Search results for: genetic difference

Authors: Dilani Wimalasiri, Robert Brkljaca, Sylvia Urban, Terrence Piva, Tien Huynh

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Momordica cochinchinensis (Cucurbitaceae) is used as food and traditional medicine in South East Asia and is commonly known as Red Gac. The fruit aril consists 70 times higher lycopene and 10 times higher β-carotene than all known fruits and vegetables. Despite its nutritional value there is little information available on its genetic variation and its influence on nutritional value. In this study; genetic and nutritional variation (lycopene and β-carotene) was investigated among 47 M. cochinchinensis samples collected from Australia, Thailand and Vietnam using molecular markers (RAPD and ISSR) and HPLC, respectively. UPGMA based cluster analysis of genetic data grouped Northern and Central Vietnam samples together but were separated from Australia, Thailand and Southern Vietnam samples. The concentration of lycopene was significantly higher among the samples collected from Central Vietnam (p<0.05) and the concentration of β-carotene was significantly higher among the samples collected from Northern Vietnam (p<0.05) indicating the existence of best varieties. This study provides vital information in genetic diversity and facilitates the selection and breeding for nutritious M. cochinchinensis varieties.

Keywords: momordica cochinchinensis, lycopene, beta carotene, genetic diversity

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Authors: Zia Amjad, Salem S. Alghamdi

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This experiment was carried out at student educational farm College of Food and Agriculture, KSU, kingdom of Saudi Arabia; in order to characterize 154 V. faba accessions based on UPOV and IBPGR descriptors. 24 agro-morphological characters including 11 quantitative and 13 qualitative were observed for genetic variation. All the results were analyzed using multivariate analysis i.e. principle component analysis (PCA). First six principle components (PC) had Eigen-value greater than one; accounted for 72% of available V. faba genetic diversity. However first three components revealed more than 10% of genetic diversity each i.e. 22.36%, 15.86% and 10.89% respectively. PCA distributed the V. faba accessions into different groups based on their performance for the characters under observation. PC-1 which represented 22.36% of the genetic diversity was positively associated with stipule spot pigmentation, intensity of streaks, pod degree of curvature and to some extent with 100 seed weight. PC-2 covered 15.86 of the genetic diversity and showed positive association for average seed weight per plant, pod length, number of seeds per plant, 100 seed weight, stipule spot pigmentation, intensity of streaks (same as in PC-1) and to some extent for pod degree of curvature and number of pods per plant. PC-3 revealed 10.89% of genetic diversity and expressed positive association for number of pods per plant and number of leaflets per plant.

Keywords: agro morphological characterization, diversity, vicia faba, PCA

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Authors: Faheema Khan

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In order to investigate the influence of genetic background on salt tolerance in Soybean (Glycine max) ten soybean genotypes released/notified in India were selected. (Pusa-20, Pusa-40, Pusa-37, Pusa-16, Pusa-24, Pusa-22, BRAGG, PK-416, PK-1042, and DS-9712). The 10-day-old seedlings were subjected to 0, 25, 50, 75, 100, 125, and 150 mM NaCl for 15 days. Plant growth, leaf osmotic adjustment, and RAPD analysis were studied. In comparison to control plants, the plant growth in all genotypes was decreased by salt stress, respectively. Salt stress decreased leaf osmotic potential in all genotypes however the maximum reduction was observed in genotype Pusa-24 followed by PK-416 and Pusa-20. The difference in osmotic adjustment between all the genotypes was correlated with the concentrations of ion examined such as Na+ and the leaf proline concentration. These results suggest that the genotypic variation for salt tolerance can be partially accounted for by plant physiological measures. The genetic polymorphisms between soybean genotypes differing in response to salt stress were characterized using 25 RAPD primers. These primers generated a total of 1640 amplification products, among which 1615 were found to be polymorphic. A very high degree of polymorphism (98.30%) was observed. UPGMA cluster analysis of genetic similarity indices grouped all the genotypes into two major clusters. Intra-clustering within the two clusters precisely grouped the 10 genotypes in sub-cluster as expected from their physiological findings. Our results show that RAPD technique is a sensitive, precise and efficient tool for genomic analysis in soybean genotypes.

Keywords: glycine max, NaCl, RAPD, proteomics

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Authors: Safa A. Mohammed Ali, Ammar S. Ahamed, Mohammed Khair Abdalla

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The objectives of this study were to estimate the means and genetic parameters of birth and weaning weight of calves of pure Holstein-Friesian cows raised in Sudan. The traits studied were:*Weight at birth *Weight at weaning. The study also included some of the important factors that affected these traits. The data were analyzed using Harvey’s Least Squares and Maximum Likelihood programme. The results obtained showed that the overall mean weight at birth of the calves under study was 34.36±0.94kg. Male calves were found to be heavier than females; the difference between the sexes was highly significant (P<0.001). The mean weight at birth of male calves was 34.27±1.17 kg while that of females was 32.51±1.14kg. The effect of sex of calves, sire and parity of dam were highly significant (P<0.001). The overall mean of weight at weaning was 67.10 ± 5.05 kg, weight at weaning was significantly (p<0.001) effected by sex of calves, sire, year and season of birth have highly significant (P<0.001) effect on either trait. Also estimates heritabilities of birth weight was (0.033±0.015) lower than heritabilities of weaning weight (0.224±0.039), and genetic correlation was 0.563, the phenotypic correlation 0.281, and the environmental correlation 0.268.

Keywords: birth, weaning, weight, friesian

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Authors: Qazi Salman Khalid, Muhammad Khalid, Shahid Maqsood

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This paper presents a solution for optimizing the cycle time in an assembly line with human-robot collaboration and diverse operators. A genetic algorithm with tailored parameters is used to address the assembly line balancing problem in the automobile sector. A mathematical model is developed, depicting the problem. Currently, the firm runs on the largest candidate rule; however, it causes a lag in orders, which ultimately gets penalized. The results of the study show that the proposed GA is effective in providing efficient solutions and that the cycle time has significantly impacted productivity.

Keywords: line balancing, cycle time, genetic algorithm, productivity

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Authors: Elsheikh Asser

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Time and cost are the main goals of the construction project management. The first schedule developed may not be a suitable schedule for beginning or completing the project to achieve the target completion time at a minimum total cost. In general, there are trade-offs between time and cost (TCT) to complete the activities of a project. This research presents genetic algorithms (GAs) multi-objective model for project scheduling considering different scenarios such as least cost, least time, and target time.

Keywords: genetic algorithms, time-cost trade-off, multi-objective model, project scheduling

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Authors: Zia Amjad, Salem Safar Alghamdi

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This experiment was carried out at student educational farm College of Food and Agriculture, KSU, kingdom of Saudi Arabia; in order to characterize 154 Vicia faba, characterization, PCA, ago-morphological diversity. Icia faba L. accessions were based on ipove and ibpgr descriptors. 24 agro-morphological characters including 11 quantitative and 13 qualitative were observed for genetic variation. All the results were analyzed using multivariate analysis i.e. principle component analysis. First 6 principle components with eigenvalue greater than one; accounted for 72% of available Vicia faba genetic diversity. However, first three components revealed more than 10% of genetic diversity each i.e. 22.36%, 15.86%, and 10.89% respectively. PCA distributed the V. faba accessions into different groups based on their performance for the characters under observation. PC-1 which represented 22.36% of the genetic diversity was positively associated with stipule spot pigmentation, intensity of streaks, pod degree of curvature and to some extent with 100 seed weight. PC-2 covered 15.86 of the genetic diversity and showed positive association for average seed weight per plant, pod length, number of seeds per plant, 100 seed weight, stipule spot pigmentation, intensity of streaks (same as in PC-1), and to some extent for pod degree of curvature and number of pods per plant. PC-3 revealed 10.89% of genetic diversity and expressed positive association for number of pods per plant and number of leaflets per plant.

Keywords: Vicia faba, characterization, PCA, ago-morphological diversity

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Authors: M. Y. Abubakar, Ipinjolu J. K., Yuzine B. Esa, Magawata I., Hassan W. A., Turaki A. A.

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Catfish (Heterobranchus spp.) is a major freshwater fish that are widely distributed in Nigeria waters and are gaining rapid aquaculture expansion. However, indiscriminate artificial crossbreeding of the species with others poses a threat to their biodiversity. There is a paucity of information about the genetic variability, hence this insight on the genetic variability is badly needed, not only for the species conservation but for aquaculture expansion. In this study, we tested the level of Genetic diversity, population differentiation and phylogenetic relationship analysis on 35 individuals of two populations of Heterobranchus bidorsalis and 29 individuals of three populations of Heterobranchus longifilis using the mitochondrial cytochrome c oxidase subunit I (mtDNA COI) gene sequence. Nucleotide sequences of 650 bp fragment of the COI gene of the two species were compared. In the whole 4 and 5 haplotypes were distinguished in the populations of H. bidorsalis & H. longifilis with accession numbers (MG334168 - MG334171 & MG334172 to MG334176) respectively. Haplotypes diversity indices revealed a range of 0.59 ± 0.08 to 0.57 ± 0.09 in H. bidorsalis and 0.000 to 0.001051 ± 0.000945 in H. longifilis population, respectively. Analysis of molecular variance (AMOVA) revealed no significant variation among H. bidorsalis population of the Niger & Benue Rivers, detected significant genetic variation was between the Rivers of Niger, Kaduna and Benue population of H. longifilis. Two main clades were recovered, showing a clear separation between H. bidorsalis and H. longifilis in the phylogenetic tree. The mtDNA COI genes studied revealed high gene flow between populations with no distinct genetic differentiation between the populations as measured by the fixation index (FST) statistic. However, a proportion of population-specific haplotypes was observed in the two species studied, suggesting a substantial degree of genetic distinctiveness for each of the population investigated. These findings present the description of the species character and accessions of the fish’s genetic resources, through gene sequence submitted in Genetic database. The data will help to protect their valuable wild resource and contribute to their recovery and selective breeding in Nigeria.

Keywords: AMOVA, genetic diversity, Heterobranchus spp., mtDNA COI, phylogenetic tree

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Authors: José A. Menezes, Giordano Cabral, Bruno T. Gomes

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Choosing good features is an essential part of machine learning. Recent techniques aim to automate this process. For instance, feature learning intends to learn the transformation of raw data into a useful representation to machine learning tasks. In automatic audio classification tasks, this is interesting since the audio, usually complex information, needs to be transformed into a computationally convenient input to process. Another technique tries to generate features by searching a feature space. Genetic algorithms, for instance, have being used to generate audio features by combining or modifying them. We find this approach particularly interesting and, despite the undeniable advances of feature learning approaches, we wanted to take a step forward in the use of genetic algorithms to find audio features, combining them with more conventional methods, like PCA, and inserting search control mechanisms, such as constraints over a confusion matrix. This work presents the results obtained on particular audio classification problems.

Keywords: feature generation, feature learning, genetic algorithm, music information retrieval

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Authors: Somayeh Akrami, Habib Onsori, Elham Tahmassebian

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Species of Anemone narcissiflora is belonged to Anemone genus of Ranunculaceae family. This species has two subspecies named narcissiflora and willdenowii which the latest is recorded in Iran in 2010. Some samples of A. narcissiflora is gathered from kuhkamar-zonouz region of East -Azerbaijan province, Iran to study the genetic diversity of the species by using RAPD molecular markers, and estimation of genetic diversity were evaluated with the using 10mer RAPD primers by PCR-RAPD method. 39 polymorphic bands were produced from the six primers used in this technique that the maximum band is related to the RP1 primer, the lowest band is related to the RP7 and the average band for all primers were 6.5 polymorphic bands. Cluster analysis of samples in done by UPGMA method in NTSYSpc 2.02 software. Dendrogram resulting from migrating bands showed that the studied samples can be divided into two groups. The first group includes samples with 1-2 flowers and the second group consists of two sub-groups which the first subgroup consists of samples with 3-5 flowers, and the second subgroup consists of samples with 6-7 flowers. The results of the comparison and analysis of the data obtained from RAPD technique and similarity matrix represents the genetic variation between collected samples. This study shows that RAPD markers can determine the polymorphisms between different genotypes of A. narcissiflora and their hybrids. So RAPD technique can serve as a suitable molecular method to determine the genetic diversity of samples.

Keywords: Anemone narcissiflora, genetic diversity, RAPD-PCR

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Authors: Shahzad Bhatti, M. Aslamkhan, Sana Abbas, Marcella Attimonelli, Hikmet Hakan Aydin, Erica Martinha Silva de Souza,

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Despite being situated at the crossroad of Asia, Pakistan has gained crucial importance because of its pivotal role in subsequent migratory events. To highlight the genetic footprints and to contribute an enigmatic picture of the relative population expansion pattern among four major Pashtun tribes in Khyber Pakhtunkhwa viz., Bangash, Khattak, Mahsuds and Orakzai, the complete mitochondrial control region of 100 Pashtun were analyzed. All Pashtun tribes studied here revealed high genetic diversity; that was comparable to the other Central Asian, Southeast Asian and European populations. The configuration of genetic variation and heterogeneity further unveiled through Multidimensional Scaling, Principal Component Analysis, and phylogenetic analysis. The results revealed that the Pashtun is a composite mosaic of West Eurasian ancestry of numerous geographic origin. They received substantial gene flow during different invasions and have a high element of the Western provenance. The most common haplogroups reported in this study are: South Asian haplogroup M (28%) and R (8%); whereas, West Asians haplogroups are present, albeit in high frequencies (67%) and widespread over all; HV (15%), U (17%), H (9%), J (8%), K (8%), W (4%), N (3%) and T (3%). Herein we linked the unexplored genetic connection between Ashkenazi Jews and Pashtun. The presence of specific haplotypes J1b (4%) and K1a1b1a (5%) point to a genetic connection of Jewish conglomeration with Khattak tribe. This was a result of an ancient genetic influx in the early Neolithic period that led to the formation of a diverse genetic substratum in present day Pashtun.

Keywords: mtDNA haplogroups, control region, Pakistan, KPK, ethnicity

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Authors: M. Vivodík, Ž. Balážová, Z. Gálová

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The aim of this work was to detect genetic variability among the set of 40 castor genotypes using 8 RAPD markers. Amplification of genomic DNA of 40 genotypes, using RAPD analysis, yielded in 66 fragments, with an average of 8.25 polymorphic fragments per primer. Number of amplified fragments ranged from 3 to 13, with the size of amplicons ranging from 100 to 1200 bp. Values of the polymorphic information content (PIC) value ranged from 0.556 to 0.895 with an average of 0.784 and diversity index (DI) value ranged from 0.621 to 0.896 with an average of 0.798. The dendrogram based on hierarchical cluster analysis using UPGMA algorithm was prepared and analyzed genotypes were grouped into two main clusters and only two genotypes could not be distinguished. Knowledge on the genetic diversity of castor can be used for future breeding programs for increased oil production for industrial uses.

Keywords: dendrogram, polymorphism, RAPD technique, Ricinus communis L.

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Authors: Pratiksha Saxena, Dipti Singh, Neha Khanna

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A self-organizing migrating genetic algorithm(C-SOMGA) is developed for animal diet formulation. This paper presents animal diet formulation using stochastic and genetic algorithm. Tri-objective models for cost minimization and shelf life maximization are developed. These objectives are achieved by combination of stochastic programming and C-SOMGA. Stochastic programming is used to introduce nutrient variability for animal diet. Self-organizing migrating genetic algorithm provides exact and quick solution and presents an innovative approach towards successful application of soft computing technique in the area of animal diet formulation.

Keywords: animal feed ration, feed formulation, linear programming, stochastic programming, self-migrating genetic algorithm, C-SOMGA technique, shelf life maximization, cost minimization, nutrient maximization

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Authors: Mariana Lima, Rodrigo Silva, Victor Stange, Teodiano Bastos

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Due to the high reliability reached by DNA tests, since the 1980s this kind of test has allowed the identification of a growing number of criminal cases, including old cases that were unsolved, now having a chance to be solved with this technology. Currently, the use of genetic profiling databases is a typical method to increase the scope of genetic comparison. Forensic laboratories must process, analyze, and generate genetic profiles of a growing number of samples, which require time and great storage capacity. Therefore, it is essential to develop methodologies capable to organize and minimize the spent time for both biological sample processing and analysis of genetic profiles, using software tools. Thus, the present work aims the development of a software system solution for laboratories of forensics genetics, which allows sample, criminal case and local database management, minimizing the time spent in the workflow and helps to compare genetic profiles. For the development of this software system, all data related to the storage and processing of samples, workflows and requirements that incorporate the system have been considered. The system uses the following software languages: HTML, CSS, and JavaScript in Web technology, with NodeJS platform as server, which has great efficiency in the input and output of data. In addition, the data are stored in a relational database (MySQL), which is free, allowing a better acceptance for users. The software system here developed allows more agility to the workflow and analysis of samples, contributing to the rapid insertion of the genetic profiles in the national database and to increase resolution of crimes. The next step of this research is its validation, in order to operate in accordance with current Brazilian national legislation.

Keywords: database, forensic genetics, genetic analysis, sample management, software solution

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Authors: Ammar Said Ahmed, M. Reissmann, R. Bortfeldt, G. A. Brockmann

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Milk protein genetic variants are of interest for characterizing domesticated mammalian species and breeds, and for studying associations with economic traits. The aim of this work was to analyze milk protein genetic variation in the Sudanese native cattle breeds, which have been gradually declining in numbers over the last years due to the breed substitution, and indiscriminate crossbreeding. The genetic variation at three milk protein genes αS1-casein (CSN1S1), αS2-casein (CSN1S2) and ƙ-casein (CSN3) was investigated in 250 animals belonging to five Bos indicus cattle breeds of Sudan (Butana, Kenana, White-nile, Erashy and Elgash). Allele specific primers were designed for five SNPs determine the CSN1S1 variants B and C, the CSN1S2 variants A and B, the CSN3 variants A, B and H. Allele, haplotype frequencies and genetic distances (D) were calculated and the phylogenetic tree was constructed. All breeds were found to be polymorphic for the studied genes. The CSN1S1*C variant was found very frequently (>0.63) in all analyzed breeds with highest frequency (0.82) in White-nile cattle. The CSN1S2*A variant (0.77) and CSN3*A variant (0.79) had highest frequency in Kenana cattle. Eleven haplotypes in casein gene cluster were inferred. Six of all haplotypes occurred in all breeds with remarkably deferent frequencies. The estimated D ranged from 0.004 to 0.049. The most distant breeds were White-nile and Kenana (D 0.0479). The results presented contribute to the genetic knowledge of indigenous cattle and can be used for proper definition and classification of the Sudanese cattle breeds as well as breeding, utilization, and potential development of conservation strategies for local breeds.

Keywords: milk protein, genetic variation, casein haplotype, Bos indicus

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Authors: H. Kalboussi, A. Aloui, W. Boughattas, M. Maoua, A. Brahem, S. Chatti, O. El Maalel, F. Debbabi, N. Mrizak, Y. Ben Youssef, A. Khlif, I. Bougmiza

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Background: In recent decades, the incidence of children's hematological malignancies has been increasing worldwide including Tunisia. Their severity is reflected in the importance of the medical, social and economic impact. This increase remains fully unexplained, and the involvement of genetic, environmental and occupational factors is strongly suspected. Materials and Methods: Our study is a cross-sectional survey of the type case-control conducted in the University Hospital of Farhat Hached of Sousse during the period ranging between 1 July 2011 and 30 June 2012,and which included children with acute leukemia compared to children unharmed by neoplastic disease . Cases and controls were matched by age and gender. Our objective was to: - Describe the socio-occupational characteristics of the parents of children with acute leukemia. - Identify potential occupational factors implicated in the genesis of acute leukemia. Result: The number of acute leukemia cases in the Hematology Service and day hospital of the University Hospital of Farhat Hached during the study period was 66 cases divided into in 40 boys and 26 girls with a sex ratio of 1.53. Our cases and controls were matched by age and gender. The risk of incidence of leukemia in children from smoking fathers was higher (p = 0.02, OR = 2.24, IC = [1.11 - 4.52]). The risk of incidence of leukemia in children from alcoholic fathers was higher with p = 0,009, OR = 3.9; CI = [1.33 - 11.39]. After adjusting different variables, the difference persisted significantly with pa = 0.03 and ORa = 3.5; ICa = [1.09 -11.6]. 25.7 % of cases had a family history of blood disease and neoplasia, whereas no control presented that. The difference was statistically significant (p = 0.006), OR = 1.46, IC = [1.38 - 1.56]. The parental occupational exposures associated to the occurrence of acute leukemia in children were: - Pesticides with a statistically significant difference (p = 0.03), OR = 2.94, IC = [1.06 - 8.13]. This difference persisted after adjustment with different variables pa = 0.01, ORa 3.75; ICa = [1.27 - 11.03]. - Cement without a statistically non-significant difference (p = 0.2). This difference has become significant after adjustment with the different variables pa = 0.03; ORa = 2.67; ICa = [1.06 - 6.7]. Conclusion: Parental exposure to occupational risk factors may play a role in the pathogenesis of acute leukemia in children.

Keywords: hematological malignancies, children, parents, occupational exposure

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Authors: Ahmed Najah Ahmed Al-Mahfoodh, Ali Najah Ahmed Al-Mahfoodh, Ahmed Al-Shafie

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In this study, genetic programming (GP) technique has been investigated in prediction of set of rainfall-runoff data. To assess the effect of input parameters on the model, the sensitivity analysis was adopted. To evaluate the performance of the proposed model, three statistical indexes were used, namely; Correlation Coefficient (CC), Mean Square Error (MSE) and Correlation of Efficiency (CE). The principle aim of this study is to develop a computationally efficient and robust approach for predict of rainfall-runoff which could reduce the cost and labour for measuring these parameters. This research concentrates on the Johor River in Johor State, Malaysia.

Keywords: genetic programming, prediction, rainfall-runoff, Malaysia

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Authors: Rachel Matar, Maxime Merheb

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Chemical drugs have been used for many centuries as the only way to cure diseases until the novel gene therapy has been created in 1960. Gene therapy is based on the insertion, correction, or inactivation of genes to treat people with genetic illness (1). Gene therapy has made wonders in Parkison’s, Alzheimer and multiple sclerosis. In addition to great promises in the healing of deadly diseases like many types of cancer and autoimmune diseases (2). This method implies the use of recombinant DNA technology with the help of different viral and non-viral vectors (3). It is nowadays used in somatic cells as well as embryos and gametes. Beside all the benefits of gene therapy, this technique is deemed by some opponents as an ethically unacceptable treatment as it implies playing with the genes of living organisms.

Keywords: gene therapy, genetic disease, cancer, multiple sclerosis

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Authors: Thananyada Buapian

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Overnutrition is emerging as a morbid disease in developing and Westernized countries. Because of its comorbidity diseases, it is cost-effective to prevent and manage this disease earlier. In Thailand, this alarming disease has long been studied, but the prevalence is still higher than that in the past. Physicians should recognize it well and have a definite direction to face and combat this dangerous disease. Rapid changes in the tremendous figure of overnutrition students indicate that genetic factors are not the primary determinants since human genes have remained unchanged for a century. This study aims to assess the prevalence of overnutrition students and to investigate the non-genetic factors affecting over nutrition students. A cross-sectional school-based survey was conducted. A two-stage sampling was adopted. Respondents included 1,850 students in grades 4 to 6 in Ayutthaya Province. An anthropometric measurement and questionnaire were developed. Childhood over nutrition was defined as a weight-for-height Z-score above +2SD of NCHS/WHO references. About thirty three percent of the children were over nutrition in Ayutthaya province. Stepwise multiple logistic regression analysis showed that 8 statistically significant non genetic factors explain the variation of childhood over nutrition by 18 percent. Sex is the prime factor to explain the variation of childhood over nutrition, followed by duration of light physical activities, duration of moderate physical activities, having been breastfed, the presence of a healthy role model of the caregiver, number of siblings, birth order, and occupation of the caregiver, respectively. Non genetic factors, especially the subjects’ demographic and physical activities, as well as the caregivers’ background and family environment, should be considered in viable approach to remedy this health imbalance in children.

Keywords: non genetic factors, non-genetic, over nutrition, over nutrition students

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Authors: Tony See

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Although much has been devoted to Deleuze’s ethics of difference, relatively little has been focused on how his political perspective is informed by his appropriation of religious ideas and theological concepts. The bulk of the scholarly works have examined his political views with the assumption that they have little or nothing to do with his ideas of religions at all. This is in spite of the fact that Deleuze has drawn heavily from religious and theological thinkers such as Duns Scotus, Spinoza and Nietzsche. This dimension can also be traced in Deleuze’s later works, when he collaborated with Felix Guattari in creating an anti-Oedipal philosophy of difference after May 68. This paper seeks to reverse the tendency in contemporary scholarship ignore Deleuze’s ‘religious’ framework in his understanding of the ethical and the political. Towards this aim, we will refer to key texts in Deleuze’s corpus such as Expressionism in Philosophy, A Thousand Plateaus and others.

Keywords: difference, haeccities, identity, religion, theology

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Authors: Dheyaa W. Abbood, Rafa H. AL-Suhaili, May S. Saleh

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A model using the artificial neural networks and genetic algorithm technique is developed for obtaining optimum dimensions of the foundation length and protections of small hydraulic structures. The procedure involves optimizing an objective function comprising a weighted summation of the state variables. The decision variables considered in the optimization are the upstream and downstream cutoffs length sand their angles of inclination, the foundation length, and the length of the downstream soil protection. These were obtained for a given maximum difference in head, depth of impervious layer and degree of anisotropy.The optimization carried out subjected to constraints that ensure a safe structure against the uplift pressure force and sufficient protection length at the downstream side of the structure to overcome an excessive exit gradient. The Geo-studios oft ware, was used to analyze 1200 different cases. For each case the length of protection and volume of structure required to satisfy the safety factors mentioned previously were estimated. An ANN model was developed and verified using these cases input-output sets as its data base. A MatLAB code was written to perform a genetic algorithm optimization modeling coupled with this ANN model using a formulated optimization model. A sensitivity analysis was done for selecting the cross-over probability, the mutation probability and level ,the number of population, the position of the crossover and the weights distribution for all the terms of the objective function. Results indicate that the most factor that affects the optimum solution is the number of population required. The minimum value that gives stable global optimum solution of this parameters is (30000) while other variables have little effect on the optimum solution.

Keywords: inclined cutoff, optimization, genetic algorithm, artificial neural networks, geo-studio, uplift pressure, exit gradient, factor of safety

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Authors: Ibrahim Ilker Ozyigit, Ertugrul Filiz, Seda Birbilener, Semsettin Kulac, Zeki Severoglu

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In this study, we have performed genetic diversity analysis of Tilia tomentosa genotypes by using randomly amplified polymorphic DNA (RAPD) primers. A total of 28 genotypes, including 25 members from the urban ecosystem and 3 genotypes from forest ecosystem as outgroup were used. 8 RAPD primers produced a total of 53 bands, of which 48 (90.6 %) were polymorphic. Percentage of polymorphic loci (P), observed number of alleles (Na), effective number of alleles (Ne), Nei's (1973) gene diversity (h), and Shannon's information index (I) were found as 94.29 %, 1.94, 1.60, 0.34, and 0.50, respectively. The unweighted pair-group method with arithmetic average (UPGMA) cluster analysis revealed that two major groups were observed. The genotypes of urban and forest ecosystems showed a high genetic similarity between 28% and 92% and these genotypes did not separate from each other in UPGMA tree. Also, urban and forest genotypes clustered together in principal component analysis (PCA).

Keywords: Tilia tomentosa, genetic diversity, urban ecosystem, RAPD, UPGMA

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Authors: Guilherme Baldo Carlos

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The flexible job-shop scheduling problem (FJSP) is an NP-hard combinatorial optimization problem, which can be applied to model several applications in a wide array of industries. This problem will have its importance increase due to the shift in the production mode that modern society is going through. The demands are increasing and for products personalized and customized. This work aims to apply a meta-heuristic called a genetic algorithm (GA) to solve this problem. A GA is a meta-heuristic inspired by the natural selection of Charles Darwin; it produces a population of individuals (solutions) and selects, mutates, and mates the individuals through generations in order to find a good solution for the problem. The results found indicate that the GA is suitable for FJSP solving.

Keywords: genetic algorithm, evolutionary algorithm, scheduling, flexible job-shop scheduling

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Authors: Han Bing, Yin Zhenjie

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In order to analyze the status of a diesel engine, as well as conduct fault prediction, a new prediction model based on a gray system is proposed in this paper, which takes advantage of the neural network and the genetic algorithm. The proposed GBPGA prediction model builds on the GM (1.5) model and uses a neural network, which is optimized by a genetic algorithm to construct the error compensator. We verify our proposed model on the diesel faulty simulation data and the experimental results show that GBPGA has the potential to employ fault prediction on diesel.

Keywords: fault prediction, neural network, GM(1, 5) genetic algorithm, GBPGA

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Authors: Yasser M. Saad, Amr A. El Hanafy, Saleh A. Alkarim, Hussein A. Almehdar, Elrashdy M. Redwan

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Camels are substantial providers of transport, milk, sport, meat, shelter, security and capital in many countries, particularly in Saudi Arabia. Inter simple sequence repeat technique was used to detect the genetic variations among some camel breeds (Majaheim, Safra, Wadah, and Hamara). Actual number of alleles, effective number of alleles, gene diversity, Shannon’s information index and polymorphic bands were calculated for each evaluated camel breed. Neighbor-joining tree that re-constructed for evaluated these camel breeds showed that, Hamara breed is distantly related from the other evaluated camels. In addition, the polymorphic sites, haplotypes and nucleotide diversity were identified for some camelidae cox1 gene sequences (obtained from NCBI). The distance value between C. bactrianus and C. dromedarius (0.072) was relatively low. Analysis of genetic diversity is an important way for conserving Camelus dromedarius genetic resources.

Keywords: camel, genetics, ISSR, neighbor-joining

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Authors: Techale B., Hongxu Dong, Mihrete Getinet, Aregash Gabizew, Andrew H. Paterson, Kassahun Bantte

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The genetic architecture of drought tolerance is expected to involve multiple loci that are unlikely to all segregate for alternative alleles in a single bi-parental population. Therefore, the identification of quantitative trait loci (QTL) that are expressed in diverse genetic backgrounds of multiple bi-parental populations provides evidence about both background-specific and common genetic variants. The purpose of this study was to map QTL related to drought tolerance using three connected mapping populations of different genetic backgrounds to gain insight into the genomic landscape of this important trait in elite Ethiopian germplasm. The three bi-parental populations, each with 207 F₂:₃ lines, were evaluated using an alpha lattice design with two replications under two moisture stress environments. Drought tolerance related traits were analyzed separately for each population using composite interval mapping, finding a total of 105 QTLs. All the QTLs identified from individual populations were projected on a combined consensus map, comprising a total of 25 meta QTLs for seven traits. The consensus map allowed us to deduce locations of a larger number of markers than possible in any individual map, providing a reference for genetic studies in different genetic backgrounds. The mQTL identified in this study could be used for marker-assisted breeding programs in sorghum after validation. Only one trait, reduced leaf senescence, showed a striking bias of allele distribution, indicating substantial standing variation among present varieties that might be employed in improving drought tolerance of Ethiopian and other sorghums.

Keywords: Drought tolerance , Mapping populations, Meta QTL, QTL mapping, Sorghum

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Authors: Reza Talebi

Abstract:

Wheat (Triticum aestivum) is one of the most important food staples in Iran. Understanding genetic variability among the landrace wheat germplasm is important for breeding. Landraces endemic to Iran are a genetic resource that is distinct from other wheat germplasm. In this study, 60 Iranian landrace wheat accessions were characterized AFLP and ISSR markers. Twelve AFLP primer pairs detected 128 polymorphic bands among the sixty genotypes. The mean polymorphism rate based on AFLP data was 31%; however, a wide polymorphism range among primer pairs was observed (22–40%). Polymorphic information content (PIC value) calculated to assess the informativeness of each marker ranged from 0.28 to 0.4, with a mean of 0.37. According to AFLP molecular data, cluster analysis grouped the genotypes in five distinct clusters. .ISSR markers generated 68 bands (average of 6 bands per primer), which 31 were polymorphic (45%) across the 60 wheat genotypes. Polymorphism information content (PIC) value for ISSR markers was calculated in the range of 0.14 to 0.48 with an average of 0.33. Based on data achieved by ISSR-PCR, cluster analysis grouped the genotypes in three distinct clusters. Both AFLP and ISSR markers able to showed that high level of genetic diversity in Iranian landrace wheat accessions has maintained a relatively constant level of genetic diversity during last years.

Keywords: wheat, genetic diversity, AFLP, ISSR

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Authors: Mercy Chepkirui, Paul Orina, Priscilla Boera, Judith Achoki

Abstract:

Oreochromis jipe is a tropical freshwater bentho-pelagic fish belonging to the Cichlid family that is endemic to the Pangani River basin and Lake Jipe in Kenya and northern Tanzania, while Oreochromis niloticus inhabits the Lake Victoria basin with reported cases in Lake jipe too. Unlike O. jipe, Oreochromis niloticus is spreading across the globe due to its cultural potential. This, however, could cause genetic purity concerns in the event of cross-breeding among the tilapiines, which is already taking place in the wild. The study envisaged establishing the possibility of hybridization among the two species under aquaculture conditions and phenotypically informing the difference between pure and cross lines. Two hundred sixteen mature brooders weighing 100-120g were selected randomly, 108 of Oreochromis Jipe and 108 of Oreochromis niloticus; for each trial, 72 males and 144 females were distributed into 3 crosses, each grouped in triplicates (Oreochromis niloticus (♀) X Oreochromis niloticus(♂);Oreochromis niloticus (♂) X Oreochromis jipe ( ♀); Oreochromis jipe (♂) X Oreochromis niloticus (♀); Oreochromis jipe (♂) X Oreochromis jipe (♀). All trials had the F1 generation, which is currently undergoing growth trials and assessing its viability for the 2nd generation. The results indicated that Oreochromis niloticus has better growth, followed by crosses (Oreochromis niloticus X Oreochromis jipe) and, finally, pure line Oreochromis jipe. Further, pure Oreochromis jipe F1 demonstrated potential for aquaculture adoption despite its recent introduction into aquaculture; thus, this will help towards the conservation of indigenous fish species of Lake Jipe fishery, which is currently under the Internationa Union for Conservation of Nature Red List of endangered fish species. However, there is a need to inform the purity of existing Oreochromis jipe wild stocks to inform genetic material conservation.

Keywords: biodiversity, climate change, fisheries, oreochromis jipe, conservation

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Authors: Ilian Badjakov, Ivayla Dincheva, Violeta Kondakova, Rossitza Batchvarova

Abstract:

In this study, we present our initial results on the assessment of genetic diversity among wild Bulgarian berry accessions (Rubus idaeus L. Fragaria Vesca L., Vaccinium vitis-idaea L., Vaccinium myrtillus L.) using Random Amplified Polymorphic DNA (RAPDs) markers. Leaves and fruits were collected from two natural habitats - the Balkan Mountain and the Mountain of Orpheus - Rhodope Mountain. All accessions were screened for their polymorphism using five RAPD primers. The phylogenetic distances calculated from RAPD data ranged from 0.29 to 0.82 thus indicating that a high level of gene diversity is present in the selected genotypes. In order to characterize further the structure and grouping of berry accessions, a dendrogram deriving from UPGMA cluster analysis based on the genetic similarity (GS) coefficient matrix was designed. RAPD analysis provided to be efficient for discrimination of accessions within the same species with similar morphological characters

Keywords: Bulgarian wild berries, genetic diversity, RAPD, UPGMA

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Authors: Hailekiros Tadesse Tekle, Yemane Tsehaye, Fetien Abay

Abstract:

Barley (Hordeum vulgare L.) is one of the most important cereal crops in the world, grown for the poor farmers in Tigray with low yield production. The purpose of this research was to estimate the performance of 166 barley genotypes against the quantitative traits with detailed analysis of the variance component, heritability, genetic advance, and genetic usefulness parameters. The finding of ANOVA was highly significant variation (p ≤ 0:01) for all the genotypes. We found significant differences in coefficient of variance (CV of 15%) for 5 traits out of the 12 quantitative traits. The topmost broad sense heritability (H2) was recorded for seeds per spike (98.8%), followed by thousand seed weight (96.5%) with 79.16% and 56.25%, respectively, of GAM. The traits with H2 ≥ 60% and GA/GAM ≥ 20% suggested the least influenced by the environment, governed by the additive genes and direct selection for improvement of such beneficial traits for the studied genotypes. Hence, the 20 outstanding recombinant inbred lines (RIL) barley genotypes performing early maturity, high yield, and 1000 seed weight traits simultaneously were the top ranked group barley genotypes out of the 166 genotypes. These are; G5, G25, G33, G118, G36, G123, G28, G34, G14, G10, G3, G13, G11, G32, G8, G39, G23, G30, G37, and G26. They were early in maturity, high TSW and GYP (TSW ≥ 55 g, GYP ≥ 15.22 g/plant, and DTM below 106 days). In general, the 166 genotypes were classified as high (group 1), medium (group 2), and low yield production (group 3) genotypes in terms of yield and yield component trait analysis by clustering; and genotype parameter analysis such as the heritability, genetic advance, and genetic usefulness traits in this investigation.

Keywords: barley, clustering, genetic advance, heritability, usefulness, variability, yield

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