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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.
Front Genet ; 12: 704075, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34394192

RESUMO

Here we report on comprehensive chloroplast (cp) genome analysis of 16 pomegranate (Punica granatum L.) genotypes representing commercial cultivars, ornamental and wild types, through large-scale sequencing and assembling using next-generation sequencing (NGS) technology. Comparative genome analysis revealed that the size of cp genomes varied from 158,593 bp (in wild, "1201" and "1181") to 158,662 bp (cultivar, "Gul-e-Shah Red") among the genotypes, with characteristic quadripartite structures separated by a pair of inverted repeats (IRs). The higher conservation for the total number of coding and non-coding genes (rRNA and tRNA) and their sizes, and IRs (IR-A and IR-B) were observed across all the cp genomes. Interestingly, high variations were observed in sizes of large single copy (LSC, 88,976 to 89,044 bp) and small single copy (SSC, 18,682 to 18,684 bp) regions. Although, the structural organization of newly assembled cp genomes were comparable to that of previously reported cp genomes of pomegranate ("Helow," "Tunisia," and "Bhagawa"), the striking differences were observed with the Lagerstroemia lines, viz., Lagerstroemia intermedia (NC_0346620) and Lagerstroemia speciosa (NC_031414), which clearly confirmed previous findings. Furthermore, phylogenetic analysis also revealed that members outside the genus Punica were clubbed into a separate clade. The contraction and expansion analysis revealed that the structural variations in IRs, LSC, and SSC have significantly accounted for the evolution of cp genomes of Punica and L. intermedia over the periods. Microsatellite survey across cp genomes resulted in the identification of a total of 233 to 234 SSRs, with majority of them being mono- (A/T or C/G, 164-165 numbers), followed by di- (AT/AT or AG/CT, 54), tri- (6), tetra- (8), and pentanucleotides (1). Furthermore, the comparative structural variant analyses across cp genomes resulted in the identification of many varietal specific SNP/indel markers. In summary, our study has offered a successful development of large-scale cp genomics resources to leverage future genetic, taxonomical, and phylogenetic studies in pomegranate.

3.
Front Genet ; 12: 722519, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34456979

RESUMO

Gene expression was analyzed at 0- and 24-h post-inoculation of two inbred sorghum cultivars known to differ in response to inoculation with Colletotrichum sublineola, the fungal pathogen that causes anthracnose. QL3 is reported to have quantitative resistance, while Theis is susceptible to most pathotypes of the pathogen; RNASeq identified over 3,000 specific genes in both cultivars as showing significant changes in expression following inoculation; in all but one gene, the changes in QL3 and Thies were in the same direction. Many other genes showed significant changes in only one of the two cultivars. Overall, more genes were downregulated than upregulated. Differences in changes in expression levels of a few genes suggested potential roles for the difference in disease response between QL3 and Theis, but did not identify known resistance genes. Gene ontology (GO) and pathway enrichment analysis identified upregulation of 23 transcription factor encoding genes as well as genes involved in the production of secondary metabolites, which are part of a typical host defense reaction.

4.
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.

5.
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
6.
Int J Mol Sci ; 22(5)2021 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-33804571

RESUMO

Blueberries (Vaccinium spp.) are highly vulnerable to changing climatic conditions, especially increasing temperatures. To gain insight into mechanisms underpinning the response to heat stress, two blueberry species were subjected to heat stress for 6 and 9 h at 45 °C, and leaf samples were used to study the morpho-physiological and transcriptomic changes. As compared with Vaccinium corymbosum, Vaccinium darrowii exhibited thermal stress adaptation features such as small leaf size, parallel leaf orientation, waxy leaf coating, increased stomatal surface area, and stomatal closure. RNAseq analysis yielded ~135 million reads and identified 8305 differentially expressed genes (DEGs) during heat stress against the control samples. In V. corymbosum, 2861 and 4565 genes were differentially expressed at 6 and 9 h of heat stress, whereas in V. darrowii, 2516 and 3072 DEGs were differentially expressed at 6 and 9 h, respectively. Among the pathways, the protein processing in the endoplasmic reticulum (ER) was the highly enriched pathway in both the species: however, certain metabolic, fatty acid, photosynthesis-related, peroxisomal, and circadian rhythm pathways were enriched differently among the species. KEGG enrichment analysis of the DEGs revealed important biosynthesis and metabolic pathways crucial in response to heat stress. The GO terms enriched in both the species under heat stress were similar, but more DEGs were enriched for GO terms in V. darrowii than the V. corymbosum. Together, these results elucidate the differential response of morpho-physiological and molecular mechanisms used by both the blueberry species under heat stress, and help in understanding the complex mechanisms involved in heat stress tolerance.


Assuntos
Mirtilos Azuis (Planta)/anatomia & histologia , Mirtilos Azuis (Planta)/fisiologia , Resposta ao Choque Térmico , Proteínas de Plantas/metabolismo , Termotolerância/genética , Transcriptoma , Mirtilos Azuis (Planta)/classificação , Biologia Computacional , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Proteínas de Plantas/genética
7.
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
8.
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.

9.
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
10.
Saudi J Biol Sci ; 27(12): 3514-3528, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33304163

RESUMO

Pomegranate (Punica granatum L.) is an important fruit crop, rich in fiber, vitamins, antioxidants, minerals and source of different biologically active compounds. The bacterial blight caused by Xanthomonas axonopodispv. punicae is a serious threat to the crop leading to 60-80% yield loss under epiphytotic conditions. In this work, we have generated comparative transcriptome profile to mark the gene expression signatures during resistance and susceptible interactions. We analyzed leaf and fruits samples of moderately resistant genotype (IC 524207) and susceptible variety (Bhagawa) of pomegranate at three progressive infection stages upon inoculation with the pathogen. RNA-Seq with the Illumina HiSeq 2500 platform revealed 1,88,337 non-redundant (nr) transcript sequences from raw sequencing data, for a total of 34,626 unigenes with size >2 kb. Moreover, 85.3% unigenes were annotated in at least one of the seven databases examined. Comparative analysis of gene-expression signatures in resistant and susceptible varieties showed that the genes known to be involved in defense mechanism in plants were up-regulated in resistant variety. Gene Ontology (GO) analysis successfully annotated 90,485 pomegranate unigenes, of which 68,464 were assigned to biological, 78,107 unigenes molecular function and 44,414 to cellular components. Significantly enriched GO terms in DEGs were related to oxidations reduction biological process, protein binding and oxidoreductase activity. This transcriptome data on pomegranate could help in understanding resistance and susceptibility nature of cultivars and further detailed fine mapping and functional validation of identified candidate gene would provide scope for resistance breeding programme in pomegranate.

11.
Int J Mol Sci ; 22(1)2020 Dec 26.
Artigo em Inglês | MEDLINE | ID: mdl-33375261

RESUMO

Blueberries (Vaccinium section Cyanococcus) are perennial shrubs widely cultivated for their edible fruits. In this study, we performed admixture and genetic relatedness analysis of northern highbush (NHB, primarily V. corymbosum) and southern highbush (SHB, V. corymbosum introgressed with V. darrowii, V. virgatum, or V. tenellum) blueberry genotypes, and progenies of the BNJ16-5 cross (V. corymbosum × V. darrowii). Using genotyping-by-sequencing (GBS), we generated more than 334 million reads (75 bp). The GBS reads were aligned to the V. corymbosum cv. Draper v1.0 reference genome sequence, and ~2.8 million reads were successfully mapped. From the alignments, we identified 2,244,039 single-nucleotide polymorphisms, which were used for principal component, haplotype, and admixture analysis. Principal component analysis revealed three main groups: (1) NHB cultivars, (2) SHB cultivars, and (3) BNJ16-5 progenies. The overall fixation index (FST) and nucleotide diversity for NHB and SHB cultivars indicated wide genetic differentiation, and haplotype analysis revealed that SHB cultivars are more genetically diverse than NHB cultivars. The admixture analysis identified a mixture of various lineages of parental genomic introgression. This study demonstrated the effectiveness of GBS-derived single-nucleotide polymorphism markers in genetic and admixture analyses to reveal genetic relatedness and to examine parental lineages in blueberry, which may be useful for future breeding plans.


Assuntos
Mirtilos Azuis (Planta)/genética , Linhagem da Célula , Marcadores Genéticos , Haplótipos , Melhoramento Vegetal , Proteínas de Plantas/genética , Polimorfismo de Nucleotídeo Único , Mirtilos Azuis (Planta)/classificação , Mirtilos Azuis (Planta)/crescimento & desenvolvimento , Regulação da Expressão Gênica de Plantas , Genótipo , Especificidade da Espécie , Transcriptoma
12.
PLoS One ; 15(11): e0242500, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33232358

RESUMO

The domestic Nili-Ravi water buffalo (Bubalus bubalis) is the best dairy animal contributing 68% to total milk production in Pakistan. In this study, we identified genome-wide single nucleotide polymorphisms (SNPs) to estimate various population genetic parameters such as diversity, pairwise population differentiation, linkage disequilibrium (LD) distribution and for genome-wide association study for milk yield and body weight traits in the Nili-Ravi dairy bulls that they may pass on to their daughters who are retained for milking purposes. The genotyping by sequencing approach revealed 13,039 reference genome-anchored SNPs with minor allele frequency of 0.05 among 167 buffalos. Population structure analysis revealed that the bulls were grouped into two clusters (K = 2), which indicates the presence of two different lineages in the Pakistani Nili-Ravi water buffalo population, and we showed the extent of admixture of these two lineages in our bull collection. LD analysis revealed 4169 significant SNP associations, with an average LD decay of 90 kb for these buffalo genome. Genome-wide association study involved a multi-locus mixed linear model for milk yield and body weight to identify genome-wide male effects. Our study further illustrates the utility of the genotyping by sequencing approach for identifying genomic regions to uncover additional demographic complexity and to improve the complex dairy traits of the Pakistani Nili-Ravi water buffalo population that would provide the lot of economic benefits to dairy industry.


Assuntos
Búfalos/genética , Polimorfismo de Nucleotídeo Único , Animais , Peso Corporal , Cruzamento , Indústria de Laticínios/métodos , Domesticação , Variação Genética , Estudo de Associação Genômica Ampla , Genótipo , Haplótipos , Desequilíbrio de Ligação , Masculino , Leite , Paquistão , Característica Quantitativa Herdável , Amostragem
13.
Sci Rep ; 10(1): 18649, 2020 10 29.
Artigo em Inglês | MEDLINE | ID: mdl-33122752

RESUMO

Seedling grafting could provide additional crop improvement strategies for cotton. However, there existed limited studies on interspecific grafting and approaches. Four different grafting approaches were developed and compared between lines representing three of the four cultivated cotton species G. hirsutum, G. barbadense and G. herbaceum. Grafting approaches of this study focused on the cotyledon node and cotyledon leaves retained on scions, rootstocks, without cotyledon node and cotyledon leaves on scions and rootstocks or halved cotyledon node and single cotyledon leaf on scions and rootstocks. Evaluations of the grafting approaches were made by comparing survival and growth rate during the second and fifth weeks after transplantation, respectively. The formation of any lateral shoots at the grafted sites were studied in two of four grafting approaches in the first and the second year during flowering stage. DNA alterations due to grafting were investigated using microsatellite markers. There were no statistically significant differences between grafts and their control in survival rate and locus specific DNA alteration. Growth rate and lateral shoot formation, on the other hand, were different among grafting types and grafts. We concluded that grafting without cotyledon node and cotyledon leaves on rootstocks, and with cotyledon node but without cotyledon leaves on scions were easy to perform and suitable for interspecific cotton grafting. Results suggested that grafting seedlings and allowing time to heal graft wounds prior to spring transplanting or double cropping is suitable for wheat-cotton intercropping to prevent late or early chilling damage associated with seed sowing or conventional transplanting of susceptible seedlings. Furthermore, the rapid and consistent wound healing in seedling grafts along with lateral shoot formation occurring in two of four grafting approaches make them a suitable approach to investigate possible genetic and epigenetic movement between scions and rootstocks, especially across species.


Assuntos
Gossypium/genética , Cotilédone/crescimento & desenvolvimento , Gossypium/classificação , Gossypium/crescimento & desenvolvimento , Folhas de Planta/crescimento & desenvolvimento , Raízes de Plantas/crescimento & desenvolvimento , Plântula/crescimento & desenvolvimento , Especificidade da Espécie
14.
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
15.
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
16.
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
17.
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
18.
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
19.
BMC Genomics ; 20(1): 448, 2019 Jun 03.
Artigo em Inglês | MEDLINE | ID: mdl-31159730

RESUMO

BACKGROUND: The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although an integrated analysis of these collections in a global diversity perspective has not been possible. In this study, a sample of Indian collections together with a selection of world-wide cultivars to analyze the genetic diversity structure based on Genotype by Sequence data. RESULTS: A set of 6158 informative Single Nucleotide Polymorphism (SNP) in 175 melon accessions was generated. Melon germplasm could be classified into six major groups, in concordance with horticultural groups. Indian group was in the center of the diversity plot, with the highest genetic diversity. No strict genetic differentiation between wild and cultivated accessions was appreciated in this group. Genomic regions likely involved in the process of diversification were also found. Interestingly, some SNPs differentiating inodorus and cantalupensis groups are linked to Quantitiative Trait Loci involved in ripening behavior (a major characteristic that differentiate those groups). Linkage disequilibrium was found to be low (17 kb), with more rapid decay in euchromatic (8 kb) than heterochromatic (30 kb) regions, demonstrating that recombination events do occur within heterochromatn, although at lower frequency than in euchromatin. Concomitantly, haplotype blocks were relatively small (59 kb). Some of those haplotype blocks were found fixed in different melon groups, being therefore candidate regions that are involved in the diversification of melon cultivars. CONCLUSIONS: The results support the hypothesis that India is the primary center of diversity of melon, Occidental and Far-East cultivars have been developed by divergent selection. Indian germplasm is genetically distinct from African germplasm, supporting independent domestication events. The current set of traditional Indian accessions may be considered as a population rather than a standard collection of fixed landraces with high intercrossing between cultivated and wild melons.


Assuntos
Cucurbitaceae/classificação , Cucurbitaceae/genética , DNA de Plantas/genética , Polimorfismo de Nucleotídeo Único , Sementes/genética , Análise de Sequência de DNA/métodos , Genoma de Planta , Genótipo , Índia , Desequilíbrio de Ligação
20.
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
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