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The Ensemble Method. The Ensemble Method: An example with 4 chromosomes each with an orientation and a distinct color above. (i) The chromosomes are first arranged as a circular ring. (ii) Then they are randomly permuted and randomly flipped. Then a random cut is placed on the ring, shown as a dashed line. (iii) Then the ring is flattened out and is staged as input to the IRiS pipeline.
Source publication
Background
Ancestral recombinations graph (ARG) is a topological structure that captures the relationship between the extant genomic sequences in terms of genetic events including recombinations. IRiS is a system that estimates the ARG on sequences of individuals, at genomic scales, capturing the relationship between these individuals of the specie...
Contexts in source publication
Context 1
... G ' chromosomes are used to produce a single sequence that is staged as input to the IRiS pipeline. This single ensemble is produced from the G ' chromosomes in the following three steps (see Figure 2). First, the G' chro- mosomes are placed in some random order in the 5' to 3' order in a circle. ...Context 2
... E(T) denotes the number of edges of T that are not incident on a leaf and v(T 1 , T 2 ) denotes the number of identical splits of the taxon induced by deleting an internal edge from each T 1 and T 2 . Note that, by The IRiS pipeline is used on an ensemble sequence (see Fig. 2) of the G' chromosomes some N times and the results are consolidated. definition, 0 ≤ d p (T 1 ,T 2 ) ≤ E(T 1 ) + E(T 2 ). To make this value comparable across different trees, we define an agreement index based on Eqn 3 as ...Similar publications
Background: Witches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm.
Results: We developed a dense genetic linkage...
Background
Witches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. ResultsWe developed a dense genetic linkage ma...
Citations
... Cilas C. [259][260][261][262][263][264][265][266] analyzes the relationship between the genetic diversity of Cocoa and its advantage in resisting diseases or increasing reproduction. Motamayor J. C. [172,[266][267][268][269][270] studied Cocoa crop ecosystems, including a genetic characterization for crop production and disease resistance. Dewettinck K. [271][272][273][274][275][276][277][278] explored ...
We are pleased to announce that our recent preprint, "A Bibliometric Analysis of Computational and Mathematical Techniques in the Cocoa Sustainable Food Value Chain" is being revised in "Heliyon". This comprehensive study offers an in-depth look into the role of computational and mathematical techniques in cocoa farming from 2000-2020.
I would like to thank my esteemed co-authors, Dr. Diana Teresa Parra-Sánchez and Dr.Henry Lamos Diaz. Their expertise, dedication, and insightful contributions have been invaluable in this research endeavor. I am privileged to have the opportunity to work with such diligent and knowledgeable co-researchers, and look forward to our continued collaboration in the future.
In this paper, we have taken an interdisciplinary approach, gathering insights from various fields such as Chemistry, Biology, Social Sciences, Econometrics and Finance, Health, and Computer Science. We have proposed a unique Cocoa Sustainable Food Value Chain framework that accentuates research use in areas such as genetic improvement, machinery optimization, health implications of food composition, and crop yield enhancement.
An emergent trend we have noticed is the increasing application of machine learning techniques to address several critical challenges in cocoa farming - from post-production issues, bean quality assessment, and cocoa ripeness identification, to bean fermentation optimization and cocoa machinery industrialization.
We have also identified four research gaps that could provide substantial value to smallholder cocoa farmers: optimal cocoa aggregation and distribution management, development of user-friendly high-tech solutions, agricultural technology adoption, and the evaluation of policy impacts.
Our research contributes significantly to the body of knowledge by expanding agri-food supply chain concepts, recognizing the underdevelopment of ICT and IoT solutions for cocoa production management, and emphasizing the need to develop and transfer high-tech tools to enhance Good Agricultural Practices.
We believe a digital transformation focused on smallholder farmers is vital to improving the Cocoa Sustainable Food Value Chain.
We invite you all to delve into our paper, share it within your networks, and discuss it. Your thoughts, comments, and constructive criticisms are welcomed and highly appreciated.
Let's together explore the potential of computational and mathematical techniques to transform the world of cocoa farming and contribute to a more sustainable food chain!
🔗 Access our preprint here: https://lnkd.in/e6HdCsJh
#CocoaFarming #SustainableFoodChain #ComputationalTechniques #MathematicalTechniques #AgricultureTechnology #DigitalTransformation #AgriFood #SupplyChain #ICT #IoT #MachineLearning #Research #Preprint #Review #LiteratureReview
... Some studies also focused on understanding plant resistance mechanisms through characterization of a genome-wide pattern recognition receptors and R genes, which make up the system innate immune T. cacao (Santana Silva and Micheli 2020;Li et al. 2016). As for the evolutionary aspect, studies of cacao ancestral gene recombination contributed to a better understanding of the relationship between cocoa species (Utro et al. 2012). In general, the literature on T. cacao is rich in information, data and omics studies related to evolutionary, agronomic and responses to biotic and abiotic stresses. ...
Cocoa tree (Theobroma cacao L.) is cultivated mainly in tropical regions and produces beans that are used for chocolate manufacture. Worldwide, cocoa bean production is threatened by biotic stresses, mainly fungus, oomycetes, virus and other pests. The understanding of the determinism of the plant-pathogen interactions as well as the different and integrated ways to manage the cocoa diseases at field level began the focus of several research groups. Here, we did an overview of the several cocoa diseases, of the traditional breeding methods as well as the molecular assisted ones recently developed, of the molecular and omics resources currently available, and of the new biotechnology approaches—including genome edition and nanotechnologies—that are used at basic and applied research levels. We also described the main germplasm and collections worldwide as well as the use of the cocoa diversity as main source of disease resistance.
... The centre of origin and diversity is in Amazonian South America (Cuatrecasas 1964;Motamayor et al. 2008) with the greatest diversity and earliest use occurring in the upper Amazon region of northwest South America (Zarrillo et al. 2018). Cacao is a commercially important industrial tree crop within the top 10 global agricultural commodities (Utro et al. 2012). The fermented and dried cotyledons of the seeds are raw ingredients in the multi-billion dollar confectionery industry. ...
Single nucleotide polymorphisms (SNPs) are preferred markers for DNA fingerprinting and diversity studies in cacao ( Theobroma cacao L.). Yet, a consensus SNP panel with a minimum number of SNPs for optimal identity analysis is unavailable for cacao. An initial set of 146 SNP panels of varying sizes were assembled based on heterozygosity, linkage disequilibrium (LD), linkage group (LG) distribution, major allele frequency, minor allele frequency (M<sub>i</sub>AF), polymorphism information content (PIC) and random distribution. These panels were assessed to determine their ability to distinguish among a training set of 155 accessions. The panels with the best separation ability were supplemented with additional SNPs to create 16 designer panels, which separated all 155 accessions. The 16 designer SNP panels were then assessed on a dataset of 1,220 accessions coming from 10 ancestral groups. Increasing the number of SNPs generally yielded improved resolution of genetic identities with concomitant reduction of synonymous groups. The number and choice of SNPs were critical factors with LD, M<sub>i</sub>AF and PIC being important selection attributes but an even LG distribution was unnecessary. A robust set of 96 SNPs is recommended as a minimal core SNP panel for cacao DNA fingerprinting to the international cacao community.
... Trinitario has been recognised as a 'Criollo × Forastro' hybrid (Cheesman, 1944). Recently, molecular markers and chromosome analyses have been used to classify cacao germplasm into 10 major groups: Amelonado, Contamana, Curaray, Guiana, Iquitos, Maraňón, Nanay, Purús, Criollo, and Nacional (Motamayor et al., 2008;Utro et al., 2012). The genomes of Criollo and Amelonado have been sequenced and cover 76% and 92% of the estimated genome size, respectively (Argout et al., 2011;Motamayor et al., 2013). ...
... In Malaysia, they are the primary limitation on the cocoa industry (and can destroy 50% of a crop) (Day, 1985). Given the genetic diversity of cocoa and the diversity of resistance to pod borers, a search for genetic markers of resistance seemed feasible (Utro et al., 2012;Motamayor et al. 2013). While pod borer resistance is a quantitative trait, with varying amounts of borer activity in different varieties, the trait can also be classified in a binary fashion as " resistant " and " susceptible ". ...
We have sequenced and de-novo assembled 14 cocoa genomes, 7 susceptible to pod borers and 7 resistant varieties. Comparison of the genomes revealed multi megabase regions deleted and inserted between varieties. Six million single nucleotide polymorphisms (SNPs) were identified across the genomes. Statistical analysis of SNP distributions between the resistant and susceptible groups identified 6 SNPs that were enriched in the resistant group compared to the susceptible group. Though the SNPs were independently tested, they are tightly genomically clustered in 2 haplotype blocks of 3 SNPs each. Both blocks are statistically significant and the most significant block contains a gene known to regulate plant structure. SNPs in this region are likely to make excellent breeding markers for pod borer resistance.
... ing of relationships among lineages, timing of recombination events and genetic exchange (e.g., Utro et al., 2012). 2. The ARG can be used in a variety of population genetics inferences related with demographics, population divergence times, migration and selection. ...
... The ARG is indispensable to study evolutionary scenarios where recombination has occurred. With the development of next-generation sequencing (NGS) technologies there is a growing number of genomes at our disposal, many of which could have evolved under recombination (e.g., Utro et al., 2012;Rasmussen and Siepel, 2013). As a consequence, the importance and application of ARGs is expected to increase over the next years. ...
One of the most important evolutionary forces is recombination, it increases genetic diversity and promotes adaptation through exchange of genetic material and where existent mutations are shuffled. Knowledge about recombination is, for example, fundamental to understand genome structure (Reich et al., 2001), phenotypic diversity (Zhang et al., 2002), and diverse genetic diseases (Daly et al., 2001). Indeed, recombination should be considered to properly study molecular evolution and perform phylogenetic inferences (e.g., Schierup and Hein, 2000; Anisimova et al., 2003; Arenas and Posada, 2010c). The recombination evolutionary history is commonly represented by the ancestral recombination graph (ARG) (Griffiths and Marjoram, 1997), an illustrative example is shown in Figure Figure1.1. Counterintuitively, ARGs have not been widely used, perhaps as a consequence of the difficulties to infer explicit ARGs and the complexity of the ARG representation. The aim of this general commentary is to describe the importance and application of the ARG.
Figure 1
Illustrative example of an ARG. RE indicates recombination events. Numbers in nodes indicate intervals of ancestral material. Note that each recombinant fragment (1–2, 3–6, and 7–9) has its own most recent common ancestor (MRCA), ...
Cocoa is among the top foreign exchange earners in Uganda’s agriculture sector and has benefited the livelihood of farmers involved in production. Although cacao cultivation was adopted in the early 1900s, little is known about the on-farm diversity of the crop. A total of 125 cacao landraces were surveyed from eight districts in the Central and Western Regions to evaluate the morphological and genetic diversity of cacao in Uganda. Passport data included site, tree, fruit and seed information. Trees were genotyped using 96 single nucleotide polymorphism markers on a Fluidigm platform. Low heterozygosity was detected in the germplasm in both the Central [observed heterozygosity (Ho) = 0.295, expected heterozygosity (He) = 0.334] and Western Regions (Ho = 0.317, He- = 0.322). Genetic variation in both regions was generally comparable but the regions could be differentiated from each other. Inbreeding was noted in the Central Region while a greater sharing of genetic material was observed in the Western Region. The morphological and genetic data
indicated that the Ugandan collection was an interspersed group with low to moderate variation with some separation of the Central from Western regions. Ancestry analysis indicated that the majority of the accessions were hybrids of Maranon lineage but also had Amelonado and Iquitos
genetic backgrounds. These findings are consistent with the history of the movement of cacao into Uganda. A core collection of 18 individuals to represent the genetic diversity as well as 12 additional trees with possible advantageous traits is proposed.
I shall discuss the application of algorithmic and combinatorial tools in the area of population genomics, which has not been the traditional stomping ground for algorithmicists.
The modeling of the evolutionary dynamics of evolving populations as random graphs offers a new methodology for analysis. This exploration begins as a quest for understanding the reconstructability of common evolutionary history of populations. It provides new insights including a purely topological (or graph theoretic definition) of traditional population genomic entity like the GMRCA (Grand Most Common Ancestor) of individuals under mutations as well as recombinations. Apart from giving interesting characterizations of another important structure called the ARG (Ancestral Recombinations Graph), it provides the basis for identifying a mathematical minimal nonredundant structure in the ARG and for adapting very naturally the coalescence theory (a wellstudied notion in population genetics) in designing ARG sampling algorithms. This connection also opens the door for many interesting questions ranging from human migration paths, to genetic diversity study in plant (cacao) cultivars.
Background
Proximity of food stores is associated with dietary intake and obesity; however, individuals frequently shop at stores that are not the most proximal. Little is known about other factors that influence food store choice. The current research describes the development of the Food Store Selection Questionnaire (FSSQ) and describes preliminary results of field testing the questionnaire.
Methods
Development of the FSSQ involved a multidisciplinary literature review, qualitative analysis of focus group transcripts, and expert and community reviews. Field testing consisted of 100 primary household food shoppers (93% female, 64% African American), in rural and urban Arkansas communities, rating FSSQ items as to their importance in store choice and indicating their top two reasons. After eliminating 14 items due to low mean importance scores and high correlations with other items, the final FSSQ questionnaire consists of 49 items.
Results
Items rated highest in importance were: meat freshness; store maintenance; store cleanliness; meat varieties; and store safety. Items most commonly rated as top reasons were: low prices; proximity to home; fruit/vegetable freshness; fruit/vegetable variety; and store cleanliness.
Conclusions
The FSSQ is a comprehensive questionnaire for detailing key reasons in food store choice. Although proximity to home was a consideration for participants, there were clearly other key factors in their choice of a food store. Understanding the relative importance of these different dimensions driving food store choice in specific communities may be beneficial in informing policies and programs designed to support healthy dietary intake and obesity prevention.
