scholarly journals SeedExtractor: An Open-Source GUI for Seed Image Analysis

2021 ◽  
Vol 11 ◽  
Author(s):  
Feiyu Zhu ◽  
Puneet Paul ◽  
Waseem Hussain ◽  
Kyle Wallman ◽  
Balpreet K. Dhatt ◽  
...  
Keyword(s):  
Open Source ◽  
Seed Size ◽  
Graphical User Interface ◽  
Basic Research ◽  
Seed Color ◽  
Seed Length ◽  
Efficient Manner ◽  
Genetic Components ◽  
Genome Wide ◽  
Length Width

Accurate measurement of seed size parameters is essential for both breeding efforts aimed at enhancing yields and basic research focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 s for analyzing an image, i.e., significantly less compared to the other tools. As this software is open-source, it can be modified by users to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were used for genome-wide association analysis. We identified known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrates the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops.

scholarly journals SeedExtractor: an open-source GUI for seed image analysis

2020 ◽  
Author(s):  
Feiyu Zhu ◽  
Puneet Paul ◽  
Waseem Hussain ◽  
Kyle Wallman ◽  
Balpreet K Dhatt ◽  
...  
Keyword(s):  
Open Source ◽  
Seed Size ◽  
Graphical User Interface ◽  
Basic Research ◽  
Seed Color ◽  
Seed Length ◽  
Efficient Manner ◽  
Genetic Components ◽  
Genome Wide ◽  
Length Width

ABSTRACTAccurate measurement of seed size parameters is essential for both: breeding efforts□aimed at□enhancing yields and basic research□focused on discovering genetic components that regulate seed size. To address this need, we have developed an open-source graphical user interface (GUI) software, SeedExtractor that□determines seed size and shape (including area, perimeter, length, width, circularity, and centroid), and seed color with capability to process a large number of images in a time-efficient manner. In this context, our application takes ∼2 seconds for analyzing an image, i.e. significantly less compared to the other tools. As this software is open-source, it can be modified by users□to serve more specific needs. The adaptability of SeedExtractor was demonstrated by analyzing scanned seeds from multiple crops. We further validated the utility of this application by analyzing mature-rice seeds from 231 accessions in Rice Diversity Panel 1. The derived seed-size traits, such as seed length, width, were subjected to genome-wide association analysis. We identified well-known loci for regulating seed length (GS3) and width (qSW5/GW5) in rice, which demonstrated the accuracy of this application to extract seed phenotypes and accelerate trait discovery. In summary, we present a publicly available application that can be used to determine key yield-related traits in crops.HIGHLIGHTSeedExtractor is an open-source application designed to accurately measure seed size and seed color in a time-efficient manner for a wide variety of plant species.

Shell and Seed Size Relationships in Peanuts1

1981 ◽  
Vol 8 (1) ◽  
pp. 21-24 ◽  
Author(s):  
Ignacio J. de Godoy ◽  
A. J. Norden
Keyword(s):  
Seed Size ◽  
Plant Density ◽  
Wide Distribution ◽  
Seed Length ◽  
Arachis Hypogaea L ◽  
Length Width ◽  
Pericarp Color ◽  
The Difference ◽  
F2 Generation ◽  
F1 Generation

Abstract Three crosses and their reciprocals between peanut (Arachis hypogaea L.) genotypes differing in pod and seed sizes were made to investigate relationships between the pericarp (shell) and seed. Length, width, and weight of the fruit and seed from the F1 generation and selfed parentals were compared. The F2 generation along with plants from the parental lines were grown in the field. The weight, width, and volume of dried fruits and seeds, as well as shell thickness, were obtained from samples of 30 visually mature pods from each plant. Density of fruits and seeds, internal pericarp color, and shelling percentage were also recorded. Length, width, and weight of the F1 seeds tended to be similar to the selfed seeds from the same plants, showing possible maternal influence. The wide distribution in fruit volume obtained among F2 plants is indicative of quantitative inheritance. The larger the difference in fruit and seed size between the parents, the more pronounced was the skewness of the size distributions of the progeny toward the smaller parent. Estimates of pheno-typic correlations for fruit and seed volume were high and positive in most cases. However, fruit density vs fruit volume correlations were essentially negative suggesting that seeds grown inside pods with genetically smaller cavities may be compacted by the shell.

scholarly journals High-Density SNP-Based Association Mapping of Seed Traits in Fenugreek Reveals Homology with Clover

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 893
Author(s):  
Mustafa M. H. Abd El-Wahab ◽  
Maha Aljabri ◽  
Mohamed S. Sarhan ◽  
Gamal Osman ◽  
Shichen Wang ◽  
...  
Keyword(s):  
Association Mapping ◽  
Complex Traits ◽  
Seed Color ◽  
Marker Assisted Breeding ◽  
Seed Length ◽  
Breeding Programs ◽  
Polymorphic Snps ◽  
Lack Of Information ◽  
Genome Wide ◽  
Seed Width

Fenugreek as a self-pollinated plant is ideal for genome-wide association mapping where traits can be marked by their association with natural mutations. However, fenugreek is poorly investigated at the genomic level due to the lack of information regarding its genome. To fill this gap, we genotyped a collection of 112 genotypes with 153,881 SNPs using double digest restriction site-associated DNA sequencing. We used 38,142 polymorphic SNPs to prove the suitability of the population for association mapping. One significant SNP was associated with both seed length and seed width, and another SNP was associated with seed color. Due to the lack of a comprehensive genetic map, it is neither possible to align the newly developed markers to chromosomes nor to predict the underlying genes. Therefore, systematic targeting of those markers to homologous genomes of other legumes can overcome those problems. A BLAST search using the genomic fenugreek sequence flanking the identified SNPs showed high homology with several members of the Trifolieae tribe indicating the potential of translational approaches to improving our understanding of the fenugreek genome. Using such a comprehensively-genotyped fenugreek population is the first step towards identifying genes underlying complex traits and to underpin fenugreek marker-assisted breeding programs.

scholarly journals Quantitative characteristics of fruits and seeds of Pouteria pachycarpa Pires - Sapotaceae

2005 ◽  
Vol 27 (2) ◽  
pp. 159-164 ◽  
Author(s):  
Eniel David Cruz
Keyword(s):  
Seedling Emergence ◽  
Brazilian Amazon ◽  
Germination Percentage ◽  
Native Forest ◽  
Seed Color ◽  
Seed Length ◽  
Quantitative Characteristics ◽  
Length Width ◽  
Fruit Mass ◽  
Yellowish Orange

Pouteria pachycarpa is a tree species, found in the Brazilian Amazon and Bolivia whose wood has been exploited from the native forest. The present research describes the quantitative characteristics of fruits and seeds and quantifies the seed germination of this species. The fruit and seed color were characterized and measurements taken of the mass, length, diameter and number of seeds per fruit, the seed length, width and thickness, the germination percentage, abnormal seedlings and dead seeds. Sowing was carried out on a substrate containing sand and sawdust (1:1), in four replications of 50 seeds. The predominant fruit and seed colors were vivid yellowish orange (9YR) and dark grayish brown (6YR), respectively. Fruit mass, length and diameter ranged from 37.7 to 192.4g, 41.3 to 87.3mm and 39.7 to 71.7mm, respectively. Fruits had from two to seven seeds, and 42.6% were damaged by insects. Seed length, width and thickness ranged from 22.4 to 35.2mm, 9.7 to 15.5mm and 5.5 to 10.8mm, respectively. Seedling emergence began 18 days after sowing. Maximum germination, 86%, was recorded 33 days after sowing. The germination curve was sigmoid, similar to the majority of species. The percentage of abnormal seedlings and dead seeds were 3% and 11%, respectively. Both fruits and seeds show great variation in quantitative characteristics and the germination is slow and non-uniform.

scholarly journals Diversity of common bean in Jammu and Kashmir, India: a DIVAgeographic information system and cluster analysis

2014 ◽  
Vol 6 (1) ◽  
pp. 226-233 ◽  
Author(s):  
Sheikh Mohammad Sultan ◽  
Sher Ahmad Dar ◽  
Suheel Ahmad Dand ◽  
Natarajan Sivaraj
Keyword(s):  
Common Bean ◽  
Seed Size ◽  
Seed Weight ◽  
Genetic Relationships ◽  
Farming Systems ◽  
Seed Color ◽  
Seed Length ◽  
Jammu And Kashmir ◽  
And Cluster Analysis ◽  
100 Seed Weight

A total of 80 diverse germplasm accessions of common bean (Phaseolus vulgaris L.) were collected from 31 different locations known for marginal and risk prone farming systems in remote and hilly areas of North-Western Indian Himalayan state of Jammu and Kashmir. The variability was observed in seed color, shape, size and 100- seed weight. Thirteen colors of bean seeds were represented in these 80 accessions with high predominance of red colored seeds. Cuboid, kidney and oval seed shapes observed were represented respectively in 61.25%, 25% and 13.75% of the accessions. There were significant variations in seed length, width and 100-seed weight being highly significant in the later case. All the three seed size classes (small, medium and large according to CIAT categorization) were represented in the collected accessions. 22.5% accessions have 100-seed weight less than 25g, 53.75% accessions have 100-seed weight between 25-40g while 100-seed weight of more than 40g was recorded in 23.75% of the accessions. Highly positive correlations were found between 100-seed weight and seed length and width and between seed length and seed width. The 80 accessions were grouped in three clusters at a coefficient level of 0.3 with largest cluster of 59 accessions followed by a medium cluster with 20 accessions and the least with a single accession. Grid maps generated through DIVA-GIS software indicated that diverse accessions of common bean in terms of seed size and weight can be sourced from the areas falling in Budgam, Shopian and Kulgam districts of the state. Conservation of this remarkable genetic diversity is recommended for future propagation, breeding and the investigation of the genetic relationships.

Detection and Mapping of RAPD Markers Associated with QTL Affecting Seed Size and Shape in Common Bean

HortScience ◽  
1998 ◽  
Vol 33 (3) ◽  
pp. 547b-547
Author(s):  
Soon O. Park ◽  
Dermot P. Coyne ◽  
Geunhwa Jung ◽  
E. Arnaud-Santana ◽  
H. Ariyarathne
Keyword(s):  
Linkage Group ◽  
Common Bean ◽  
Seed Size ◽  
Phenotypic Variation ◽  
Seed Weight ◽  
Rapd Markers ◽  
Rapd Marker ◽  
Seed Shape ◽  
Seed Length ◽  
Ri Lines

Seed size is an important trait in common bean. The objective was to identify RAPD markers associated with QTL for seed weight, seed length, and seed height in a molecular marker-based linkage map in a recombinant inbred (RI) population from the common bean cross of the larger seeded (100 seed/39 to 47 g) PC-50 (ovate seed shape) × smaller seeded (100 seed/26 to 35 g) XAN-159 (flat rhomboidal seed shape). The parents and RI lines were grown in two separate greenhouse and two field (Wisconsin, Dominican Republic) experiments using a RCBD. Continuous distributions for seed weight, seed length, and seed height were observed for RI lines indicating quantitative inheritance. One to three QTLs affecting seed weight explained 17% to 41% of the phenotypic variation. Two to three QTLs for seed length explained 23% to 45% of the phenotypic variation. One to four QTL associated with seed height explained 17% to 39% of the phenotypic variation. A RAPD marker M5.850 in linkage group 3 was consistently associated with seed weight, seed length, and seed height in all experiments and explained 7% to 13% of the phenotypic variation for these traits. A seedcoat pattern morphological marker (C) in linkage group 1 was associated with seed weight and seed height in two greenhouse experiments.

scholarly journals Genetic components of human pain sensitivity: a protocol for a genome-wide association study of experimental pain in healthy volunteers

BMJ Open ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. e025530 ◽  
Author(s):  
Annina B Schmid ◽  
Kaustubh Adhikari ◽  
Luis Miguel Ramirez-Aristeguieta ◽  
Juan-Camilo Chacón-Duque ◽  
Giovanni Poletti ◽  
...  
Keyword(s):  
Latin American ◽  
Pain Sensitivity ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Healthy Individuals ◽  
Genetic Components ◽  
Genome Wide ◽  
A Genome ◽  
The University ◽  
Genetic Contributions

IntroductionPain constitutes a major component of the global burden of diseases. Recent studies suggest a strong genetic contribution to pain susceptibility and severity. Whereas most of the available evidence relies on candidate gene association or linkage studies, research on the genetic basis of pain sensitivity using genome-wide association studies (GWAS) is still in its infancy. This protocol describes a proposed GWAS on genetic contributions to baseline pain sensitivity and nociceptive sensitisation in a sample of unrelated healthy individuals of mixed Latin American ancestry.Methods and analysisA GWAS on genetic contributions to pain sensitivity in the naïve state and following nociceptive sensitisation will be conducted in unrelated healthy individuals of mixed ancestry. Mechanical and thermal pain sensitivity will be evaluated with a battery of quantitative sensory tests evaluating pain thresholds. In addition, variation in mechanical and thermal sensitisation following topical application of mustard oil to the skin will be evaluated.Ethics and disseminationThis study received ethical approval from the University College London research ethics committee (3352/001) and from the bioethics committee of the Odontology Faculty at the University of Antioquia (CONCEPTO 01–2013). Findings will be disseminated to commissioners, clinicians and service users via papers and presentations at international conferences.

scholarly journals Genome-wide association study identified candidate genes for seed size and seed composition improvement in M. truncatula

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhijuan Chen ◽  
Vanessa Lancon-Verdier ◽  
Christine Le Signor ◽  
Yi-Min She ◽  
Yun Kang ◽  
...  
Keyword(s):  
Association Study ◽  
Protein Content ◽  
Seed Size ◽  
Seed Protein ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Strong Positive Correlation ◽  
Seed Composition ◽  
Seed Traits ◽  
Genome Wide

AbstractGrain legumes are highly valuable plant species, as they produce seeds with high protein content. Increasing seed protein production and improving seed nutritional quality represent an agronomical challenge in order to promote plant protein consumption of a growing population. In this study, we used the genetic diversity, naturally present in Medicago truncatula, a model plant for legumes, to identify genes/loci regulating seed traits. Indeed, using sequencing data of 162 accessions from the Medicago HAPMAP collection, we performed genome-wide association study for 32 seed traits related to seed size and seed composition such as seed protein content/concentration, sulfur content/concentration. Using different GWAS and postGWAS methods, we identified 79 quantitative trait nucleotides (QTNs) as regulating seed size, 41 QTNs for seed composition related to nitrogen (i.e. storage protein) and sulfur (i.e. sulfur-containing amino acid) concentrations/contents. Furthermore, a strong positive correlation between seed size and protein content was revealed within the selected Medicago HAPMAP collection. In addition, several QTNs showed highly significant associations in different seed phenotypes for further functional validation studies, including one near an RNA-Binding Domain protein, which represents a valuable candidate as central regulator determining both seed size and composition. Finally, our findings in M. truncatula represent valuable resources to be exploitable in many legume crop species such as pea, common bean, and soybean due to its high synteny, which enable rapid transfer of these results into breeding programs and eventually help the improvement of legume grain production.

A genomewide study of body mass index and its genetic correlation with thromboembolic risk

2014 ◽  
Vol 112 (11) ◽  
pp. 1036-1043 ◽  
Author(s):  
Geórgia Pena ◽  
Andrey Ziyatdinov ◽  
Alfonso Buil ◽  
Sonia López ◽  
Jordi Fontcuberta ◽  
...  
Keyword(s):  
Body Mass Index ◽  
Genetic Correlation ◽  
Body Mass ◽  
Thromboembolic Disease ◽  
Thromboembolic Risk ◽  
Genetic Components ◽  
Genome Wide ◽  
Thrombosis Risk ◽  
Bivariate Linkage Analysis ◽  
Genome Wide Scan

SummaryThrombosis and obesity are complex epidemiologically associated diseases. The mechanism of this association is not yet understood. It was the objective of this study to identify genetic components of body mass index (BMI) and their possible role in the risk of thromboembolic disease. With the self-reported BMI of 397 individuals from 21 extended families enrolled in the GAIT (Genetic Analysis of Idiopathic Thrombophilia) Project, we estimated the heritability of BMI and the genetic correlation with the risk of thrombosis. Subjects were genotyped for an autosomal genome-wide scan with 363 highly-informative DNA markers. Univariate and bivariate multipoint linkage analyses were performed. The heritability for BMI was 0.31 (p= 2.9×10–5). Thromboembolic disease (including venous and arterial) and BMI had a significant genetic correlation (ρG= 0.54, p= 0.005). Two linkage signals for BMI were obtained, one at 13q34 (LOD= 3.36, p= 0.0004) and other at 2q34, highly suggestive of linkage (LOD= 1.95). Bivariate linkage analysis with BMI and thrombosis risk also showed a significant signal at 13q34 (LOD= 3), indicating that this locus influences at the same time normal variation in the BMI phenotype as well as susceptibility to thrombosis. In conclusion, BMI and thrombosis are genetically correlated. The locus 13q34, which showed pleiotropy with both phenotypes, contains two candidate genes, which may explain our linkage pleiotropic signal and deserve further investigation as possible risk factors for obesity and thrombosis.

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