scholarly journals Automatic morphology phenotyping of tetra- and hexaploid wheat spike using computer vision methods

2021 ◽  
Vol 25 (1) ◽  
pp. 71-81
Author(s):  
A. Yu. Pronozin ◽  
A. A. Paulish ◽  
E. A. Zavarzin ◽  
A. Yu. Prikhodko ◽  
N. M. Prokhoshin ◽  
...  
Keyword(s):  
Ploidy Level ◽  
Biological Diversity ◽  
Visual Analysis ◽  
Tetraploid Wheat ◽  
Morphological Characteristics ◽  
Cultivated Plants ◽  
Isogenic Line ◽  
Wheat Species ◽  
Hexaploid Species ◽  
Wheat Spike

Intraspecific classification of cultivated plants is necessary for the conservation of biological diversity, study of their origin and their phylogeny. The modern cultivated wheat species originated from three wild diploid ancestors as a result of several rounds of genome doubling and are represented by di-, tetra- and hexaploid species. The identification of wheat ploidy level is one of the main stages of their taxonomy. Such classification is possible based on visual analysis of the wheat spike traits. The aim of this study is to investigate the morphological characteristics of spikes for hexa- and tetraploid wheat species based on the method of high-performance phenotyping. Phenotyping of the quantitative characteristics of the spike of 17 wheat species (595 plants, 3348 images), including eight tetraploids (Triticum aethiopicum, T. dicoccoides, T. dicoccum, T. durum, T. militinae, T. polonicum, T. timopheevii, and T. turgidum) and nine hexaploids (T. compactum, T. aestivum, i:ANK-23 (near-isogenic line of T. aestivum cv. Novosibirskaya 67), T. antiquorum, T. spelta (including cv. Rother Sommer Kolben), T. petropavlovskyi, T. yunnanense, T. macha, T. sphaerococcum, and T. vavilovii), was performed. Wheat spike morphology was described on the basis of nine quantitative traits including shape, size and awns area of the spike. The traits were obtained as a result of image analysis using the WERecognizer program. A cluster analysis of plants according to the characteristics of the spike shape and comparison of their distributions in tetraploid and hexaploid species showed a higher variability of traits in hexaploid species compared to tetraploid ones. At the same time, the species themselves form two clusters in the visual characteristics of the spike. One type is predominantly hexaploid species (with the exception of one tetraploid, T. dicoccoides). The other group includes tetraploid ones (with the exception of three hexaploid ones, T. compactum, T. antiquorum, T. sphaerococcum, and i:ANK-23). Thus, it has been shown that the morphological characteristics of spikes for hexaploid and tetraploid wheat species, obtained on the basis of computer analysis of images, include differences, which are further used to develop methods for plant classifications by ploidy level and their species in an automatic mode.

scholarly journals Fungi causing powdery mildew on plants of a Botanical Garden in Southern Finland

Karstenia ◽  
2021 ◽  
pp. 13-29
Author(s):  
Ville J. Heiskanen ◽  
Jari P. T. Valkonen
Keyword(s):  
Powdery Mildew ◽  
Urban Areas ◽  
Biological Diversity ◽  
Morphological Characteristics ◽  
Cultivated Plants ◽  
Its Sequencing ◽  
Species Determination ◽  
Morphological Studies ◽  
Wide Range ◽  
The Impact

Fungi that cause powdery mildew on plants are plant pathogenic parasites (<em>Erysiphales</em>) and can significantly reduce the ornamental value of plants and cause significant yield losses among cultivated plants. In this study, 94 plant accessions infected with powdery mildew were observed in Kumpula Botanic Garden, Helsinki, Finland, in 2015. The taxonomic affiliation and species richness of powdery mildew fungi were investigated. Morphological studies by microscope distinguished only 14 fungal species, whereas further comparisons of internal transcribed spacer (ITS) sequences enabled the identification of 28 species. Hence, ITS sequencing improved the reliability of species determination, as compared with the use of morphological characteristics only. The vegetation in an area of six hectares supported a wide range of fungi that cause powdery mildew as well as hyperparasitic microbes, which may balance the impact of pathogens in host plants. The findings of this study emphasize the role of botanical gardens in protecting biological diversity in urban areas.

scholarly journals The Independent Domestication of Timopheev’s Wheat: Insights from Haplotype Analysis of the Brittle rachis 1 (BTR1-A) Gene

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 338
Author(s):  
Moran Nave ◽  
Mihriban Taş ◽  
John Raupp ◽  
Vijay K. Tiwari ◽  
Hakan Ozkan ◽  
...  
Keyword(s):  
Promoter Region ◽  
Haplotype Analysis ◽  
Common Ancestor ◽  
Triticum Turgidum ◽  
Tetraploid Wheat ◽  
Wheat Species ◽  
Loss Of Function ◽  
Brittle Rachis ◽  
Gene Level ◽  
Large Panel

Triticum turgidum and T. timopheevii are two tetraploid wheat species sharing T. urartu as a common ancestor, and domesticated accessions from both of these allopolyploids exhibit nonbrittle rachis (i.e., nonshattering spikes). We previously described the loss-of-function mutations in the Brittle Rachis 1 genes BTR1-A and BTR1-B in the A and B subgenomes, respectively, that are responsible for this most visible domestication trait in T. turgidum. Resequencing of a large panel of wild and domesticated T. turgidum accessions subsequently led to the identification of the two progenitor haplotypes of the btr1-A and btr1-B domesticated alleles. Here, we extended the haplotype analysis to other T. turgidum subspecies and to the BTR1 homologues in the related T. timopheevii species. Our results showed that all the domesticated wheat subspecies within T. turgidum share common BTR1-A and BTR1-B haplotypes, confirming their common origin. In T. timopheevii, however, we identified a novel loss-of-function btr1-A allele underlying a partially brittle spike phenotype. This novel recessive allele appeared fixed within the pool of domesticated Timopheev’s wheat but was also carried by one wild timopheevii accession exhibiting partial brittleness. The promoter region for BTR1-B could not be amplified in any T. timopheevii accessions with any T. turgidum primer combination, exemplifying the gene-level distance between the two species. Altogether, our results support the concept of independent domestication processes for the two polyploid, wheat-related species.

scholarly journals Identification key for anuran amphibians in a protected area in the northeastern Atlantic Forest

2021 ◽  
Vol 61 ◽  
pp. e20216176
Author(s):  
Marcos Jorge Matias Dubeux ◽  
Filipe Augusto Cavalcanti do Nascimento ◽  
Ubiratan Gonçalves ◽  
Tamí Mott
Keyword(s):  
Atlantic Forest ◽  
Biological Diversity ◽  
Morphological Characteristics ◽  
Identification Key ◽  
Anuran Amphibians ◽  
Anuran Species ◽  
Starting Point ◽  
Environmental Protection Area ◽  
Baseline Information ◽  
Northeastern Atlantic

The identification of anuran amphibians is still a challenge in megadiverse assemblages. In the Neotropics, the Atlantic Forest harbors more than 600 anuran species, and many studies in this ecoregion report anuran assemblages surpassing 30 species. Taxonomic keys facilitate the identification of biological diversity, however only a few are available for anuran assemblages in the Atlantic Forest. Herein we present an identification key for 40 anuran species distributed across 20 genera and nine families, occurring in the Environmental Protection Area of Catolé and Fernão Velho, northeastern Atlantic Forest. Thirty-five morphological characteristics were used in the key, all of which can be easily observed in living and museum specimens. This pioneer study provides the first identification key for an amphibian assemblage in the northeastern Atlantic Forest and this baseline information acts as the starting point for the development of evolutionary and ecological research in this conservation unit.

scholarly journals A new species of Coccoloba P. Browne (Polygonaceae) from the Brazilian Amazon with exceptionally large leaves

2019 ◽  
Vol 49 (4) ◽  
pp. 324-329 ◽  
Author(s):  
Efigenia de MELO ◽  
Carlos Alberto CID FERREIRA ◽  
Rogério GRIBEL
Keyword(s):  
New Species ◽  
Conservation Status ◽  
Natural Habitat ◽  
Morphological Characteristics ◽  
Brazilian Amazon ◽  
Cultivated Plants ◽  
New Taxon ◽  
Madeira River ◽  
Individual Trees ◽  
A New Species

ABSTRACT We describe and illustrate a new species of Coccoloba (Polygonaceae), named Coccoloba gigantifolia, from the Brazilian Amazon. It resembles Coccoloba mollis Casar, but differs from the latter species by its much larger leaves in the fertile branches. The species has only been recorded in the Madeira River basin, in the states of Amazonas and Rondônia, in the central and southwestern Brazilian Amazon. The description was based on herbarium material, cultivated plants, and individual trees in their natural habitat. We provide illustrations, photographs, and an identification key with morphological characteristics that distinguish the new taxon from the other two related taxa of the Coccoloba sect. Paniculatae, as well as comments on the geographic distribution and conservation status of the species.

scholarly journals Research Concerning Cucumber (Cucumis Sativus L. Mill) Genetic Diversity

2011 ◽  
Vol 68 (2) ◽  
Author(s):  
Aurel MAXIM ◽  
Mignon ŞANDOR ◽  
Lucia MIHALESCU ◽  
Ovidiu MAXIM ◽  
Oana MARE ROŞCA
Keyword(s):  
Genetic Diversity ◽  
Biological Diversity ◽  
Genetic Erosion ◽  
Farming Systems ◽  
Convention On Biological Diversity ◽  
Cultivated Plants ◽  
Cucumis Sativus L ◽  
Local Varieties ◽  
Industrial Farming ◽  
The University

During the second part of the twentieth century the cultivated plants have been faced with genetic erosion, because of the expandinding industrial farming systems. The sustainable agriculture can not exist without a rich genetic diversity. After the United Nations Conference from Rio de Janeiro (1992), when the Convention on Biological Diversity was adopted, a series of acts and european references that protect agrobiodiversity had emerged. Between 2007 and 2010, at the University of Agricultural Sciences and Veterinary Medicine a program which aims to identify and conserve local vegetable varieties was conducted. Out of 290 cultivars, 171 (58.9%) were genuine local varieties. There were collected 12 cucumber cultivars from the following counties: Salaj (7), Cluj (3), Bistrita-Nasaud (1) and Satu-Mare (1). The morphologic caractheristics proved that all this 12 cultivars were authentic and valuable local varieties. The local varieties were agronomical, biological and biochemical characterized, both in field and laboratory. The seeds achieved from those 12 local varieties were preserved in the Suceava Gene Bank, from where stakeholders (farmers, agronomists, researchers) can obtain seeds.

scholarly journals First Report of Leaf Blight Caused by Septoria allii on Garlic Chives in Korea

Plant Disease ◽  
2013 ◽  
Vol 97 (1) ◽  
pp. 147-147
Author(s):  
J. H. Park ◽  
S. E. Cho ◽  
K. S. Han ◽  
H. D. Shin
Keyword(s):  
Disease Incidence ◽  
Morphological Characteristics ◽  
Its Region ◽  
Leaf Blight ◽  
Plant Diseases ◽  
Cultivated Plants ◽  
Sequence Information ◽  
Conidial Suspension ◽  
Korean Society ◽  
First Report

Garlic chives, Allium tuberosum Roth., are widely cultivated in Asia and are the fourth most important Allium crop in Korea. In June 2011, a leaf blight of garlic chives associated with a Septoria spp. was observed on an organic farm in Hongcheon County, Korea. Similar symptoms were also found in fields within Samcheok City and Yangku County of Korea during the 2011 and 2012 seasons. Disease incidence (percentage of plants affected) was 5 to 10% in organic farms surveyed. Diseased voucher specimens (n = 5) were deposited at the Korea University Herbarium (KUS). The disease first appeared as yellowish specks on leaves, expanding to cause a leaf tip dieback. Half of the leaves may be diseased within a week, especially during wet weather. Pycnidia were directly observed in leaf lesions. Pycnidia were amphigenous, but mostly epigenous, scattered, dark brown to rusty brown, globose, embedded in host tissue or partly erumpent, separate, unilocular, 50 to 150 μm in diameter, with ostioles of 20 to 40 μm in diameter. Conidia were acicular, straight to sub-straight, truncate at the base, obtuse at the apex, hyaline, aguttulate, 22 to 44 × 1.8 to 3 μm, mostly 3-septate, occasionally 1- or 2-septate. These morphological characteristics matched those of Septoria allii Moesz, which is differentiated from S. alliacea on conidial dimensions (50 to 60 μm long) (1,2). A monoconidial isolate was cultured on potato dextrose agar (PDA). Two isolates have been deposited in the Korean Agricultural Culture Collection (Accession Nos. KACC46119 and 46688). Genomic DNA was extracted using the DNeasy Plant Mini DNA Extraction Kit (Qiagen Inc., Valencia, CA). The internal transcribed spacer (ITS) region of rDNA was amplified using the ITS1/ITS4 primers and sequenced. The resulting sequence of 482-bp was deposited in GenBank (JX531648 and JX531649). ITS sequence information was at least 99% similar to those of many Septoria species, however no information was available for S. allii. Pathogenicity was tested by spraying leaves of three potted young plants with a conidial suspension (2 × 105 conidia/ml), which was harvested from a 4-week-old culture on PDA. Control leaves were sprayed with sterile water. The plants were placed in humid chambers (relative humidity 100%) for the first 48 h. After 7 days, typical leaf blight symptoms started to develop on the leaves of inoculated plants. S. allii was reisolated from the lesions of inoculated plants, confirming Koch's postulates. No symptoms were observed on control plants. The host-parasite association of A. tuberosum and S. allii has been known only from China (1). S. alliacea has been recorded on several species of Allium, e.g. A. cepa, A. chinense, A. fistulosum, and A. tuberosum from Japan (4) and A. cepa from Korea (3). To the best of our knowledge, this is the first report of S. allii on garlic chives. No diseased plants were observed in commercial fields of garlic chives which involved regular application of fungicides. The disease therefore seems to be limited to organic garlic chive production. References: (1) P. K. Chi et al. Fungous Diseases on Cultivated Plants of Jilin Province, Science Press, Beijing, China, 1966. (2) P. A. Saccardo. Sylloge Fungorum Omnium Hucusque Congnitorum. XXV. Berlin, 1931. (3) The Korean Society of Plant Pathology. List of Plant Diseases in Korea, Suwon, Korea, 2009. (4) The Phytopathological Society of Japan. Common Names of Plant Diseases in Japan, Tokyo, Japan, 2000.

scholarly journals First Report of Powdery Mildew Caused by Golovinomyces sp. on Plantago australis in Brazil

Plant Disease ◽  
2013 ◽  
Vol 97 (3) ◽  
pp. 421-421
Author(s):  
L. J. Dallagnol ◽  
F. R. de Castro ◽  
E. N. Garcia ◽  
L. E. A. Camargo
Keyword(s):  
Powdery Mildew ◽  
Morphological Characteristics ◽  
Its Region ◽  
Plant Size ◽  
Wild Plants ◽  
Cultivated Plants ◽  
Its2 Region ◽  
Leaf Extracts ◽  
Galium Aparine ◽  
Galium Spurium

The plantain Plantago australis Lam. (Plantaginaceae) is a herbaceous species native to southern Brazil that is known for the analgesic, antibiotic, and anti-inflammatory properties of its leaf extracts (2). Powdery mildew was observed on wild P. australis plants in the cities of Tapejara, Jari, and Santa Maria (State of Rio Grande do Sul, Brazil) during the summer of 2011. Affected plants were more often observed in shaded areas. Signs included sparse to abundant white powdery masses of conidia and mycelium on pseudo-petioles and leaves, mostly on the adaxial surface. Severely affected plants (≥80% of foliar area affected) had small chlorotic leaves and reduced size compared to healthy ones. Mycelia were superficial and presented nipple-shaped appressoria. Conidiophores were often curved at the base, unbranched, cylindrical, 81 to 125 μm long (average 97.3 ± 14.9 μm) and composed of a cylindrical foot cell 52 to 73 μm long (average 65.4 ± 7.5 μm) and 9 to 14 μm wide (average 11.6 ± 1.5 μm) followed by one to two shorter cells 17 to 29 μm long (average 23.4 ± 3.6 μm). Conidia were produced in chains of up to eight cells, did not contain fibrosin bodies, ranged from ellipsoid-ovoid to subcylindrical, and measured 24 to 35 μm long (average 30.5 ± 3.7 μm) and 12 to 19 μm wide (average 15.8 ± 1.7 μm). Germ tubes were produced apically (reticuloidium type). Chasmothecia were not observed on sampled leaves. Genomic DNA was extracted from conidia, conidiophores, and mycelium and used to amplify the internal transcribed spacer (ITS) (ITS1-5.8s-ITS2) region using the ITS1 and ITS4 primers. The resulting sequence (558 bp) was deposited under accession number JX312220 in GenBank. Searches with the BLASTn algorithm revealed similarity of 100% with Golovinomyces orontii (Castagne) V.P. Heluta 1988 from Veronica arvensis L. (AB077652.1) (3), 99% with G. orontii from Galium spurium L. and Galium aparine L. (AB430818.1 and AB430813.1) (2) and 99% with G. sordidus (L. Junell) V.P. Heluta 1988 from P. lanceolata L. (AB077665.1) (3). Based on morphological characteristics and sequence analysis of the ITS region, the fungus was identified as belonging to Golovinomyces sp. To fulfill Koch's postulates, five cultivated plants of P. australis with four to five expanded leaves were inoculated by dusting conidia (10 to 15 conidia cm–2) on their leaves. Inoculated and non-inoculated control plants were kept in a greenhouse at 27 ± 5°C and relative humidity of 80 ± 15%. Powdery mildew symptoms identical to those of wild plants were observed 8 to 10 days after in inoculated plants. Although G. sordidus was previously reported on P. australis subsp. hirtella in Argentina and on several species of Plantago in others world regions (1), to our knowledge, Golovinomyces sp. has not been previously reported as a pathogen of P. australis in Brazil. Although the economic impact of the disease is limited, the reduction in plant size and leaves affects biomass production used in the extraction of pharmaceutical compounds. References: (1) U. Braun and R. T. A. Cook. Taxonomic Manual of the Erysiphales (Powdery Mildews), CBS Biodiversity Series 11, 2012. (2) G. C. Sousa et al. J. Ethnopharmacol. 90:135, 2004. (3) S. Takamatsu et al. Mycol. Res. 113:117, 2009.

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