Pub Date : 2020-05-18DOI: 10.11648/J.IJGG.20200802.15
E. Andrew, O. Dorcas, Olaoye Olawale
Trace elements are very critical for rice growth of which Cu is one of the essential trace elements for rice and excess of cupper becomes toxic to rice growth. The aim of this study was to determine the productivity increase in rice crop and genotype reactions to application of Copper under the tropical rainforest condition. Three experiments were established concurrently in randomized complete block design in three replications in pots. Treatment comprised of 6 breeding lines each from two rice populations of F2 and F3 generations and two popular checks. Experiment one is the control without CuSO4 treatment, while experiment two and three is the F2 and F3 populations, respectively treated with CuSO4 solution. Three concentration levels of CuSO4 solution (15mg Cu /kg of soil, 30mg Cu /kg of soil and 60mg Cu /kg of soil) were applied into each pots a week before transplanting in the treated experiments. This study observed that at 30mg of Cu/kg of soil is the optimum level for rice performance based on these experiments beyond, reduction in rice performance. Reduction of 24.92% and 22.12% of total grain yield of F2 and F3 populations at 60mg of Cu/kg of soil as compared to the control were recorded, stable and high yielding genotypes across the copper concentration levels were identified for copper breeding programme.
微量元素对水稻生长至关重要，其中铜是水稻必需的微量元素之一，过量的铜对水稻生长有毒害作用。本研究旨在研究热带雨林条件下施用铜对水稻产量的影响及其基因型反应。采用随机完全区组设计，3个重复，同时建立3个试验。处理包括F2和F3代两个水稻群体各6个选育系和2个普通对照。试验1为未加CuSO4处理的对照，试验2和试验3分别为加CuSO4溶液处理的F2和F3群体。在移栽前一周，每盆分别施用15mg Cu /kg土壤、30mg Cu /kg土壤和60mg Cu /kg土壤3种浓度的CuSO4溶液。本研究发现，在这些试验基础上，30mg Cu/kg土壤是水稻生产性能的最佳水平，超出了水稻生产性能的降低。结果表明，与对照相比，在60mg Cu/kg土壤处理下，F2和F3群体的籽粒总产量分别降低了24.92%和22.12%，并在铜育种计划中确定了不同铜浓度水平下稳定和高产的基因型。
{"title":"Effects of Copper (Cu) on Yield Components and Associated Traits in Segregating Populations of Lowland Rice (O. sativa L.)","authors":"E. Andrew, O. Dorcas, Olaoye Olawale","doi":"10.11648/J.IJGG.20200802.15","DOIUrl":"https://doi.org/10.11648/J.IJGG.20200802.15","url":null,"abstract":"Trace elements are very critical for rice growth of which Cu is one of the essential trace elements for rice and excess of cupper becomes toxic to rice growth. The aim of this study was to determine the productivity increase in rice crop and genotype reactions to application of Copper under the tropical rainforest condition. Three experiments were established concurrently in randomized complete block design in three replications in pots. Treatment comprised of 6 breeding lines each from two rice populations of F2 and F3 generations and two popular checks. Experiment one is the control without CuSO4 treatment, while experiment two and three is the F2 and F3 populations, respectively treated with CuSO4 solution. Three concentration levels of CuSO4 solution (15mg Cu /kg of soil, 30mg Cu /kg of soil and 60mg Cu /kg of soil) were applied into each pots a week before transplanting in the treated experiments. This study observed that at 30mg of Cu/kg of soil is the optimum level for rice performance based on these experiments beyond, reduction in rice performance. Reduction of 24.92% and 22.12% of total grain yield of F2 and F3 populations at 60mg of Cu/kg of soil as compared to the control were recorded, stable and high yielding genotypes across the copper concentration levels were identified for copper breeding programme.","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"4 1","pages":"85"},"PeriodicalIF":0.0,"publicationDate":"2020-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78807966","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-04-08DOI: 10.11648/J.IJGG.20200802.14
Mohammed Youssif Mohammed, Afra M. Al Bkrye, H. A. Elnasri, M. A. Khaier
Background: The AGT gene is gene responsible for regulation of protein called angiotensinogen which regulates blood pressure and balances fluids in the body. Hypertension happens due to many causes one of this is the defect in AGT gene. Hypertension usually has no symptoms. However, it is a major risk factor for heart diseases, stroke, kidney failure, and eye problems. Objectives: in this study we use software to analyze the gene using different software and represented statistically and to detect the SNPs that can cause the disease. Material and Method: In this analysis using many software tools that can analyze the nsSNPs retrieved from NCBI website. These software include SIFT, I-mutant, Polyphen-2, PHD SNP and SNP& Go, Projecthop and GeneMANIA. Results: The study showed that from 172 nsSNPs only 46 nsSNPs were deleterious while 126 were tolerated using SIFT. Two were benign, 11 were possibly damaging and 33 were probably damaging by Polyphen-2. Using Provean, 19 nsSNPs were neutral and 27 were deleterious. For PHD-SNP software 20 nsSNPs were disease related and 18 were neutral. Also SNPs were checked using SNP & Go software that showed 32 neutral nsSNPs and 14 nsSNPs were disease associated variants. Using I-Mutant software 13 nsSNPs increase the stability of the protein and 33 decrease the protein stability. Conclusions: In conclusion, extensive functional and structural analyses are carried out to predict potentially damaging and deleterious nsSNPs of AGT gene using bioinformatics and computational methods. In the study, 14 high confidence damaging nsSNPs are identified from 172 nsSNPs. Although bioinformatics tools have their limitations, the results from the present study may be convenient in future for further population based research activities and towards development of accuracy medicines.
{"title":"Data Analysis of Single Nucleotide Polymorphism in Human AGT Gene Using Computational Approach","authors":"Mohammed Youssif Mohammed, Afra M. Al Bkrye, H. A. Elnasri, M. A. Khaier","doi":"10.11648/J.IJGG.20200802.14","DOIUrl":"https://doi.org/10.11648/J.IJGG.20200802.14","url":null,"abstract":"Background: The AGT gene is gene responsible for regulation of protein called angiotensinogen which regulates blood pressure and balances fluids in the body. Hypertension happens due to many causes one of this is the defect in AGT gene. Hypertension usually has no symptoms. However, it is a major risk factor for heart diseases, stroke, kidney failure, and eye problems. Objectives: in this study we use software to analyze the gene using different software and represented statistically and to detect the SNPs that can cause the disease. Material and Method: In this analysis using many software tools that can analyze the nsSNPs retrieved from NCBI website. These software include SIFT, I-mutant, Polyphen-2, PHD SNP and SNP& Go, Projecthop and GeneMANIA. Results: The study showed that from 172 nsSNPs only 46 nsSNPs were deleterious while 126 were tolerated using SIFT. Two were benign, 11 were possibly damaging and 33 were probably damaging by Polyphen-2. Using Provean, 19 nsSNPs were neutral and 27 were deleterious. For PHD-SNP software 20 nsSNPs were disease related and 18 were neutral. Also SNPs were checked using SNP & Go software that showed 32 neutral nsSNPs and 14 nsSNPs were disease associated variants. Using I-Mutant software 13 nsSNPs increase the stability of the protein and 33 decrease the protein stability. Conclusions: In conclusion, extensive functional and structural analyses are carried out to predict potentially damaging and deleterious nsSNPs of AGT gene using bioinformatics and computational methods. In the study, 14 high confidence damaging nsSNPs are identified from 172 nsSNPs. Although bioinformatics tools have their limitations, the results from the present study may be convenient in future for further population based research activities and towards development of accuracy medicines.","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"31 1","pages":"78"},"PeriodicalIF":0.0,"publicationDate":"2020-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81560188","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-03-24DOI: 10.11648/J.IJGG.20200802.13
Gueye Rokhaya, Tendeng Jacques Noël, Kénémé Bineta, S. Mbacke
Fibroadenoma is the most common benign breast tumor in women under 30 years. This study aimed to contribute to the knowledge of the genetic factors involved in the occurrence and progression of mammary fibroadenomas. MED12 and CYP17A1 were sequenced in fibroadenomas and blood in 43 Senegalese women. The Alamut-visual software, which includes the pathogenicity prediction software SIFT, Polyphen2 and MutationTaster, was used to search for mutations. DnaSP version 5.10.01, MEGA version 7.0.14 and Arlequin version 3.5.1.3 were used to determine phylogenetic parameters including indices of genetic variability and diversity and genetic differentiation parameters. A deletion in the poly-A tail of MED12 was identified in our study population. An alteration of Methionine (M1) was observed on exon 1 of CYP17A1. Our results also show that most of the variants found on exon 2 of MED12 and exon 1 of CYP17A1 have the probability of causing the appearance of breast fibroadenomas according by the three pathogenicity prediction software. We found 23 new variants on the MED12 gene and 109 new variants on the CYP17A1 gene. The amino acid frequency distribution between blood and fibroadenomas shows a statistically significant difference in Glycine, Arginine and Valine for MED12 and Cysteine, Phenylalanine, Histidine, Asparagine, Arginine, Tryptophan and Tyrosine for CYP17A1. In addition the selection test shows that codon 20 of exon 1 of CYP17A1 which codes for Arginine (p.20Arg) is under positive selection in mammary fibroadenomas. Genetic differentiation parameters show a clear difference between blood and breast fibroadenomas. These results show for the first time the involvement of the CYP17A1 gene in breast fibroadenomas and confirm the involvement of MED12. Codon 20 of exon 1 of CYP17A1 being under positive selection could be used as a biomarker in breast fibroadenomas.
{"title":"Prevalence of Mutations of the MED12 and CYP17A1 Genes in Mammary Fibroadenomas in Senegalese Women","authors":"Gueye Rokhaya, Tendeng Jacques Noël, Kénémé Bineta, S. Mbacke","doi":"10.11648/J.IJGG.20200802.13","DOIUrl":"https://doi.org/10.11648/J.IJGG.20200802.13","url":null,"abstract":"Fibroadenoma is the most common benign breast tumor in women under 30 years. This study aimed to contribute to the knowledge of the genetic factors involved in the occurrence and progression of mammary fibroadenomas. MED12 and CYP17A1 were sequenced in fibroadenomas and blood in 43 Senegalese women. The Alamut-visual software, which includes the pathogenicity prediction software SIFT, Polyphen2 and MutationTaster, was used to search for mutations. DnaSP version 5.10.01, MEGA version 7.0.14 and Arlequin version 3.5.1.3 were used to determine phylogenetic parameters including indices of genetic variability and diversity and genetic differentiation parameters. A deletion in the poly-A tail of MED12 was identified in our study population. An alteration of Methionine (M1) was observed on exon 1 of CYP17A1. Our results also show that most of the variants found on exon 2 of MED12 and exon 1 of CYP17A1 have the probability of causing the appearance of breast fibroadenomas according by the three pathogenicity prediction software. We found 23 new variants on the MED12 gene and 109 new variants on the CYP17A1 gene. The amino acid frequency distribution between blood and fibroadenomas shows a statistically significant difference in Glycine, Arginine and Valine for MED12 and Cysteine, Phenylalanine, Histidine, Asparagine, Arginine, Tryptophan and Tyrosine for CYP17A1. In addition the selection test shows that codon 20 of exon 1 of CYP17A1 which codes for Arginine (p.20Arg) is under positive selection in mammary fibroadenomas. Genetic differentiation parameters show a clear difference between blood and breast fibroadenomas. These results show for the first time the involvement of the CYP17A1 gene in breast fibroadenomas and confirm the involvement of MED12. Codon 20 of exon 1 of CYP17A1 being under positive selection could be used as a biomarker in breast fibroadenomas.","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"11 1","pages":"66"},"PeriodicalIF":0.0,"publicationDate":"2020-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87243539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2020-03-18DOI: 10.11648/J.IJGG.20200802.12
Fidelis Charles Bugoye, Elias Zakaria Mulima, D. L. Elias, Fidelis Saimon Segumba, Leticia Nchagwa Waitara
The Government Chemist Laboratory Authority (GCLA) in Tanzania is the only institution offering DNA testing in solving various human identification challenges using Human DNA technology. Globally, forensic DNA typing has undeniably been a useful tool employed in cases such as criminal investigation,, missing persons and parentage testing. In Tanzania, the indispensable need for Human DNA technology in human identification was greatly emphasized in August 2009 following the inferno at Idodi secondary school in Iringa region whereby the fire burnt and razed a girl’s dormitory to the ground killing twelve girls student while leaving twenty students severely wounded. The cause of the fire was later determined to have been due to a lit candle by a student aiming to study late into the night even after the power generator had been switched off. DNA typing of 15 autosomal Short Tandem Repeat markers using ABI 3100 Genetic Analyser was performed on samples collected from the recovered deceased bodies and their relatives. Successful human identification was achieved for all twelve recovered bodies and their reunification with their respective families. Therefore, the Idodi gruesome incident marked both an icon in scientific approach towards the utilization of DNA technology for disaster victim identification and usefulness of experts’ collaborations from different disciplines in mass fatalities and human identification in Tanzania.
{"title":"DNA Identification of Human Remains in Disaster Victim Identification (DVI): An Identification of Burned Girls Students in Tanzania","authors":"Fidelis Charles Bugoye, Elias Zakaria Mulima, D. L. Elias, Fidelis Saimon Segumba, Leticia Nchagwa Waitara","doi":"10.11648/J.IJGG.20200802.12","DOIUrl":"https://doi.org/10.11648/J.IJGG.20200802.12","url":null,"abstract":"The Government Chemist Laboratory Authority (GCLA) in Tanzania is the only institution offering DNA testing in solving various human identification challenges using Human DNA technology. Globally, forensic DNA typing has undeniably been a useful tool employed in cases such as criminal investigation,, missing persons and parentage testing. In Tanzania, the indispensable need for Human DNA technology in human identification was greatly emphasized in August 2009 following the inferno at Idodi secondary school in Iringa region whereby the fire burnt and razed a girl’s dormitory to the ground killing twelve girls student while leaving twenty students severely wounded. The cause of the fire was later determined to have been due to a lit candle by a student aiming to study late into the night even after the power generator had been switched off. DNA typing of 15 autosomal Short Tandem Repeat markers using ABI 3100 Genetic Analyser was performed on samples collected from the recovered deceased bodies and their relatives. Successful human identification was achieved for all twelve recovered bodies and their reunification with their respective families. Therefore, the Idodi gruesome incident marked both an icon in scientific approach towards the utilization of DNA technology for disaster victim identification and usefulness of experts’ collaborations from different disciplines in mass fatalities and human identification in Tanzania.","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"3 1","pages":"63"},"PeriodicalIF":0.0,"publicationDate":"2020-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87513926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Of all mammals the rodents have an importance and great diversity. The phylogenetic relationships between the different species of the order Rodentia has an interest and investigations for many researchers. The current study suggests the ability of Random Amplified Polymorphic DNA (RAPD)-PCR to estimate the genetic distance and reflect the genetic relations and variability among eight rodent species of order Rodentia in Egypt. After the use of five arbitrary short primers (OPA-4, OPT-7, OPG-2, OPN-4 and OPM-1) to generate polymorphic, reproducible and score able bands. The results explained that, the highest genetic distance 1 was pronounced between Rattus norvegicus and Mus musculus praetextus similarly between Mus musculus domesticus and Rattus norvegicus. This is followed by the genetic distance between Mesocricetus auratus and Mus musculus domesticus as well as between Cavia porcellus and Rattus norvegicus. Nonetheless, the lowest genetic distance 0.31 was noticeable between Mus musculus praetextus and Mus musculus musculus.
{"title":"Genetic Diversity and Phylogenetic Relationship Among Eight Species of Order: Rodentia in Egypt Based on Random Amplified Polymorphic DNA (RAPD) Marker","authors":"Fawzeya Abdelhadi Zayed, SobhyHasab El‐Naby, Fatma Ahmady Al-Zahaby, Sabha Elsayed Elballat","doi":"10.11648/J.IJGG.20200802.11","DOIUrl":"https://doi.org/10.11648/J.IJGG.20200802.11","url":null,"abstract":"Of all mammals the rodents have an importance and great diversity. The phylogenetic relationships between the different species of the order Rodentia has an interest and investigations for many researchers. The current study suggests the ability of Random Amplified Polymorphic DNA (RAPD)-PCR to estimate the genetic distance and reflect the genetic relations and variability among eight rodent species of order Rodentia in Egypt. After the use of five arbitrary short primers (OPA-4, OPT-7, OPG-2, OPN-4 and OPM-1) to generate polymorphic, reproducible and score able bands. The results explained that, the highest genetic distance 1 was pronounced between Rattus norvegicus and Mus musculus praetextus similarly between Mus musculus domesticus and Rattus norvegicus. This is followed by the genetic distance between Mesocricetus auratus and Mus musculus domesticus as well as between Cavia porcellus and Rattus norvegicus. Nonetheless, the lowest genetic distance 0.31 was noticeable between Mus musculus praetextus and Mus musculus musculus.","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"2 1","pages":"54"},"PeriodicalIF":0.0,"publicationDate":"2020-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82598433","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
T. Zohoncon, P. Ouedraogo, M. Belemgnégré, A. Ouattara, L. B. Tingueri, J. Simporé
Genetic diseases are poorly reported in sub-Saharan Africa, especially in Burkina Faso. The reasons for this reality are multifactorial including, the difficulty of diagnostic confirmation, financial accessibility and even the difficulty with referral of cases by medical staff. Genetic diseases, although relatively rare, exist in families and deserve special attention in our paraclinical assessments. Few cases can be diagnosed in sub-Saharan Africa. The clinical case we are reporting here is a dystrophynopathy by mutation of the Duchenne muscular dystrophy (DMD) gene. This is the first confirmed detection of a frameshift mutation in the DMD gene in a boy received at Saint Camille Hospital in Ouagadougou, Burkina Faso. This is a 13-year-old MR boy, from a family of four siblings, all male, from the eastern region of Burkina Faso. The boy had a clinical picture of myopathy with difficulty in walking, frequent falls, myogenic syndrome with stool sign, Gowers sign and scapula alata, all leading to a suspicion of dystrophinopathy with a request for genetic analysis. The DMD gene responsible for the disease is located on the X chromosome (Xp21.2-p21.1). The study of the dystrophin gene (DMD) was done using three methods, namely MLPA, high throughput sequencing and Sanger sequencing. The results led to the identification of a frameshift mutation of exon 71 in the DMD gene: it is a hemizygotic variant with ribosomal shift of the DMD gene NM_004006.2 (DMD): c.10258del p.(Ser3420Leufs*25). This clinical case led for the first time in Burkina Faso to the confirmed diagnosis of hereditary muscular dystrophy resulting from a mutation with a frameshift in exon 71 of the DMD gene in the hemizygotic state in a 13-year-old boy, a student and the eldest sibling of 4 boys, three of whom have myopathy. Key words: Mutation, Duchenne muscular dystrophy (DMD) gene, dystrophinopathy, duchenne versus becker, case report.
{"title":"First detection of the hemizygote frameshift variant of the DMD gene in a 13-year-old patient affected by dystrophinopathy (Duchenne DMD and Becker BMD) at Saint Camille Hospital of Ouagadougou, Burkina Faso: Case report","authors":"T. Zohoncon, P. Ouedraogo, M. Belemgnégré, A. Ouattara, L. B. Tingueri, J. Simporé","doi":"10.5897/IJGMB2020.0195","DOIUrl":"https://doi.org/10.5897/IJGMB2020.0195","url":null,"abstract":"Genetic diseases are poorly reported in sub-Saharan Africa, especially in Burkina Faso. The reasons for this reality are multifactorial including, the difficulty of diagnostic confirmation, financial accessibility and even the difficulty with referral of cases by medical staff. Genetic diseases, although relatively rare, exist in families and deserve special attention in our paraclinical assessments. Few cases can be diagnosed in sub-Saharan Africa. The clinical case we are reporting here is a dystrophynopathy by mutation of the Duchenne muscular dystrophy (DMD) gene. This is the first confirmed detection of a frameshift mutation in the DMD gene in a boy received at Saint Camille Hospital in Ouagadougou, Burkina Faso. This is a 13-year-old MR boy, from a family of four siblings, all male, from the eastern region of Burkina Faso. The boy had a clinical picture of myopathy with difficulty in walking, frequent falls, myogenic syndrome with stool sign, Gowers sign and scapula alata, all leading to a suspicion of dystrophinopathy with a request for genetic analysis. The DMD gene responsible for the disease is located on the X chromosome (Xp21.2-p21.1). The study of the dystrophin gene (DMD) was done using three methods, namely MLPA, high throughput sequencing and Sanger sequencing. The results led to the identification of a frameshift mutation of exon 71 in the DMD gene: it is a hemizygotic variant with ribosomal shift of the DMD gene NM_004006.2 (DMD): c.10258del p.(Ser3420Leufs*25). This clinical case led for the first time in Burkina Faso to the confirmed diagnosis of hereditary muscular dystrophy resulting from a mutation with a frameshift in exon 71 of the DMD gene in the hemizygotic state in a 13-year-old boy, a student and the eldest sibling of 4 boys, three of whom have myopathy. \u0000 \u0000 \u0000 \u0000 Key words: Mutation, Duchenne muscular dystrophy (DMD) gene, dystrophinopathy, duchenne versus becker, case report.","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"10 1","pages":"30-35"},"PeriodicalIF":0.0,"publicationDate":"2020-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81631539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
S. Shibeshi, V. Adetimirin, L. Kumar, M. Abebe, M. Gedil
Maize streak virus (MSV) is a devastating viral disease of maize in sub-Saharan Africa. The disease may cause up to 100% yield loss in susceptible crops. The use of molecular markers can facilitate the development of varieties resistant to the virus. The objective of this study is to assess the usefulness of Single Nucleotide Polymorphism (SNP) markers linked to MSV resistance in selecting for resistance at early generations of inbred line development in maize. A total of 160 maize lines were genotyped with three SNP markers that are linked to MSV resistance. These lines were tested for their reaction to MSV through artificial inoculation using viruliferous Cicadulina triangular at the three leaf stage; maize streak virus symptom was scored from 7 days after inoculation for six weeks at weekly interval on a scale of 1 to 5. MSV titer on the upper and lower leaves was determined using Direct Antigen Coating Enzyme linked Immunosorbent Assay (DAC-ELISA). One hundred and forty-two (142) of the 160 maize lines had the favourable marker allele for MSV resistance while 18 maize lines did not have the allele. Differences among the 160 maize lines for MSV symptom on upper leaves at six week after inoculation were significant (P< 0.01). Favourable allele of the SNP markers was significantly associated with MSV symptom score at 6 week after inoculation and MSV titer status. The percentage of maize lines with desirable marker allele with resistance based on symptoms score and ELISA were 97.9 and 93%, respectively. The three SNP markers showed high efficiency in the identification of MSV resistant maize lines and therefore have potential for use in marker-assisted selection. The SNP markers were not effective in detecting MSV resistance in few genotypes, indicating a need to develop other markers for resistance. Key words: ELISA, genotyping, inoculation, maize streak virus, SNPs. See: Notice of Retraction
{"title":"Retracted: Verification of single nucleotide polymorphism (SNP) markers associated with maize (Zea mays. L) streak virus resistance in early generation maize lines","authors":"S. Shibeshi, V. Adetimirin, L. Kumar, M. Abebe, M. Gedil","doi":"10.5897/IJGMB2019.0182","DOIUrl":"https://doi.org/10.5897/IJGMB2019.0182","url":null,"abstract":"Maize streak virus (MSV) is a devastating viral disease of maize in sub-Saharan Africa. The disease may cause up to 100% yield loss in susceptible crops. The use of molecular markers can facilitate the development of varieties resistant to the virus. The objective of this study is to assess the usefulness of Single Nucleotide Polymorphism (SNP) markers linked to MSV resistance in selecting for resistance at early generations of inbred line development in maize. A total of 160 maize lines were genotyped with three SNP markers that are linked to MSV resistance. These lines were tested for their reaction to MSV through artificial inoculation using viruliferous Cicadulina triangular at the three leaf stage; maize streak virus symptom was scored from 7 days after inoculation for six weeks at weekly interval on a scale of 1 to 5. MSV titer on the upper and lower leaves was determined using Direct Antigen Coating Enzyme linked Immunosorbent Assay (DAC-ELISA). One hundred and forty-two (142) of the 160 maize lines had the favourable marker allele for MSV resistance while 18 maize lines did not have the allele. Differences among the 160 maize lines for MSV symptom on upper leaves at six week after inoculation were significant (P< 0.01). Favourable allele of the SNP markers was significantly associated with MSV symptom score at 6 week after inoculation and MSV titer status. The percentage of maize lines with desirable marker allele with resistance based on symptoms score and ELISA were 97.9 and 93%, respectively. The three SNP markers showed high efficiency in the identification of MSV resistant maize lines and therefore have potential for use in marker-assisted selection. The SNP markers were not effective in detecting MSV resistance in few genotypes, indicating a need to develop other markers for resistance. \u0000 \u0000 \u0000 \u0000 Key words: ELISA, genotyping, inoculation, maize streak virus, SNPs. \u0000 \u0000 \u0000 \u0000 See: Notice of Retraction","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"2 1","pages":"36-45"},"PeriodicalIF":0.0,"publicationDate":"2020-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86008173","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
T. Zohoncon, W. F. Djigma, A. Ouattara, I. M. Traore, R. A. Ouédraogo, Esther M.A Traor e, P. Bado, T. C. Ouédraogo, B. Diarra, M. Ilboudo, C. D. Capo-chichi, D. Obiri-Yeboah, S. Karou, M. Nayama, A. Horo, K. P. Kouakou, M. Gomina, S. Ouattara, A. Sanni, A. Simon, C. Ouedraogo, J. Simporé
The aim of this study was to determine the distribution of high-risk human papillomavirus genotypes (HR-HPV) in women from the general population of five West African countries. This was a cross-sectional descriptive study, involving 2133 women from nine cities of five West African countries: Benin, Burkina Faso, Cote d'Ivoire, Niger and Togo. Women were screened for precancerous cervical lesions and HR-HPV infection. The detection of HR-HPV was done by a multiplex real-time PCR on extracted viral DNA. The average age of the women in this study was 35.06 ± 10.00 years with a range of 15 to 65 years. The overall prevalence of high-risk HPV infection among general population sample of women in five West African countries was 33.61% (717/2133). The prevalence of dysplasia was 8.81%. In decreasing order of frequency, the genotypes found were: HPV 52 followed by HPV 31, 59, 51, 66, 45, 68, 56, 56, 58, 35, 39, 18, 33 and 16. The prevalence of HPV16/18 (bivalent vaccine types) was 7.02%. This study reveals a high prevalence of HPV 52 in West Africa. The extent and diversity of HR-HPV genotypes in these West African countries deserve special attention for prevention. Key words: High-risk HPV, real time PCR, genotypes, women, epidemiology, West Africa.
{"title":"Mapping of fourteen high-risk human papillomavirus genotypes by molecular detection in sexually active women in the West African sub-region","authors":"T. Zohoncon, W. F. Djigma, A. Ouattara, I. M. Traore, R. A. Ouédraogo, Esther M.A Traor e, P. Bado, T. C. Ouédraogo, B. Diarra, M. Ilboudo, C. D. Capo-chichi, D. Obiri-Yeboah, S. Karou, M. Nayama, A. Horo, K. P. Kouakou, M. Gomina, S. Ouattara, A. Sanni, A. Simon, C. Ouedraogo, J. Simporé","doi":"10.5897/IJGMB2019.0193","DOIUrl":"https://doi.org/10.5897/IJGMB2019.0193","url":null,"abstract":"The aim of this study was to determine the distribution of high-risk human papillomavirus genotypes (HR-HPV) in women from the general population of five West African countries. This was a cross-sectional descriptive study, involving 2133 women from nine cities of five West African countries: Benin, Burkina Faso, Cote d'Ivoire, Niger and Togo. Women were screened for precancerous cervical lesions and HR-HPV infection. The detection of HR-HPV was done by a multiplex real-time PCR on extracted viral DNA. The average age of the women in this study was 35.06 ± 10.00 years with a range of 15 to 65 years. The overall prevalence of high-risk HPV infection among general population sample of women in five West African countries was 33.61% (717/2133). The prevalence of dysplasia was 8.81%. In decreasing order of frequency, the genotypes found were: HPV 52 followed by HPV 31, 59, 51, 66, 45, 68, 56, 56, 58, 35, 39, 18, 33 and 16. The prevalence of HPV16/18 (bivalent vaccine types) was 7.02%. This study reveals a high prevalence of HPV 52 in West Africa. The extent and diversity of HR-HPV genotypes in these West African countries deserve special attention for prevention. \u0000 \u0000 \u0000 \u0000 Key words: High-risk HPV, real time PCR, genotypes, women, epidemiology, West Africa.","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"78 1","pages":"11-21"},"PeriodicalIF":0.0,"publicationDate":"2020-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83927402","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
B. Mukoye, A. Mabele, M. Ndonga, B. Mangeni, H. Wéré
Production of groundnuts (Arachis hypogaea L.) in Western Kenya is mainly constrained by groundnut rosette disease (GRD) which cause up to 100% yield loss. This disease expresses different symptoms as a result of variations in the groundnut rosette virus (GRV) associated satellite-ribonucleic acid (GRV Sat-RNA). Over the past 20 years, no work had been done to document the status of the disease in Kenya. Additionally, no sequences of any of the GRD associated viruses were available in the GeneBank from Kenya. This study determined the distribution of GRD and the genetic diversity of GRV Sat-RNA. Sampling was done in main groundnut growing areas of Western Kenya during the long and short rain seasons in 2016/2017. Total RNA was extracted from the leafy samples collected using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol and used for double stranded cDNA synthesis using the SuperScript II kit. DNA libraries were sequenced on the Illumina MiSeq platform (Illumina). Reads were used for de novo assembly and contigs aligned to the viral genomes database using CLC Genomics Workbench 10.1.2. The assembled contigs were subjected to a BLASTn search against the GenBank database. Average GRD incidence was 53 and 41% in the short and long rain seasons, respectively. Chlorotic rosette was the dominant symptom followed by green rosette and mosaic. Nucleotide sequences of Sat-RNA revealed identities of 88 to 100% between the Kenyan isolates and those from Malawi, Nigeria and Ghana. All Kenya isolates clustered closest with green rosette variants of Malawi except one which clustered with chlorotic/yellow blotch variants. Rosette is widely distributed in Western Kenya and occurs wherever groundnuts are grown. The variations of GRD symptoms in Western Kenya could be due to the existence of different variants of Sat-RNA or other agents. Key words: Groundnuts, satellite-ribonucleic acid (Sat-RNA), diversity, Western Kenya.
{"title":"Distribution of groundnut rosette disease and sequence diversity of groundnut rosette virus associated satellite RNA (Sat-RNA) in Western Kenya","authors":"B. Mukoye, A. Mabele, M. Ndonga, B. Mangeni, H. Wéré","doi":"10.5897/IJGMB2019.0178","DOIUrl":"https://doi.org/10.5897/IJGMB2019.0178","url":null,"abstract":"Production of groundnuts (Arachis hypogaea L.) in Western Kenya is mainly constrained by groundnut rosette disease (GRD) which cause up to 100% yield loss. This disease expresses different symptoms as a result of variations in the groundnut rosette virus (GRV) associated satellite-ribonucleic acid (GRV Sat-RNA). Over the past 20 years, no work had been done to document the status of the disease in Kenya. Additionally, no sequences of any of the GRD associated viruses were available in the GeneBank from Kenya. This study determined the distribution of GRD and the genetic diversity of GRV Sat-RNA. Sampling was done in main groundnut growing areas of Western Kenya during the long and short rain seasons in 2016/2017. Total RNA was extracted from the leafy samples collected using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol and used for double stranded cDNA synthesis using the SuperScript II kit. DNA libraries were sequenced on the Illumina MiSeq platform (Illumina). Reads were used for de novo assembly and contigs aligned to the viral genomes database using CLC Genomics Workbench 10.1.2. The assembled contigs were subjected to a BLASTn search against the GenBank database. Average GRD incidence was 53 and 41% in the short and long rain seasons, respectively. Chlorotic rosette was the dominant symptom followed by green rosette and mosaic. Nucleotide sequences of Sat-RNA revealed identities of 88 to 100% between the Kenyan isolates and those from Malawi, Nigeria and Ghana. All Kenya isolates clustered closest with green rosette variants of Malawi except one which clustered with chlorotic/yellow blotch variants. Rosette is widely distributed in Western Kenya and occurs wherever groundnuts are grown. The variations of GRD symptoms in Western Kenya could be due to the existence of different variants of Sat-RNA or other agents. \u0000 \u0000 \u0000 \u0000 Key words: Groundnuts, satellite-ribonucleic acid (Sat-RNA), diversity, Western Kenya.","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"31 1","pages":"22-29"},"PeriodicalIF":0.0,"publicationDate":"2020-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72741208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yao Saraka Didier Martial, D. Nafan, Attikora Affi Jean Paul, Fofana Inza Jesus, D. Noel, Silué Souleymane
Agromorphological diversity structure of the elite shea trees identified in village lands and conserved in situ in the districts of Bagoue and Tchologo by the shea breeding program of the University of Peleforo Gon Coulibaly (UPGC, Cote d’Ivoire), are not known. In the present study, we characterized the agromorphological parameters of 220 elite shea trees using a set of 12 quantitative traits. The results showed that elite shea trees population has been structured into three morphological clusters or genetic pools that do not overlap with the original geographic areas. Morphological Cluster I contain elite shea trees with small trunk diameters carrying large leaves and producing fewer fruits per tree. Morphological Cluster II consisted of elite shea trees with stronger trunks bearing small leaves and producing a high number of fruits per tree. Morphological Cluster III regrouped elite shea trees of medium trunk diameters carrying medium sized leaves; fruit production level is intermediate compare to preceding groups. The elite shea trees of morphological Clusters II, which are more interesting from an agronomic point of view, can be used as grafting trees for the production of high-yielding grafted plants for farmers in Cote d'Ivoire. Key words: elite shea trees, genetic improvement, phenotypic variability, Northern Cote d’Ivoire.
{"title":"Morphological diversity patterns among selected elite Shea trees (Vitellaria paradoxa C.F. Gaertn.) from Tchologo and Bagou districts in Northern \u0000Cte dIvoire","authors":"Yao Saraka Didier Martial, D. Nafan, Attikora Affi Jean Paul, Fofana Inza Jesus, D. Noel, Silué Souleymane","doi":"10.5897/ijgmb2019.0189","DOIUrl":"https://doi.org/10.5897/ijgmb2019.0189","url":null,"abstract":"Agromorphological diversity structure of the elite shea trees identified in village lands and conserved in situ in the districts of Bagoue and Tchologo by the shea breeding program of the University of Peleforo Gon Coulibaly (UPGC, Cote d’Ivoire), are not known. In the present study, we characterized the agromorphological parameters of 220 elite shea trees using a set of 12 quantitative traits. The results showed that elite shea trees population has been structured into three morphological clusters or genetic pools that do not overlap with the original geographic areas. Morphological Cluster I contain elite shea trees with small trunk diameters carrying large leaves and producing fewer fruits per tree. Morphological Cluster II consisted of elite shea trees with stronger trunks bearing small leaves and producing a high number of fruits per tree. Morphological Cluster III regrouped elite shea trees of medium trunk diameters carrying medium sized leaves; fruit production level is intermediate compare to preceding groups. The elite shea trees of morphological Clusters II, which are more interesting from an agronomic point of view, can be used as grafting trees for the production of high-yielding grafted plants for farmers in Cote d'Ivoire. \u0000 \u0000 \u0000 \u0000 Key words: elite shea trees, genetic improvement, phenotypic variability, Northern Cote d’Ivoire.","PeriodicalId":88902,"journal":{"name":"International journal of genetics and molecular biology","volume":"12 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2020-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85688037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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