scholarly journals Microsatellite Markers as Reliable Tools for Fig Cultivar Identification

2009 ◽  
Vol 134 (6) ◽  
pp. 624-631 ◽  
Author(s):  
Hafid Achtak ◽  
Ahmed Oukabli ◽  
Mohammed Ater ◽  
Sylvain Santoni ◽  
Finn Kjellberg ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Cultivar Identification ◽  
Unknown Origin ◽  
Ex Situ ◽  
Discrimination Power ◽  
Crop Species ◽  
Fruit Species ◽  
Ssr Loci ◽  
Ex Situ Collection ◽  
Material Identity

Accurate and reliable cultivar identification of crop species is essential to ensure plant material identity for registration and for cultivar protection. In this article, we proposed six simple sequence repeat (SSR) loci as a sufficient tool to characterize fig (Ficus carica L.) germplasm in Morocco maintained in an ex situ collection. A set of 17 microsatellite loci was used to characterize 75 accessions representing eight caprifigs, 51 local accessions, 11 foreign accessions, and five accessions of unknown origin. Eighty-five alleles with a mean number of six alleles per locus were observed in 62 distinct genotypes. Suspected synonyms and homonyms were confirmed, some of which maybe resulted from somatic mutation. Based on genetic criteria, including linkage disequilibrium, discrimination power, and molecular criteria as polymerase chain reaction conditions of loci multiplexing, we proposed a key identification set using six microsatellite markers to discriminate all genotypes present in the ex situ collection. Our selected SSR loci set can be used for larger genetic studies of fig germplasm, and a similar approach can be adopted for other fruit species.

scholarly journals MFCIS: an automatic leaf-based identification pipeline for plant cultivars using deep learning and persistent homology

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yanping Zhang ◽  
Jing Peng ◽  
Xiaohui Yuan ◽  
Lisi Zhang ◽  
Dongzi Zhu ◽  
...  
Keyword(s):  
Prunus Avium ◽  
Cultivar Identification ◽  
Leaf Shape ◽  
Persistent Homology ◽  
Growth Period ◽  
Image Features ◽  
Crop Species ◽  
Score Level Fusion ◽  
Level Fusion ◽  
Leaf Image

AbstractRecognizing plant cultivars reliably and efficiently can benefit plant breeders in terms of property rights protection and innovation of germplasm resources. Although leaf image-based methods have been widely adopted in plant species identification, they seldom have been applied in cultivar identification due to the high similarity of leaves among cultivars. Here, we propose an automatic leaf image-based cultivar identification pipeline called MFCIS (Multi-feature Combined Cultivar Identification System), which combines multiple leaf morphological features collected by persistent homology and a convolutional neural network (CNN). Persistent homology, a multiscale and robust method, was employed to extract the topological signatures of leaf shape, texture, and venation details. A CNN-based algorithm, the Xception network, was fine-tuned for extracting high-level leaf image features. For fruit species, we benchmarked the MFCIS pipeline on a sweet cherry (Prunus avium L.) leaf dataset with >5000 leaf images from 88 varieties or unreleased selections and achieved a mean accuracy of 83.52%. For annual crop species, we applied the MFCIS pipeline to a soybean (Glycine max L. Merr.) leaf dataset with 5000 leaf images of 100 cultivars or elite breeding lines collected at five growth periods. The identification models for each growth period were trained independently, and their results were combined using a score-level fusion strategy. The classification accuracy after score-level fusion was 91.4%, which is much higher than the accuracy when utilizing each growth period independently or mixing all growth periods. To facilitate the adoption of the proposed pipelines, we constructed a user-friendly web service, which is freely available at http://www.mfcis.online.

scholarly journals Diversity and Relationships among Neglected Apricot (Prunus armeniaca L.) Landraces Using Morphological Traits and SSR Markers: Implications for Agro-Biodiversity Conservation

Plants ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1341
Author(s):  
Giandomenico Corrado ◽  
Marcello Forlani ◽  
Rosa Rao ◽  
Boris Basile
Keyword(s):  
Prunus Armeniaca ◽  
Ex Situ ◽  
Skin Colour ◽  
Maintenance Breeding ◽  
Prunus Armeniaca L ◽  
Ex Situ Collection ◽  
Loss Of Diversity ◽  
Ssrs Markers ◽  
On Farm ◽  
Simple Sequence

Apricot (Prunus armeniaca L.) is an economically important tree species globally cultivated in temperate areas. Italy has an ample number of traditional varieties, but numerous landraces are abandoned and at risk of extinction because of increasing urbanization, agricultural intensification, and varietal renewal. In this work, we investigated the morphological and genetic diversity present in an ex-situ collection of 28 neglected varieties belonging to the so-called “Vesuvian apricot”. Our aim was to understand the level of diversity and the possible link between the promotion of specific fruit types (e.g., by public policies) and the intraspecific variation in apricot. The combination of five continuous and seven categorical traits allowed us to phenotypically distinguish the varieties; while fruit quality-related attributes displayed high variation, both apricot size and skin colour were more uniform. The twelve fluorescent-based Simple Sequence Repeats (SSRs) markers identified cultivar-specific molecular profiles and revealed a high molecular diversity, which poorly correlated with that described by the morphological analysis. Our results highlighted the complementary information provided by the two sets of descriptors and that DNA markers are necessary to separate morphologically related apricot landraces. The observed morphological and genetic differences suggest a loss of diversity influenced by maintenance breeding of specific pomological traits (e.g., skin colour and size). Finally, our study provided evidence to recommend complementary strategies to avoid the loss of diversity in apricot. Actions should pivot on both the promotion of easily identified premium products and more inclusive biodiversity-centred on-farm strategies.

Development of microsatellite markers at the National Agrobiodiversity Center in Korea for the genetic assessment of underutilized crops

2014 ◽  
Vol 12 (S1) ◽  
pp. S125-S129
Author(s):  
Gi-An Lee ◽  
Sok-Young Lee ◽  
Ho-Sun Lee ◽  
Kyung-Ho Ma ◽  
Jae-Gyun Gwag ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Germplasm Management ◽  
Underutilized Crops ◽  
Crop Species ◽  
Closely Related Species ◽  
Polymorphic Loci ◽  
Allele Number ◽  
The Mean ◽  
Genetic Assessment

The RDA Genebank at the National Agrobiodiversity Center (NAAS, RDA, Republic of Korea) has conserved about 182,000 accessions in 1777 species and is working at preserving agricultural genetic resources for the conservation and sustainable utilization of genetic diversity. The detection of genetic variability in conserved resources is important for germplasm management, but the molecular evaluation tools providing genetic information are insufficient for underutilized crops, unlike those for major crops. In this regard, the Korean National Agrobiodiversity Center has been developing microsatellite markers for several underutilized crops. We designed 3640 primer pairs flanking simple sequence repeat (SSR) motifs for 6310 SSR clones in 21 crop species. Polymorphic loci were revealed in each species (7–36), and the mean ratio of polymorphic loci to all the loci tested was 12%. The average allele number was 5.1 (2.8–10.3) and the expected heterozygosity 0.51 (0.31–0.74). Some SSRs were transferable to closely related species, such as within the genera Fagopyrum and Allium. These SSR markers might be used for studying the genetic diversity of conserved underutilized crops.

scholarly journals Structure of the phenotypic variability of fruit and seeds of Dipteryx alata vogel (Fabaceae)

2020 ◽  
Vol 42 (5) ◽  
Author(s):  
Elias Emanuel Silva Mota ◽  
Carolina Ribeiro Diniz Boaventura Novaes ◽  
Luciana Borges e Silva ◽  
Lázaro José Chaves
Keyword(s):  
Phenotypic Variability ◽  
Descriptive Analysis ◽  
Germplasm Collection ◽  
Ex Situ ◽  
Brazilian Cerrado ◽  
Phenotypic Differentiation ◽  
Fruit Species ◽  
Mother Plants ◽  
Priority Species ◽  
Dipteryx Alata

Abstract Dipteryx alata Vogel (“baru tree”) is a fruit species native to the Brazilian Cerrado and presents a multiplicity of uses, constituting a priority species for domestication and cultivation studies. The objective of the current study was to characterize fruit and seeds of D. alata from several regions of the Brazilian Cerrado biome to support strategies for ex situ conservation and utilization of the genetic variability of the species. Fruits were collected from 25 subpopulations, sampling six mother plants per subpopulation, with collection of at least 25 fruits per plant. The physical trait data of the fruits and seeds were submitted to descriptive analysis, analysis of variance and correlation among traits. There was significant variation for all traits among subpopulations and among individuals within subpopulations. The highest proportion of variability was observed among individuals within subpopulations. The phenotypic differentiation among subpopulations was higher for fruit traits compared to seed traits. The correlation analysis showed the existence of significant correlations for most of the traits pairs in the different hierarchical levels. It was concluded that D. alata presents phenotypic variability to support germplasm collection programsand formation of base populations for breeding programs, recommending the sampling in several locations to ensure an adequate representativeness of the phenotypic variability.

scholarly journals Genetic Divergence of Flax Genotypes (Linum Usitatissimum L.) Utilizing Microsatellite Markers

2017 ◽  
Vol 5 (1) ◽  
pp. 123-129 ◽  
Author(s):  
Sumita Nag ◽  
Jiban Mitra
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Linum Usitatissimum ◽  
Rank Correlation ◽  
Natural Fibre ◽  
Similarity Coefficients ◽  
Oilseed Crops ◽  
Linum Usitatissimum L ◽  
Ssr Primers ◽  
Ssr Loci

Flax (Linum usitatissimum L.), stoods in position third, being the largest natural fibre crop and simultaneously one of the five preeminent oilseed crops in the world. SSR/microsatellite markers are extensively utilized for genetic diversity analysis and cultivar identification considering their myriad abundance, co-dominant inheritance, steep polymorphism, reproducibility, and comfort of assay by PCR. Ten microsatellites were amplified in 27 genotypes of Flax. The study was undertaken to assess the genetic diversity in flax and to select most diverse genotypes for future breeding program. Primer efficiency parameters were studied. The 10 SSR loci amplified a total of 41 alleles that were used for genetic analysis. Most primers have PIC value greater than 0.5 and the LU6 marker was highly polymorphic PIC = 0.95. Estimates of RP̅ were highest for the primer LU1 (0.68). The maximum MI was observed for the primer LU10 (3.56). The H and D ranged from 0.26 to 1.78 and 0.36 to 5.40, respectively. According to Spearman rank correlation, PIC and MI were most important parameters in assessing the efficiency of whole set of 10 SSR primers. Dendrogram was constructed using the genetic similarity coefficients using UPGMA. PCo-A was also performed in support. Genetic diversity in Flax was revealed at molecular level.

scholarly journals Pengelolaan Sumber Daya Genetik Tanaman Obat Spesifik Kalimantan Tengah

2016 ◽  
Vol 12 (1) ◽  
pp. 16 ◽  
Author(s):  
Amik Krismawati ◽  
M. Sabran
Keyword(s):  
Medicinal Plants ◽  
Ex Situ Conservation ◽  
Coastal Region ◽  
Ex Situ ◽  
Central Kalimantan ◽  
Acid Sulphate ◽  
Medicinal Crops ◽  
Continental Area ◽  
Ex Situ Collection

<p>Central Kalimantan Province covers an area of 15,38 million ha which consist of 61,140 ha coastal region, 1,53 million ha open waters, and 13,79 million ha as inland area. The continental area consisted of various type of lands e.g. acid sulphate, peats soil, and up land. In order to explore and conserve potential medicinal plants indigenous to Central Kalimantan, these exploration and characterization activities were conducted. Method of study: (1) exploration, (2) ex situ conservation, (3) characterization, and (4) documentation. The result of these activities are ex situ collection of 15 acessions of medicinal crops. This exploration obtained 15 accessions of medicinal plants which were characterized and conserved in ex situ condition.</p><p> </p><p><strong>Abstrak</strong></p><p>Kalimantan Tengah memiliki luas wilayah 15,38 juta ha yang terdiri dari 61,1 ribu ha daerah pantai, 1,53 juta ha daerah perairan umum, dan 17,79 juta ha daratan. Wilayah daratan yang luas ini terdiri atas berbagai tipologi lahan seperti lahan sulfat masam, gambut, dan lahan kering. Untuk menggali potensi dan melestarikan plasma nutfah tanaman obat spesifik Kalimantan Tengah telah dilaksanakan kegiatan eksplorasi dan karakterisasi. Dari kegiatan ini dapat disusun deskripsi berbagai jenis tanaman tersebut untuk inventarisasi, karakterisasi, dan koleksi tanaman obat secara ex situ dalam bentuk kebun pembibitan. Metode kegiatan meliputi (1) eksplorasi, (2) konservasi ex situ, (3) karakterisasi, dan (4) dokumentasi. Hasil kegiatan adalah koleksi secara ex situ tanaman obat sebanyak 15 aksesi.</p>

EX SITU CONSERVATION OF TROPICAL RARE FRUIT SPECIES

2002 ◽  
pp. 221-230 ◽  
Author(s):  
M.N. Normah ◽  
M.M. Clyde ◽  
E.G. Cho ◽  
V. Ramanatha Rao
Keyword(s):  
Ex Situ Conservation ◽  
Ex Situ ◽  
Fruit Species

scholarly journals  Genetic diversity of Czech apple cultivars inferred from microsatellite markers analysis

2012 ◽  
Vol 39 (No. 4) ◽  
pp. 149-157 ◽  
Author(s):  
J. Patzak ◽  
F. Paprštein ◽  
A. Henychová ◽  
J. Sedlák
Keyword(s):  
Genetic Diversity ◽  
Microsatellite Markers ◽  
Simple Sequence Repeat ◽  
Cultivar Identification ◽  
Genetic Relationships ◽  
Similarity Coefficient ◽  
Collection Management ◽  
Apple Cultivars ◽  
Repeat Primer ◽  
Simple Sequence

Genetic diversity and genetic relationships of Czech apple cultivars were evaluated. Trees of 33&nbsp;Czech apple cultivars and 97 reference foreign cultivars were analysed using the set of 10 SSR (simple sequence repeat) primer pairs. The total of 89 polymorphic alleles were amplified, while the number of alleles per locus ranged from 4 to 14. The SSR dendrogram, based on the Jaccard&rsquo;s similarity coefficient, divided apple cultivars into three major groups: Cox&rsquo;s Orange Pippin, McIntosh and Golden Delicious ancestries. The clustering highly depended on pedigree and origin of apple cultivars. Spontaneous mutated cultivars were identical with their progenitors. We proved that microsatellite markers were useful for evaluation of genetic resources, collection management and cultivar identification. &nbsp;

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