qualidade dos Alimentos , Genes de Plantas/genética , Estudos de Associação Genética , Variação Genética , Triticum/enzimologia , Triticum/metabolismo
19.
BMC Plant Biol ; 21(1): 300, 2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34187360

RESUMO

BACKGROUND: A major limiting factor for plant growth is the aluminum (Al) toxicity in acidic soils, especially in tropical regions. The exclusion of Al from the root apex through root exudation of organic acids such as malate and citrate is one of the most ubiquitous tolerance mechanisms in the plant kingdom. Two families of anion channels that confer Al tolerance are well described in the literature, ALMT and MATE family. RESULTS: In this study, sugarcane plants constitutively overexpressing the Sorghum bicolor MATE gene (SbMATE) showed improved tolerance to Al when compared to non-transgenic (NT) plants, characterized by sustained root growth and exclusion of aluminum from the root apex based on the result obtained with hematoxylin staining. In addition, genome-wide analysis of the recently released sugarcane genome identified 11 ALMT genes and molecular studies showed potential new targets for aluminum tolerance. CONCLUSIONS: Our results indicate that the transgenic plants overexpressing the Sorghum bicolor MATE has an improved tolerance to Al. The expression profile of ALMT genes revels potential candidate genes to be used has an alternative for agricultural expansion in Brazil and other areas with aluminum toxicity in poor and acid soils.


Assuntos
Alumínio/metabolismo , Proteínas de Transporte de Ânions/genética , Genes de Plantas/genética , Proteínas de Plantas/genética , Saccharum/genética , Alumínio/toxicidade , Proteínas de Transporte de Ânions/metabolismo , Regulação da Expressão Gênica de Plantas , Genes de Plantas/fisiologia , Estudo de Associação Genômica Ampla , Filogenia , Proteínas de Plantas/metabolismo , Raízes de Plantas/metabolismo , Plantas Geneticamente Modificadas , Saccharum/metabolismo , Sorghum/genética , Sorghum/metabolismo , Transcriptoma
20.
BMC Plant Biol ; 21(1): 301, 2021 Jun 29.
Artigo em Inglês | MEDLINE | ID: mdl-34187365

RESUMO

BACKGROUND: Mustard (Brassica juncea) is an important economic vegetable, and some cultivars have purple leaves and accumulate more anthocyanins than the green. The genetic and evolution of purple trait in mustard has not been well studied. RESULT: In this study, free-hand sections and metabolomics showed that the purple leaves of mustard accumulated more anthocyanins than green ones. The gene controlling purple leaves in mustard, Mustard Purple Leaves (MPL), was genetically mapped and a MYB113-like homolog was identified as the candidate gene. We identified three alleles of the MYB113-like gene, BjMYB113a from a purple cultivar, BjMYB113b and BjMYB113c from green cultivars. A total of 45 single nucleotide polymorphisms (SNPs) and 8 InDels were found between the promoter sequences of the purple allele BjMYB113a and the green allele BjMYB113b. On the other hand, the only sequence variation between the purple allele BjMYB113a and the green allele BjMYB113c is an insertion of 1,033-bp fragment in the 3'region of BjMYB113c. Transgenic assay and promoter activity studies showed that the polymorphism in the promoter region was responsible for the up-regulation of the purple allele BjMYB113a and high accumulation of anthocyanin in the purple cultivar. The up-regulation of BjMYB113a increased the expression of genes in the anthocyanin biosynthesis pathway including BjCHS, BjF3H, BjF3'H, BjDFR, BjANS and BjUGFT, and consequently led to high accumulation of anthocyanin. However, the up-regulation of BjMYB113 was compromised by the insertion of 1,033-bp in 3'region of the allele BjMYB113c. CONCLUSIONS: Our results contribute to a better understanding of the genetics and evolution of the BjMYB113 gene controlling purple leaves and provide useful information for further breeding programs of mustard.


Assuntos
Genes de Plantas/genética , Mutação com Perda de Função/genética , Mostardeira/genética , Folhas de Planta/anatomia & histologia , Proteínas de Plantas/genética , Fatores de Transcrição/genética , Alelos , Antocianinas/metabolismo , Arabidopsis , Clonagem Molecular , Cor , Genes de Plantas/fisiologia , Mostardeira/anatomia & histologia , Mostardeira/metabolismo , Folhas de Planta/metabolismo , Proteínas de Plantas/fisiologia , Plantas Geneticamente Modificadas , Fatores de Transcrição/fisiologia
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