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1.
PeerJ ; 9: e12343, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34722000

RESUMO

Background: Watermelon seeds are a powerhouse of value-added traits such as proteins, free amino acids, vitamins, and essential minerals, offering a paleo-friendly dietary option. Despite the availability of substantial genetic variation, there is no sufficient information on the natural variation in seed-bound amino acids or proteins across the watermelon germplasm. This study aimed to analyze the natural variation in watermelon seed amino acids and total protein and explore underpinning genetic loci by genome-wide association study (GWAS). Methods: The study evaluated the distribution of seed-bound free amino acids and total protein in 211 watermelon accessions of Citrullus spp, including 154 of Citrullus lanatus, 54 of Citrullus mucosospermus (egusi) and three of Citrullus amarus. We used the GWAS approach to associate seed phenotypes with 11,456 single nucleotide polymorphisms (SNPs) generated by genotyping-by-sequencing (GBS). Results: Our results demonstrate a significant natural variation in different free amino acids and total protein content across accessions and geographic regions. The accessions with high protein content and proportion of essential amino acids warrant its use for value-added benefits in the food and feed industries via biofortification. The GWAS analysis identified 188 SNPs coinciding with 167 candidate genes associated with watermelon seed-bound amino acids and total protein. Clustering of SNPs associated with individual amino acids found by principal component analysis was independent of the speciation or cultivar groups and was not selected during the domestication of sweet watermelon. The identified candidate genes were involved in metabolic pathways associated with amino acid metabolism, such as Argininosuccinate synthase, explaining 7% of the variation in arginine content, which validate their functional relevance and potential for marker-assisted analysis selection. This study provides a platform for exploring potential gene loci involved in seed-bound amino acids metabolism, useful in genetic analysis and development of watermelon varieties with superior seed nutritional values.

2.
Genomics ; 113(5): 3002-3014, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34229041

RESUMO

Phenotype diversity within cultivated Capsicum chinense is particularly evident for fruit shape and size. We used this diversity in C. chinense to further unravel the genetic mechanisms underlying fruit shape variation in pepper and related Solanaceous species. We identified candidate genes for C. chinense fruit shape, explored their contribution to population structure, and characterized their potential function in pepper fruit shape. Using genotyping by sequencing, we identified 43,081 single nucleotide polymorphisms (SNPs) from diverse collections of C. chinense. Principal component, neighbor-joining tree, and population structure analyses resolved 3 phylogenetically robust clusters associated with fruit shapes. Genome-wide association study (GWAS) was used to identify associated genomic regions with various fruit shape traits obtained from image analysis with Tomato Analyzer software. In our GWAS, we selected 12 SNPs associated with locule number trait and 8 SNP markers associated with other fruit shape traits such as perimeter, area, obovoid, ellipsoid and morphometrics (5y, 6y and 7y). The SNPs in CLAVATA1, WD-40, Auxin receptor, AAA type ATPase family protein, and RNA polymerase III genes were the major markers identified for fruit locule number from our GWAS results. Furthermore, we found SNPs in tetratricopeptide-repeat thioredoxin-like 3, enhancer of ABA co-receptor 1, subunit of exocyst complex 8 and pleiotropic drug resistance proteins associated with various fruit shape traits. CLAVATA1, WD-40 and Auxin receptor genes are known genes that affect tomato fruit shape. In this study, we used Arabidopsis thaliana T-DNA insertion knockout mutants and expression profiles for functional characterization of newly identified genes and to understand their role in fruit shape.

3.
Int J Mol Sci ; 22(9)2021 May 04.
Artigo em Inglês | MEDLINE | ID: mdl-34064462

RESUMO

MicroRNAs (miRNAs) are regulators of the post-transcription stage of gene activity documented to play central roles in flower and fruit development in model plant species. However, little is known about their roles and differences in domesticated and wild Capsicum species. In this study, we used high-throughput sequencing to analyze the miRNA content at three developmental stages (flower, small fruit, and middle fruit) from two cultivated (C. baccatum and C. annuum) and two wild (C. chacoense and C. eximium) pepper species. This analysis revealed 22 known and 27 novel miRNAs differentially expressed across species and tissues. A number of stage- and species-specific miRNAs were identified, and Gene Ontology terms were assigned to 138 genes targeted by the miRNAs. Most Gene Ontology terms were for the categories "genetic information processing", "signaling and cellular processes", "amino acid metabolism", and "carbohydrate metabolism". Enriched KEGG analysis revealed the pathways amino acids, sugar and nucleotide metabolism, starch and sucrose metabolism, and fructose-mannose metabolism among the principal ones regulated by miRNAs during pepper fruit ripening. We predicted miRNA-target gene interactions regulating flowering time and fruit development, including miR156/157 with SPL genes, miR159 with GaMYB proteins, miR160 with ARF genes, miR172 with AP2-like transcription factors, and miR408 with CLAVATA1 gene across the different Capsicum species. In addition, novel miRNAs play an important role in regulating interactions potentially controlling plant pathogen defense and fruit quality via fructokinase, alpha-L-arabinofuranosidase, and aromatic and neutral amino acid transporter. Overall, the small RNA-sequencing results from this study represent valuable information that provides a solid foundation for uncovering the miRNA-mediated mechanisms of flower and fruit development between domesticated and wild Capsicum species.


Assuntos
Capsicum/genética , Flores/genética , Frutas/genética , Regulação da Expressão Gênica de Plantas , MicroRNAs/genética , Proteínas de Plantas/genética , Sistemas de Transporte de Aminoácidos/genética , Sistemas de Transporte de Aminoácidos/metabolismo , Capsicum/classificação , Capsicum/crescimento & desenvolvimento , Capsicum/metabolismo , Domesticação , Flores/crescimento & desenvolvimento , Flores/metabolismo , Frutoquinases/genética , Frutoquinases/metabolismo , Frutas/crescimento & desenvolvimento , Frutas/metabolismo , Perfilação da Expressão Gênica , Regulação da Expressão Gênica no Desenvolvimento , Ontologia Genética , Glicosídeo Hidrolases/genética , Glicosídeo Hidrolases/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Humanos , Redes e Vias Metabólicas/genética , MicroRNAs/classificação , MicroRNAs/metabolismo , Anotação de Sequência Molecular , Proteínas de Plantas/classificação , Proteínas de Plantas/metabolismo , RNA de Plantas/genética , RNA de Plantas/metabolismo , Fatores de Transcrição/classificação , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
4.
Plant J ; 106(3): 588-600, 2021 05.
Artigo em Inglês | MEDLINE | ID: mdl-33788333

RESUMO

Polyploidy has played a crucial role in plant evolution, development and function. Synthetic autopolyploid represents an ideal system to investigate the effects of polyploidization on transcriptional regulation. In this study, we deciphered the impact of genome duplication at phenotypic and molecular levels in watermelon. Overall, 88% of the genes in tetraploid watermelon followed a >1:1 dosage effect, and accordingly, differentially expressed genes were largely upregulated. In addition, a great number of hypomethylated regions (1688) were identified in an isogenic tetraploid watermelon. These differentially methylated regions were localized in promoters and intergenic regions and near transcriptional start sites of the identified upregulated genes, which enhances the importance of methylation in gene regulation. These changes were reflected in sophisticated higher-order chromatin structures. The genome doubling caused switching of 108 A and 626 B compartments that harbored genes associated with growth, development and stress responses.


Assuntos
Cromatina/ultraestrutura , Citrullus/genética , Duplicação Gênica/genética , Regulação da Expressão Gênica de Plantas/genética , Cromatina/genética , Cromatina/metabolismo , Cromossomos de Plantas/genética , Cromossomos de Plantas/metabolismo , Cromossomos de Plantas/ultraestrutura , Citrullus/metabolismo , Epigenoma/genética , Estudos de Associação Genética , Genoma de Planta/genética , Poliploidia , Tetraploidia
5.
Plants (Basel) ; 10(2)2021 Jan 20.
Artigo em Inglês | MEDLINE | ID: mdl-33498421

RESUMO

Acid mine drainage (AMD) is a huge environmental problem in mountain-top mining regions worldwide, including the Appalachian Mountains in the United States. This study applied a genome-wide association study (GWAS) to uncover genomic loci in Arabidopsis associated with tolerance to AMD toxicity. We characterized five major root phenotypes-cumulative root length, average root diameter, root surface area, root volume, and primary root length-in 180 Arabidopsis accessions in response to AMD-supplemented growth medium. GWAS of natural variation in the panel revealed genes associated with tolerance to an acidic environment. Most of these genes were transcription factors, anion/cation transporters, metal transporters, and unknown proteins. Two T-DNA insertion mutants, At1g63005 (miR399b) and At2g05635 (DEAD helicase RAD3), showed enhanced acidity tolerance. Our GWAS and the reverse genetic approach revealed genes involved in conferring tolerance to coal AMD. Our results indicated that proton resistance in hydroponic conditions could be an important index to improve plant growth in acidic soil, at least in acid-sensitive plant species.

6.
J Hazard Mater ; 407: 124831, 2021 04 05.
Artigo em Inglês | MEDLINE | ID: mdl-33340971

RESUMO

Arsenic (As), a non-biodegradable contaminant, is extremely toxic to plants and animals in its inorganic form. As negatively affects plant growth and development, primarily by inducing oxidative stress through redox imbalance. Here we characterized the Arabidopsis F-box protein gene AT2G16220 (Arsenic Stress-Related F-box (ASRF)) that we identified in the genome-wide association study. The asrf mutant seedlings showed high sensitivity to arsenate (AsV) stress. AsV significantly affected asrf seedling growth when germinated on or exposed to AsV-supplemented growth regimes. AsV stress significantly induced production of reactive oxygen species and proline accumulation in asrf, so the asrf maintained high proline content, possibly for cellular protection and redox homeostasis. Heterozygous seedlings (Col-0 x asrf, F1 progeny) were relatively less affected by AsV stress than asrf mutant but showed slightly reduced growth compared with the Col-0 wild type, which suggests that the homozygous ASRF locus is important for AsV stress resistance. Transcriptome analysis involving the mutant and wild type revealed altered phosphate homeostasis in asrf seedlings, which implies that ASRF is required for maintaining phosphate and cellular- homeostasis under excess AsV. Our findings confirm the roles of ASRF in As stress tolerance in plants, for a novel way to mitigate arsenic stress.


Assuntos
Proteínas de Arabidopsis , Arabidopsis , Arsênio , Arabidopsis/genética , Arabidopsis/metabolismo , Proteínas de Arabidopsis/genética , Proteínas de Arabidopsis/metabolismo , Arsênio/metabolismo , Arsênio/toxicidade , Regulação da Expressão Gênica de Plantas , Estudo de Associação Genômica Ampla , Plântula/genética , Plântula/metabolismo
7.
Sci Rep ; 10(1): 4044, 2020 03 04.
Artigo em Inglês | MEDLINE | ID: mdl-32132613

RESUMO

The ankyrin (ANK) repeat protein family is largely distributed across plants and has been found to participate in multiple processes such as plant growth and development, hormone response, response to biotic and abiotic stresses. It is considered as one of the major markers of capsaicin content in pepper fruits. In this study, we performed a genome-wide identification and expression analysis of genes encoding ANK proteins in three Capsicum species: Capsicum baccatum, Capsicum annuum and Capsicum chinense. We identified a total of 87, 85 and 96 ANK genes in C. baccatum, C. annuum and C. chinense genomes, respectively. Next, we performed a comprehensive bioinformatics analysis of the Capsicum ANK gene family including gene chromosomal localization, Cis-elements, conserved motif identification, intron/exon structural patterns and gene ontology classification as well as profile expression. Phylogenetic and domain organization analysis grouped the Capsicum ANK gene family into ten subfamilies distributed across all 12 pepper chromosomes at different densities. Analysis of the expression of ANK genes in leaf and pepper fruits suggested that the ANKs have specific expression patterns at various developmental stages in placenta tissue. Our results provide valuable information for further studies of the evolution, classification and putative functions of ANK genes in pepper.


Assuntos
Capsicum , Regulação da Expressão Gênica de Plantas/fisiologia , Genes de Plantas/fisiologia , Família Multigênica/fisiologia , Proteínas de Plantas , Transcriptoma/fisiologia , Repetição de Anquirina/fisiologia , Capsicum/genética , Capsicum/metabolismo , Estudo de Associação Genômica Ampla , Proteínas de Plantas/biossíntese , Proteínas de Plantas/genética , Especificidade da Espécie
8.
Int J Mol Sci ; 21(3)2020 Jan 31.
Artigo em Inglês | MEDLINE | ID: mdl-32023882

RESUMO

One of the greatest impacts on the gastrointestinal microbiome is diet because the host and microbiome share the same food source. In addition, the effect of diet can diverge depending on the host genotype. Diets supplemented with phytochemicals found in peppers might cause shifts in the microbiome. Thus, understanding how these interactions occur can reveal potential health implications associated with such changes. This study aims to explore the gut microbiome of different Drosophila genetic backgrounds and the effects of dietary pepper treatments on its composition and structure. We analyzed the gut microbiomes of three Drosophila melanogaster genetic backgrounds (Canton-S, Oregon-RC, and Berlin-K) reared on control and pepper-containing diets (bell, serrano, and habanero peppers). Results of 16S rRNA gene sequencing revealed that the variability of Drosophila gut microbiome can be driven mainly by genetic factors. When the abundance of these communities is considered, pepper-containing diets also appear to have an effect. The most relevant change in microbial composition was the increment of Lactobacillaceae and Acetobacteraceae abundance in the pepper-containing diets in comparison with the controls in Oregon-RC and Berlin-K. Regression analysis demonstrated that this enhancement was associated with the content of phenolic compounds and carotenoids of the peppers utilized in this study; specifically, to the concentration of ß-carotene, ß-cryptoxanthin, myricetin, quercetin, and apigenin.


Assuntos
Bactérias/classificação , Bactérias/genética , Dieta/métodos , Drosophila melanogaster/microbiologia , Microbioma Gastrointestinal/efeitos dos fármacos , Compostos Fitoquímicos/farmacologia , Piper nigrum/química , Animais , Bactérias/isolamento & purificação , Drosophila melanogaster/efeitos dos fármacos , Drosophila melanogaster/crescimento & desenvolvimento , Feminino , Masculino
9.
Int J Mol Sci ; 21(4)2020 Feb 19.
Artigo em Inglês | MEDLINE | ID: mdl-32092953

RESUMO

Habanero peppers constantly face biotic and abiotic stresses such as pathogen/pest infections, extreme temperature, drought and UV radiation. In addition, the fruit cutin lipid composition plays an important role in post-harvest water loss rates, which in turn causes shriveling and reduced fruit quality and storage. In this study, we integrated metabolome and transcriptome profiling pertaining to cutin in two habanero genotypes: PI 224448 and PI 257145. The fruits were selected by the waxy or glossy phenotype on their surfaces. Metabolomics analysis showed a significant variation in cutin composition, with about 6-fold higher cutin in PI 257145 than PI 224448. It also revealed that 10,16-dihydroxy hexadecanoic acid is the most abundant monomer in PI 257145. Transcriptomic analysis of high-cutin PI 257145 and low-cutin PI 224448 resulted in the identification of 2703 statistically significant differentially expressed genes, including 1693 genes upregulated and 1010 downregulated in high-cutin PI 257145. Genes and transcription factors such as GDSL lipase, glycerol-3 phosphate acyltransferase 6, long-chain acyltransferase 2, cytochrome P450 86A/77A, SHN1, ANL2 and HDG1 highly contributed to the high cutin content in PI 257145. We predicted a putative cutin biosynthetic pathway for habanero peppers based on deep transcriptome analysis. This is the first study of the transcriptome and metabolome pertaining to cutin in habanero peppers. These analyses improve our knowledge of the molecular mechanisms regulating the accumulation of cutin in habanero pepper fruits. These resources can be built on for developing cultivars with high cutin content that show resistance to biotic and abiotic stresses with superior postharvest appearance.


Assuntos
Capsicum/genética , Frutas/metabolismo , Lipídeos de Membrana/biossíntese , Metabolômica/métodos , Transcriptoma/genética , Vias Biossintéticas/genética , Vias Biossintéticas/fisiologia , Capsicum/química , Capsicum/metabolismo , Hidrolases de Éster Carboxílico/metabolismo , Sistema Enzimático do Citocromo P-450/metabolismo , Regulação para Baixo , Frutas/genética , Cromatografia Gasosa-Espectrometria de Massas , Regulação da Expressão Gênica de Plantas/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Ontologia Genética , Genótipo , Glicerol-3-Fosfato O-Aciltransferase/metabolismo , Proteínas de Homeodomínio/metabolismo , Lipídeos de Membrana/análise , Lipídeos de Membrana/química , Ácidos Palmíticos/metabolismo , Fenótipo , RNA-Seq , Fatores de Transcrição/metabolismo , Transcriptoma/fisiologia , Regulação para Cima
10.
Plant Mol Biol ; 102(1-2): 213-223, 2020 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-31845303

RESUMO

KEY MESSAGE: Transcriptome landscape reveals the molecular mechanisms involved in the improvement of fruit traits by the grafting of watermelon and bottle gourd. Grafting has been used as a sustainable alternative for watermelon breeding to control soil-borne pathogens and to increase tolerance to various abiotic stresses. However, some reports have shown that grafting can negatively affect the quality of fruits. Despite several field studies on the effects of grafting on fruit quality, the regulation of this process at the molecular level has not been revealed. The aim of this study was to elucidate various molecular mechanisms involved in different tissues of heterografted watermelon and bottle gourd plants. Grafting with bottle gourd rootstock increased the size and rind thickness of watermelon fruits, whereas that with watermelon rootstock produced bottle gourd fruits with higher total soluble solid content and thinner rinds. Correspondingly, genes related to ripening, softening, cell wall strengthening, stress response and disease resistance were differentially expressed in watermelon fruits. Moreover, genes associated mainly with sugar metabolism were differentially expressed in bottle gourd fruits. RNA-seq revealed more than 400 mobile transcripts across the heterografted sets. More than half of these were validated from PlaMoM, a database for plant mobile macromolecules. In addition, some of these mobile transcripts contained a transfer RNA-like structure. Other RNA motifs were also enriched in these transcripts, most with a biological role based on GO analysis. This transcriptome study provided a comprehensive understanding of various molecular mechanisms underlying grafted tissues in watermelon.


Assuntos
Citrullus/metabolismo , Frutas/crescimento & desenvolvimento , Frutas/metabolismo , Transcriptoma , Transplante Heterólogo , Metabolismo dos Carboidratos , Citrullus/genética , Resistência à Doença/genética , Frutas/genética , Regulação da Expressão Gênica de Plantas , Ontologia Genética , Melhoramento Vegetal , Raízes de Plantas/metabolismo , RNA Mensageiro/metabolismo , RNA de Plantas , Análise de Sequência , Estresse Fisiológico
11.
Int J Mol Sci ; 20(21)2019 Oct 29.
Artigo em Inglês | MEDLINE | ID: mdl-31671884

RESUMO

Watermelon is a good source of citrulline, a non-protein amino acid. Citrulline has several therapeutic and clinical implications as it produces nitric oxide via arginine. In plants, citrulline plays a pivotal role in nitrogen transport and osmoprotection. The purpose of this study was to identify single nucleotide polymorphism (SNP) markers associated with citrulline metabolism using a genome-wide association study (GWAS) and understand the role of citrulline in watermelon domestication. A watermelon collection consisting of 187 wild, landraces, and cultivated accessions was used to estimate citrulline content. An association analysis involved a total of 12,125 SNPs with a minor allele frequency (MAF) >0.05 in understanding the population structure and phylogeny in light of citrulline accumulation. Wild egusi types and landraces contained low to medium citrulline content, whereas cultivars had higher content, which suggests that obtaining higher content of citrulline is a domesticated trait. GWAS analysis identified candidate genes (ferrochelatase and acetolactate synthase) showing a significant association of SNPs with citrulline content. Haplotype networking indicated positive selection from wild to domesticated watermelon. To our knowledge, this is the first study showing genetic regulation of citrulline variation in plants by using a GWAS strategy. These results provide new insights into the citrulline metabolism in plants and the possibility of incorporating high citrulline as a trait in watermelon breeding programs.


Assuntos
Citrulina/genética , Citrulina/metabolismo , Citrullus/genética , Citrullus/metabolismo , Domesticação , Estudo de Associação Genômica Ampla/métodos , Haplótipos/genética , Acetolactato Sintase/genética , Acetolactato Sintase/metabolismo , Arginina , Ferroquelatase/genética , Ferroquelatase/metabolismo , Frequência do Gene , Ontologia Genética , Genes de Plantas/genética , Genoma de Planta , Óxido Nítrico , Osmorregulação , Fenótipo , Filogenia , Polimorfismo de Nucleotídeo Único
12.
PLoS One ; 14(4): e0215901, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-31039176

RESUMO

ATP-binding cassette (ABC) transporter genes act as transporters for different molecules across biological membranes and are involved in a diverse range of biological processes. In this study, we performed a genome-wide identification and expression analysis of genes encoding ABC transporter proteins in three Capsicum species, i.e., Capsicum annuum, Capsicum baccatum and Capsicum chinense. Capsicum is a valuable horticultural crop worldwide as an important constituent of many foods while containing several medicinal compounds including capsaicin and dihydrocapsaicin. Our results identified the presence of a total of 200, 185 and 187 ABC transporter genes in C. annuum, C. baccatum and C. chinense genomes, respectively. Capsaicin and dihydrocapsaicin content were determined in green pepper fruits (16 dpa). Additionally, we conducted different bioinformatics analyses including ABC genes classification, gene chromosomal location, Cis elements, conserved motifs identification and gene ontology classification, as well as profile expression of selected genes. Based on phylogenetic analysis and domain organization, the Capsicum ABC gene family was grouped into eight subfamilies. Among them, members within the ABCG, ABCB and ABCC subfamilies were the most abundant, while ABCD and ABCE subfamilies were less abundant throughout all species. ABC members within the same subfamily showed similar motif composition. Furthermore, common cis-elements involved in the transcriptional regulation were also identified in the promoter regions of all Capsicum ABC genes. Gene expression data from RNAseq and reverse transcription-semi-quantitative PCR analysis revealed development-specific stage expression profiles in placenta tissues. It suggests that ABC transporters, specifically the ABCC and ABCG subfamilies, may be playing important roles in the transport of secondary metabolites such as capsaicin and dihydrocapsaicin to the placenta vacuoles, effecting on their content in pepper fruits. Our results provide a more comprehensive understanding of ABC transporter gene family in different Capsicum species while allowing the identification of important candidate genes related to capsaicin content for subsequent functional validation.


Assuntos
Transportadores de Cassetes de Ligação de ATP/genética , Capsicum/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Proteínas de Plantas/genética , Transportadores de Cassetes de Ligação de ATP/química , Transportadores de Cassetes de Ligação de ATP/metabolismo , Alelos , Motivos de Aminoácidos , Capsaicina/análogos & derivados , Capsaicina/análise , Cromossomos de Plantas/genética , Ontologia Genética , Genes de Plantas , Marcadores Genéticos , Anotação de Sequência Molecular , Filogenia , Proteínas de Plantas/química , Proteínas de Plantas/metabolismo , Polimorfismo de Nucleotídeo Único/genética , Regiões Promotoras Genéticas/genética
13.
Plant Biotechnol J ; 17(12): 2246-2258, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31022325

RESUMO

Years of selection for desirable fruit quality traits in dessert watermelon (Citrullus lanatus) has resulted in a narrow genetic base in modern cultivars. Development of novel genomic and genetic resources offers great potential to expand genetic diversity and improve important traits in watermelon. Here, we report a high-quality genome sequence of watermelon cultivar 'Charleston Gray', a principal American dessert watermelon, to complement the existing reference genome from '97103', an East Asian cultivar. Comparative analyses between genomes of 'Charleston Gray' and '97103' revealed genomic variants that may underlie phenotypic differences between the two cultivars. We then genotyped 1365 watermelon plant introduction (PI) lines maintained at the U.S. National Plant Germplasm System using genotyping-by-sequencing (GBS). These PI lines were collected throughout the world and belong to three Citrullus species, C. lanatus, C. mucosospermus and C. amarus. Approximately 25 000 high-quality single nucleotide polymorphisms (SNPs) were derived from the GBS data using the 'Charleston Gray' genome as the reference. Population genomic analyses using these SNPs discovered a close relationship between C. lanatus and C. mucosospermus and identified four major groups in these two species correlated to their geographic locations. Citrullus amarus was found to have a distinct genetic makeup compared to C. lanatus and C. mucosospermus. The SNPs also enabled identification of genomic regions associated with important fruit quality and disease resistance traits through genome-wide association studies. The high-quality 'Charleston Gray' genome and the genotyping data of this large collection of watermelon accessions provide valuable resources for facilitating watermelon research, breeding and improvement.


Assuntos
Citrullus/genética , Genoma de Planta , Mapeamento Cromossômico , Resistência à Doença , Frutas , Estudos de Associação Genética , Genômica , Polimorfismo de Nucleotídeo Único
14.
Funct Integr Genomics ; 19(1): 171-190, 2019 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-30244303

RESUMO

Elevated CO2 along with drought is a serious global threat to crop productivity. Therefore, understanding the molecular mechanisms plants use to protect these stresses is the key for plant growth and development. In this study, we mimicked natural stress conditions under a controlled Soil-Plant-Atmosphere-Research (SPAR) system and provided the evidence for how miRNAs regulate target genes under elevated CO2 and drought conditions. Significant physiological and biomass data supported the effective utilization of source-sink (leaf to root) under elevated CO2. Additionally, elevated CO2 partially rescued the effect of drought on total biomass. We identified both known and novel miRNAs differentially expressed during drought, CO2, and combined stress, along with putative targets. A total of 32 conserved miRNAs belonged to 23 miRNA families, and 25 novel miRNAs were identified by deep sequencing. Using the existing sweet potato genome database and stringent analyses, a total of 42 and 22 potential target genes were predicted for the conserved and novel miRNAs, respectively. These target genes are involved in drought response, hormone signaling, photosynthesis, carbon fixation, sucrose and starch metabolism, etc. Gene ontology and KEGG ontology functional enrichment revealed that these miRNAs might target transcription factors (MYB, TCP, NAC), hormone signaling regulators (ARF, AP2/ERF), cold and drought factors (corA), carbon metabolism (ATP synthase, fructose-1,6-bisphosphate), and photosynthesis (photosystem I and II complex units). Our study is the first report identifying targets of miRNAs under elevated CO2 levels and could support the molecular mechanisms under elevated CO2 in sweet potato and other crops in the future.


Assuntos
Dióxido de Carbono/metabolismo , Regulação da Expressão Gênica de Plantas , Genoma de Planta , Ipomoea batatas/genética , MicroRNAs/genética , Folhas de Planta/genética , Raízes de Plantas/genética , Biomassa , Ciclo do Carbono/genética , Secas , Regulação da Expressão Gênica no Desenvolvimento , Ontologia Genética , Sequenciamento de Nucleotídeos em Larga Escala , Ipomoea batatas/crescimento & desenvolvimento , Ipomoea batatas/metabolismo , MicroRNAs/metabolismo , Anotação de Sequência Molecular , Fotossíntese/genética , Folhas de Planta/crescimento & desenvolvimento , Folhas de Planta/metabolismo , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raízes de Plantas/crescimento & desenvolvimento , Raízes de Plantas/metabolismo , Transdução de Sinais , Estresse Fisiológico/genética
15.
PLoS One ; 13(10): e0206183, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-30379886

RESUMO

Chili peppers are an important constituent of many foods and contain medicinally valuable compounds, such as capsaicin and dihydrocapsaicin. As various dietary botanicals have anticancer properties, this study was aimed to examine the effect of Ghost pepper (Bhut Jolokia), one of the hottest chili peppers in the world, on cell proliferation, apoptosis, senescence and the global proteomic profile in human renal cell adenocarcinoma in vitro. 769-P human renal adenocarcinoma cells were cultured on RPMI-1640 media supplemented with fetal bovine serum (10%) and antibiotic-antimycotic solution (1%). Treatment stock solutions were prepared in ethanol. Cell proliferation was tested with phenol red-free media with capsaicin (0-400 µM), dihydrocapsaicin (0-400 µM), capsaicin + dihydrocapsaicin (5:1), and dry Ghost peppers (0-3 g L-1) for 24, 48 and 72 h. Polycaspase and senescence associated-beta-galactosidase (SA-beta-gal) activities were tested with capsaicin (400 µM), dihydrocapsaicin (400 µM), capsaicin (400 µM) + dihydrocapsaicin (80 µM), and ghost pepper (3 g L-1) treatments. Global proteomic profile of cells in control and ghost pepper treatment (3 g L-1) was analyzed after 6 h by a shotgun proteomic approach using tandem mass spectrometry. At 24 h after treatment (24 HAT), relative to control, cell proportion with capsaicin (400 µM), dihydrocapsaicin (400 µM), capsaicin (400 µM) + dihydrocapsaicin (80 µM), and ghost pepper (3 g L-1) treatments was reduced to 36%, 18%, 33% and 20%, respectively, and further reduced at 48 and 72 HAT. All treatments triggered an early polycaspase response. SA-beta-gal activity was normal or suppressed with all treatments. About 68,220 protein isoforms were identified by shotgun proteomic approach. Among these, about 8.2% were significantly affected by ghost pepper. Ghost pepper regulated various proteins involved in intrinsic and extrinsic apoptotic pathways, Ras, Rb/E2F, p53, TGF-beta, WNT-beta catenin, and calcium induced cell death pathways. Ghost pepper also induced changes in proteins related to methylation, acetylation, genome stability, cell cycle check points, carbohydrate, protein and other metabolism and cellular mechanisms. Ghost pepper exhibited antiproliferation activity by inducing apoptosis through a complex network of proteins in human renal cell adenocarcinoma in vitro.


Assuntos
Capsicum/química , Carcinoma de Células Renais/metabolismo , Neoplasias Renais/metabolismo , Extratos Vegetais/farmacologia , Proteômica/métodos , Capsaicina/análogos & derivados , Capsaicina/farmacologia , Carcinoma de Células Renais/tratamento farmacológico , Caspases/metabolismo , Linhagem Celular Tumoral , Proliferação de Células/efeitos dos fármacos , Sobrevivência Celular/efeitos dos fármacos , Senescência Celular , Regulação Neoplásica da Expressão Gênica/efeitos dos fármacos , Humanos , Neoplasias Renais/tratamento farmacológico , Extratos Vegetais/química , Transdução de Sinais/efeitos dos fármacos , Espectrometria de Massas em Tandem
16.
Front Plant Sci ; 9: 4, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29403516

RESUMO

The plant microbiome is a key determinant of plant health and productivity, and changes in the plant microbiome can alter the tolerance to biotic and abiotic stresses and the quality of end produce. Little is known about the microbial diversity and its effect on carbohydrate metabolism in ripe fruits. In this study, we aimed to understand the diversity and function of microorganisms in relation to carbohydrate metabolism of ripe watermelon fruits. We used 16S metagenomics and RNAseq metatranscriptomics for analysis of red (PI459074, Congo, and SDRose) and yellow fruit-flesh cultivars (PI227202, PI435990, and JBush) of geographically and metabolically diverse watermelon cultivars. Metagenomics data showed that Proteobacteria were abundant in SDRose and PI227202, whereas Cyanobacteria were most abundant in Congo and PI4559074. In the case of metatranscriptome data, Proteobacteria was the most abundant in all cultivars. High expression of genes linked to infectious diseases and the expression of peptidoglycan hydrolases associated to pathogenicity of eukaryotic hosts was observed in SDRose, which could have resulted in low microbial diversity in this cultivar. The presence of GH28, associated with polygalacturonase activity in JBush and SDRose could be related to cell wall modifications including de-esterification and depolymerization, and consequent loss of galacturonic acid and neutral sugars. Moreover, based on the KEGG annotation of the expressed genes, nine α-galactosidase genes involved in key processes of galactosyl oligosaccharide metabolism, such as raffinose family were identified and galactose metabolism pathway was reconstructed. Results of this study underline the links between the host and fruit-associated microbiome in carbohydrate metabolism of the ripe fruits. The cultivar difference in watermelon reflects the quantum and diversity of the microbiome, which would benefit watermelon and other plant breeders aiming at the holobiont concept to incorporate associated microbiomes in breeding programs.

17.
Sci Rep ; 7: 41285, 2017 01 27.
Artigo em Inglês | MEDLINE | ID: mdl-28128280

RESUMO

Use of 10,129 singleton SNPs of known genomic location in tetraploid cotton provided unique opportunities to characterize genome-wide diversity among 440 Gossypium hirsutum and 219 G. barbadense cultivars and landrace accessions of widespread origin. Using the SNPs distributed genome-wide, we examined genetic diversity, haplotype distribution and linkage disequilibrium patterns in the G. hirsutum and G. barbadense genomes to clarify population demographic history. Diversity and identity-by-state analyses have revealed little sharing of alleles between the two cultivated allotetraploid genomes, with a few exceptions that indicated sporadic gene flow. We found a high number of new alleles, representing increased nucleotide diversity, on chromosomes 1 and 2 in cultivated G. hirsutum as compared with low nucleotide diversity on these chromosomes in landrace G. hirsutum. In contrast, G. barbadense chromosomes showed negative Tajima's D on several chromosomes for both cultivated and landrace types, which indicate that speciation of G. barbadense itself, might have occurred with relatively narrow genetic diversity. The presence of conserved linkage disequilibrium (LD) blocks and haplotypes between G. hirsutum and G. barbadense provides strong evidence for comparable patterns of evolution in their domestication processes. Our study illustrates the potential use of population genetic techniques to identify genomic regions for domestication.


Assuntos
Domesticação , Genética Populacional , Genoma de Planta/genética , Gossypium/genética , Alelos , Mapeamento Cromossômico , Variação Genética , Haplótipos , Filogenia , Polimorfismo de Nucleotídeo Único , Tetraploidia
18.
Sci Rep ; 6: 38081, 2016 11 30.
Artigo em Inglês | MEDLINE | ID: mdl-27901114

RESUMO

Accumulated capsaicinoid content and increased fruit size are traits resulting from Capsicum annuum domestication. In this study, we used a diverse collection of C. annuum to generate 66,960 SNPs using genotyping by sequencing. The study identified 1189 haplotypes containing 3413 SNPs. Length of individual linkage disequilibrium (LD) blocks varied along chromosomes, with regions of high and low LD interspersed with an average LD of 139 kb. Principal component analysis (PCA), Bayesian model based population structure analysis and an Euclidean tree built based on identity by state (IBS) indices revealed that the clustering pattern of diverse accessions are in agreement with capsaicin content (CA) and fruit weight (FW) classifications indicating the importance of these traits in shaping modern pepper genome. PCA and IBS were used in a mixed linear model of capsaicin and dihydrocapsaicin content and fruit weight to reduce spurious associations because of confounding effects of subpopulations in genome-wide association study (GWAS). Our GWAS results showed SNPs in Ankyrin-like protein, IKI3 family protein, ABC transporter G family and pentatricopeptide repeat protein are the major markers for capsaicinoids and of 16 SNPs strongly associated with FW in both years of the study, 7 are located in known fruit weight controlling genes.


Assuntos
Capsaicina/análogos & derivados , Capsicum , Frutas , Polimorfismo de Nucleotídeo Único , Capsaicina/metabolismo , Capsicum/genética , Capsicum/metabolismo , Frutas/genética , Frutas/metabolismo , Estudo de Associação Genômica Ampla
19.
Front Plant Sci ; 7: 1646, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27857720

RESUMO

Principal component analysis (PCA) with 36,621 polymorphic genome-anchored single nucleotide polymorphisms (SNPs) identified collectively for Capsicum annuum and Capsicum baccatum was used to characterize population structure and species domestication of these two important incompatible cultivated pepper species. Estimated mean nucleotide diversity (π) and Tajima's D across various chromosomes revealed biased distribution toward negative values on all chromosomes (except for chromosome 4) in cultivated C. baccatum, indicating a population bottleneck during domestication of C. baccatum. In contrast, C. annuum chromosomes showed positive π and Tajima's D on all chromosomes except chromosome 8, which may be because of domestication at multiple sites contributing to wider genetic diversity. For C. baccatum, 13,129 SNPs were available, with minor allele frequency (MAF) ≥0.05; PCA of the SNPs revealed 283 C. baccatum accessions grouped into 3 distinct clusters, for strong population structure. The fixation index (FST ) between domesticated C. annuum and C. baccatum was 0.78, which indicates genome-wide divergence. We conducted extensive linkage disequilibrium (LD) analysis of C. baccatum var. pendulum cultivars on all adjacent SNP pairs within a chromosome to identify regions of high and low LD interspersed with a genome-wide average LD block size of 99.1 kb. We characterized 1742 haplotypes containing 4420 SNPs (range 9-2 SNPs per haplotype). Genome-wide association study (GWAS) of peduncle length, a trait that differentiates wild and domesticated C. baccatum types, revealed 36 significantly associated genome-wide SNPs. Population structure, identity by state (IBS) and LD patterns across the genome will be of potential use for future GWAS of economically important traits in C. baccatum peppers.

20.
Front Plant Sci ; 7: 1437, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27713759

RESUMO

Melon (Cucumis melo L.) is a phenotypically diverse eudicot diploid (2n = 2x = 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (Fst) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. The FST between accessions of cantalupensis and inodorus was 0.23. The FST between cantalupensis and various agrestis accessions was in a range of 0.19-0.53 and between inodorus and agrestis accessions was in a range of 0.21-0.59 indicating sporadic to wide ranging introgression. The EM (Expectation Maximization) algorithm was used for estimation of 1436 haplotypes. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. In the current research, we focused on the genome-wide divergence underlying diverse melon horticultural groups. A high-resolution genetic map with 7153 loci was constructed. Genome-wide segregation distortion and recombination rate across various chromosomes were characterized. Melon has climacteric and non-climacteric morphotypes and wide variation for fruit firmness, a very important trait for transportation and shelf life. Various levels of QTLs were identified with high to moderate stringency and linked to fruit firmness using both genome-wide association study (GWAS) and biparental mapping. Gene annotation revealed some of the SNPs are located in ß-D-xylosidase, glyoxysomal malate synthase, chloroplastic anthranilate phosphoribosyltransferase, and histidine kinase, the genes that were previously characterized for fruit ripening and softening in other crops.

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