scholarly journals Genetic diversity, variety identification and gene detection in some Egyptian grape varieties by SSR and SCoT markers

Plant Omics ◽  
2016 ◽  
Vol 9 (5) ◽  
pp. 311-318 ◽  
Author(s):  
Shafik D. Ibrahim ◽  
◽  
S. S. Adawy ◽  
M. A. M Atia ◽  
A. M. Alsamman ◽  
...  
Sensors ◽  
2019 ◽  
Vol 19 (22) ◽  
pp. 4850 ◽  
Author(s):  
Carlos S. Pereira ◽  
Raul Morais ◽  
Manuel J. C. S. Reis

Frequently, the vineyards in the Douro Region present multiple grape varieties per parcel and even per row. An automatic algorithm for grape variety identification as an integrated software component was proposed that can be applied, for example, to a robotic harvesting system. However, some issues and constraints in its development were highlighted, namely, the images captured in natural environment, low volume of images, high similarity of the images among different grape varieties, leaf senescence, and significant changes on the grapevine leaf and bunch images in the harvest seasons, mainly due to adverse climatic conditions, diseases, and the presence of pesticides. In this paper, the performance of the transfer learning and fine-tuning techniques based on AlexNet architecture were evaluated when applied to the identification of grape varieties. Two natural vineyard image datasets were captured in different geographical locations and harvest seasons. To generate different datasets for training and classification, some image processing methods, including a proposed four-corners-in-one image warping algorithm, were used. The experimental results, obtained from the application of an AlexNet-based transfer learning scheme and trained on the image dataset pre-processed through the four-corners-in-one method, achieved a test accuracy score of 77.30%. Applying this classifier model, an accuracy of 89.75% on the popular Flavia leaf dataset was reached. The results obtained by the proposed approach are promising and encouraging in helping Douro wine growers in the automatic task of identifying grape varieties.


PLoS ONE ◽  
2012 ◽  
Vol 7 (2) ◽  
pp. e32507 ◽  
Author(s):  
Dorit Schuller ◽  
Filipa Cardoso ◽  
Susana Sousa ◽  
Paula Gomes ◽  
Ana C. Gomes ◽  
...  

2014 ◽  
Vol 143 ◽  
pp. 506-513 ◽  
Author(s):  
Livio Muccillo ◽  
Angelita Gambuti ◽  
Luigi Frusciante ◽  
Massimo Iorizzo ◽  
Luigi Moio ◽  
...  

2011 ◽  
Vol 39 (5) ◽  
pp. 5307-5313 ◽  
Author(s):  
Da-Long Guo ◽  
Jun-Yu Zhang ◽  
Chong-Huai Liu

2005 ◽  
Vol 83 (1) ◽  
pp. 66-72 ◽  
Author(s):  
L S Zhang ◽  
V Le Clerc ◽  
S Li ◽  
D Zhang

The objective of this study was to identify an efficient set of simple sequence repeat (SSR) markers for sunflower (Helianthus annuus L.) variety fingerprinting, relying on semi-automated analysis conditions. Based on criteria such as quality of amplification products, co-dominant and single locus, 78 SSR markers were selected and used to assess the genetic variability among a large set of 124 sunflower inbred lines, including 67 female maintainers (M lines) and 57 male restorers (R lines). They revealed a total of 276 alleles across the 124 elite inbred lines, with a mean of 3.5 alleles per SSR locus. The polymorphism index content per locus varied from 0.06 to 0.81, with an average of 0.51. Relationships among the inbred lines were studied using estimations of Rogers' distances. The great majority of the distance estimates ranged between 0.4 and 0.6, but distances between some pairs of lines were less than 0.1. The genetic diversity value was similar within each subset of R and M lines and low, but significant differentiation was found (GST = 0.049) between the two pools. The selected set of SSRs proved to be useful both for sunflower fingerprinting and genetic diversity assessment.Key words: genetic diversity, genotyping, Helianthus annuus, multiplex PCR, simple sequence repeats (SSR).


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yusha Meng ◽  
Wenjin Su ◽  
Yanping Ma ◽  
Lei Liu ◽  
Xingguo Gu ◽  
...  

AbstractSweet potato, a dicotyledonous and perennial plant, is the third tuber/root crop species behind potato and cassava in terms of production. Long terminal repeat (LTR) retrotransposons are highly abundant in sweet potato, contributing to genetic diversity. Retrotransposon-based insertion polymorphism (RBIP) is a high-throughput marker system to study the genetic diversity of plant species. To date, there have been no transposon marker-based genetic diversity analyses of sweet potato. Here, we reported a structure-based analysis of the sweet potato genome, a total of 21555 LTR retrotransposons, which belonged to the main LTR-retrotransposon subfamilies Ty3-gypsy and Ty1-copia were identified. After searching and selecting using Hidden Markov Models (HMMs), 1616 LTR retrotransposon sequences containing at least two models were screened. A total of 48 RBIP primers were synthesized based on the high copy numbers of conserved LTR sequences. Fifty-six amplicons with an average polymorphism of 91.07% were generated in 105 sweet potato germplasm resources based on RBIP markers. A Unweighted Pair Group Method with Arithmatic Mean (UPGMA) dendrogram, a model-based genetic structure and principal component analysis divided the sweet potato germplasms into 3 groups containing 8, 53, and 44 germplasms. All the three analyses produced significant groupwise consensus. However, almost all the germplasms contained only one primary locus. The analysis of molecular variance (AMOVA) among the groups indicated higher intergroup genetic variation (53%) than intrapopulation genetic variation. In addition, long-term self-retention may cause some germplasm resources to exhibit variable segregation. These results suggest that these sweet potato germplasms are not well evolutionarily diversified, although geographic speciation could have occurred at a limited level. This study highlights the utility of RBIP markers for determining the intraspecies variability of sweet potato and have the potential to be used as core primer pairs for variety identification, genetic diversity assessment and linkage map construction. The results could provide a good theoretical reference and guidance for germplasm research and breeding.


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