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Abah SP, Mbe JO, Dzidzienyo DK, Njoku D, Onyeka J, Danquah EY, Offei SK, Kulakow P, Egesi CN. Determination of genomic regions associated with early storage root formation and bulking in cassava. FRONTIERS IN PLANT SCIENCE 2024; 15:1391452. [PMID: 38988637 PMCID: PMC11233741 DOI: 10.3389/fpls.2024.1391452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2024] [Accepted: 04/30/2024] [Indexed: 07/12/2024]
Abstract
Early cassava storage root formation and bulking is a medium of escape that farmers and processors tend to adopt in cases of abiotic and biotic stresses like drought, flood, and destruction by domestic animals. In this study, 220 cassava genotypes from the International Institute of Tropical Agriculture (IITA), National Root Crops Research Institute (NRCRI), International Center for Tropical Agriculture (CIAT), local farmers (from farmer's field), and NextGen project were evaluated in three locations (Umudike, Benue, and Ikenne). The trials were laid out using a split plot in a randomized incomplete block design (alpha lattice) with two replications in 2 years. The storage roots for each plant genotype were sampled or harvested at 3, 6, 9, and 12 month after planting (MAP). All data collected were analyzed using the R-statistical package. The result showed moderate to high heritability among the traits, and there were significant differences (p< 0.05) among the performances of the genotypes. The genome-wide association mapping using the BLINK model detected 45 single-nucleotide polymorphism (SNP) markers significantly associated with the four early storage root bulking and formation traits on Chromosomes 1, 2, 3, 4, 5, 6, 8, 9, 10, 13, 14, 17, and 18. A total of 199 putative candidate genes were found to be directly linked to early storage root bulking and formation. The functions of these candidate genes were further characterized to regulate i) phytohormone biosynthesis, ii) cellular growth and development, and iii) biosynthesis of secondary metabolites for accumulation of starch and defense. Genome-wide association study (GWAS) also revealed the presence of four pleiotropic SNPs, which control starch content, dry matter content, dry yield, and bulking and formation index. The information on the GWAS could be used to develop improved cassava cultivars by breeders. Five genotypes (W940006, NR090146, TMS982123, TMS13F1060P0014, and NR010161) were selected as the best early storage root bulking and formation genotypes across the plant age. These selected cultivars should be used as sources of early storage root bulking and formation in future breeding programs.
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Affiliation(s)
- Simon Peter Abah
- Bioscience, National Root Crops Research Institute, Umudike, Nigeria
- Cassava Breeding, International Institute for Tropical Agriculture, Ibadan, Nigeria
- West African Centers for Crop Improvement, University of Ghana, Accra, Ghana
| | - Joseph Okpani Mbe
- Bioscience, National Root Crops Research Institute, Umudike, Nigeria
- West African Centers for Crop Improvement, University of Ghana, Accra, Ghana
| | | | - Damian Njoku
- Bioscience, National Root Crops Research Institute, Umudike, Nigeria
| | - Joseph Onyeka
- Bioscience, National Root Crops Research Institute, Umudike, Nigeria
| | | | - Samuel Kwane Offei
- West African Centers for Crop Improvement, University of Ghana, Accra, Ghana
- Biotechnology Centre, University of Ghana, Accra, Ghana
| | - Peter Kulakow
- Cassava Breeding, International Institute for Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Ngozi Egesi
- Bioscience, National Root Crops Research Institute, Umudike, Nigeria
- Cassava Breeding, International Institute for Tropical Agriculture, Ibadan, Nigeria
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Karim KY, Ifie B, Dzidzienyo D, Danquah EY, Blay ET, Whyte JBA, Kulakow P, Rabbi I, Parkes E, Omoigui L, Norman PE, Iluebbey P. Genetic characterization of cassava ( Manihot esculenta Crantz) genotypes using agro-morphological and single nucleotide polymorphism markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:317-330. [PMID: 32158137 PMCID: PMC7036393 DOI: 10.1007/s12298-019-00740-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/15/2019] [Accepted: 11/24/2019] [Indexed: 06/01/2023]
Abstract
Dearth of information on extent of genetic variability in cassava limits the genetic improvement of cassava genotypes in Sierra Leone. The aim of this study was to assess the genetic diversity and relationships within 102 cassava genotypes using agro-morphological and single nucleotide polymorphism markers. Morphological classification based on qualitative traits categorized the germplasm into five different groups, whereas the quantitative trait set had four groups. The SNP markers classified the germplasm into three main cluster groups. A total of seven principal components (PCs) in the qualitative and four PCs in the quantitative trait sets accounted for 79.03% and 72.30% of the total genetic variation, respectively. Significant and positive correlations were observed between average yield per plant and harvest index (r = 0.76***), number of storage roots per plant and harvest index (r = 0.33*), height at first branching and harvest index (0.26*), number of storage roots per plant and average yield per plant (r = 0.58*), height at first branching and average yield per plant (r = 0.24*), length of leaf lobe and petiole length (r = 0.38*), number of leaf lobe and petiole length (r = 0.31*), width of leaf lobe and length of leaf lobe (r = 0.36*), number of leaf lobe and length of leaf lobe (r = 0.43*), starch content and dry matter content (r = 0.99***), number of leaf lobe and root dry matter (r = 0.30*), number of leaf lobe and starch content (r = 0.28*), and height at first branching and plant height (r = 0.45**). Findings are useful for conservation, management, short term recommendation for release and genetic improvement of the crop.
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Affiliation(s)
- Kumba Y. Karim
- Sierra Leone Agricultural Research Institute, Tower Hill, Freetown, PMB 1313 Sierra Leone
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Beatrice Ifie
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Daniel Dzidzienyo
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Eric Y. Danquah
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Essie T. Blay
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Jim B. A. Whyte
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Ismail Rabbi
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Lucky Omoigui
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
| | - Prince E. Norman
- Sierra Leone Agricultural Research Institute, Tower Hill, Freetown, PMB 1313 Sierra Leone
- West Africa Centre for Crop Improvement, College of Basic and Applied Sciences, University of Ghana, P.O. Box LG 30, Legon, Accra, Greater Accra Ghana
| | - Peter Iluebbey
- International Institute of Tropical Agriculture, Ibadan, PMB 5320 Nigeria
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SNP and SCAR Markers for Specific Discrimination of Antler-Shaped Ganoderma lucidum. Microorganisms 2019; 7:microorganisms7010012. [PMID: 30634458 PMCID: PMC6352128 DOI: 10.3390/microorganisms7010012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 12/31/2018] [Accepted: 01/08/2019] [Indexed: 11/17/2022] Open
Abstract
In this study we identified single nucleotide polymorphism (SNP) and sequence characteristic amplification region (SCAR) markers for specific identification of antler-shaped Ganoderma lucidum strains. When the partial mitochondrial SSU rDNA gene sequence of various antler- and kidney-shaped G. lucidum strains were analyzed and aligned, an SNP was found only in the antler-shaped G. lucidum strain at position 456 bp. In addition, this SNP of antler-shaped strains was digested by HinfI restriction enzyme. We further analyzed the polymorphism of various G. lucidum strains by random amplified polymorphic DNA (RAPD) analysis. In RAPD analysis, we isolated and sequenced a fragment, specific for antler-shaped G. lucidum strains. Based on this specific fragment sequence, two sets of specific primer pairs for antler-shaped G. lucidum strains were designed. PCR analysis revealed that two specific bands were observed only from antler-shaped strains. These two molecular markers will be helpful for identification of morphological characteristics of G. lucidum.
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Feasibility of mini-sequencing schemes based on nucleotide polymorphisms for microbial identification and population analyses. Appl Microbiol Biotechnol 2015; 99:2513-21. [DOI: 10.1007/s00253-015-6427-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 01/20/2015] [Accepted: 01/21/2015] [Indexed: 11/26/2022]
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Yang L, Sun H, Chen D, Lu M, Wang J, Xu F, Hu L, Xiao J. Application of multiplex SNaPshot assay in measurement of PLAC4 RNA-SNP allelic ratio for noninvasive prenatal detection of trisomy 21. Prenat Diagn 2013; 34:139-44. [PMID: 24214739 DOI: 10.1002/pd.4271] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Revised: 10/11/2013] [Accepted: 11/01/2013] [Indexed: 11/07/2022]
Affiliation(s)
- Lan Yang
- Department of Prenatal Diagnosis Center; Wuxi Maternal and Child Health Hospital Affiliated Nanjing Medical University; 214002 Wuxi Jiangsu China
| | - Haiyan Sun
- State Key Laboratory of Genetic Engineering; Fu Dan University; 200433 Shanghai China
| | - Daozhen Chen
- Department of Prenatal Diagnosis Center; Wuxi Maternal and Child Health Hospital Affiliated Nanjing Medical University; 214002 Wuxi Jiangsu China
| | - Mudan Lu
- Department of Prenatal Diagnosis Center; Wuxi Maternal and Child Health Hospital Affiliated Nanjing Medical University; 214002 Wuxi Jiangsu China
| | - Junfeng Wang
- Department of Prenatal Diagnosis Center; Wuxi Maternal and Child Health Hospital Affiliated Nanjing Medical University; 214002 Wuxi Jiangsu China
| | - Fei Xu
- Department of Prenatal Diagnosis Center; Wuxi Maternal and Child Health Hospital Affiliated Nanjing Medical University; 214002 Wuxi Jiangsu China
| | - Lingqing Hu
- Department of Prenatal Diagnosis Center; Wuxi Maternal and Child Health Hospital Affiliated Nanjing Medical University; 214002 Wuxi Jiangsu China
| | - Jianpin Xiao
- Department of Prenatal Diagnosis Center; Wuxi Maternal and Child Health Hospital Affiliated Nanjing Medical University; 214002 Wuxi Jiangsu China
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Caramalho R, Gusmão L, Lackner M, Amorim A, Araujo R. SNaPAfu: a novel single nucleotide polymorphism multiplex assay for aspergillus fumigatus direct detection, identification and genotyping in clinical specimens. PLoS One 2013; 8:e75968. [PMID: 24204585 PMCID: PMC3799902 DOI: 10.1371/journal.pone.0075968] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Accepted: 08/16/2013] [Indexed: 12/01/2022] Open
Abstract
Objective Early diagnosis of invasive aspergillosis is essential for positive patient outcome. Likewise genotyping of fungal isolates is desirable for outbreak control in clinical setting. We designed a molecular assay that combines detection, identification, and genotyping of Aspergillus fumigatus in a single reaction. Methods To this aim we combined 20 markers in a multiplex reaction and the results were seen following mini-sequencing readings. Pure culture extracts were firstly tested. Thereafter, Aspergillus-DNA samples obtained from clinical specimens of patients with possible, probable, or proven aspergillosis according to European Organization for the Research and Treatment of Cancer/Mycoses Study Group (EORTC/MSG) criteria. Results A new set of designed primers allowed multilocus sequence typing (MLST) gene amplification in a single multiplex reaction. The newly proposed SNaPAfu assay had a specificity of 100%, a sensitivity of 89% and detection limit of 1 ITS copy/mL (∼0.5 fg genomic Aspergillus-DNA/mL). The marker A49_F was detected in 89% of clinical samples. The SNaPAfu assay was accurately performed on clinical specimens using only 1% of DNA extract (total volume 50 µL) from 1 mL of used bronchoalveolar lavage. Conclusions The first highly sensitive and specific, time- and cost-economic multiplex assay was implemented that allows detection, identification, and genotyping of A. fumigatus strains in a single amplification followed by mini-sequencing reaction. The new test is suitable to clinical routine and will improve patient management.
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Affiliation(s)
- Rita Caramalho
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Leonor Gusmão
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- DNA Diagnostic Laboratory, State University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Michaela Lackner
- Division of Hygiene and Medical Microbiology, Innsbruck Medical University, Innsbruck, Austria
| | - António Amorim
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
| | - Ricardo Araujo
- Institute of Molecular Pathology and Immunology of the University of Porto, Porto, Portugal
- Faculty of Sciences, University of Porto, Porto, Portugal
- * E-mail:
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SNaPBcen: a novel and practical tool for genotyping Burkholderia cenocepacia. J Clin Microbiol 2013; 51:2646-53. [PMID: 23761147 DOI: 10.1128/jcm.01019-13] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Burkholderia cenocepacia is the most prevalent and feared member of the Burkholderia cepacia complex in lung infections of cystic fibrosis (CF). Genotyping and monitoring of long-term colonization are critical at clinical units; however, the differentiation of specific lineages performed by multilocus sequence typing (MLST) is still limited to a small number of isolates due to the high cost and time-consuming procedure. The aim of this study was to optimize a protocol (the SNaPBcen assay) for extensive bacterial population studies. The strategy used for the SNaPBcen assay is based on targeting single nucleotide polymorphisms (SNPs) located in MLST genes instead of sequencing full MLST sequences. Nonpolymorphic and redundant MLST positions were eliminated, and a set of 24 polymorphisms included in the SNaPBcen assay ensures a high-resolution genomic characterization. These polymorphisms were identified based on the comparative analysis of 137 B. cenocepacia MLST profiles available online (http://pubmlst.org/bcc/). The group of 81 clinical isolates of B. cenocepacia examined in this study using the SNaPBcen assay revealed 51 distinct profiles, and a final discriminatory power of 0.9997 compared with MLST was determined. The SNaPBcen assay was able to reveal isolates with microvariations and the presence of multiple clonal variants in patients chronically colonized with B. cenocepacia. Main phylogenetic subgroups IIIA, IIIB, and IIIC of B. cenocepacia could be separated by the Gl94R polymorphism included in the panel. The SNaPBcen assay proved to be a rapid and robust alternative to the standard MLST for B. cenocepacia, allowing the simultaneous analysis of multiple polymorphisms following amplification and mini-sequencing reactions.
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Lambiase A, Del Pezzo M, Cerbone D, Raia V, Rossano F, Catania MR. Rapid identification of Burkholderia cepacia complex species recovered from cystic fibrosis patients using matrix-assisted laser desorption ionization time-of-flight mass spectrometry. J Microbiol Methods 2012. [PMID: 23201483 DOI: 10.1016/j.mimet.2012.11.010] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aim of this study was to establish the identification ability of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for bacteria of Burkholderia cepacia complex (Bcc) and to compare these results with those obtained by a molecular method (PCR-RFLP). A total of 57 isolates was used in the study. Isolates were collected from 31 patients attending the Regional Cystic Fibrosis Unit from January 2001 to December 2005. For phenotypic identification, both automated and manual systems were used. Using mass spectrometry, we identified all 57 isolates, previously identified by molecular method. Of these, 28 isolates were identified as B. cenocepacia, although not differentiated further into lineages. Moreover, other isolates were identified as B. cepacia (12 isolates), B. stabilis (12 isolates), and B. vietnamiensis (5 isolates). Our data indicate a good correlation between the two approaches.
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Affiliation(s)
- Antonietta Lambiase
- Department of Cellular and Molecular Biology and Pathology Luigi Califano, Medicine School, University Federico II, Naples, Italy.
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Huang CH, Chang MT, Huang MC, Wang LT, Huang L, Lee FL. Discrimination of the Lactobacillus acidophilus group using sequencing, species-specific PCR and SNaPshot mini-sequencing technology based on the recA gene. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2012; 92:2703-2708. [PMID: 22555934 DOI: 10.1002/jsfa.5692] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/20/2012] [Accepted: 03/06/2012] [Indexed: 05/31/2023]
Abstract
BACKGROUND To clearly identify specific species and subspecies of the Lactobacillus acidophilus group using phenotypic and genotypic (16S rDNA sequence analysis) techniques alone is difficult. The aim of this study was to use the recA gene for species discrimination in the L. acidophilus group, as well as to develop a species-specific primer and single nucleotide polymorphism primer based on the recA gene sequence for species and subspecies identification. RESULTS The average sequence similarity for the recA gene among type strains was 80.0%, and most members of the L. acidophilus group could be clearly distinguished. The species-specific primer was designed according to the recA gene sequencing, which was employed for polymerase chain reaction with the template DNA of Lactobacillus strains. A single 231-bp species-specific band was found only in L. delbrueckii. A SNaPshot mini-sequencing assay using recA as a target gene was also developed. The specificity of the mini-sequencing assay was evaluated using 31 strains of L. delbrueckii species and was able to unambiguously discriminate strains belonging to the subspecies L. delbrueckii subsp. bulgaricus. CONCLUSION The phylogenetic relationships of most strains in the L. acidophilus group can be resolved using recA gene sequencing, and a novel method to identify the species and subspecies of the L. delbrueckii and L. delbrueckii subsp. bulgaricus was developed by species-specific polymerase chain reaction combined with SNaPshot mini-sequencing.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 30062, Taiwan, ROC.
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Almeida LA, Araujo R. Highlights on molecular identification of closely related species. INFECTION GENETICS AND EVOLUTION 2012; 13:67-75. [PMID: 22982158 DOI: 10.1016/j.meegid.2012.08.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 08/06/2012] [Accepted: 08/08/2012] [Indexed: 10/27/2022]
Abstract
The term "complex" emerged in the literature at the beginning of the genomic era associated to taxonomy and grouping organisms that belong to different species but exhibited similar patterns according to their morphological, physiological and/or other phenotypic features. DNA-DNA hybridization values ~70% and high identity on 16S rRNA gene sequences were recommended for species delineation. Electrophoretic methods showed in some cases to be useful for species identification and population structure but the reproducibility was questionable. Later, the implementation of polyphasic approaches involving phenotypic and molecular methods brought new insights into the analysis of population structure and phylogeny of several "species complexes", allowing the identification of new closely related species. Likewise, the introduction of multilocus sequence typing and sequencing analysis of several genes offered an evolutionary perspective to the term "species complex". Several centres worldwide have recently released increasing genetic information on distinct microbial species. A brief review will be presented to highlight the definition of "species complex" for selected microorganisms, mainly the prokaryotic Acinetobacter calcoaceticus -Acinetobacter baumannii, Borrelia burgdorferi sensu lato, Burkholderia cepacia, Mycobacterium tuberculosis and Nocardia asteroides complexes, and the eukaryotic Aspergillus fumigatus, Leishmania donovani and Saccharomyces sensu stricto complexes. The members of these complexes may show distinct epidemiology, pathogenicity and susceptibility, turning critical their correct identification. Dynamics of prokaryotic and eukaryotic genomes can be very distinct and the term "species complex" should be carefully extended.
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Affiliation(s)
- Lígia A Almeida
- IPATIMUP, Institute of Molecular Pathology and Immunology, University of Porto, Rua Dr. Roberto Frias s/n, 4200-465 Porto, Portugal.
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Huang CH, Chang MT, Huang MC, Lee FL. Rapid identification of Lactobacillus plantarum group using the SNaPshot minisequencing assay. Syst Appl Microbiol 2012; 34:586-9. [PMID: 21641139 DOI: 10.1016/j.syapm.2011.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2010] [Revised: 02/15/2011] [Accepted: 02/16/2011] [Indexed: 10/18/2022]
Abstract
This study used SNaPshot minisequencing for species identification within the Lactobacillus plantarum group. A SNaPshot minisequencing assay using dnaK as a target gene was developed, and five SNP primers were designed by analysing the conserved regions of the dnaK sequences. The specificity of the minisequencing assay was evaluated using 35 strains of L. plantarum group species. The results showed that the SNaPshot minisequencing assay was able to unambiguously and simultaneously discriminate strains belonging to the species L. plantarum subsp. plantarum, L. plantarum subsp. argentoratensis, Lactobacillus paraplantarum, Lactobacillus pentosus and Lactobacillus fabifermentans. In conclusion, a rapid, accurate and cost-effective assay was successfully developed for species identification of the members of the L. plantarum group.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, P.O. Box 246, Hsinchu 30099, Taiwan, ROC
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Huang CH, Chang MT, Huang MC, Lee FL. Application of the SNaPshot minisequencing assay to species identification in the Lactobacillus casei group. Mol Cell Probes 2011; 25:153-7. [PMID: 21440058 DOI: 10.1016/j.mcp.2011.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2011] [Revised: 03/14/2011] [Accepted: 03/14/2011] [Indexed: 10/18/2022]
Abstract
This study used group-specific PCR combined with SNaPshot minisequencing for species identification within the Lactobacillus casei group. The L. casei group-specific PCR primer pair was designed using the rpoA gene sequence. A SNaPshot minisequencing assay using dnaK as a target gene was developed, and five SNP primers were designed by analysing the conserved regions of the dnaK sequences. The specificity of the minisequencing assay was evaluated using 63 strains of L. casei group species. The results showed that the group-specific PCR could assign Lactobacillus strains into the L. casei group, and the SNaPshot minisequencing assay was able to unambiguously and simultaneously discriminate strains belonging to the species L. casei, Lactobacillus paracasei, and Lactobacillus rhamnosus. In conclusion, we have successfully developed a rapid, accurate and cost-effective assay for species identification of members of the L. casei group.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan, ROC
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Arif IA, Bakir MA, Khan HA, Al Farhan AH, Al Homaidan AA, Bahkali AH, Sadoon MA, Shobrak M. A brief review of molecular techniques to assess plant diversity. Int J Mol Sci 2010; 11:2079-96. [PMID: 20559503 PMCID: PMC2885095 DOI: 10.3390/ijms11052079] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2010] [Revised: 04/24/2010] [Accepted: 04/28/2010] [Indexed: 02/05/2023] Open
Abstract
Massive loss of valuable plant species in the past centuries and its adverse impact on environmental and socioeconomic values has triggered the conservation of plant resources. Appropriate identification and characterization of plant materials is essential for the successful conservation of plant resources and to ensure their sustainable use. Molecular tools developed in the past few years provide easy, less laborious means for assigning known and unknown plant taxa. These techniques answer many new evolutionary and taxonomic questions, which were not previously possible with only phenotypic methods. Molecular techniques such as DNA barcoding, random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), microsatellites and single nucleotide polymorphisms (SNP) have recently been used for plant diversity studies. Each technique has its own advantages and limitations. These techniques differ in their resolving power to detect genetic differences, type of data they generate and their applicability to particular taxonomic levels. This review presents a basic description of different molecular techniques that can be utilized for DNA fingerprinting and molecular diversity analysis of plant species.
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Affiliation(s)
| | | | - Haseeb A. Khan
- Author to whom correspondence should be addressed; E-Mail:
; Tel.: +966-1-4674-712
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