A Systematic Approach to Species–Level Identification of Chile Pepper (Capsicum spp.) Seeds: Establishing the Groundwork for Tracking the Domestication and Movement of Chile Peppers through the Americas and Beyond

Abstract Chile peppers (Capsicum spp.) are among the most important vegetable crops in the world due to their health-related, economic, and industrial uses. In recent years, quantitative trait loci (QTL) mapping approaches have been widely implemented to identify genomic regions affecting variation for different traits for marker-assisted selection (MAS) in peppers. Meta-QTL analysis for different traits in Capsicum remains lacking, and therefore it would be necessary to re-evaluate identified QTL for a more precise MAS for genetic improvement. We report the first known meta-QTL analysis for diverse traits in the chile pepper QTLome. A literature survey using 29 published linkage mapping studies identified 766 individual QTL from five different trait classes. A total of 311 QTL were projected into a consensus map. Meta-analysis identified 30 meta-QTL regions distributed across the 12 chromosomes of Capsicum. MQTL5.1 and MQTL5.2 related to Phytophthora capsici fruit and root rot resistance were delimited to < 1.0 cM confidence intervals in chromosome P5. Candidate gene analysis for the flanking sequences for the P5 meta-QTL revealed biological functions related to DNA repair and transcription regulation. Moreover, epigenetic mechanisms such as histone and RNA methylation and demethylation were predicted, indicating the potential role of epigenetics for P. capsici resistance. Allele specific SNP markers for the meta-QTL will be developed and validated using different breeding populations of Capsicum for MAS of P. capsici resistant lines. Altogether, results from meta-QTL analysis for chile pepper QTLome rendered further insights into the genetic architecture of different traits for this valuable horticultural crop.

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Genetic Architecture of Chile Pepper (Capsicum spp.) QTLome Revealed Using Meta-QTL Analysis

Horticulturae ◽

10.3390/horticulturae7080227 ◽

2021 ◽

Vol 7 (8) ◽

pp. 227

Author(s):

Dennis N. Lozada ◽

Madelin Whelpley ◽

Andrea Acuña-Galindo

Keyword(s):

Qtl Analysis ◽

Genetic Architecture ◽

Meta Analysis ◽

Phytophthora Capsici ◽

Chile Pepper ◽

Resistant Lines ◽

Capsicum Spp ◽

Allele Specific ◽

Chile Peppers ◽

Genomic Regions

In recent years, quantitative trait loci (QTL) mapping approaches have been widely implemented to identify genomic regions affecting variation for different traits for marker-assisted selection (MAS). Meta-QTL analysis for different traits in chile peppers (Capsicum spp.) remains lacking, and therefore it would be necessary to re-evaluate identified QTL for a more precise MAS for genetic improvement. We report the first known meta-QTL analysis for diverse traits in the chile pepper QTLome. A literature survey using 29 published linkage mapping studies identified 766 individual QTL from five different trait classes. A total of 311 QTL were projected into a consensus map. Meta-analysis identified 30 meta-QTL regions distributed across the 12 chromosomes of Capsicum. MQTL5.1 and MQTL5.2 related to Phytophthora capsici fruit and root rot resistance were delimited to < 1.0 cM confidence intervals in chromosome P5. Candidate gene analysis for the P5 meta-QTL revealed functions related to histone methylation and demethylation, indicating the potential role of epigenetics for P. capsici resistance. Allele-specific markers for the meta-QTL will be developed and validated for MAS of P. capsici resistant lines. Altogether, results from meta-QTL analysis for chile pepper QTLome rendered further insights into the genetic architecture of different traits for this valuable horticultural crop.

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First Report of a Gall Midge Species (Diptera: Cecidomyiidae) Associated With Pistachios

Journal of Integrated Pest Management ◽

10.1093/jipm/pmaa022 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Farshid O Sirjani ◽

Edwin E Lewis

Keyword(s):

Gall Midge ◽

Species Level ◽

Plant Tissues ◽

First Report ◽

Branch Dieback ◽

First Time ◽

Level Identification

Abstract A new dipterous pest is reported, for the first time, on commercial pistachios from Sirjan, Kerman province, Iran. The genus of the insect was determined to be Resseliella Seitner (Diptera: Cecidomyiidae). Adults are light brown to brown in color and 0.8–1.5 mm in length with females, generally, slightly larger than males. Females have an elongated ovipositor, which is characteristic of the genus. Larvae are orange in color, 2–3 mm in length in the later instars, feed under bark without inducing galls, and cause branch dieback on trees of various ages. Brown to black discolorations are observed on plant tissues under bark where the larvae feed. Infestations observed on current and the previous—year’s growths, ranged from 0.5 to 1.2 cm in diameter, and all located in outer branches. Dry leaves and fruit clusters on infested branches remain attached, which may be used to recognize infestation by the gall midge. Dark-colored, sunken spots with splits on the bark located at the base of the wilted sections of the shoots also are symptoms of Resseliella sp. larval activity. Species-level identification of the gall midge is currently underway.

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Matrix-assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) as a Reliable Tool to Identify Species of Catalase-negative Gram-positive Cocci not Belonging to the Streptococcus Genus

The Open Microbiology Journal ◽

10.2174/1874285801610010202 ◽

2016 ◽

Vol 10 (1) ◽

pp. 202-208 ◽

Cited By ~ 7

Author(s):

Marisa Almuzara ◽

Claudia Barberis ◽

Viviana Rojas Velázquez ◽

Maria Soledad Ramirez ◽

Angela Famiglietti ◽

...

Keyword(s):

Extraction Methods ◽

Species Level ◽

Ionization Time ◽

Maldi Tof Ms ◽

Genus Level ◽

Maldi Tof ◽

Flight Mass Spectrometry ◽

Level Identification ◽

Gram Positive Cocci ◽

Tof Ms

Objective:To evaluate the performance of matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) by using 190 Catalase-negative Gram-Positive Cocci (GPC) clinical isolates.Methods:All isolates were identified by conventional phenotypic tests following the proposed scheme by Ruoff and Christensen and MALDI-TOF MS (Bruker Daltonics, BD, Bremen, Germany). Two different extraction methods (direct transfer formic acid method on spot and ethanol formic acid extraction method) and different cut-offs for genus/specie level identification were used. The score cut-offs recommended by the manufacturer (≥ 2.000 for species-level, 1.700 to 1.999 for genus level and <1.700 no reliable identification) and lower cut-off scores (≥1.500 for genus level, ≥ 1.700 for species-level and score <1.500 no reliable identification) were considered for identification. A minimum difference of 10% between the top and next closest score was required for a different genus or species.MALDI-TOF MS identification was considered correct when the result obtained from MS database agreed with the phenotypic identification result.When both methods gave discordant results, the 16S rDNA orsodAgenes sequencing was considered as the gold standard identification method. The results obtained by MS concordant with genes sequencing, although discordant with conventional phenotyping, were considered correct. MS results discordant with 16S orsodA identification were considered incorrect.Results:Using the score cut-offs recommended by the manufacturer, 97.37% and 81.05% were correctly identified to genus and species level, respectively. On the other hand, using lower cut-off scores for identification, 97.89% and 94.21% isolates were correctly identified to genus and species level respectively by MALDI-TOF MS and no significant differences between the results obtained with two extraction methods were obtained.Conclusion:The results obtained suggest that MALDI-TOF MS has the potential of being an accurate tool for Catalase-negative GPC identification even for those species with difficult diagnosis asHelcococcus,Abiotrophia,Granulicatella, among others. Nevertheless, expansion of the library, especially including more strains with different spectra on the same species might overcome potential “intraspecies” variability problems. Moreover, a decrease of the identification scores for species and genus-level identification must be considered since it may improve the MALDI-TOF MS accuracy.

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Assessing universality of DNA barcoding in geographically isolated selected desert medicinal species of Fabaceae and Poaceae

PeerJ ◽

10.7717/peerj.4499 ◽

2018 ◽

Vol 6 ◽

pp. e4499 ◽

Cited By ~ 1

Author(s):

Aisha Tahir ◽

Fatma Hussain ◽

Nisar Ahmed ◽

Abdolbaset Ghorbani ◽

Amer Jamil

Keyword(s):

Dna Barcoding ◽

Species Identification ◽

Phylogenetic Trees ◽

Sequence Similarity ◽

Sequence Divergence ◽

Species Level ◽

Practical Implementation ◽

Medicinal Species ◽

Level Identification ◽

Geographically Isolated

In pursuit of developing fast and accurate species-level molecular identification methods, we tested six DNA barcodes, namely ITS2, matK, rbcLa, ITS2+matK, ITS2+rbcLa, matK+rbcLa and ITS2+matK+rbcLa, for their capacity to identify frequently consumed but geographically isolated medicinal species of Fabaceae and Poaceae indigenous to the desert of Cholistan. Data were analysed by BLASTn sequence similarity, pairwise sequence divergence in TAXONDNA, and phylogenetic (neighbour-joining and maximum-likelihood trees) methods. Comparison of six barcode regions showed that ITS2 has the highest number of variable sites (209/360) for tested Fabaceae and (106/365) Poaceae species, the highest species-level identification (40%) in BLASTn procedure, distinct DNA barcoding gap, 100% correct species identification in BM and BCM functions of TAXONDNA, and clear cladding pattern with high nodal support in phylogenetic trees in both families. ITS2+matK+rbcLa followed ITS2 in its species-level identification capacity. The study was concluded with advocating the DNA barcoding as an effective tool for species identification and ITS2 as the best barcode region in identifying medicinal species of Fabaceae and Poaceae. Current research has practical implementation potential in the fields of pharmaco-vigilance, trade of medicinal plants and biodiversity conservation.

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Chile Peppers (Capsicum spp.)

Ethnobotany of Mexico - Ethnobiology ◽

10.1007/978-1-4614-6669-7_17 ◽

2016 ◽

pp. 417-437 ◽

Cited By ~ 4

Author(s):

Barbara Pickersgill

Keyword(s):

Capsicum Spp ◽

Chile Peppers

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Utility of species-level identification of Chironomus larvae in biological assessment of prairie lakes

SIL Proceedings 1922-2010 ◽

10.1080/03680770.1998.11901239 ◽

2000 ◽

Vol 27 (1) ◽

pp. 273-277

Author(s):

M. G. Butler ◽

R. L. Rezanka ◽

K. M. Giovannielli

Keyword(s):

Species Level ◽

Biological Assessment ◽

Prairie Lakes ◽

Level Identification

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Identification and broth-microdilution antifungal susceptibility testing of yeast directly from automated blood cultures

Future Microbiology ◽

10.2217/fmb-2020-0077 ◽

2020 ◽

Vol 15 (15) ◽

pp. 1453-1464

Author(s):

Sourav Das ◽

Yamini Tawde ◽

Shreya Singh ◽

Arunaloke Chakrabarti ◽

Pallab Ray ◽

...

Keyword(s):

Susceptibility Testing ◽

Antifungal Susceptibility ◽

High Sensitivity ◽

Turnaround Time ◽

Blood Cultures ◽

Species Level ◽

Robust Method ◽

Broth Microdilution ◽

Level Identification ◽

Tof Ms

Aim: To standardize MALDI-TOF-MS based identification and antifungal susceptibility (AFST) for yeasts directly from automated blood cultures to reduce turnaround time. Materials & methods: Direct-ID after lysis-centrifugation (0.5% SDS) standardized in 40 and validated in 250 yeast positive samples. Direct-AFST was standardized with fluconazole (28 samples) and evaluated (70 samples) for seven antifungals. Results: Direct-ID had a high sensitivity (97.2%) and specificity (94.3%). Correct species-level identification showed 100% in C. tropicalis, C. krusei, C. parapsilosis. Direct-AFST had a 100% categorical agreement with culture-AFST for posaconazole, anidulafungin and >90% categorical agreement for amphotericin B, voriconazole and fluconazole. Conclusion: Direct-ID and subsequent direct-AFST is a rapid and robust method to reduce the turnaround time for the diagnosis of invasive candidiasis.

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Multi-centric evaluation of the online MSI platform for the identification of cryptic and rare species of Aspergillus by MALDI-TOF

Medical Mycology ◽

10.1093/mmy/myz004 ◽

2019 ◽

Vol 57 (8) ◽

pp. 962-968 ◽

Cited By ~ 9

Author(s):

Sébastien Imbert ◽

Anne Cécile Normand ◽

Frédéric Gabriel ◽

Sophie Cassaing ◽

Christine Bonnal ◽

...

Keyword(s):

Mass Spectrometry ◽

Cryptic Species ◽

Rare Species ◽

Sensu Stricto ◽

Species Level ◽

Identification Accuracy ◽

Mass Spectrometry Identification ◽

Almost All ◽

Level Identification ◽

Section Level

Abstract The taxonomy of Aspergillus species has recently been revolutionized with the introduction of cryptic species and section concepts. However, their species-level identification in routine laboratories remains a challenge. The aim of this study was to prospectively assess the identification accuracy of cryptic species of Aspergillus in various laboratories using the mass spectrometry identification (MSI) platform, an independent and freely accessible online mass spectrometry database. Over a 12-month period, when a select set of MSI users identified cryptic species, they were contacted and requested to send the isolates to our laboratory for sequence-based identification. Sequence and MSI identification results were then compared. During the study period, 5108 Aspergillus isolates were identified using MSI including 1477 (28.9%) cryptic species. A total of 245 isolates that corresponded to 56 cryptic species and 13 sections were randomly selected for DNA sequencing confirmation. Agreement between the two methods was 99.6% at the section level and 66.1% at the species level. However, almost all discrepancies (72/83, 86.7%) were misidentifications between closely related cryptic species belonging to the same section. Fifty-one isolates from noncryptic species were also identified, thus yielding 100% and 92.2% agreement at the section and species level, respectively. Although the MSI fungus database is a reliable tool to identify Aspergillus at the section level, the database still requires adjustment to correctly identify rare or cryptic species at the species level. Nevertheless, the application properly differentiated between cryptic and sensu stricto species in the same section, thus alerting on possible specific isolate characteristics.

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