1
|
Patel R, Menon J, Kumar S, Nóbrega MB, Patel DA, Sakure AA, Vaja MB. Modern day breeding approaches for improvement of castor. Heliyon 2024; 10:e27048. [PMID: 38463846 PMCID: PMC10920369 DOI: 10.1016/j.heliyon.2024.e27048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 02/12/2024] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
Castor (Ricinus communis L.) is an industrially important oil producing crop belongs to Euphorbiaceae family. Castor oil has unique chemical properties make it industrially important crop. It is a member of monotypic genus even though it has ample amount of variability. Using this variability, conventionally many varieties and hybrids have been developed. But, like other crops, the modern and unconventional methods of crop improvement has not fully explored in castor. This article discusses the use of polyploidy induction, distant/wide hybridization and mutation breeding as tools for generating variety. Modern approaches accelerate the speed of crop breeding as an alternative tool. To achieve this goal, molecular markers are employed in breeding to capture the genetic variability through molecular analysis and population structuring. Allele mining is used to trace the evolution of alleles, identify new haplotypes and produce allele specific markers for use in marker aided selection using Genome wide association studies (GWAS) and quantitative trait loci (QTL) mapping. Plant genetic transformation is a rapid and effective mode of castor improvement is also discussed here. The efforts towards developing stable regeneration protocol provide a wide range of utility like embryo rescue in distant crosses, development of somaclonal variation, haploid development using anther culture and callus development for stable genetic transformation has reviewed in this article. Omics has provided intuitions to the molecular mechanisms of (a)biotic stress management in castor along with dissected out the possible genes for improving the yield. Relating genes to traits offers additional scientific inevitability leading to enhancement and sympathetic mechanisms of yield improvement and several stress tolerance.
Collapse
Affiliation(s)
- Rumit Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
- Department of Genetics & Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388110, India
| | - Juned Menon
- Department of Genetics & Plant Breeding, B. A. College of Agriculture, Anand Agricultural University, Anand, 388110, India
| | - Sushil Kumar
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Márcia B.M. Nóbrega
- Embrapa Algodão, Rua Oswaldo Cruz, nº 1.143, Centenário, CEP 58428-095, Campina Grande, PB, Brazil
| | - Dipak A. Patel
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Amar A. Sakure
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| | - Mahesh B. Vaja
- Department of Agricultural Biotechnology, Anand Agricultural University, Anand, 388110, India
| |
Collapse
|
2
|
Wu S, Wu Z, Chen M, Zhong X, Gu H, Du W, Liu W, Lang L, Wang J. Interactions of genetic variations in FAS, GJB2 and PTPRN2 are associated with noise-induced hearing loss: a case-control study in China. BMC Med Genomics 2024; 17:18. [PMID: 38212800 PMCID: PMC10785407 DOI: 10.1186/s12920-023-01790-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND This study aimed to screen and validate noise-induced hearing loss (NIHL) associated single nucleotide polymorphisms (SNPs), construct genetic risk prediction models, and evaluate higher-order gene-gene, gene-environment interactions for NIHL in Chinese population. METHODS First, 83 cases and 83 controls were recruited and 60 candidate SNPs were genotyped. Then SNPs with promising results were validated in another case-control study (153 cases and 252 controls). NIHL-associated SNPs were identified by logistic regression analysis, and a genetic risk model was constructed based on the genetic risk score (GRS), and classification and regression tree (CART) analysis was used to evaluate interactions among gene-gene and gene-environment. RESULTS Six SNPs in five genes were significantly associated with NIHL risk (p < 0.05). A positive dose-response relationship was found between GRS values and NIHL risk. CART analysis indicated that strongest interaction was among subjects with age ≥ 45 years and cumulative noise exposure ≥ 95 [dB(A)·years], without personal protective equipment, and carried GJB2 rs3751385 (AA/AB) and FAS rs1468063 (AA/AB) (OR = 10.038, 95% CI = 2.770, 47.792), compared with the referent group. CDH23, FAS, GJB2, PTPRN2 and SIK3 may be NIHL susceptibility genes. CONCLUSION GRS values may be utilized in the evaluation of the cumulative effect of genetic risk for NIHL based on NIHL-associated SNPs. Gene-gene, gene-environment interaction patterns play an important role in the incidence of NIHL.
Collapse
Affiliation(s)
- Shan Wu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of public health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhidan Wu
- Guangzhou Baiyun District Center for Disease Prevention and Control, Guangzhou, China
| | - Manlian Chen
- The Sixth people's Hospital Of Dongguan, Dongguan, China
| | - Xiangbin Zhong
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of public health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Haoyan Gu
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of public health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Wenjing Du
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of public health, Guangdong Pharmaceutical University, Guangzhou, China
| | - Weidong Liu
- The Sixth people's Hospital Of Dongguan, Dongguan, China
| | - Li Lang
- Guangdong Province Hospital for Occupational Disease Prevention and Treatment, Guangzhou, China.
| | - Junyi Wang
- Guangdong Provincial Engineering Research Center of Public Health Detection and Assessment, School of public health, Guangdong Pharmaceutical University, Guangzhou, China.
| |
Collapse
|
3
|
Yuan Z, Liu X, Deng S, He G, Zhang J, He Q, Chi Y, Jiang X, Xia X, Deng R. Single-Cell Genotyping of Single-Nucleotide Mutations Using In Situ Allele-Specific Loop-Mediated Isothermal Amplification. ACS Sens 2023; 8:4315-4322. [PMID: 37862679 DOI: 10.1021/acssensors.3c01679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2023]
Abstract
Single-nucleotide mutations (SNMs) in the bacterial genome may cause antibiotic resistance. The visualization of SNMs can indicate antibiotic resistance phenotypes at the single-cell level but remains challenging. Herein, we proposed an in situ allele-specific isothermal amplification proceeded inside cells, allowing us to image bacterial genes with single-nucleotide resolution. The primer for loop-mediated isothermal amplification (LAMP) was designed with artificial mismatch bases to serve as an allele-specific probe, endowing LAMP to specifically amplify genes with SNMs. Due to the high amplification efficiency of LAMP, the method termed AlleLAMP can generate high gain for imaging SNMs and precisely quantify mutated quinolone-resistant Salmonella in bacterial mixture. We utilized AlleLAMP to survey the selection of antibiotic resistance under the preservative stress and found that the mutant quinolone-resistant strain owned a survival advantage over the wild-type quinolone-sensitive strain under the stress of preservatives. AlleLAMP can serve as a single-cell tool for analyzing the relationship between bacterial genotype and phenotype.
Collapse
Affiliation(s)
- Zilan Yuan
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Xinmiao Liu
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Sha Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Guiping He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Jiaqi Zhang
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Qiang He
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Yuanlong Chi
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Xiue Jiang
- Research Center for Analytical Science, College of Chemistry, Nankai University, Tianjin 300071, China
| | - Xuhan Xia
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| | - Ruijie Deng
- College of Biomass Science and Engineering, Healthy Food Evaluation Research Center, Sichuan University, Chengdu 610065, Sichuan, China
| |
Collapse
|
4
|
de Olazarra AS, Wang SX. Advances in point-of-care genetic testing for personalized medicine applications. BIOMICROFLUIDICS 2023; 17:031501. [PMID: 37159750 PMCID: PMC10163839 DOI: 10.1063/5.0143311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 04/12/2023] [Indexed: 05/11/2023]
Abstract
Breakthroughs within the fields of genomics and bioinformatics have enabled the identification of numerous genetic biomarkers that reflect an individual's disease susceptibility, disease progression, and therapy responsiveness. The personalized medicine paradigm capitalizes on these breakthroughs by utilizing an individual's genetic profile to guide treatment selection, dosing, and preventative care. However, integration of personalized medicine into routine clinical practice has been limited-in part-by a dearth of widely deployable, timely, and cost-effective genetic analysis tools. Fortunately, the last several decades have been characterized by tremendous progress with respect to the development of molecular point-of-care tests (POCTs). Advances in microfluidic technologies, accompanied by improvements and innovations in amplification methods, have opened new doors to health monitoring at the point-of-care. While many of these technologies were developed with rapid infectious disease diagnostics in mind, they are well-suited for deployment as genetic testing platforms for personalized medicine applications. In the coming years, we expect that these innovations in molecular POCT technology will play a critical role in enabling widespread adoption of personalized medicine methods. In this work, we review the current and emerging generations of point-of-care molecular testing platforms and assess their applicability toward accelerating the personalized medicine paradigm.
Collapse
Affiliation(s)
- A. S. de Olazarra
- Department of Electrical Engineering, Stanford University, Stanford, California 94305, USA
| | - S. X. Wang
- Author to whom correspondence should be addressed:
| |
Collapse
|
5
|
Chen Y, Li R, Sun J, Li C, Xiao H, Chen S. Genome-Wide Population Structure and Selection Signatures of Yunling Goat Based on RAD-seq. Animals (Basel) 2022; 12:ani12182401. [PMID: 36139261 PMCID: PMC9495202 DOI: 10.3390/ani12182401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/07/2022] [Accepted: 09/10/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary Goats are important domestic animals that provide meat, milk, fur, and other products for humans. The demand for these products has increased in recent years. Disease resistance among goat breeds is different, but the genetic basis of the differences in resistance to diseases is still unclear and needs to be further studied. In this study, many genes and pathways related to immunity and diseases were identified to be under positive selection between Yunling and Nubian goats using RAD-seq technology. This study on the selection signatures of Yunling goats provides the scientific basis and technical support for the breeding of domestic goats for disease resistance, which has important social and economic significance. Abstract Animal diseases impose a huge burden on the countries where diseases are endemic. Conventional control strategies of vaccines and veterinary drugs are to control diseases from a pharmaceutical perspective. Another alternative approach is using pre-existing genetic disease resistance or tolerance. We know that the Yunling goat is an excellent local breed from Yunnan, southwestern China, which has characteristics of strong disease resistance and remarkable adaptability. However, genetic information about the selection signatures of Yunling goats is limited. We reasoned that the genes underlying the observed difference in disease resistance might be identified by investigating selection signatures between two different goat breeds. Herein, we selected the Nubian goat as the reference group to perform the population structure and selection signature analysis by using RAD-seq technology. The results showed that two goat breeds were divided into two clusters, but there also existed gene flow. We used Fst (F-statistics) and π (pi/θπ) methods to carry out selection signature analysis. Eight selected regions and 91 candidate genes were identified, in which some genes such as DOK2, TIMM17A, MAVS, and DOCK8 related to disease and immunity and some genes such as SPEFI, CDC25B, and MIR103 were associated with reproduction. Four GO (Gene Ontology) terms (GO:0010591, GO:001601, GO:0038023, and GO:0017166) were associated with cell migration, signal transduction, and immune responses. The KEGG (Kyoto Encyclopedia of Genes and Genomes) signaling pathways were mainly associated with immune responses, inflammatory responses, and stress reactions. This study preliminarily revealed the genetic basis of strong disease resistance and adaptability of Yunling goats. It provides a theoretical basis for the subsequent genetic breeding of disease resistance of goats.
Collapse
Affiliation(s)
- Yuming Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
- School of Life Sciences, Yunnan University, Kunming 650500, China;
| | - Rong Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
- College of Life Science, Yunnan Normal University, Kunming 650500, China
| | - Jianshu Sun
- School of Life Sciences, Yunnan University, Kunming 650500, China;
| | - Chunqing Li
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
| | - Heng Xiao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
| | - Shanyuan Chen
- School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; (Y.C.); (R.L.); (C.L.); (H.X.)
- Correspondence: ; Tel.: +86-18687122260
| |
Collapse
|
6
|
Radhakrishnan A, Kuppusamy G, Ponnusankar S, Mutalik S. Towards next-generation personalization of tacrolimus treatment: a review on advanced diagnostic and therapeutic approaches. Pharmacogenomics 2021; 22:1151-1175. [PMID: 34719935 DOI: 10.2217/pgs-2021-0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The benefit of personalized medicine is that it allows the customization of drug therapy - maximizing efficacy while avoiding side effects. Genetic polymorphisms are one of the major contributors to interindividual variability. Currently, the only gold standard for applying personalized medicine is dose titration. Because of technological advancements, converting genotypic data into an optimum dose has become easier than in earlier years. However, for many medications, determining a personalized dose may be difficult, leading to a trial-and-error method. On the other hand, the technologically oriented pharmaceutical industry has a plethora of smart drug delivery methods that are underutilized in customized medicine. This article elaborates the genetic polymorphisms of tacrolimus as case study, and extensively covers the diagnostic and therapeutic technologies which aid in the delivery of personalized tacrolimus treatment for better clinical outcomes, thereby providing a new strategy for implementing personalized medicine.
Collapse
Affiliation(s)
- Arun Radhakrishnan
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Gowthamarajan Kuppusamy
- Department of Pharmaceutics, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Sivasankaran Ponnusankar
- Department of Pharmacy Practice, JSS College of Pharmacy, JSS Academy of Higher Education & Research, Ooty, Nilgiris, Tamilnadu, India
| | - Srinivas Mutalik
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Karnataka, India
| |
Collapse
|
7
|
Discovery of SNPs in important legumes through comparative genome analysis and conversion of SNPs into PCR-based markers. J Genet 2021. [DOI: 10.1007/s12041-021-01320-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
|
8
|
Mukhtar M, Sargazi S, Barani M, Madry H, Rahdar A, Cucchiarini M. Application of Nanotechnology for Sensitive Detection of Low-Abundance Single-Nucleotide Variations in Genomic DNA: A Review. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:1384. [PMID: 34073904 PMCID: PMC8225127 DOI: 10.3390/nano11061384] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 01/02/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) are the simplest and most common type of DNA variations in the human genome. This class of attractive genetic markers, along with point mutations, have been associated with the risk of developing a wide range of diseases, including cancer, cardiovascular diseases, autoimmune diseases, and neurodegenerative diseases. Several existing methods to detect SNPs and mutations in body fluids have faced limitations. Therefore, there is a need to focus on developing noninvasive future polymerase chain reaction (PCR)-free tools to detect low-abundant SNPs in such specimens. The detection of small concentrations of SNPs in the presence of a large background of wild-type genes is the biggest hurdle. Hence, the screening and detection of SNPs need efficient and straightforward strategies. Suitable amplification methods are being explored to avoid high-throughput settings and laborious efforts. Therefore, currently, DNA sensing methods are being explored for the ultrasensitive detection of SNPs based on the concept of nanotechnology. Owing to their small size and improved surface area, nanomaterials hold the extensive capacity to be used as biosensors in the genotyping and highly sensitive recognition of single-base mismatch in the presence of incomparable wild-type DNA fragments. Different nanomaterials have been combined with imaging and sensing techniques and amplification methods to facilitate the less time-consuming and easy detection of SNPs in different diseases. This review aims to highlight some of the most recent findings on the aspects of nanotechnology-based SNP sensing methods used for the specific and ultrasensitive detection of low-concentration SNPs and rare mutations.
Collapse
Affiliation(s)
- Mahwash Mukhtar
- Faculty of Pharmacy, Institute of Pharmaceutical Technology and Regulatory Affairs, University of Szeged, 6720 Szeged, Hungary;
| | - Saman Sargazi
- Cellular and Molecular Research Center, Resistant Tuberculosis Institute, Zahedan University of Medical Sciences, Zahedan 98167-43463, Iran;
| | - Mahmood Barani
- Department of Chemistry, Shahid Bahonar University of Kerman, Kerman 76169-14111, Iran;
| | - Henning Madry
- Center of Experimental Orthopaedics, Saarland University Medical Center, D-66421 Homburg/Saar, Germany;
| | - Abbas Rahdar
- Department of Physics, Faculty of Science, University of Zabol, Zabol 538-98615, Iran
| | - Magali Cucchiarini
- Center of Experimental Orthopaedics, Saarland University Medical Center, D-66421 Homburg/Saar, Germany;
| |
Collapse
|
9
|
Islam MT, Alam ARU, Sakib N, Hasan MS, Chakrovarty T, Tawyabur M, Islam OK, Al-Emran HM, Jahid MIK, Anwar Hossain M. A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades. J Med Virol 2021; 93:2962-2970. [PMID: 33491822 DOI: 10.1101/2020.10.08.20209692] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 05/23/2023]
Abstract
Tracing the globally circulating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) phylogenetic clades by high-throughput sequencing is costly, time-consuming, and labor-intensive. We here propose a rapid, simple, and cost-effective amplification refractory mutation system (ARMS)-based multiplex reverse-transcription polymerase chain reaction (PCR) assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. Our multiplex PCR is designed in a mutually exclusive way to identify V-S and G-GH-GR clade variants separately. The pentaplex assay included all five variants and the quadruplex comprised of the triplex variants alongside either V or S clade mutations that created two separate subsets. The procedure was optimized with 0.2-0.6 µM primer concentration, 56-60°C annealing temperature, and 3-5 ng/µl complementary DNA to validate on 24 COVID-19-positive samples. Targeted Sanger sequencing further confirmed the presence of the clade-featured mutations with another set of primers. This multiplex ARMS-PCR assay is a fast, low-cost alternative and convenient to discriminate the circulating phylogenetic clades of SARS-CoV-2.
Collapse
Affiliation(s)
- Mohammad Tanvir Islam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Asm Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Najmuj Sakib
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Mohammad Shazid Hasan
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Tanay Chakrovarty
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Mohammad Tawyabur
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Ovinu Kibria Islam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hassan M Al-Emran
- Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Mohammad Anwar Hossain
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
- Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| |
Collapse
|
10
|
Islam MT, Alam ARU, Sakib N, Hasan MS, Chakrovarty T, Tawyabur M, Islam OK, Al-Emran HM, Jahid MIK, Anwar Hossain M. A rapid and cost-effective multiplex ARMS-PCR method for the simultaneous genotyping of the circulating SARS-CoV-2 phylogenetic clades. J Med Virol 2021; 93:2962-2970. [PMID: 33491822 PMCID: PMC8014803 DOI: 10.1002/jmv.26818] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 01/15/2021] [Accepted: 01/20/2021] [Indexed: 01/09/2023]
Abstract
Tracing the globally circulating severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) phylogenetic clades by high‐throughput sequencing is costly, time‐consuming, and labor‐intensive. We here propose a rapid, simple, and cost‐effective amplification refractory mutation system (ARMS)‐based multiplex reverse‐transcription polymerase chain reaction (PCR) assay to identify six distinct phylogenetic clades: S, L, V, G, GH, and GR. Our multiplex PCR is designed in a mutually exclusive way to identify V–S and G–GH–GR clade variants separately. The pentaplex assay included all five variants and the quadruplex comprised of the triplex variants alongside either V or S clade mutations that created two separate subsets. The procedure was optimized with 0.2–0.6 µM primer concentration, 56–60°C annealing temperature, and 3–5 ng/µl complementary DNA to validate on 24 COVID‐19‐positive samples. Targeted Sanger sequencing further confirmed the presence of the clade‐featured mutations with another set of primers. This multiplex ARMS‐PCR assay is a fast, low‐cost alternative and convenient to discriminate the circulating phylogenetic clades of SARS‐CoV‐2. Multiplex ARMS‐PCR (amplification refractory mutation system‐polymerase chain reaction) method for genotyping major severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2 clades). Identify the mutated region of circulating phylogenetically SARS‐CoV‐2 clades. PCR conditions were optimized and validated to identify V–S and G–GH–GR clade.
Collapse
Affiliation(s)
- Mohammad Tanvir Islam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Asm Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Najmuj Sakib
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Mohammad Shazid Hasan
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Tanay Chakrovarty
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Mohammad Tawyabur
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Ovinu Kibria Islam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh
| | - Hassan M Al-Emran
- Department of Biomedical Engineering, Jashore University of Science and Technology, Jashore, Bangladesh
| | | | - Mohammad Anwar Hossain
- Department of Microbiology, Jashore University of Science and Technology, Jashore, Bangladesh.,Department of Microbiology, University of Dhaka, Dhaka, Bangladesh
| |
Collapse
|
11
|
Yang S, Gill RA, Zaman QU, Ulhassan Z, Zhou W. Insights on SNP types, detection methods and their utilization in Brassica species: Recent progress and future perspectives. J Biotechnol 2020; 324:11-20. [PMID: 32979432 DOI: 10.1016/j.jbiotec.2020.09.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2020] [Revised: 09/15/2020] [Accepted: 09/20/2020] [Indexed: 01/09/2023]
Abstract
The genus Brassica, family Brassicaceae (Cruciferae), comprises many important species of oil crops, vegetables and medicinal plants including B. rapa, B. oleracea, B. nigra, B. napus, B. juncea, B. carinata. Genomic researches in Brassica species is constrained by polyploidization, mainly due to its complicated genomic structure. However, rapid development of methods for detecting single nucleotide polymorphisms (SNP), such as next generation sequencing and SNP microarray, has accelerated release of reference Brassica species genomes as well as discovery of large numbers and genome-wide SNPs, thus intensifying forward genetics in this genus. In this review, we summarize biological characteristics, classification and various methods for detecting SNPs, focusing on high-throughput techniques. Moreover, we describe the pivotal roles of SNPs in genetic diversity, linkage map construction and QTL mapping, comparative genomics, linkage disequilibrium and genome-wide association studies. These insights are expected to deepen our understanding and guide further advancements in Brassica species research.
Collapse
Affiliation(s)
- Su Yang
- College of Life Sciences, China Jiliang University, Hangzhou 310018, China
| | - Rafaqat Ali Gill
- Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan 430062, China.
| | - Qamar U Zaman
- Oil Crops Research Institute, Chinese Academy of Agricultural Science, Wuhan 430062, China
| | - Zaid Ulhassan
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| | - Weijun Zhou
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou 310058, China
| |
Collapse
|
12
|
Zhang J, Yang J, Zhang L, Luo J, Zhao H, Zhang J, Wen C. A new SNP genotyping technology Target SNP-seq and its application in genetic analysis of cucumber varieties. Sci Rep 2020; 10:5623. [PMID: 32221398 PMCID: PMC7101363 DOI: 10.1038/s41598-020-62518-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 03/11/2020] [Indexed: 01/18/2023] Open
Abstract
To facilitate the utility of SNP-based genotyping, we developed a new method called target SNP-seq which combines the advantages of multiplex PCR amplification and high throughput sequencing. Compared with KASP, Microarrays, GBS and other SNP genotyping methods, target SNP-seq is flexible both in SNPs and samples, yields high accuracy, especially when genotyping genome wide perfect SNPs with high polymorphism and conserved flanking sequences, and is cost-effective, requiring 3 days and $7 for per DNA sample to genotype hundreds of SNP loci. The present study established a DNA fingerprint of 261 cucumber varieties by target SNP-seq with 163 perfect SNPs from 4,612,350 SNPs based on 182 cucumber resequencing datasets. Four distinct subpopulations were found in 261 Chinese cucumber varieties: the north China type, the south China type, the Europe type, and the Xishuangbanna type. The north China type and Xishuangbanna type harbored lower genetic diversity, indicating greater risk of genetic erosion in these two subpopulations. Furthermore, a core set of 24 SNPs was able to distinguish 99% of the 261 cucumber varieties. 29 core cucumber backbone varieties in China were identified. Therefore, target SNP-seq provides a new way to screen out core SNP loci from the whole genome for DNA fingerprinting of crop varieties. The high efficiency and low cost of target SNP-seq is more competitive than the current SNP genotyping methods, and it has excellent application prospects in genetic research, as well as in promoting plant breeding processes in the near future.
Collapse
Affiliation(s)
- Jian Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Like Zhang
- National Agricultural Technology Extension and Service Center, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jiang Luo
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Hong Zhao
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jianan Zhang
- Molbreeding Biotechnology Company, Shijiazhuang, 050000, China
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China. .,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
| |
Collapse
|
13
|
Ahmed M, Goh C, Saunders E, Cieza-Borrella C, Kote-Jarai Z, Schumacher FR, Eeles R. Germline genetic variation in prostate susceptibility does not predict outcomes in the chemoprevention trials PCPT and SELECT. Prostate Cancer Prostatic Dis 2019; 23:333-342. [PMID: 31776447 PMCID: PMC7237354 DOI: 10.1038/s41391-019-0181-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 06/02/2019] [Accepted: 06/24/2019] [Indexed: 12/11/2022]
Abstract
Background The development of prostate cancer can be influenced by genetic and environmental factors. Numerous germline SNPs influence prostate cancer susceptibility. The functional pathways in which these SNPs increase prostate cancer susceptibility are unknown. Finasteride is currently not being used routinely as a chemoprevention agent but the long term outcomes of the PCPT trial are awaited. The outcomes of the SELECT trial have not recommended the use of chemoprevention in preventing prostate cancer. This study investigated whether germline risk SNPs could be used to predict outcomes in the PCPT and SELECT trial. Methods Genotyping was performed in European men entered into the PCPT trial (n = 2434) and SELECT (n = 4885). Next generation genotyping was performed using Affymetrix® Eureka™ Genotyping protocols. Logistic regression models were used to test the association of risk scores and the outcomes in the PCPT and SELECT trials. Results Of the 100 SNPs, 98 designed successfully and genotyping was validated for samples genotyped on other platforms. A number of SNPs predicted for aggressive disease in both trials. Men with a higher polygenic score are more likely to develop prostate cancer in both trials, but the score did not predict for other outcomes in the trial. Conclusion Men with a higher polygenic risk score are more likely to develop prostate cancer. There were no interactions of these germline risk SNPs and the chemoprevention agents in the SELECT and PCPT trials.
Collapse
Affiliation(s)
- Mahbubl Ahmed
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK.
| | - Chee Goh
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Edward Saunders
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Clara Cieza-Borrella
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | | | - Zsofia Kote-Jarai
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| | - Fredrick R Schumacher
- Department of Epidemiology and Biostatistics, Case Western Reserve University; Seidman Cancer Center, University Hospitals, Cleveland, OH, USA
| | - Ros Eeles
- The Institute of Cancer Research, Royal Marsden Hospital, NHS Foundation Trust, 123 Old Brompton Road, London, SW7 3RP, UK
| |
Collapse
|
14
|
Raizada A, Souframanien J. Transcriptome sequencing, de novo assembly, characterisation of wild accession of blackgram (Vigna mungo var. silvestris) as a rich resource for development of molecular markers and validation of SNPs by high resolution melting (HRM) analysis. BMC PLANT BIOLOGY 2019; 19:358. [PMID: 31419947 PMCID: PMC6697964 DOI: 10.1186/s12870-019-1954-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 07/31/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Blackgram [Vigna mungo (L.) Hepper], is an important legume crop of Asia with limited genomic resources. We report a comprehensive set of genic simple sequence repeat (SSR) and single nucleotide polymorphism (SNPs) markers using Illumina MiSeq sequencing of transcriptome and its application in genetic variation analysis and mapping. RESULTS Transcriptome sequencing of immature seeds of wild blackgram, V. mungo var. silvestris by Illumina MiSeq technology generated 1.9 × 107 reads, which were assembled into 40,178 transcripts (TCS) with an average length of 446 bp covering 2.97 GB of the genome. A total of 38,753 CDS (Coding sequences) were predicted from 40,178 TCS and 28,984 CDS were annotated through BLASTX and mapped to GO and KEGG database resulting in 140 unique pathways. The tri-nucleotides were most abundant (39.9%) followed by di-nucleotide (30.2%). About 60.3 and 37.6% of SSR motifs were present in the coding sequences (CDS) and untranslated regions (UTRs) respectively. Among SNPs, the most abundant substitution type were transitions (Ts) (61%) followed by transversions (Tv) type (39%), with a Ts/Tv ratio of 1.58. A total of 2306 DEGs were identified by RNA Seq between wild and cultivar and validation was done by quantitative reverse transcription polymerase chain reaction. In this study, we genotyped SNPs with a validation rate of 78.87% by High Resolution Melting (HRM) Assay. CONCLUSION In the present study, 1621genic-SSR and 1844 SNP markers were developed from immature seed transcriptome sequence of blackgram and 31 genic-SSR markers were used to study genetic variations among different blackgram accessions. Above developed markers contribute towards enriching available genomic resources for blackgram and aid in breeding programmes.
Collapse
Affiliation(s)
- Avi Raizada
- Nuclear Agriculture and Biotechnology Division, BARC, Trombay, Mumbai, Trombay, 400085, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Anushakti Nagar, 400094, India
| | - J Souframanien
- Nuclear Agriculture and Biotechnology Division, BARC, Trombay, Mumbai, Trombay, 400085, India.
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai, Anushakti Nagar, 400094, India.
| |
Collapse
|
15
|
Roques S, Chancerel E, Boury C, Pierre M, Acolas M. From microsatellites to single nucleotide polymorphisms for the genetic monitoring of a critically endangered sturgeon. Ecol Evol 2019; 9:7017-7029. [PMID: 31380030 PMCID: PMC6662312 DOI: 10.1002/ece3.5268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 02/12/2019] [Accepted: 04/04/2019] [Indexed: 01/06/2023] Open
Abstract
The use of genetic information is crucial in conservation programs for the establishment of breeding plans and for the evaluation of restocking success. Short tandem repeats (STRs) have been the most widely used molecular markers in such programs, but next-generation sequencing approaches have prompted the transition to genome-wide markers such as single nucleotide polymorphisms (SNPs). Until now, most sturgeon species have been monitored using STRs. The low diversity found in the critically endangered European sturgeon (Acipenser sturio), however, makes its future genetic monitoring challenging, and the current resolution needs to be increased. Here, we describe the discovery of a highly informative set of 79 SNPs using double-digest restriction-associated DNA (ddRAD) sequencing and its validation by genotyping using the MassARRAY system. Comparing with STRs, the SNP panel proved to be highly efficient and reproducible, allowing for more accurate parentage and kinship assignments' on 192 juveniles of known pedigree and 40 wild-born adults. We explore the effectiveness of both markers to estimated relatedness and inbreeding, using simulated and empirical datasets. Interestingly, we found significant correlations between STRs and SNPs at individual heterozygosity and inbreeding that give support to a reasonable representation of whole genome diversity for both markers. These results are useful for the conservation program of A. sturio in building a comprehensive studbook, which will optimize conservation strategies. This approach also proves suitable for other case studies in which highly discriminatory genetic markers are needed to assess parentage and kinship.
Collapse
Affiliation(s)
- Séverine Roques
- Aquatic Ecosystems and Global ChangesIRSTEA, EABX URCestasFrance
| | | | | | - Maud Pierre
- Aquatic Ecosystems and Global ChangesIRSTEA, EABX URCestasFrance
| | | |
Collapse
|
16
|
Bi R, Lohithaswa HC, Lokesh S, Kumar KRS, Shilpa HB, Jyothi K, Vinutha K, Hittalmani S. Development and application of genomic resources for comparative and translational genomics in legumes through leveraging genomic sequence of Medicago truncatula. J Genet 2018. [DOI: 10.1007/s12041-018-0995-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
17
|
Shen T, You Y, Joseph C, Mirzaei M, Klistorner A, Graham SL, Gupta V. BDNF Polymorphism: A Review of Its Diagnostic and Clinical Relevance in Neurodegenerative Disorders. Aging Dis 2018; 9:523-536. [PMID: 29896439 PMCID: PMC5988606 DOI: 10.14336/ad.2017.0717] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/17/2017] [Indexed: 12/17/2022] Open
Abstract
Brain-derived neurotrophic factor (BDNF) has a unique role in the neuronal development, differentiation, and survival in the developing and adult nervous system. A common single-nucleotide polymorphism in the pro-region of the human BDNF gene, resulting in a valine to methionine substitution (Val66Met), has been associated with the susceptibility, incidence, and clinical features of several neurodegenerative disorders. Much research has been dedicated to evaluating the effects of polymorphism in the past decade, and functional effects of this genetic variation. A better understanding of how this naturally occurring polymorphism associates with or influences physiology, anatomy, and cognition in both healthy and diseased adults in neurodegenerative conditions will help understand neurochemical mechanisms and definable clinical outcomes in humans. Here we review the role and relevance of the BDNF Val66Met polymorphism in neurodegenerative diseases, with particular emphasis on glaucoma, multiple sclerosis (MS), Alzheimer’s disease (AD) and Parkinson’s disease (PD). Several controversies and unresolved issues, including small effect sizes, possible ethnicity, gender, and age effects of the BDNF Val66Met are also discussed with respect to future research.
Collapse
Affiliation(s)
- Ting Shen
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia
| | - Yuyi You
- 2Save Sight Institute, Sydney University, Sydney, Australia
| | - Chitra Joseph
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia
| | - Mehdi Mirzaei
- 3Faculty of Science and Engineering, Macquarie University, Australia
| | - Alexander Klistorner
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia.,2Save Sight Institute, Sydney University, Sydney, Australia
| | - Stuart L Graham
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia.,2Save Sight Institute, Sydney University, Sydney, Australia
| | - Vivek Gupta
- 1Faculty of Medicine and Health Sciences, Macquarie University, Australia
| |
Collapse
|
18
|
Puggioni V, Chiesa O, Panini M, Mazzoni E. Qualitative Sybr Green real-time detection of single nucleotide polymorphisms responsible for target-site resistance in insect pests: the example of Myzus persicae and Musca domestica. BULLETIN OF ENTOMOLOGICAL RESEARCH 2017; 107:96-105. [PMID: 27444359 DOI: 10.1017/s0007485316000675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Chemical insecticides have been widely used to control insect pests, leading to the selection of resistant populations. To date, several single nucleotide polymorphisms (SNPs) have already been associated with insecticide resistance, causing reduced sensitivity to many classes of products. Monitoring and detection of target-site resistance is currently one of the most important factors for insect pest management strategies. Several methods are available for this purpose: automated and high-throughput techniques (i.e. TaqMan or pyrosequencing) are very costly; cheaper alternatives (i.e. RFLP or PASA-PCRs) are time-consuming and limited by the necessity of a final visualization step. This work presents a new approach (QSGG, Qualitative Sybr Green Genotyping) which combines the specificity of PASA-PCR with the rapidity of real-time PCR analysis. The specific real-time detection of Cq values of wild-type or mutant alleles (amplified used allele-specific primers) allows the calculation of ΔCqW-M values and the consequent identification of the genotypes of unknown samples, on the basis of ranges previously defined with reference clones. The methodology is applied here to characterize mutations described in Myzus persicae and Musca domestica and we demonstrate it represents a valid, rapid and cost-effective technique that can be adopted for monitoring target-site resistance in field populations of these and other insect species.
Collapse
Affiliation(s)
- V Puggioni
- Department of Sustainable Crop Production,Section Sustainable Crop and Food Protection,Università Cattolica del Sacro Cuore,Via Emilia Parmense,84, I-29122 Piacenza,Italy
| | - O Chiesa
- Department of Sustainable Crop Production,Section Sustainable Crop and Food Protection,Università Cattolica del Sacro Cuore,Via Emilia Parmense,84, I-29122 Piacenza,Italy
| | - M Panini
- Department of Sustainable Crop Production,Section Sustainable Crop and Food Protection,Università Cattolica del Sacro Cuore,Via Emilia Parmense,84, I-29122 Piacenza,Italy
| | - E Mazzoni
- Department of Sustainable Crop Production,Section Sustainable Crop and Food Protection,Università Cattolica del Sacro Cuore,Via Emilia Parmense,84, I-29122 Piacenza,Italy
| |
Collapse
|
19
|
Heidari Sharafdarkolaei S, Motovali-Bashi M, Gill P. Fluorescent detection of point mutation via ligase reaction assisted by quantum dots and magnetic nanoparticle-based probes. RSC Adv 2017. [DOI: 10.1039/c7ra03767h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A nanodiagnostic genotyping method was presented for point mutation detection directly in human genomic DNA based on ligase reaction coupled with quantum dots and magnetic nanoparticle-based probes.
Collapse
Affiliation(s)
| | | | - P. Gill
- Nanomedicine Group
- Immunogenetics Research Center
- Mazandaran University of Medical Sciences
- Sari
- Iran
| |
Collapse
|
20
|
Genetic characterization and founder effect analysis of recently introduced Salers cattle breed population. Animal 2016; 11:24-32. [PMID: 27278345 DOI: 10.1017/s1751731116001063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Salers are a native French breed used for beef and dairy production that has expanded to all the continents. The Salers breed was introduced to the north of Spain in 1985 with only 15 individuals from France and has successfully increased to over 20 000 animals. Although over time new animals have been imported from France for breeding, it is possible that the limiting number of founder animals could have resulted in a reduction of the genetic diversity found in Spanish Salers. Thus, the purpose of the present study has been to characterize the genetic diversity of Salers breed in Spain and evaluate a possible founder effect due to reduced number of the first reproducers. A total of 403 individuals from 12 Salers herds were analyzed using 12 microsatellite markers and compared with phylogenetically and geographically close related Blonde d'Aquitaine, Limousin and Charolais French breeds but also other 16 European breeds. Microsatellites in Salers were polymorphic, with a mean allelic richness of 5.129 and an expected heterozygosity of 0.621 across loci (0.576 to 0.736 among all breeds). Average observed heterozygosity was 0.618. All the loci fit the Hardy-Weinberg (HW) equilibrium except TGLA227 locus due to a significant deficit of heterozygotes in only one of the herds, probably attributable to a sampling effect. When all loci were combined, Salers inbreeding coefficient did not differ statistically from 0 (F IS=0.005), indicating not significant excess or deficit of heterozygotes (P=0.309). Based in allelic distribution, Salers revealed a frequency of 0.488 in BM2113-131 and 0.064 in BM2113-143 diagnostic alleles, which are specific to the African zebu. These zebu alleles are also found in some French breeds, supported by STR data previously postulated hypothesis of a migration route through Mediterranean route by which North African cattle may have left a genetic signature in southern Europe. Phylogenetic tree and population structure analyses could unambiguously differentiate Salers cattle from the other populations and 10% of the total genetic variability could be attributed to differences among breeds (mean R ST=0.105; P<0.01). Mutation-drift equilibrium tests (sign test and Wilcoxon's sign rank test) were in correspondence to the absence of founder effect when Bonferroni was applied. Gene diversity previously reported in French Salers was comparable with the observed in our population. Thus, high genetic diversity in Spanish Salers highlights the resources of this population, which looks toward future breeding and selection programs.
Collapse
|
21
|
Huang CW, Lin YT, Ding ST, Lo LL, Wang PH, Lin EC, Liu FW, Lu YW. Efficient SNP Discovery by Combining Microarray and Lab-on-a-Chip Data for Animal Breeding and Selection. ACTA ACUST UNITED AC 2015; 4:570-95. [PMID: 27600241 PMCID: PMC4996412 DOI: 10.3390/microarrays4040570] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 10/16/2015] [Accepted: 10/28/2015] [Indexed: 11/16/2022]
Abstract
The genetic markers associated with economic traits have been widely explored for animal breeding. Among these markers, single-nucleotide polymorphism (SNPs) are gradually becoming a prevalent and effective evaluation tool. Since SNPs only focus on the genetic sequences of interest, it thereby reduces the evaluation time and cost. Compared to traditional approaches, SNP genotyping techniques incorporate informative genetic background, improve the breeding prediction accuracy and acquiesce breeding quality on the farm. This article therefore reviews the typical procedures of animal breeding using SNPs and the current status of related techniques. The associated SNP information and genotyping techniques, including microarray and Lab-on-a-Chip based platforms, along with their potential are highlighted. Examples in pig and poultry with different SNP loci linked to high economic trait values are given. The recommendations for utilizing SNP genotyping in nimal breeding are summarized.
Collapse
Affiliation(s)
- Chao-Wei Huang
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Yu-Tsung Lin
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Shih-Torng Ding
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Ling-Ling Lo
- Department of Animal Science, Chinese Culture University, Taipei 11114, Taiwan.
| | - Pei-Hwa Wang
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - En-Chung Lin
- Department of Animal Science, National Taiwan University, Taipei 10617, Taiwan.
| | - Fang-Wei Liu
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| | - Yen-Wen Lu
- Department of Bio-Industrial Mechatronics Engineering, National Taiwan University, Taipei 10617, Taiwan.
| |
Collapse
|
22
|
Jang JP, Baek IC, Choi EJ, Kim TG. Multiplex genotyping of cytokine gene SNPs using fluorescence bead array. PLoS One 2015; 10:e0118008. [PMID: 25689696 PMCID: PMC4331502 DOI: 10.1371/journal.pone.0118008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 01/05/2015] [Indexed: 01/02/2023] Open
Abstract
Single nucleotide polymorphisms (SNPs) of genes that affect cytokine production and function are known to influence the susceptibility and progression of immune-related conditions such as infection, autoimmune diseases, transplantation, and cancer. We established a multiplex genotyping method to analyze the SNPs of cytokine genes by combining the multiplex PCR and bead array platform. Thirteen cytokine gene regions, including 20 SNPs, were amplified, and allele-specific primer extension was performed in a single tube. High-quality allele-specific primers were selected for signals greater than 1000 median fluorescence intensity (MFI) for positive alleles, and less than 500 MFI for negative alleles. To select and improve the extension primers, modifications for the reverse direction, length or refractory were performed. 24 primers in the forward or reverse direction step and 12 primers in length or refractory modifications were selected and showed high concordance with results by nucleotide sequencing. Among the 13 candidate cytokine genes, the SNPs of 12 cytokine genes, including IL-1α, IL-1R, IL-1RA, IL-1β, IL-2, IL-4, IL-4Rα, IL-6, IL-10, IL-12, TGF-β1, and TNF-α, were successfully defined with the selected allele-specific primers in healthy Korean subjects. Our genotyping system provides a fast and accurate detection for SNPs of multiple cytokine genes to investigate their association with immune-related diseases and transplantation outcomes.
Collapse
Affiliation(s)
- Jung-Pil Jang
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - In-Cheol Baek
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Eun-Jeong Choi
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
| | - Tai-Gyu Kim
- Department of Microbiology, College of Medicine, The Catholic University of Korea, Seoul, Korea
- Hematopoietic Stem Cell Bank, College of Medicine, The Catholic University of Korea, Seoul, Korea
- * E-mail:
| |
Collapse
|
23
|
Sajjanar B, Deb R, Singh U, Kumar S, Brahmane M, Nirmale A, Bal SK, Minhas PS. Identification of SNP inHSP90AB1and its Association with the Relative Thermotolerance and Milk Production Traits in Indian Dairy Cattle. Anim Biotechnol 2014; 26:45-50. [DOI: 10.1080/10495398.2014.882846] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
|
24
|
Sathyendra V, Donahue HJ, Vrana KE, Berg A, Fryzel D, Gandhi J, Reid JS. Single Nucleotide Polymorphisms in Osteogenic Genes in Atrophic Delayed Fracture-Healing: A Preliminary Investigation. J Bone Joint Surg Am 2014; 96:1242-1248. [PMID: 25100770 DOI: 10.2106/jbjs.m.00453] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
UNLABELLED UpdateThis article was updated on September 10, 2014, because of a previous error. On page 1242, in the byline, and on page 1247, in the author addresses, the academic degree for Henry J. Donahue had previously read "MD." The degree now reads "PhD." BACKGROUND We propose that fracture-healing potential is affected by the patient's genome. This genotype is then phenotypically expressed by the patient at the time of injury. We examined the hypothesis that patients who exhibit delayed or impaired fracture-healing may have one or more single nucleotide polymorphisms (SNPs) within a series of genes related to bone formation. METHODS We performed a population-based, case-controlled study of delayed fracture-healing. Sixty-two adults with a long-bone fracture were identified from a surgical database. Thirty-three patients had an atrophic nonunion (delayed healing), and twenty-nine displayed normal fracture-healing. These patients underwent buccal mucosal cell harvesting. SNP genotyping was performed with use of bead array technology. One hundred and forty-four SNPs (selected from HapMap) within thirty genes associated with fracture-healing were investigated. Three SNPs did not segregate in the population and were excluded from the analysis. Eight of the remaining SNPs failed the test for Hardy-Weinberg equilibrium (p value smaller than the Bonferroni-corrected level of 0.05/141 = 0.000355) and were excluded. RESULTS Five SNPs on four genes were found to have a p value of <0.05 in the additive genetic model. Of these five significant SNPs, three had an odds ratio (OR) of >1, indicating that the presence of the allele increased the risk of nonunion. The rs2853550 SNP, which had the largest effect (OR = 5.9, p = 0.034), was on the IL1B gene, which codes for interleukin 1 beta. The rs2297514 SNP (OR = 3.98, p = 0.015) and the rs2248814 SNP (OR = 2.27, p = 0.038) were on the NOS2 gene coding for nitric oxide synthase. The remaining two SNPs had an OR of <1, indicating that the presence of the allele may be protective against nonunion. The rs3819089 SNP (OR = 0.26, p = 0.026) was on the MMP13 gene for matrix metallopeptidase 13, and the rs270393 SNP (OR = 0.30, p = 0.015) was on the BMP6 gene for bone morphogenetic protein 6. CONCLUSIONS Variations in the IL1B and NOS2 genes may contribute to delayed fracture-healing and warrant further investigation. CLINICAL RELEVANCE Impaired fracture union may have genetic contributions.
Collapse
Affiliation(s)
- Vikram Sathyendra
- Departments of Orthopaedics and Rehabilitation (V.S., H.J.D., D.F., J.G., and J.S.R.), Pharmacology (K.E.V.), and Public Health Sciences (A.B.), Penn State Hershey College of Medicine, 500 University Drive, Hershey, PA 17033. E-mail address for J.S. Reid:
| | - Henry J Donahue
- Departments of Orthopaedics and Rehabilitation (V.S., H.J.D., D.F., J.G., and J.S.R.), Pharmacology (K.E.V.), and Public Health Sciences (A.B.), Penn State Hershey College of Medicine, 500 University Drive, Hershey, PA 17033. E-mail address for J.S. Reid:
| | - Kent E Vrana
- Departments of Orthopaedics and Rehabilitation (V.S., H.J.D., D.F., J.G., and J.S.R.), Pharmacology (K.E.V.), and Public Health Sciences (A.B.), Penn State Hershey College of Medicine, 500 University Drive, Hershey, PA 17033. E-mail address for J.S. Reid:
| | - Arthur Berg
- Departments of Orthopaedics and Rehabilitation (V.S., H.J.D., D.F., J.G., and J.S.R.), Pharmacology (K.E.V.), and Public Health Sciences (A.B.), Penn State Hershey College of Medicine, 500 University Drive, Hershey, PA 17033. E-mail address for J.S. Reid:
| | - David Fryzel
- Departments of Orthopaedics and Rehabilitation (V.S., H.J.D., D.F., J.G., and J.S.R.), Pharmacology (K.E.V.), and Public Health Sciences (A.B.), Penn State Hershey College of Medicine, 500 University Drive, Hershey, PA 17033. E-mail address for J.S. Reid:
| | - Jonathan Gandhi
- Departments of Orthopaedics and Rehabilitation (V.S., H.J.D., D.F., J.G., and J.S.R.), Pharmacology (K.E.V.), and Public Health Sciences (A.B.), Penn State Hershey College of Medicine, 500 University Drive, Hershey, PA 17033. E-mail address for J.S. Reid:
| | - J Spence Reid
- Departments of Orthopaedics and Rehabilitation (V.S., H.J.D., D.F., J.G., and J.S.R.), Pharmacology (K.E.V.), and Public Health Sciences (A.B.), Penn State Hershey College of Medicine, 500 University Drive, Hershey, PA 17033. E-mail address for J.S. Reid:
| |
Collapse
|
25
|
Jin YL, Kong LF, Yu H, Li Q. Development, inheritance and evaluation of 55 novel single nucleotide polymorphism markers for parentage assignment in the Pacific oyster (Crassostrea gigas). Genes Genomics 2013. [DOI: 10.1007/s13258-013-0150-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
26
|
Kwon S, Simko I, Hellier B, Mou B, Hu J. Genome-wide association of 10 horticultural traits with expressed sequence tag-derived SNP markers in a collection of lettuce lines. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.cj.2013.07.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
27
|
Tan C, Han Z, Yu H, Zhan W, Xie W, Chen X, Zhao H, Zhou F, Xing Y. QTL scanning for rice yield using a whole genome SNP array. J Genet Genomics 2013; 40:629-38. [PMID: 24377869 DOI: 10.1016/j.jgg.2013.06.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 05/29/2013] [Accepted: 06/20/2013] [Indexed: 01/04/2023]
Abstract
High-throughput SNP genotyping is widely used for plant genetic studies. Recently, a RICE6K SNP array has been developed based on the Illumina Bead Array platform and Infinium SNP assay technology for genome-wide evaluation of allelic variations and breeding applications. In this study, the RICE6K SNP array was used to genotype a recombinant inbred line (RIL) population derived from the cross between the indica variety, Zhenshan 97, and the japonica variety, Xizang 2. A total of 3324 SNP markers of high quality were identified and were grouped into 1495 recombination bins in the RIL population. A high-density linkage map, consisting of the 1495 bins, was developed, covering 1591.2 cM and with average length of 1.1 cM per bin. Segregation distortions were observed in 24 regions of the 11 chromosomes in the RILs. One half of the distorted regions contained fertility genes that had been previously reported. A total of 23 QTLs were identified for yield. Seven QTLs were firstly detected in this study. The positive alleles from about half of the identified QTLs came from Zhenshan 97 and they had lower phenotypic values than Xizang 2. This indicated that favorable alleles for breeding were dispersed in both parents and pyramiding favorable alleles could develop elite lines. The size of the mapping population for QTL analysis using high throughput SNP genotyping platform is also discussed.
Collapse
Affiliation(s)
- Cong Tan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhongmin Han
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Huihui Yu
- Life Science and Technology Center, China National Seed Group Co., Ltd., Wuhan 430075, China
| | - Wei Zhan
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Weibo Xie
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Xun Chen
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Hu Zhao
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China
| | - Fasong Zhou
- Life Science and Technology Center, China National Seed Group Co., Ltd., Wuhan 430075, China
| | - Yongzhong Xing
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
28
|
Coates BS, Johnson H, Kim KS, Hellmich RL, Abel CA, Mason C, Sappington TW. Frequency of hybridization between Ostrinia nubilalis E-and Z-pheromone races in regions of sympatry within the United States. Ecol Evol 2013; 3:2459-70. [PMID: 24567821 PMCID: PMC3930039 DOI: 10.1002/ece3.639] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 05/07/2013] [Accepted: 05/08/2013] [Indexed: 01/13/2023] Open
Abstract
Female European corn borer, Ostrinia nubilalis, produce and males respond to sex pheromone blends with either E- or Z-Δ11-tetradecenyl acetate as the major component. E- and Z-race populations are sympatric in the Eastern United States, Southeastern Canada, and the Mediterranean region of Europe. The E- and Z-pheromone races of O. nubilalis are models for incipient species formation, but hybridization frequencies within natural populations remain obscure due to lack of a high-throughput phenotyping method. Lassance et al. previously identified a pheromone gland-expressed fatty-acyl reductase gene (pgfar) that controls the ratio of Δ11-tetradecenyl acetate stereoisomers. We identified three single nucleotide polymorphism (SNP) markers within pgfar that are differentially fixed between E- and Z-race females, and that are ≥98.2% correlated with female pheromone ratios measured by gas chromatography. Genotypic data from locations in the United States demonstrated that pgfar-z alleles were fixed within historically allopatric Z-pheromone race populations in the Midwest, and that hybrid frequency ranged from 0.00 to 0.42 within 11 sympatric sites where the two races co-occur in the Eastern United States (mean hybridization frequency or heterozygosity (H O) = 0.226 ± 0.279). Estimates of hybridization between the E- and Z-races are important for understanding the dynamics involved in maintaining race integrity, and are consistent with previous estimates of low levels of genetic divergence between E- and Z-races and the presence of weak prezygotic mating barriers. This work describes the development of new single nucleotide polymorphism (SNP) markers within the pheromone gland expressed fatty acyl reductase (pgfar) gene of Ostrinia nubilalis. These SNPs were shown to segregate based upon female pheromone production, and thus provide the first description of an assay for genetic determination of O. nubilalis pheromone strain from field-collected samples. These assays were applied to estimate hybridization within field populations, and represent valuable tools for future population genetic studies of this species.
Collapse
Affiliation(s)
- Brad S Coates
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University Ames, Iowa, 50011 ; Department of Entomology, Iowa State University Ames, Iowa, 50011
| | - Holly Johnson
- Entomology and Wildlife Ecology, University of Delaware 531 S College Ave RM 250, Newark, Delaware, 19716-2160
| | - Kyung-Seok Kim
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University Ames, Iowa, 50011
| | - Richard L Hellmich
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University Ames, Iowa, 50011 ; Department of Entomology, Iowa State University Ames, Iowa, 50011
| | - Craig A Abel
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University Ames, Iowa, 50011
| | - Charles Mason
- Entomology and Wildlife Ecology, University of Delaware 531 S College Ave RM 250, Newark, Delaware, 19716-2160
| | - Thomas W Sappington
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Genetics Laboratory, Iowa State University Ames, Iowa, 50011 ; Department of Entomology, Iowa State University Ames, Iowa, 50011
| |
Collapse
|
29
|
Garvin MR, Saitoh K, Gharrett AJ. Application of single nucleotide polymorphisms to non-model species: a technical review. Mol Ecol Resour 2013; 10:915-34. [PMID: 21565101 DOI: 10.1111/j.1755-0998.2010.02891.x] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Single nucleotide polymorphisms (SNPs) have gained wide use in humans and model species and are becoming the marker of choice for applications in other species. Technology that was developed for work in model species may provide useful tools for SNP discovery and genotyping in non-model organisms. However, SNP discovery can be expensive, labour intensive, and introduce ascertainment bias. In addition, the most efficient approaches to SNP discovery will depend on the research questions that the markers are to resolve as well as the focal species. We discuss advantages and disadvantages of several past and recent technologies for SNP discovery and genotyping and summarize a variety of SNP discovery and genotyping studies in ecology and evolution.
Collapse
Affiliation(s)
- M R Garvin
- Fisheries Division, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK 99801, USA National Research Institute of Fisheries Science, Fukuura, Kanazawa, Yokohama 236-8648 Japan
| | | | | |
Collapse
|
30
|
Abstract
Techniques involving whole-genome sequencing and whole-population sequencing (metagenomics) are beginning to revolutionize the study of ecology and evolution. This revolution is furthest advanced in the Bacteria and Archaea, and more sequence data are required for genomic ecology to be fully applied to the majority of eukaryotes. Recently developed next-generation sequencing technologies provide practical, massively parallel sequencing at lower cost and without the requirement for large, automated facilities, making genome and transcriptome sequencing and resequencing possible for more projects and more species. These sequencing methods include the 454 implementation of pyrosequencing, Solexa/Illumina reversible terminator technologies, polony sequencing and AB SOLiD. All of these methods use nanotechnology to generate hundreds of thousands of small sequence reads at one time. These technologies have the potential to bring the genomics revolution to whole populations, and to organisms such as endangered species or species of ecological and evolutionary interest. A future is now foreseeable where ecologists may resequence entire genomes from wild populations and perform population genetic studies at a genome, rather than gene, level. The new technologies for high throughput sequencing, their limitations and their applicability to evolutionary and environmental studies, are discussed in this review.
Collapse
Affiliation(s)
- Matthew E Hudson
- Department of Crop Sciences, University of Illinois, Urbana, 334 NSRC, 1101 W. Peabody Blvd., IL 61801, USA
| |
Collapse
|
31
|
Gheyas AA, Burt DW. Microarray resources for genetic and genomic studies in chicken: a review. Genesis 2013; 51:337-56. [PMID: 23468091 DOI: 10.1002/dvg.22387] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Revised: 02/21/2013] [Accepted: 02/22/2013] [Indexed: 11/08/2023]
Abstract
Advent of microarray technologies revolutionized the nature and scope of genetic and genomic research in human and other species by allowing massively parallel analysis of thousands of genomic sites. They have been used for diverse purposes such as for transcriptome analysis, CNV detection, SNP and CNV genotyping, studying DNA-protein interaction, and detection of genome methylation. Microarrays have also made invaluable contributions to research in chicken which is an important model organism for studying embryology, immunology, oncology, virology, evolution, genetics, and genomics and also for other avian species. Despite their huge contributions in life science research, the future of microarrays is now being questioned with the advent of massively parallel next generation sequencing (NGS) technologies, which promise to overcome some of the limitations of microarray platforms. In this article we review the various microarray resources developed for chicken and their past and potential future applications. We also discuss about the future of microarrays in the NGS era particularly in the context of livestock genetics. We argue that even though NGS promises some major advantages-in particular, offers the opportunity to discover novel elements in the genome-microarrays will continue to be major tools for research and practice in the field of livestock genetics/genomics due to their affordability, high throughput nature, mature established technologies and ease of application. Moreover, with advent of new microarray technologies like capture arrays, the NGS and microarrays are expected to complement each other in future research in life science.
Collapse
Affiliation(s)
- Almas A Gheyas
- Department of Genetics and Genomics, The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom
| | | |
Collapse
|
32
|
Song Y, Zhang Y, Wang TH. Single quantum dot analysis enables multiplexed point mutation detection by gap ligase chain reaction. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2013; 9:1096-105. [PMID: 23239594 PMCID: PMC3963288 DOI: 10.1002/smll.201202242] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Indexed: 05/10/2023]
Abstract
Gene point mutations present important biomarkers for genetic diseases. However, existing point mutation detection methods suffer from low sensitivity, specificity, and a tedious assay processes. In this report, an assay technology is proposed which combines the outstanding specificity of gap ligase chain reaction (Gap-LCR), the high sensitivity of single-molecule coincidence detection, and the superior optical properties of quantum dots (QDs) for multiplexed detection of point mutations in genomic DNA. Mutant-specific ligation products are generated by Gap-LCR and subsequently captured by QDs to form DNA-QD nanocomplexes that are detected by single-molecule spectroscopy (SMS) through multi-color fluorescence burst coincidence analysis, allowing for multiplexed mutation detection in a separation-free format. The proposed assay is capable of detecting zeptomoles of KRAS codon 12 mutation variants with near 100% specificity. Its high sensitivity allows direct detection of KRAS mutation in crude genomic DNA without PCR pre-amplification.
Collapse
Affiliation(s)
- Yunke Song
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine. 3400 N. Charles Street, 122 Clark Baltimore, MD, 21218 (USA)
| | - Yi Zhang
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine. 3400 N. Charles Street, 122 Clark Baltimore, MD, 21218 (USA)
| | - Tza-Huei Wang
- Department of Mechanical Engineering, Department of Biomedical Engineering, Sidney Kimmel Comprehensive Cancer Center, and Center of Cancer Nanotechnology Excellence, The Johns Hopkins University. 3400 N. Charles Street, 108 Latrobe Baltimore, MD, 21218 (USA)
| |
Collapse
|
33
|
Fedick A, Su J, Jalas C, Northrop L, Devkota B, Ekstein J, Treff NR. High-throughput carrier screening using TaqMan allelic discrimination. PLoS One 2013; 8:e59722. [PMID: 23555759 PMCID: PMC3608587 DOI: 10.1371/journal.pone.0059722] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2012] [Accepted: 02/17/2013] [Indexed: 12/29/2022] Open
Abstract
Members of the Ashkenazi Jewish community are at an increased risk for inheritance of numerous genetic diseases such that carrier screening is medically recommended. This paper describes the development and evaluation of 30 TaqMan allelic discrimination qPCR assays for 29 mutations on 2 different high-throughput platforms. Four of these mutations are in the GBA gene and are successfully examined using short amplicons due to the qualitative nature of TaqMan allelic discrimination. Two systems were tested for their reliability (call rate) and consistency with previous diagnoses (diagnostic accuracy) indicating a call rate of 99.04% and a diagnostic accuracy of 100% (+/−0.00%) from one platform, and a call rate of 94.66% and a diagnostic accuracy of 93.35% (+/−0.29%) from a second for 9,216 genotypes. Results for mutations tested at the expected carrier frequency indicated a call rate of 97.87% and a diagnostic accuracy of 99.96% (+/−0.05%). This study demonstrated the ability of a high throughput qPCR methodology to accurately and reliably genotype 29 mutations in parallel. The universally applicable nature of this technology provides an opportunity to increase the number of mutations that can be screened simultaneously, and reduce the cost and turnaround time for accommodating newly identified and clinically relevant mutations.
Collapse
Affiliation(s)
- Anastasia Fedick
- Department of Microbiology and Molecular Genetics, University of Medicine and Dentistry of New Jersey-Robert Wood Johnson Medical School, Piscataway, New Jersey, United States of America.
| | | | | | | | | | | | | |
Collapse
|
34
|
Yang W, Kang X, Yang Q, Lin Y, Fang M. Review on the development of genotyping methods for assessing farm animal diversity. J Anim Sci Biotechnol 2013; 4:2. [PMID: 23343204 PMCID: PMC3563493 DOI: 10.1186/2049-1891-4-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 01/21/2013] [Indexed: 11/10/2022] Open
Abstract
Advances in molecular biotechnology have introduced new generations of molecular markers for use in the genetic improvement of farm animals. Consequently, more accurate genetic information can be obtained to better understand existing animal genetic resources. This review gives a brief summary on the development of genetic markers including both the classical genetic markers and more advanced DNA-based molecular markers. This review will help us better understand the characteristics of different genetic markers and the genetic diversity of animal genetic resources.
Collapse
Affiliation(s)
- Wanjie Yang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, P, R, China.
| | | | | | | | | |
Collapse
|
35
|
High-throughput discovery of chloroplast and mitochondrial DNA polymorphisms in Brassicaceae species by ORG-EcoTILLING. PLoS One 2012. [PMID: 23185237 PMCID: PMC3504036 DOI: 10.1371/journal.pone.0047284] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Background Information on polymorphic DNA in organelle genomes is essential for evolutionary and ecological studies. However, it is challenging to perform high-throughput investigations of chloroplast and mitochondrial DNA polymorphisms. In recent years, EcoTILLING stands out as one of the most universal, low-cost, and high-throughput reverse genetic methods, and the identification of natural genetic variants can provide much information about gene function, association mapping and linkage disequilibrium analysis and species evolution. Until now, no report exists on whether this method is applicable to organelle genomes and to what extent it can be used. Methodology/Principal Findings To address this problem, we adapted the CEL I-based heteroduplex cleavage strategy used in Targeting Induced Local Lesions in Genomes (TILLING) for the discovery of nucleotide polymorphisms in organelle genomes. To assess the applicability and accuracy of this technology, designated ORG-EcoTILLING, at different taxonomic levels, we sampled two sets of taxa representing accessions from the Brassicaceae with three chloroplast genes (accD, matK and rbcL) and one mitochondrial gene (atp6). The method successfully detected nine, six and one mutation sites in the accD, matK and rbcL genes, respectively, in 96 Brassica accessions. These mutations were confirmed by DNA sequencing, with 100% accuracy at both inter- and intraspecific levels. We also detected 44 putative mutations in accD in 91 accessions from 45 species and 29 genera of seven tribes. Compared with DNA sequencing results, the false negative rate was 36%. However, 17 SNPs detected in atp6 were completely identical to the sequencing results. Conclusions/Significance These results suggest that ORG-EcoTILLING is a powerful and cost-effective alternative method for high-throughput genome-wide assessment of inter- and intraspecific chloroplast and mitochondrial DNA polymorphisms. It will play an important role in evolutionary and ecological biology studies, in identification of related genes associated with agronomic importance such as high yield and improved cytoplasmic quality, and for identifying mitochondrial point mutations responsible for diseases in humans and other animals.
Collapse
|
36
|
Liu J, Huang S, Sun M, Liu S, Liu Y, Wang W, Zhang X, Wang H, Hua W. An improved allele-specific PCR primer design method for SNP marker analysis and its application. PLANT METHODS 2012; 8:34. [PMID: 22920499 PMCID: PMC3495711 DOI: 10.1186/1746-4811-8-34] [Citation(s) in RCA: 151] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Accepted: 08/17/2012] [Indexed: 05/18/2023]
Abstract
BACKGROUND Although Single Nucleotide Polymorphism (SNP) marker is an invaluable tool for positional cloning, association study and evolutionary analysis, low SNP detection efficiency by Allele-Specific PCR (AS-PCR) still restricts its application as molecular marker like other markers such as Simple Sequence Repeat (SSR). To overcome this problem, primers with a single nucleotide artificial mismatch introduced within the three bases closest to the 3'end (SNP site) have been used in AS-PCR. However, for one SNP site, nine possible mismatches can be generated among the three bases and how to select the right one to increase primer specificity is still a challenge. RESULTS In this study, different from the previous reports which used a limited quantity of primers randomly (several or dozen pairs), we systematically investigated the effects of mismatch base pairs, mismatch sites and SNP types on primer specificity with 2071 primer pairs, which were designed based on SNPs from Brassica oleracea 01-88 and 02-12. According to the statistical results, we (1) found that the primers designed with SNP (A/T), in which the mismatch (CA) in the 3rd nucleotide from the 3' end, had the highest allele-specificity (81.9%). This information could be used when designing primers from a large quantity of SNP sites; (2) performed the primer design principle which forms the one and only best primer for every SNP type. This is never reported in previous studies. Additionally, we further identified its availability in rapeseed (Brassica napus L.) and sesame (Sesamum indicum). High polymorphism percent (75%) of the designed primers indicated it is a general method and can be applied in other species. CONCLUSION The method provided in this study can generate primers more effectively for every SNP site compared to other AS-PCR primer design methods. The high allele-specific efficiency of the SNP primer allows the feasibility for low- to moderate- throughput SNP analyses and is much suitable for gene mapping, map-based cloning, and marker-assisted selection in crops.
Collapse
Affiliation(s)
- Jing Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People’s Republic of China
| | - Shunmou Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People’s Republic of China
| | - Meiyu Sun
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People’s Republic of China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People’s Republic of China
| | - Yumei Liu
- Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences, Beijing, 100081, People’s Republic of China
| | - Wanxing Wang
- Institute of Vegetables and Flowers of the Chinese Academy of Agricultural Sciences, Beijing, 100081, People’s Republic of China
| | - Xiurong Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People’s Republic of China
| | - Hanzhong Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People’s Republic of China
| | - Wei Hua
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, 430062, People’s Republic of China
| |
Collapse
|
37
|
Firacative C, Trilles L, Meyer W. MALDI-TOF MS enables the rapid identification of the major molecular types within the Cryptococcus neoformans/C. gattii species complex. PLoS One 2012; 7:e37566. [PMID: 22666368 PMCID: PMC3362595 DOI: 10.1371/journal.pone.0037566] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2012] [Accepted: 04/20/2012] [Indexed: 12/14/2022] Open
Abstract
Background The Cryptococcus neoformans/C. gattii species complex comprises two sibling species that are divided into eight major molecular types, C. neoformans VNI to VNIV and C. gattii VGI to VGIV. These genotypes differ in host range, epidemiology, virulence, antifungal susceptibility and geographic distribution. The currently used phenotypic and molecular identification methods for the species/molecular types are time consuming and expensive. As Matrix-Assisted Laser Desorption Ionization-Time-of-Flight Mass Spectrometry (MALDI-TOF MS) offers an effective alternative for the rapid identification of microorganisms, the objective of this study was to examine its potential for the identification of C. neoformans and C. gattii strains at the intra- and inter-species level. Methodology Protein extracts obtained via the formic acid extraction method of 164 C. neoformans/C. gattii isolates, including four inter-species hybrids, were studied. Results The obtained mass spectra correctly identified 100% of all studied isolates, grouped each isolate according to the currently recognized species, C. neoformans and C. gattii, and detected potential hybrids. In addition, all isolates were clearly separated according to their major molecular type, generating greater spectral differences among the C. neoformans molecular types than the C. gattii molecular types, most likely reflecting a closer phylogenetic relationship between the latter. The number of colonies used and the incubation length did not affect the results. No spectra were obtained from intact yeast cells. An extended validated spectral library containing spectra of all eight major molecular types was established. Conclusions MALDI-TOF MS is a rapid identification tool for the correct recognition of the two currently recognized human pathogenic Cryptococcus species and offers a simple method for the separation of the eight major molecular types and the detection of hybrid strains within this species complex in the clinical laboratory. The obtained mass spectra provide further evidence that the major molecular types warrant variety or even species status.
Collapse
Affiliation(s)
- Carolina Firacative
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, Sydney Medical School–Westmead, The University of Sydney, Westmead Hospital, Sydney, Australia
- Grupo de Microbiología, Instituto Nacional de Salud, Bogotá, Colombia
| | - Luciana Trilles
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, Sydney Medical School–Westmead, The University of Sydney, Westmead Hospital, Sydney, Australia
- Laboratório de Micologia, Instituto de Pesquisa Clínica Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Wieland Meyer
- Molecular Mycology Research Laboratory, Centre for Infectious Diseases and Microbiology, Westmead Millennium Institute, Sydney Medical School–Westmead, The University of Sydney, Westmead Hospital, Sydney, Australia
- * E-mail:
| |
Collapse
|
38
|
Ojurongbe O, Ouf EA, Van Tong H, Toan NL, Song LH, Luz PR, Messias-Reason IJT, Nurjadi D, Zanger P, Kun JFJ, Kremsner PG, Velavan TP. Reliable and rapid characterization of functional FCN2 gene variants reveals diverse geographical patterns. BMC MEDICAL GENETICS 2012; 13:37. [PMID: 22594803 PMCID: PMC3458960 DOI: 10.1186/1471-2350-13-37] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 04/23/2012] [Indexed: 12/28/2022]
Abstract
BACKGROUND Ficolin-2 coded by FCN2 gene is a soluble serum protein and an innate immune recognition element of the complement system. FCN2 gene polymorphisms reveal distinct geographical patterns and are documented to alter serum ficolin levels and modulate disease susceptibility. METHODS We employed a real-time PCR based on Fluorescence Resonance Energy Transfer (FRET) method to genotype four functional SNPs including -986 G > A (#rs3124952), -602 G > A (#rs3124953), -4A > G (#rs17514136) and +6424 G > T (#rs7851696) in the ficolin-2 (FCN2) gene. We characterized the FCN2 variants in individuals representing Brazilian (n = 176), Nigerian (n = 180), Vietnamese (n = 172) and European Caucasian ethnicity (n = 165). RESULTS We observed that the genotype distribution of three functional SNP variants (-986 G > A, -602 G > A and -4A > G) differ significantly between the populations investigated (p < 0.0001). The SNP variants were highly linked to each other and revealed significant population patterns. Also the distribution of haplotypes revealed distinct geographical patterns (p < 0.0001). CONCLUSIONS The observed distribution of the FCN2 functional SNP variants may likely contribute to altered serum ficolin levels and this may depend on the different disease settings in world populations. To conclude, the use of FRET based real-time PCR especially for FCN2 gene will benefit a larger scientific community who extensively depend on rapid, reliable method for FCN2 genotyping.
Collapse
Affiliation(s)
- Olusola Ojurongbe
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
- Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Eman Abou Ouf
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Hoang Van Tong
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Nguyen L Toan
- Department of Pathophysiology, Vietnam Military Medical University, Hanoi, Vietnam
| | - Le H Song
- Tran Hung Dao Hospital, Hanoi, Vietnam
| | - Paola R Luz
- Laboratório de Imunopatologia Molecular-Hospital de Clínicas, Federal University of Paraná, Curitiba, Brazil
| | - Iara JT Messias-Reason
- Laboratório de Imunopatologia Molecular-Hospital de Clínicas, Federal University of Paraná, Curitiba, Brazil
| | - Dennis Nurjadi
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Philipp Zanger
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Jürgen FJ Kun
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | - Peter G Kremsner
- Institute of Tropical Medicine, University of Tübingen, Tübingen, Germany
| | | |
Collapse
|
39
|
Krithika S, Valladares-Salgado A, Peralta J, Escobedo-de La Peña J, Kumate-Rodríguez J, Cruz M, Parra EJ. Evaluation of the imputation performance of the program IMPUTE in an admixed sample from Mexico City using several model designs. BMC Med Genomics 2012; 5:12. [PMID: 22549150 PMCID: PMC3436779 DOI: 10.1186/1755-8794-5-12] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Accepted: 05/01/2012] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND We explored the imputation performance of the program IMPUTE in an admixed sample from Mexico City. The following issues were evaluated: (a) the impact of different reference panels (HapMap vs. 1000 Genomes) on imputation; (b) potential differences in imputation performance between single-step vs. two-step (phasing and imputation) approaches; (c) the effect of different INFO score thresholds on imputation performance and (d) imputation performance in common vs. rare markers. METHODS The sample from Mexico City comprised 1,310 individuals genotyped with the Affymetrix 5.0 array. We randomly masked 5% of the markers directly genotyped on chromosome 12 (n=1,046) and compared the imputed genotypes with the microarray genotype calls. Imputation was carried out with the program IMPUTE. The concordance rates between the imputed and observed genotypes were used as a measure of imputation accuracy and the proportion of non-missing genotypes as a measure of imputation efficacy. RESULTS The single-step imputation approach produced slightly higher concordance rates than the two-step strategy (99.1% vs. 98.4% when using the HapMap phase II combined panel), but at the expense of a lower proportion of non-missing genotypes (85.5% vs. 90.1%). The 1,000 Genomes reference sample produced similar concordance rates to the HapMap phase II panel (98.4% for both datasets, using the two-step strategy). However, the 1000 Genomes reference sample increased substantially the proportion of non-missing genotypes (94.7% vs. 90.1%). Rare variants (<1%) had lower imputation accuracy and efficacy than common markers. CONCLUSIONS The program IMPUTE had an excellent imputation performance for common alleles in an admixed sample from Mexico City, which has primarily Native American (62%) and European (33%) contributions. Genotype concordances were higher than 98.4% using all the imputation strategies, in spite of the fact that no Native American samples are present in the HapMap and 1000 Genomes reference panels. The best balance of imputation accuracy and efficiency was obtained with the 1,000 Genomes panel. Rare variants were not captured effectively by any of the available panels, emphasizing the need to be cautious in the interpretation of association results for imputed rare variants.
Collapse
Affiliation(s)
- S Krithika
- Department of Anthropology, University of Toronto at Mississauga, 3359 Mississauga Road North, Mississauga, ON, Canada
| | | | | | | | | | | | | |
Collapse
|
40
|
Kaur S, Francki MG, Forster JW. Identification, characterization and interpretation of single-nucleotide sequence variation in allopolyploid crop species. PLANT BIOTECHNOLOGY JOURNAL 2012; 10:125-38. [PMID: 21831136 DOI: 10.1111/j.1467-7652.2011.00644.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
An understanding of nature and extent of nucleotide sequence variation is required for programmes of discovery and characterization of single nucleotide polymorphisms (SNPs), which provide the most versatile class of molecular genetic marker. A majority of higher plant species are polyploids, and allopolyploidy, because of hybrid formation between closely related taxa, is very common. Mutational variation may arise both between allelic (homologous) sequences within individual subgenomes and between homoeologous sequences among subgenomes, in addition to paralogous variation between duplicated gene copies. Successful SNP validation in allopolyploids depends on differentiation of the sequence variation classes. A number of biological factors influence the feasibility of discrimination, including degree of gene family complexity, inbreeding or outbreeding reproductive habit, and the level of knowledge concerning progenitor diploid species. In addition, developments in high-throughput DNA sequencing and associated computational analysis provide general solutions for the genetic analysis of allopolyploids. These issues are explored in the context of experience from a range of allopolyploid species, representing grain (wheat and canola), forage (pasture legumes and grasses), and horticultural (strawberry) crop. Following SNP discovery, detection in routine genotyping applications also presents challenges for allopolyploids. Strategies based on either design of subgenome-specific SNP assays through homoeolocus-targeted polymerase chain reaction (PCR) amplification, or detection of incremental changes in nucleotide variant dosage, are described.
Collapse
Affiliation(s)
- Sukhjiwan Kaur
- Department of Primary Industries, Biosciences Research Division, Victorian AgriBiosciences Centre, La Trobe University Research and Development Park, Bundoora, Victoria, Australia
| | | | | |
Collapse
|
41
|
Kumar S, Banks TW, Cloutier S. SNP Discovery through Next-Generation Sequencing and Its Applications. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2012; 2012:831460. [PMID: 23227038 PMCID: PMC3512287 DOI: 10.1155/2012/831460] [Citation(s) in RCA: 103] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2012] [Accepted: 10/08/2012] [Indexed: 05/08/2023]
Abstract
The decreasing cost along with rapid progress in next-generation sequencing and related bioinformatics computing resources has facilitated large-scale discovery of SNPs in various model and nonmodel plant species. Large numbers and genome-wide availability of SNPs make them the marker of choice in partially or completely sequenced genomes. Although excellent reviews have been published on next-generation sequencing, its associated bioinformatics challenges, and the applications of SNPs in genetic studies, a comprehensive review connecting these three intertwined research areas is needed. This paper touches upon various aspects of SNP discovery, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses. The use of next-generation sequencing methodologies in many non-model crops leading to discovery and implementation of SNPs in various genetic studies is discussed. Development and improvement of bioinformatics software that are open source and freely available have accelerated the SNP discovery while reducing the associated cost. Key considerations for SNP filtering and associated pipelines are discussed in specific topics. A list of commonly used software and their sources is compiled for easy access and reference.
Collapse
Affiliation(s)
- Santosh Kumar
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
| | - Travis W. Banks
- Department of Applied Genomics, Vineland Research and Innovation Centre, Vineland Station, ON, Canada L0R 2E0
| | - Sylvie Cloutier
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada R3T 2N2
- Cereal Research Centre, Agriculture and Agri-Food Canada, Winnipeg, MB, Canada R3T 2M9
- *Sylvie Cloutier:
| |
Collapse
|
42
|
Giestas L, Lima JC, Baptista PV. Coupling single base extension to a spectral codification tool for increased throughput screening. J Biotechnol 2011; 154:199-204. [DOI: 10.1016/j.jbiotec.2011.05.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2011] [Revised: 05/09/2011] [Accepted: 05/25/2011] [Indexed: 10/18/2022]
|
43
|
Coates BS, Bayles DO, Wanner KW, Robertson HM, Hellmich RL, Sappington TW. The application and performance of single nucleotide polymorphism markers for population genetic analyses of lepidoptera. Front Genet 2011; 2:38. [PMID: 22303334 PMCID: PMC3268592 DOI: 10.3389/fgene.2011.00038] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 06/10/2011] [Indexed: 01/19/2023] Open
Abstract
Microsatellite markers are difficult to apply within lepidopteran studies due to the lack of locus-specific PCR amplification and the high proportion of “null” alleles, such that erroneous estimations of population genetic parameters often result. Herein single nucleotide polymorphism (SNP) markers are developed from Ostrinia nubilalis (Lepidoptera: Crambidae) using next generation expressed sequence tag (EST) data. A total of 2742 SNPs were predicted within a reference assembly of 7414 EST contigs, and a subset of 763 were incorporated into 24 multiplex PCR reactions. To validate this pipeline, 5 European and North American sample sites were genotyped at 178 SNP loci, which indicated 84 (47.2%) were in Hardy–Weinberg equilibrium. Locus-by-locus FST, analysis of molecular variance, and STRUCTURE analyses indicate significant genetic differentiation may exist between European and North American O. nubilalis. The observed genetic diversity was significantly lower among European sites, which may result from genetic drift, natural selection, a genetic bottleneck, or ascertainment bias due to North American origin of EST sequence data. SNPs are an abundant source of mutation data for molecular genetic marker development in non-model species, with shared ancestral SNPs showing application within closely related species. These markers offer advantages over microsatellite markers for genetic and genomic analyses of Lepidoptera, but the source of mutation data may affect the estimation of population parameters and likely need to be considered in the interpretation of empirical data.
Collapse
Affiliation(s)
- Brad Steven Coates
- Corn Insects and Crop Genetics Research Unit, Agricultural Research Service, United States Department of Agriculture Ames, IA, USA
| | | | | | | | | | | |
Collapse
|
44
|
Li G, Luo X, He J, Zhu Z, Yu G, Qin H, Zeng T, Liu Z, Wu S, Xu J, Ren-Heidenreich L. A novel liquidchip platform for simultaneous detection of 70 alleles of DNA somatic mutations on EGFR, KRAS, BRAF and PIK3CA from formalin-fixed and paraffin-embedded slides containing tumor tissue. Clin Chem Lab Med 2010; 49:191-5. [PMID: 21118047 DOI: 10.1515/cclm.2011.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND DNA somatic mutations of EGFR, KRAS, BRAF and PIK3CA in the epidermal growth factor receptor (EGFR) signaling pathway play critical roles in the response or resistance of tumors to targeted therapy with tyrosine kinase inhibitors (EGFR-TKIs). To provide a high-throughput (HTP) clinical testing service for detecting these mutations, we developed a novel platform, SurPlex®-xTAG70plex-EGFR liquidchip. METHODS This platform was developed based on a universal 100-tag system. The procedures for multiplex PCR, allele specific primer extension (ASPE) and hybridization were optimized and standardized. RESULTS A total of 70 alleles of somatic mutations of EGFR, KRAS, BRAF and PIK3CA can be detected simultaneously in one reaction from one formalin-fixed and paraffin-embedded (FFPE) slide within one day. Cross-reaction was < 8% between individual amplimers and 70 different ASPE primers. The sensitivity for detecting mutants in the wild-type DNA was 1%-5%. Seventy-three FFPE samples with somatic mutations were used to validate the 70plex. Seventy-one showed a complete match, while two were not detected. CONCLUSIONS A simple, accurate, sensitive HTP technology was developed and standardized for detecting simultaneously 70 different alleles of EGFR, KRAS, BRAF and PIK3CA gene mutations from FFPE tumor slides.
Collapse
Affiliation(s)
- Guoqiang Li
- SurExam Bio-Tech Co. Ltd., Guangzhou Technology Innovation Base, Science City, Guangzhou, PR China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
45
|
Integration of high-throughput genotyping data into pharmacometric analyses using nonlinear mixed effects modeling. Pharmacogenet Genomics 2010. [DOI: 10.1097/fpc.0b013e32833b747f] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
46
|
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.
Collapse
Affiliation(s)
| | | | - Haseeb A. Khan
- Author to whom correspondence should be addressed; E-Mail:
; Tel.: +966-1-4674-712
| | | | | | | | | | | |
Collapse
|
47
|
Abstract
The genetics of complex diseases has been given a tremendous boost in recent years by the introduction of high-throughput laboratory methods that make it possible to approach larger questions in larger populations and to cover the genome more comprehensively. The ability to determine genotypes of many individuals accurately and efficiently has allowed genetic studies that cover more of the variation within individual genes, instead of focusing only on one or a few coding variants, and to do so in study samples of reasonable power. Chip-based genotyping assays, combined with knowledge of the patterns of coinheritance of markers (linkage disequilibrium [LD]), have stimulated genome-wide association studies (GWAS) of complex diseases. Recent successes of GWAS in identifying specific genes that affect risk for common diseases are dramatic illustrations of how improved technology can lead to scientific breakthroughs. A key issue in high-throughput genotyping is to choose the appropriate technology for your goals and for the stage of your experiment, being cognizant of your sample numbers and resources. This article introduces some of the commonly used methods of high-throughput single-nucleotide polymorphism (SNP) genotyping for different stages of genetic studies and briefly reviews some of the high-throughput sequencing methods just coming into use. It also mentions some recent developments in "next-generation" sequencing that will enable other kinds of studies. This article is not intended to be comprehensive, and because technology in this area is rapidly changing, our comments should be taken as a starting point for further investigation.
Collapse
|
48
|
Foster JT, Allan GJ, Chan AP, Rabinowicz PD, Ravel J, Jackson PJ, Keim P. Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis). BMC PLANT BIOLOGY 2010; 10:13. [PMID: 20082707 PMCID: PMC2832895 DOI: 10.1186/1471-2229-10-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Accepted: 01/18/2010] [Indexed: 05/21/2023]
Abstract
BACKGROUND Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci. RESULTS Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74%) followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population phiPT values, p < 0.01). CONCLUSION Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.
Collapse
Affiliation(s)
- Jeffrey T Foster
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073 USA
| | - Gerard J Allan
- Department of Biological Sciences, Environmental Genetics and Genomics Laboratory, Northern Arizona University, Flagstaff, AZ 86011-5640 USA
| | - Agnes P Chan
- J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850 USA
| | - Pablo D Rabinowicz
- J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850 USA
- Institute for Genome Sciences, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201 USA
- Department of Biochemistry & Molecular Biology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201 USA
| | - Jacques Ravel
- J. Craig Venter Institute, 9712 Medical Center Drive, Rockville, MD 20850 USA
- Institute for Genome Sciences, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201 USA
- Department of Microbiology & Immunology, University of Maryland School of Medicine, 20 Penn Street, Baltimore, MD 21201 USA
| | - Paul J Jackson
- Defense Biology Division, Lawrence Livermore National Laboratory, Livermore, CA 94551 USA
| | - Paul Keim
- Center for Microbial Genetics and Genomics, Northern Arizona University, Flagstaff, AZ 86011-4073 USA
| |
Collapse
|
49
|
Lima-Neto LG, Hirata RD, Luchessi AD, Silbiger VN, Pastorelli CP, Sampaio MF, Armaganijan D, Rezende AA, Doi SQ, Hirata MH. Detection of theTLR41196C>T Polymorphism by Mismatched-Polymerase Chain Reaction Using Plasmid DNA as Internal Control in Restriction Fragment Length Polymorphism Assays. Genet Test Mol Biomarkers 2009; 13:343-7. [DOI: 10.1089/gtmb.2008.0147] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Lidio G. Lima-Neto
- Faculdade de Ciencias Farmaceuticas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Rosario D. Hirata
- Faculdade de Ciencias Farmaceuticas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Andre D. Luchessi
- Faculdade de Ciencias Farmaceuticas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Vivian N. Silbiger
- Faculdade de Ciencias Farmaceuticas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | - Carla P. Pastorelli
- Faculdade de Ciencias Farmaceuticas, Universidade de Sao Paulo, Sao Paulo, Brazil
| | | | | | | | - Sonia Q. Doi
- Uniformed Services University of the Health Sciences, Bethesda, Maryland
| | - Mario H. Hirata
- Faculdade de Ciencias Farmaceuticas, Universidade de Sao Paulo, Sao Paulo, Brazil
| |
Collapse
|
50
|
Nawrot B, Rebowska B. DNA oligonucleotides containing stereodefined phosphorothioate linkages in selected positions. ACTA ACUST UNITED AC 2009; Chapter 4:Unit 4.34. [PMID: 19319859 DOI: 10.1002/0471142700.nc0434s36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This unit describes a method for the synthesis of DNA chimeric PO/PS-oligonucleotides with a stereodefined phosphorothioate bond in the selected position. Diastereomerically pure 5'-O-DMTr-N-protected-deoxyribonucleoside-3'-O-(2-thio-spiro-4,4-pentamethylene-1,3,2-oxathiaphospholane)s obtained according to the previously described protocol (UNIT 4.17) are transformed via a stereospecific 1,3,2-oxathiaphospholane-ring opening condensation into the corresponding dinucleoside phosphorothioates. Such dimers cannot be introduced into an oligonucleotide chain via the phosphoramidite approach since the unprotected P-S(-) bond is easily oxidized during routine I(2)/Py/water oxidation of the phosphite function. In the methodology described here, the reversible alkylation of the PS function is applied. Subsequently, the 3'-phosphoramidites of such PS-protected dimers prepared in situ are used for routine synthesis of chimeric PO/PS-oligonucleotides according to the phosphoramidite method. The presence of the alkylated PS-function requires modified conditions for oligonucleotide deprotection and cleavage from the solid support. Detailed procedures for the synthesis of PS-dimers and their incorporation into an oligonucleotide chain, as well as deprotection/purification steps are presented.
Collapse
Affiliation(s)
- Barbara Nawrot
- Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Lodz, Poland
| | | |
Collapse
|