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1.
Sci Rep ; 14(1): 15755, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38977809

ABSTRACT

Guava (Psidium guajava L.) is a semi-domesticated fruit tree of moderate importance in the Neotropics, utilized for millennia due to its nutritional and medicinal benefits, but its origin of domestication remains unknown. In this study, we examine genetic diversity and population structure in 215 plants from 11 countries in Mesoamerica, the Andes, and Amazonia using 25 nuclear microsatellite loci to propose an origin of domestication. Genetic analyses reveal one gene pool in Mesoamerica (Mexico) and four in South America (Brazilian Amazonia, Peruvian Amazonia and Andes, and Colombia), indicating greater differentiation among localities, possibly due to isolation between guava populations, particularly in the Amazonian and Andean regions. Moreover, Mesoamerican populations show high genetic diversity, with moderate genetic structure due to gene flow from northern South American populations. Dispersal scenarios suggest that Brazilian Amazonia is the probable origin of guava domestication, spreading from there to the Peruvian Andes, northern South America, Central America, and Mexico. These findings present the first evidence of guava domestication in the Americas, contributing to a deeper understanding of its evolutionary history.


Subject(s)
Domestication , Genetic Variation , Microsatellite Repeats , Psidium , Psidium/genetics , Microsatellite Repeats/genetics , South America , Gene Flow , Genetics, Population , Brazil
2.
Sci Rep ; 14(1): 9811, 2024 04 29.
Article in English | MEDLINE | ID: mdl-38684872

ABSTRACT

Most research on trinucleotide repeats (TRs) focuses on human diseases, with few on the impact of TR expansions on plant gene expression. This work investigates TRs' effect on global gene expression in Psidium guajava L., a plant species with widespread distribution and significant relevance in the food, pharmacology, and economics sectors. We analyzed TR-containing coding sequences in 1,107 transcripts from 2,256 genes across root, shoot, young leaf, old leaf, and flower bud tissues of the Brazilian guava cultivars Cortibel RM and Paluma. Structural analysis revealed TR sequences with small repeat numbers (5-9) starting with cytosine or guanine or containing these bases. Functional annotation indicated TR-containing genes' involvement in cellular structures and processes (especially cell membranes and signal recognition), stress response, and resistance. Gene expression analysis showed significant variation, with a subset of highly expressed genes in both cultivars. Differential expression highlighted numerous down-regulated genes in Cortibel RM tissues, but not in Paluma, suggesting interplay between tissues and cultivars. Among 72 differentially expressed genes with TRs, 24 form miRNAs, 13 encode transcription factors, and 11 are associated with transposable elements. In addition, a set of 20 SSR-annotated, transcribed, and differentially expressed genes with TRs was selected as phenotypic markers for Psidium guajava and, potentially for closely related species as well.


Subject(s)
Gene Expression Regulation, Plant , Microsatellite Repeats , Psidium , Psidium/genetics , Microsatellite Repeats/genetics , Trinucleotide Repeats/genetics , Gene Expression Profiling , Plant Leaves/genetics , Plant Leaves/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism
3.
Sci Rep ; 14(1): 1446, 2024 01 16.
Article in English | MEDLINE | ID: mdl-38228714

ABSTRACT

Peroxidases (PRXs) play multifaceted roles in plant growth, development, and stress responses. Here, we present a comprehensive analysis of the PRX gene family in guava, a globally significant fruit. In the guava genome, we identified 37 PRX genes, a number lower than that of Arabidopsis, suggesting a distinctive gene family expansion pattern. Phylogenetic analysis unveiled close relationships with Arabidopsis PRXs, with 12 PgPRX genes forming ortholog pairs, indicating a specific expansion pattern. Predictions placed most PRX proteins in the chloroplast and extracellular regions. Structural analysis of PgPRX proteins revealed commonalities in domain structures and motif organization. Synteny analysis underscored the dynamic role of segmental duplication in the evolution of guava's PRX genes. We explored the dynamic expression of PgPRX genes across guava tissues, exposing functional diversity. Furthermore, we examined changes in peroxidase levels and gene expressions during postharvest fruit storage, providing insights for preserving fruit quality. This study offers an initial genome-wide identification and characterization of Class III peroxidases in guava, laying the foundation for future functional analyses.


Subject(s)
Arabidopsis , Psidium , Psidium/genetics , Arabidopsis/genetics , Phylogeny , Genomics , Peroxidases/genetics , Multigene Family , Plant Proteins/genetics , Plant Proteins/chemistry , Gene Expression Regulation, Plant , Genome, Plant
4.
Sci Rep ; 14(1): 574, 2024 01 05.
Article in English | MEDLINE | ID: mdl-38182724

ABSTRACT

Psidium guajava L., a fruit crop belonging to the Myrtaceae family, is highly valued for its nutritional and medicinal properties. The family exhibits a diverse chemical profile of essential oils and serves as a valuable resource due to its ecological interactions, adaptability, and dispersal capacity. The Myrtaceae family has been extensively studied for its terpenoids. Genetic studies have focused on foliar terpene yield in species from the Eucalypteae and Melaleucaceae tribes. To understand the evolutionary trends in guava breeding, this study predicted terpene synthase genes (TPS) from different cultivars. Through this analysis, 43 full-length TPS genes were identified, and approximately 77% of them exhibited relative expression in at least one of the five investigated plant tissues (root, leaf, bud, flower, and fruit) of two guava cultivars. We identified intra-species variation in the terpene profile and single nucleotide polymorphisms (SNPs) in twelve TPS genes, resulting in the clustering of 62 genotypes according to their essential oil chemotypes. The high concentration of sesquiterpenes is supported by the higher number of TPS-a genes and their expression. The expansion for TPS sub-families in P. guajava occurred after the expansion of other rosids species. Providing insight into the origin of structural diversification and expansion in each clade of the TPS gene family within Myrtaceae. This study can provide insights into the diversity of genes for specialized metabolites such as terpenes, and their regulation, which can lead to a diverse chemotype of essential oil in different tissues and genotypes. This suggests a mode of enzymatic evolution that could lead to high sesquiterpene production, act as a chemical defense and contribute to the adaptive capacity of this species to different habitats.


Subject(s)
Myrtaceae , Oils, Volatile , Psidium , Psidium/genetics , Plant Breeding , Terpenes
5.
Genes (Basel) ; 14(11)2023 Oct 31.
Article in English | MEDLINE | ID: mdl-38002972

ABSTRACT

The guava (Psidium guajava L.) is a climacteric fruit with an accelerated post-harvest overripening. miRNAs are small RNA sequences that function as gene regulators in eukaryotes and are essential for their survival and development. In this study, miRNA libraries were constructed, sequenced and analyzed from the breaker and ripe stages of guava fruit cv. Siglo XXI. One hundred and seventy-four mature miRNA sequences from 28 miRNA families were identified. The taxonomic distribution of the guava miRNAs showed a high level of conservation among the dicotyledonous plants. Most of the predicted miRNA target genes were transcription factors and genes involved in the metabolism of phytohormones such as abscisic acid, auxins, and ethylene, as revealed through an ontology enrichment analysis. The miRNA families miR168, miR169, miR396, miR397, and miR482 were classified as being directly associated with maturation, whereas the miRNA families miR160, miR165, miR167, miR3930, miR395, miR398, and miR535 were classified as being indirectly associated. With this study, we intended to increase our knowledge and understanding of the regulatory process involved in the ripening process, thereby providing valuable information for future research on the ripening of guava fruit.


Subject(s)
MicroRNAs , Psidium , Humans , MicroRNAs/genetics , MicroRNAs/metabolism , Psidium/genetics , Psidium/metabolism , Fruit , Gene Expression Regulation, Plant , Plants, Genetically Modified/genetics
6.
An Acad Bras Cienc ; 95(4): e20190120, 2023.
Article in English | MEDLINE | ID: mdl-37729294

ABSTRACT

The introgression of M. enterolobii resistance-related genes in guava breeding programs can be compromised by incompatibility among Psidium species. This study aimed to evaluate the female parent preference and genetic diversity of Psidium interspecific hybrids using morphoagronomic traits and resistance to M. enterolobii. There were evaluated cross successes and germination from crosses between accesses of P. cattleyanum, P. guineense and P. guajava and the genetic diversity by Ward-MLM method of hybrids according to descriptors developed for the genus. Crosses were more successful when P. cattleyanum was the female parent. Germination was more successful in crosses involving P. cattleyanum and P. guajava. Four groups were formed. The group IV clustered the most resistant genotypes, composed by genotypes of P. cattleyanum x P. guineense, while the group II was the most susceptible. The groups I and III grouped some genotypes of P. cattleyanum x P. guajava with low levels of susceptibility. There are preferences of female parent species among crosses. Some individuals of groups I and III can be used as source of resistance genes for the breeding program, due the presence of favorable alleles inherited from guava parent. The high susceptibility leads to reduction in root development.


Subject(s)
Psidium , Tylenchoidea , Humans , Female , Animals , Psidium/genetics , Plant Breeding , Phenotype , Genetic Variation/genetics
7.
Sci Rep ; 13(1): 3930, 2023 03 09.
Article in English | MEDLINE | ID: mdl-36894661

ABSTRACT

Terpenoids are essential for plant growth, development, defense, and adaptation mechanisms. Psidium cattleyanum (Myrtaceae) is a fleshy fruit tree species endemics from Atlantic Forest, known for its pleasant fragrance and sweet taste, attributed to terpenoids in its leaves and fruits. In this study, we conducted genome-wide identification, evolutionary and expression analyses of the terpene synthase gene (TPS) family in P. cattleyanum red guava (var. cattleyanum), and yellow guava (var. lucidum Hort.) morphotypes. We identified 32 full-length TPS in red guava (RedTPS) and 30 in yellow guava (YlwTPS). We showed different expression patterns of TPS paralogous in the two morphotypes, suggesting the existence of distinct gene regulation mechanisms and their influence on the final essential oil content in both morphotypes. Moreover, the oil profile of red guava was dominated by 1,8-cineole and linalool and yellow guava was enriched in α-pinene, coincident in proportion to TPS-b1 genes, which encode enzymes that produce cyclic monoterpenes, suggesting a lineage-specific subfamily expansion of this family. Finally, we identified amino acid residues near the catalytic center and functional areas under positive selection. Our findings provide valuable insights into the terpene biosynthesis in a Neotropical Myrtaceae species and their potential involvement in adaptation mechanisms.


Subject(s)
Myrtaceae , Psidium , Fruit/chemistry , Myrtaceae/metabolism , Psidium/genetics , Psidium/chemistry , Terpenes/metabolism , Genome, Plant
8.
Sci Rep ; 12(1): 22367, 2022 12 26.
Article in English | MEDLINE | ID: mdl-36572739

ABSTRACT

Crossing and developing inbred lines have been promising options for guava breeding programs. The purpose of this study was to evaluate the genetic divergence among genotypes of S1 inbred guava families by means of the Gower's technique and the Ward-MLM methodology, to verify the correlation and relative contribution of traits, as well as to identify descriptors with minimum efficiency for this species. The experiment was implemented at the Estação Experimental da Ilha Barra do Pomba, in the municipality of Itaocara, RJ, Brazil. A randomized block design with 18 inbred families, three replicates, and ten plants per plot was used for the experimental design. After 19 months from the planting of the experiment, the 61 earliest and most productive genotypes (individual plants) were evaluated. For this purpose, 29 descriptors were evaluated, of which fifteen were qualitative and fourteen, quantitative. The characteristics required to obtain the distance matrix were analyzed based on the Gower algorithm, and a comparative cluster between the dendrograms of the morphoagronomic variables was achieved from this matrix. Lastly, the Ward-MLM procedure was applied to form the clusters of inbred families. By using all 29 descriptors, greater efficiency was achieved in cluster discrimination. Hence, according to the results identified, it is not possible to indicate minimum descriptors for the culture. Using the Ward-MLM method, the descriptors that most contributed to the divergence among the genotypes were fruit flesh mass, fruit weight, fruit diameter, fruit flesh thickness, fruit placental mass, and fruit length. The most divergent genotypes can be recommended for further crosses or self-pollinations to develop new lines in the guava breeding program of UENF.


Subject(s)
Genetic Variation , Psidium , Female , Humans , Pregnancy , Psidium/genetics , Plant Breeding/methods , Placenta , Genetic Drift , Fruit/genetics
9.
PLoS One ; 17(11): e0273959, 2022.
Article in English | MEDLINE | ID: mdl-36322533

ABSTRACT

Tropical fruit tree species constitute a yet untapped supply of outstanding diversity of taste and nutritional value, barely developed from the genetics standpoint, with scarce or no genomic resources to tackle the challenges arising in modern breeding practice. We generated a de novo genome assembly of the Psidium guajava, the super fruit "apple of the tropics", and successfully transferred 14,268 SNP probesets from Eucalyptus to Psidium at the nucleotide level, to detect genomic loci linked to resistance to the root knot nematode (RKN) Meloidogyne enterolobii derived from the wild relative P. guineense. Significantly associated loci with resistance across alternative analytical frameworks, were detected at two SNPs on chromosome 3 in a pseudo-assembly of Psidium guajava genome built using a syntenic path approach with the Eucalyptus grandis genome to determine the order and orientation of the contigs. The P. guineense-derived resistance response to RKN and disease onset is conceivably triggered by mineral nutrients and phytohormone homeostasis or signaling with the involvement of the miRNA pathway. Hotspots of mapped resistance quantitative trait loci and functional annotation in the same genomic region of Eucalyptus provide further indirect support to our results, highlighting the evolutionary conservation of genomes across genera of Myrtaceae in the adaptation to pathogens. Marker assisted introgression of the resistance loci mapped should accelerate the development of improved guava cultivars and hybrid rootstocks.


Subject(s)
Eucalyptus , Myrtaceae , Psidium , Tylenchoidea , Animals , Tylenchoidea/genetics , Psidium/genetics , Eucalyptus/genetics , Myrtaceae/genetics , Polymorphism, Single Nucleotide , Plant Breeding , Genomics
10.
Biochem Genet ; 60(6): 2503-2514, 2022 Dec.
Article in English | MEDLINE | ID: mdl-35577994

ABSTRACT

The Atlantic Forest is one of the most threatened biomes in the world. Here, we use a common set of microsatellite markers to assess the genetic diversity and population structure of three species from the genus Psidium (P. guajava, P. macahense, and P. guineense), located in a disturbed environment of the Atlantic Forest, the restinga, in Espírito Santo, Brazil. Psidium guajava populations presented the highest number of alleles (95) followed by P. guineense (81) and P. macahense (68). The genetic variability was high (P. guajava = 0.71; P. guineense = 0.74; P. macahense = 0.63), with greater variation within populations (72 to 84%) than among populations (15 to 27%), reflecting elevated values of genetic differentiation (P. guajava, FST: 0.15; P. macahense, ØST: 0.27; P. guineense, ØST: 0.21). The populations were clustered into two main groups and considered moderately structured. This is the first report of genetic studies and evidence of polyploidy to P. macahense. Our results may provide information that can be used in management and conservation strategies, to preserve the diversity of Psidium populations.


Subject(s)
Psidium , Psidium/genetics , Ecosystem , Brazil , Forests , Polyploidy , Genetic Variation
11.
Ann Bot ; 129(4): 367-388, 2022 03 23.
Article in English | MEDLINE | ID: mdl-35034117

ABSTRACT

BACKGROUND AND AIMS: Psidium is the fourthth largest genus of Myrtaceae in the Neotropics. Psidium guajava is widely cultivated in the tropics for its edible fruit. It is commercially under threat due to the disease guava decline. Psidium cattleyanum is one of the 100 most invasive organisms in the world. Knowledge of the phylogenetic relationships within Psidium is poor. We aim to provide a review of the biology, morphology and ecology of Psidium, a phylogenetic tree, an infrageneric classification and a list of species. METHODS: Morphological and geographic data were obtained by studying Psidium in herbaria and in the field between 1988 and 2020. Forty-six herbaria were visited personally. A database of approx. 6000 specimens was constructed, and the literature was reviewed. Thirty species (about a third of the species in the genus) were sampled for molecular phylogenetic inference. Two chloroplast (psbA-trnH and ndhF) and two nuclear (external transcribed spacer and internal transcribed spacer) regions were targeted. Phylogenetic trees were constructed using maximum likelihood (ML; RaxML) and Bayesian inference (BI; MrBayes). KEY RESULTS: Psidium is a monophyletic genus with four major clades recognized as sections. Section Psidium (ten species), to which P. guajava belongs, is sister to the rest of the genus; it is widespread across the Neotropics. Section Obversifolia (six species; restricted to the Brazilian Atlantic Forest), which includes P. cattleyanum, is sister to the innermost clade composed of sister sections Apertiflora (31 species; widespread but most diverse in the Brazilian Atlantic Forest) + Mitranthes (26 species; widespread in dry forests and probably diverse in the Caribbean). Characters associated with diversification within Psidium are discussed. CONCLUSIONS: Research on pre-foliation, colleters, leaf anatomy, leaf physiology, staminal development, placentation and germination associated with the anatomy of the opercular plug is desirable. Studies are biased towards sections Psidium and Obversifolia, with other sections poorly known.


Subject(s)
Myrtaceae , Psidium , Bayes Theorem , Forests , Myrtaceae/anatomy & histology , Myrtaceae/genetics , Phylogeny , Psidium/genetics
12.
PLoS One ; 16(7): e0255245, 2021.
Article in English | MEDLINE | ID: mdl-34310664

ABSTRACT

Acquiring high-quality RNA in sufficient amounts is crucial in plant molecular biology and genetic studies. Several methods for RNA extraction from plants are available in the literature, mainly due to the great biochemical diversity present in each species and tissue, which can complicate or prevent the extraction. Psidium guajava (Myrtaceae family) is a perennial fruit tree of medicinal and economic value; nevertheless, only a few molecular studies are available for the species. One reason is the difficulty in obtaining RNA due to the content of the samples, which are rich in polyphenols, polysaccharides, and secondary metabolites. Furthermore, there are few studies available for the isolation of RNA from guava or Psidium samples, which hampers advances in the study of the genus. Here, quality and yields of RNA isolates were compared using six extraction protocols: two protocols based on the application of cetyltrimethylammonium bromide (CTAB) lysis buffer, one protocol which uses the TRIzol reagent, one which applies guanidine thiocyanate lysis buffer followed by organic phase extraction, and two commercial kits (PureLink RNA Mini Kit and RNeasy Plant Mini Kit). The CTAB-based method provided the highest RNA yields and quality for five different tissues (flower bud, immature leaf, young leaf, mature leaf, and root), genotypes, and stress conditions. For the most efficient protocol, the average yield of RNA from guava leaves was 203.06 µg/g of tissue, and the A260/A280 and A260/A230 ratios were 2.1 and 2.2, respectively. RT-qPCR analysis demonstrated that the purity of the samples was sufficient for molecular biology experiments. CTAB-based methods for RNA isolation were found to be the most efficient, providing the highest RNA yields and quality for tissues from P. guajava. Additionally, they were compatible for downstream RNA-based applications, besides being simple and cost-effective.


Subject(s)
Cetrimonium/chemistry , Psidium/genetics , RNA, Plant/isolation & purification , Flowers/genetics , Genotype , Guanidines/chemistry , Phenols/chemistry , Plant Leaves/genetics , Plant Roots/genetics , Polyphenols/chemistry , Polysaccharides/chemistry , RNA, Plant/metabolism , Real-Time Polymerase Chain Reaction
13.
Biochem Genet ; 59(1): 219-234, 2021 Feb.
Article in English | MEDLINE | ID: mdl-32980958

ABSTRACT

Polyploidy is a phenomenon that alters the genetic diversity of populations and has been reported as one of the most important evolutionary forces for plant diversification. The Psidium cattleyanum complex comprises a group of wild populations with several ploidy levels reported in the literature. The multiple cytotypes, associated with its wide distribution area, make this species a potential key model for understanding evolutionary processes related to polyploidization. In this study, we isolated and characterized nuclear microsatellite markers of P. cattleyanum and tested their transferability to other nine species of the genus. We performed a preliminary analysis of genetic diversity and population structure in three populations of P. cattleyanum. The three populations analyzed had different chromosome numbers, being polyploid cytotypes (2n = 6x = 66, 2n = 7x = 77 and 2n = 8x = 88). We designed 46 primer pairs and successfully amplified 37 markers, from which the 10 best were selected for analysis. Considering both the PIC and DP values, most of markers were highly informative. The new SSR markers were used to assess the levels of genetic diversity of the populations and detected one population with predominance of sexual reproduction. DAPC analysis pointed the formation of three groups, which corresponded to the populations analyzed. The markers were successfully amplified in related species, with some species presenting 80% transferability. By producing this panel of polymorphic microsatellites, we contribute to the understanding evolution in groups of natural polyploids for future studies.


Subject(s)
Genes, Plant , Genetic Variation , Genetics, Population , Microsatellite Repeats , Ploidies , Psidium/genetics , DNA, Plant/genetics , Gene Library , Genetic Markers , Introduced Species , Polymorphism, Genetic , Polyploidy , Species Specificity
14.
J Sci Food Agric ; 101(7): 2767-2778, 2021 May.
Article in English | MEDLINE | ID: mdl-33140438

ABSTRACT

BACKGROUND: Dietary intervention is an important approach to improve intestinal function of weaned piglets. Phytogenic and herbal products have received increasing attention as in-feed antibiotic alternatives. This study investigated the chemical composition of guava leaf extract (GE) by ultrahigh-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Meanwhile, we investigated the effects of dietary supplementation with GE on diarrhea in relation to immune responses and intestinal health in weaned piglets challenged by enterotoxigenic Escherichia coli (ETEC). RESULTS: In total, 323 characterized compounds, which including 91 phenolic compounds and 232 other compounds were identified. Animal experiment results showed that the supplementation of 50-200 mg kg-1 of GE in the diet could reduce diarrhea incidence, increase activities of superoxide dismutase, glutathione peroxidase and total anti-oxidant capacity in the serum (P < 0.05), decrease the levels of interleukin 1ß, interleukin 6 and tumor necrosis factor α in the serum or jejunum mucosa (P < 0.05), and increase villus height and villus height to crypt depth ratio (P < 0.05) in the jejuna of piglets challenged by oral ETEC compared with negative control group (NC). Meanwhile, diet supplementation with 50-200 mg kg-1 GE reduced the levels of D-lactate, endothelin-1 and diamine oxidase in the serum, and increased the expression of zonula occludens-1, Claudin-1, Occludin and Na+ /H+ exchanger 3 (P < 0.05) in the jejuna mucosa of piglets challenged by ETEC compared with the NC. CONCLUSIONS: These results suggested that GE could attenuate diarrhea and improve intestinal barrier function of piglets challenged by ETEC. © 2020 Society of Chemical Industry.


Subject(s)
Diarrhea/veterinary , Intestinal Mucosa/metabolism , Plant Extracts/metabolism , Plant Leaves/metabolism , Psidium/chemistry , Swine Diseases/prevention & control , Animal Feed/analysis , Animals , Chromatography, Liquid , Diarrhea/metabolism , Diarrhea/microbiology , Diarrhea/prevention & control , Diet/veterinary , Enterotoxigenic Escherichia coli/physiology , Intestinal Mucosa/growth & development , Intestinal Mucosa/microbiology , Plant Extracts/chemistry , Plant Leaves/chemistry , Psidium/genetics , Psidium/metabolism , Swine/growth & development , Swine/metabolism , Swine Diseases/metabolism , Swine Diseases/microbiology , Tandem Mass Spectrometry , Weaning
15.
Plant Biotechnol J ; 19(4): 717-730, 2021 04.
Article in English | MEDLINE | ID: mdl-33098334

ABSTRACT

Guava (Psidium guajava) is an important fleshy-fruited tree of the Myrtaceae family that is widely cultivated in tropical and subtropical areas of the world and has attracted considerable attention for the richness of ascorbic acid in its fruits. However, studies on the evolution and genetic breeding potential of guava are hindered by the lack of a reference genome. Here, we present a chromosome-level genomic assembly of guava using PacBio sequencing and Hi-C technology. We found that the genome assembly size was 443.8 Mb with a contig N50 of ~15.8 Mb. We annotated a total of 25 601 genes and 193.2 Mb of repetitive sequences for this genome. Comparative genomic analysis revealed that guava has undergone a recent whole-genome duplication (WGD) event shared by all species in Myrtaceae. In addition, through metabolic analysis, we determined that the L-galactose pathway plays a major role in ascorbic acid biosynthesis in guava fruits. Moreover, the softening of fruits of guava may result from both starch and cell wall degradation according to analyses of gene expression profiles and positively selected genes. Our data provide a foundational resource to support molecular breeding of guava and represent new insights into the evolution of soft, fleshy fruits in Myrtaceae.


Subject(s)
Psidium , Ascorbic Acid , Chromosomes , Fruit/genetics , Plant Breeding , Psidium/genetics
16.
PLoS One ; 15(8): e0237538, 2020.
Article in English | MEDLINE | ID: mdl-32804981

ABSTRACT

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


Subject(s)
Microsatellite Repeats , Psidium/classification , Sequence Analysis, DNA/methods , DNA, Plant/genetics , Evolution, Molecular , Gene Frequency , Genetic Variation , Genetics, Population , Genomic Library , Psidium/genetics , Species Specificity
17.
BMC Genomics ; 21(1): 484, 2020 Jul 15.
Article in English | MEDLINE | ID: mdl-32669108

ABSTRACT

BACKGROUND: Guava (Psidium guajava L.) is an important fruit crop of tropical and subtropical areas of the world. Genomics resources in guava are scanty. RNA-Seq based tissue specific expressed genomic information, de novo transcriptome assembly, functional annotation and differential expression among contrasting genotypes has a potential to set the stage for the functional genomics for traits of commerce like colored flesh and apple color peel. RESULTS: Development of fruit from flower involves orchestration of myriad molecular switches. We did comparative transcriptome sequencing on leaf, flower and fruit tissues of cv. Allahabad Safeda to understand important genes and pathways controlling fruit development. Tissue specific RNA sequencing and de novo transcriptome assembly using Trinity pipeline provided us the first reference transcriptome for guava consisting of 84,206 genes comprising 279,792 total transcripts with a N50 of 3603 bp. Blast2GO assigned annotation to 116,629 transcripts and PFam based HMM profile annotated 140,061 transcripts with protein domains. Differential expression with EdgeR identified 3033 genes in Allahabad Safeda tissues. Mapping the differentially expressed transcripts over molecular pathways indicate significant Ethylene and Abscisic acid hormonal changes and secondary metabolites, carbohydrate metabolism and fruit softening related gene transcripts during fruit development, maturation and ripening. Differential expression analysis among colored tissue comparisons in 3 cultivars Allahabad Safeda, Punjab Pink and Apple Color identified 68 candidate genes that might be controlling color development in guava fruit. Comparisons of red vs green peel in Apple Color, white pulp vs red pulp in Punjab Pink and fruit maturation vs ripening in non-colored Allahabad Safeda indicates up-regulation of ethylene biosynthesis accompanied to secondary metabolism like phenylpropanoid and monolignol pathways. CONCLUSIONS: Benchmarking Universal Single-Copy Orthologs analysis of de novo transcriptome of guava with eudicots identified 93.7% complete BUSCO genes. In silico differential gene expression among tissue types of Allahabad Safeda and validation of candidate genes with qRT-PCR in contrasting color genotypes promises the utility of this first guava transcriptome for its potential of tapping the genetic elements from germplasm collections for enhancing fruit traits.


Subject(s)
Psidium/genetics , Transcriptome , Color , Flowers/genetics , Flowers/metabolism , Fruit/genetics , Fruit/growth & development , Fruit/metabolism , Genes, Plant , Genotype , Metabolic Networks and Pathways/genetics , Plant Leaves/genetics , Plant Leaves/metabolism , Psidium/growth & development , Psidium/metabolism , RNA-Seq , Secondary Metabolism/genetics , Up-Regulation
18.
Sci Rep ; 10(1): 1999, 2020 02 06.
Article in English | MEDLINE | ID: mdl-32029823

ABSTRACT

Perennial breeding species demand substantial investment in various resources, mainly the required time to obtain adult and productive plants. Estimating several genetic parameters in these species, in a more confidence way, means saving resources when selecting a new genotype. A model using the Bayesian approach was compared with the frequentist methodology for selecting superior genotypes. A population of 17 families of full-siblings of guava tree was evaluated, and the yield, fruit mass, and pulp mass were measured. The Bayesian methodology suggest more accurate estimates of variance components, as well as better results to fit of model in a cross-validation. Proper priori for Bayesian model is very important to convergency of chains, mainly for small datasets. Even with poor priori, Bayesian was better than frequentist approach.


Subject(s)
Models, Genetic , Plant Breeding/methods , Psidium/genetics , Selection, Genetic , Bayes Theorem , Brazil , Datasets as Topic , Fruit , Genotype
19.
PLoS One ; 14(3): e0203737, 2019.
Article in English | MEDLINE | ID: mdl-30865637

ABSTRACT

The threat of invasive plant species in island populations prompts the need to better understand their population genetics and dynamics. In the Galapagos islands, this is exemplified by the introduced guava (Psidium guajava), considered one of the greatest threats to the local biodiversity due to its effective spread in the archipelago and its ability to outcompete endemic species. To better understand its history and genetics, we analyzed individuals from three inhabited islands in the Galapagos archipelago with 11 SSR markers. Our results reveal similar genetic diversity between islands, and the populations appear to be distinct: the islands of San Cristobal and Isabela are genetically different while the population of Santa Cruz is a mixture from both. Additional evidence for genetic bottlenecks and the inference of introduction events suggests an original introduction of the species in San Cristobal, from where it was later introduced to Isabela, and finally into Santa Cruz. Alternatively, a second introduction in Isabela might have occurred. These results are contrasted with the historical record, providing a first overview of the history of P. guajava in the Galapagos islands and its current population dynamics.


Subject(s)
Genetic Variation , Genetics, Population , Genome, Plant , Introduced Species , Population Dynamics , Psidium/genetics , Biodiversity , DNA, Plant/analysis , DNA, Plant/genetics , Ecosystem , Ecuador
20.
Phytochemistry ; 153: 129-137, 2018 Sep.
Article in English | MEDLINE | ID: mdl-29913321

ABSTRACT

The essential oil of Psidium guajava L. has been studied for pharmacological and industrial purposes, without considering the plant's genotype regarding the heterogeneity of its composition. The present study aimed to characterize the chemotype diversity of the essential oil extracted from the leaves of 22 genotypes of P. guajava grown in two different environments in the state of Espírito Santo, Brazil, and to identify the different chemical markers present in these plants. Essential oil from the leaves of the P. guajava genotypes was extracted by hydrodistillation, and its chemical composition was analyzed by gas chromatography-flame ionization detection (GC-FID) and gas chromatography-mass spectrometry (GC-MS). Thirty-three compounds were identified, comprising 87.5-99.0% of the total composition, with a prevalence of sesquiterpenes in all samples. The major compounds identified consisted of (E)-trans-Caryophyllene, α-Humulene, trans-Nerolidol, ß-Bisabolene, ß-Bisabolol, and Hinesol, the first of which was identified as a possible chemical marker for the species. Multivariate factor analysis of the chemical composition of P. guajava oil identified three chemotypes: Commercial - PAL, SEC, PS, PET, C7, C11, and C17MI, characterized by high levels of ß-Selinene, α-Selinene, Hinesol, and 14-hydroxy-epi-(E)-caryophyllene, with ß-Selinene and α-Selinene as the chemical markers; C10 and C13, exhibiting high levels of Elemol, trans-Nerolidol, trans-ß-Eudesmol, and (2Z, 6Z)-Farnesol, which were indicated as chemical markers, and Cortibel - C1, C2, C3, C4, C5, C6, C8, C9, C12, C14, C15, C16, C17LI, which retained high levels of α-Cedrene, cis-α-Bergamotene, α-Humulene, Humulene epoxide, epi-α-Cadinol, ß-Bisabolol, and α-Bisabolol, with ß-Bisabolol and α-Bisabolol as the chemical markers. The use of guava genotypes with different chemotypes, that are agronomically favorable to fruit production and essential oil exploitation adds value to the crop and renders it more sustainable. Given guava crops produce large amounts of leaf biomass, resulting from successive prunings, the extraction of their essential oil, which retains commercially valuable compounds, can be feasible.


Subject(s)
Oils, Volatile/isolation & purification , Phytochemicals/isolation & purification , Plant Leaves/chemistry , Psidium/chemistry , Genotype , Oils, Volatile/chemistry , Phytochemicals/chemistry , Psidium/genetics
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