1
|
Tran HT, Schramm C, Huynh MM, Shavrukov Y, Stangoulis JCR, Jenkins CLD, Anderson PA. An accurate, reliable, and universal qPCR method to identify homozygous single insert T-DNA with the example of transgenic rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1221790. [PMID: 37900763 PMCID: PMC10600460 DOI: 10.3389/fpls.2023.1221790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/22/2023] [Indexed: 10/31/2023]
Abstract
Early determination of transgenic plants that are homozygous for a single locus T-DNA insert is highly desirable in most fundamental and applied transgenic research. This study aimed to build on an accurate, rapid, and reliable quantitative real-time PCR (qPCR) method to fast-track the development of multiple homozygous transgenic rice lines in the T1 generation, with low copy number to single T-DNA insert for further analyses. Here, a well-established qPCR protocol, based on the OsSBE4 reference gene and the nos terminator, was optimized in the transgenic Japonica rice cultivar Nipponbare, to distinguish homozygous single-insert plants with 100% accuracy. This method was successfully adapted to transgenic Indica rice plants carrying three different T-DNAs, without any modifications to quickly develop homozygous rice plants in the T1 generation. The accuracy of this qPCR method when applied to transgenic Indica rice approached 100% in 12 putative transgenic lines. Moreover, this protocol also successfully detected homozygous single-locus T-DNA transgenic rice plants with two-transgene T-DNAs, a feature likely to become more popular in future transgenic research. The assay was developed utilizing universal primers targeting common sequence elements of gene cassettes (the nos terminator). This assay could therefore be applied to other transgenic plants carrying the nos terminator. All procedures described here use standardized qPCR reaction conditions and relatively inexpensive dyes, such as SYBR Green, thus the qPCR method could be cost-effective and suitable for lower budget laboratories that are involved in rice transgenic research.
Collapse
Affiliation(s)
- Hai Thanh Tran
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | | | | | | | | | | | - Peter A. Anderson
- College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| |
Collapse
|
2
|
Saravanan K, Vidya N, Appunu C, Gurusaravanan P, Arun M. A simple and efficient genetic transformation system for soybean ( Glycine max (L.) Merrill) targeting apical meristem of modified half-seed explant. 3 Biotech 2023; 13:293. [PMID: 37547916 PMCID: PMC10403444 DOI: 10.1007/s13205-023-03715-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023] Open
Abstract
The present study is an attempt to establish a fast, highly reproducible transformation with a simplified regeneration system in soybean targeting the apical meristem. The modified half-seed explants from soybean cultivar (cv.) JS335 were subjected to different time intervals of sonication (0, 1, 10, 20, and 30 min) and vacuum infiltration (0, 1, 10, 20, and 30 min) in the presence of Agrobacterium tumefaciens strain EHA105 harbouring pCAMBIA1301. The explants were then co-cultivated and subjected to a modified plant regeneration process that involves only two steps (1) primary shoot regeneration, and (2) in vitro rooting of primary shoot. The rooted plantlets were hardened and maintained in the greenhouse until maturity. Sonication treatment of 10 min, followed by plant regeneration using a modified method, recorded the highest transformation efficiency of 26.3% compared to other time duration tested. Furthermore, 10 min of vacuum infiltration alone resulted in even higher transformation efficiency after regeneration, reaching 28.0%. Interestingly, coupling sonication and vacuum infiltration for 10 min respectively produced the highest transformation efficiency after regeneration of 38.0%. The putative transformants showed gus expression in mature leaves, trifoliate leaves, flowers, and pods. The presence of hpt II was also confirmed in putative transformants, with an amplicon size of 500 bp. Quantitative real-time PCR confirmed the existence of hpt II as one to two copies in the soybean genome of T0 plants. Furthermore, the segregation pattern was observed in the T1 generation soybean plants which were confirmed using PCR for hpt II. The optimized protocol when tested with other Indian soybean cultivars showed an enhanced transformation efficiency ranging from 19.3% (cv. MAUS47) to 36.5% (cv. CO1). This optimized protocol could provide a reliable platform to overcome the challenges that are associated with the genetic engineering of soybean. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03715-8.
Collapse
Affiliation(s)
- Krishnagowdu Saravanan
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641 046 India
| | - Nandakumar Vidya
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641 046 India
| | - Chinnaswamy Appunu
- Division of Crop Improvement, ICAR-Sugarcane Breeding Institute, Coimbatore, Tamil Nadu 641 007 India
| | | | - Muthukrishnan Arun
- Department of Biotechnology, Bharathiar University, Coimbatore, Tamil Nadu 641 046 India
| |
Collapse
|
3
|
High-Throughput and Accurate Determination of Transgene Copy Number and Zygosity in Transgenic Maize: From DNA Extraction to Data Analysis. Int J Mol Sci 2021; 22:ijms222212487. [PMID: 34830369 PMCID: PMC8619409 DOI: 10.3390/ijms222212487] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/10/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
It is vital to develop high-throughput methods to determine transgene copy numbers initially and zygosity during subsequent breeding. In this study, the target sequence of the previously reported endogenous reference gene hmg was analyzed using 633 maize inbred lines, and two SNPs were observed. These SNPs significantly increased the PCR efficiency, while the newly developed hmg gene assay (hmg-taq-F2/R2) excluding these SNPs reduced the efficiency into normal ranges. The TaqMan amplification efficiency of bar and hmg with newly developed primers was calculated as 0.993 and 1.000, respectively. The inter-assay coefficient of variation (CV) values for the bar and hmg genes varied from 1.18 to 2.94%. The copy numbers of the transgene bar using new TaqMan assays were identical to those using dPCR. Significantly, the precision of one repetition reached 96.7% of that of three repetitions of single-copy plants analyzed by simple random sampling, and the actual accuracy reached 95.8%, confirmed by T1 and T2 progeny. With the high-throughput DNA extraction and automated data analysis procedures developed in this study, nearly 2700 samples could be analyzed within eight hours by two persons. The combined results suggested that the new hmg gene assay developed here could be a universal maize reference gene system, and the new assay has high throughput and high accuracy for large-scale screening of maize varieties around the world.
Collapse
|
4
|
Xia T, Yang Y, Zheng H, Han X, Jin H, Xiong Z, Qian W, Xia L, Ji X, Li G, Wang D, Zhang K. Efficient expression and function of a receptor-like kinase in wheat powdery mildew defence require an intron-located MYB binding site. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:897-909. [PMID: 33225586 PMCID: PMC8131041 DOI: 10.1111/pbi.13512] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 05/10/2023]
Abstract
The LRK10-like receptor kinases (LRK10L-RLKs) are ubiquitously present in higher plants, but knowledge of their expression and function is still limited. Here, we report expression and functional analysis of TtdLRK10L-1, a typical LRK10L-RLK in durum wheat (Triticum turgidum L. ssp. durum). The introns of TtdLRK10L-1 contained multiple kinds of predicted cis-elements. To investigate the potential effect of these cis-elements on TtdLRK10L-1 expression and function, two types of transgenic wheat lines were prepared, which expressed a GFP-tagged TtdLRK10L-1 protein (TtdLRK10L-1:GFP) from the cDNA or genomic DNA (gDNA) sequence of TtdLRK10L-1 under the native promoter. TtdLRK10L-1:GFP expression was up-regulated by the powdery mildew pathogen Blumeria graminis f. sp. tritici (Bgt) in both types of transgenic plants, with the scale of the elevation being much stronger in the gDNA lines. Both types of transgenic plants exhibited enhanced resistance to Bgt infection relative to wild type control. Notably, the Bgt defence activated in the gDNA lines was significantly stronger than that in the cDNA lines. Further analysis revealed that a putative MYB transcription factor binding site (MYB-BS, CAGTTA) located in TtdLRK10L-1 intron I was critical for the efficient expression and function of TtdLRK10L-1 in Bgt defence. This MYB-BS could also increase the activity of a superpromoter widely used in ectopic gene expression studies in plants. Together, our results deepen the understanding of the expression and functional characteristics of LRK10L-RLKs. TtdLRK10L-1 is likely useful for further dissecting the molecular processes underlying wheat defence against Bgt and for developing Bgt resistant wheat crops.
Collapse
Affiliation(s)
- Tengfei Xia
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Yanping Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Hongyuan Zheng
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Xinyun Han
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Huaibing Jin
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| | - Zijun Xiong
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking UniversityBeijingChina
| | - Lanqi Xia
- Institute of Crop SciencesChinese Academy of Agricultural SciencesBeijingChina
| | - Xiang Ji
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Guangwei Li
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
| | - Daowen Wang
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Kunpu Zhang
- College of AgronomyState Key Laboratory of Wheat and Maize Crop Science, and Center for Crop Genome EngineeringHenan Agricultural UniversityZhengzhouChina
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
| |
Collapse
|
5
|
Zeng X, Li H, Li K, Yuan R, Zhao S, Li J, Luo J, Li X, Ma H, Wu G, Yan X. Evolution of the Brassicaceae-specific MS5-Like family and neofunctionalization of the novel MALE STERILITY 5 gene essential for male fertility in Brassica napus. THE NEW PHYTOLOGIST 2021; 229:2339-2356. [PMID: 33128826 PMCID: PMC7894334 DOI: 10.1111/nph.17053] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 10/08/2020] [Indexed: 05/22/2023]
Abstract
New genes (or lineage-specific genes) can facilitate functional innovations. MALE STERILITY 5 (MS5) in Brassica napus is a fertility-related new gene, which has two wild-type alleles (BnMS5a and BnMS5c ) and two mutant alleles (BnMS5b and BnMS5d ) that could induce male sterility. Here, we studied the history and functional evolution of MS5 homologs in plants by phylogenetic analysis and molecular genetic experiments. We identified 727 MS5 homologs and found that they define a Brassicaceae-specific gene family that has expanded partly via multiple tandem gene duplications and also probably transpositions. The MS5 in B. napus is inherited from a basic diploid ancestor of B. rapa. Molecular genetic experiments indicate that BnMS5a and BnMS5c are functionally distinct in B. napus and that BnMS5d can inhibit BnMS5a in B. napus in a dosage-dependent manner. The BnMS5a protein can move in coordination with meiotic telomeres and interact with the nuclear envelope protein SUN1, with a possible crucial role in meiotic chromosome behavior. In summary, BnMS5 belongs to a Brassicaceae-specific new gene family, and has gained a novel function that is essential for male fertility in B. napus through neofunctionalization that has likely occurred since the origin of B. rapa.
Collapse
Affiliation(s)
- Xinhua Zeng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Hao Li
- Department of Biologythe Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Keqi Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Rong Yuan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Shengbo Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Jun Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Junling Luo
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Xiaofei Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Hong Ma
- Department of Biologythe Huck Institutes of the Life Sciencesthe Pennsylvania State UniversityUniversity ParkPA16802USA
| | - Gang Wu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| | - Xiaohong Yan
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil CropsMinistry of AgricultureWuhan430062China
| |
Collapse
|
6
|
Real-Time PCR for the Detection of Precise Transgene Copy Number in Wheat. Methods Mol Biol 2017. [PMID: 28913805 DOI: 10.1007/978-1-4939-7337-8_15] [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: 10/31/2023]
Abstract
Despite the unceasing advances in genetic transformation techniques, the success of common delivery methods still lies on the behavior of the integrated transgenes in the host genome. Stability and expression of the introduced genes are influenced by several factors such as chromosomal location, transgene copy number and interaction with the host genotype. Such factors are traditionally characterized by Southern blot analysis, which can be time-consuming, laborious, and often unable to detect the exact copy number of rearranged transgenes. Recent research in crop field suggests real-time PCR as an effective and reliable tool for the precise quantification and characterization of transgene loci. This technique overcomes most problems linked to phenotypic segregation analysis and can analyze hundreds of samples in a day, making it an efficient method for estimating a gene copy number integrated in a transgenic line. This protocol describes the use of real-time PCR for the detection of transgene copy number in durum wheat transgenic lines by means of two different chemistries (SYBR® Green I dye and TaqMan® probes).
Collapse
|
7
|
Li S, Cong Y, Liu Y, Wang T, Shuai Q, Chen N, Gai J, Li Y. Optimization of Agrobacterium-Mediated Transformation in Soybean. FRONTIERS IN PLANT SCIENCE 2017; 8:246. [PMID: 28286512 PMCID: PMC5323423 DOI: 10.3389/fpls.2017.00246] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/09/2017] [Indexed: 05/20/2023]
Abstract
High transformation efficiency is a prerequisite for study of gene function and molecular breeding. Agrobacterium tumefaciens-mediated transformation is a preferred method in many plants. However, the transformation efficiency in soybean is still low. The objective of this study is to optimize Agrobacterium-mediated transformation in soybean by improving the infection efficiency of Agrobacterium and regeneration efficiency of explants. Firstly, four factors affecting Agrobacterium infection efficiency were investigated by estimation of the rate of GUS transient expression in soybean cotyledonary explants, including Agrobacterium concentrations, soybean explants, Agrobacterium suspension medium, and co-cultivation time. The results showed that an infection efficiency of over 96% was achieved by collecting the Agrobacterium at a concentration of OD650 = 0.6, then using an Agrobacterium suspension medium containing 154.2 mg/L dithiothreitol to infect the half-seed cotyledonary explants (from mature seeds imbibed for 1 day), and co-cultured them for 5 days. The Agrobacterium infection efficiencies for soybean varieties Jack Purple and Tianlong 1 were higher than the other six varieties. Secondly, the rates of shoot elongation were compared among six different concentration combinations of gibberellic acid (GA3) and indole-3-acetic acid (IAA). The shoot elongation rate of 34 and 26% was achieved when using the combination of 1.0 mg/L GA3 and 0.1 mg/L IAA for Jack Purple and Tianlong 1, respectively. This rate was higher than the other five concentration combinations of GA3 and IAA, with an 18 and 11% increase over the original laboratory protocol (a combination of 0.5 mg/L GA3 and 0.1 mg/L IAA), respectively. The transformation efficiency was 7 and 10% for Jack Purple and Tianlong 1 at this optimized hormone concentration combination, respectively, which was 2 and 6% higher than the original protocol, respectively. Finally, GUS histochemical staining, PCR, herbicide (glufosinate) painting, and QuickStix Kit for Liberty Link (bar) were used to verify the positive transgenic plants, and absolute quantification PCR confirmed the exogenous gene existed as one to three copies in the soybean genome. This study provides an improved protocol for Agrobacterium-mediated transformation in soybean and a useful reference to improve the transformation efficiency in other plant species.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), National Center for Soybean Improvement, Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural UniversityNanjing, China
| |
Collapse
|
8
|
Lee S, Sohn KC, Choi DK, Won M, Park KA, Ju SK, Kang K, Bae YK, Hur GM, Ro H. Ecdysone Receptor-based Singular Gene Switches for Regulated Transgene Expression in Cells and Adult Rodent Tissues. MOLECULAR THERAPY-NUCLEIC ACIDS 2016; 5:e367. [PMID: 27673563 PMCID: PMC5056996 DOI: 10.1038/mtna.2016.74] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022]
Abstract
Controlled gene expression is an indispensable technique in biomedical research. Here, we report a convenient, straightforward, and reliable way to induce expression of a gene of interest with negligible background expression compared to the most widely used tetracycline (Tet)-regulated system. Exploiting a Drosophila ecdysone receptor (EcR)-based gene regulatory system, we generated nonviral and adenoviral singular vectors designated as pEUI(+) and pENTR-EUI, respectively, which contain all the required elements to guarantee regulated transgene expression (GAL4-miniVP16-EcR, termed GvEcR hereafter, and 10 tandem repeats of an upstream activation sequence promoter followed by a multiple cloning site). Through the transient and stable transfection of mammalian cell lines with reporter genes, we validated that tebufenozide, an ecdysone agonist, reversibly induced gene expression, in a dose- and time-dependent manner, with negligible background expression. In addition, we created an adenovirus derived from the pENTR-EUI vector that readily infected not only cultured cells but also rodent tissues and was sensitive to tebufenozide treatment for regulated transgene expression. These results suggest that EcR-based singular gene regulatory switches would be convenient tools for the induction of gene expression in cells and tissues in a tightly controlled fashion.
Collapse
Affiliation(s)
- Seoghyun Lee
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| | - Kyung-Cheol Sohn
- Department of Dermatology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Dae-Kyoung Choi
- Department of Dermatology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Minho Won
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Kyeong Ah Park
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Sung-Kyu Ju
- Affiliated Research (and Development) Institute, Daejeon, Republic of Korea
| | - Kidong Kang
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Young-Ki Bae
- Comparative Biomedical Research Branch, Research Institute, National Cancer Center, Goyang, Republic of Korea
| | - Gang Min Hur
- Department of Pharmacology, College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Hyunju Ro
- Department of Biological Sciences, College of Bioscience and Biotechnology, Chungnam National University, Daejeon, Republic of Korea
| |
Collapse
|
9
|
Xu X, Peng C, Wang X, Chen X, Wang Q, Xu J. Comparison of droplet digital PCR with quantitative real-time PCR for determination of zygosity in transgenic maize. Transgenic Res 2016; 25:855-864. [PMID: 27632191 DOI: 10.1007/s11248-016-9982-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 08/29/2016] [Indexed: 11/29/2022]
Abstract
This study evaluated the applicability of droplet digital PCR (ddPCR) as a tool for maize zygosity determination using quantitative real-time PCR (qPCR) as a reference technology. Quantitative real-time PCR is commonly used to determine transgene copy number or GMO zygosity characterization. However, its effectiveness is based on identical reaction efficiencies for the transgene and the endogenous reference gene. Additionally, a calibrator sample should be utilized for accuracy. Droplet digital PCR is a DNA molecule counting technique that directly counts the absolute number of target and reference DNA molecules in a sample, independent of assay efficiency or external calibrators. The zygosity of the transgene can be easily determined using the ratio of the quantity of the target gene to the reference single copy endogenous gene. In this study, both the qPCR and ddPCR methods were used to determine insect-resistant transgenic maize IE034 zygosity. Both methods performed well, but the ddPCR method was more convenient because of its absolute quantification property.
Collapse
Affiliation(s)
- Xiaoli Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Cheng Peng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaofu Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Xiaoyun Chen
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Qiang Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Junfeng Xu
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China.
| |
Collapse
|
10
|
Passricha N, Saifi S, Khatodia S, Tuteja N. Assessing zygosity in progeny of transgenic plants: current methods and perspectives. J Biol Methods 2016; 3:e46. [PMID: 31453212 PMCID: PMC6706148 DOI: 10.14440/jbm.2016.114] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Revised: 04/29/2016] [Accepted: 05/25/2016] [Indexed: 01/20/2023] Open
Abstract
Homozygosity is highly desirable in transgenic plants research to ensure the stable integration and inheritance of transgene(s). Simple, reliable and high-throughput techniques to detect the zygosity of transgenic events in plants are invaluable tools for biotechnology and plant breeding companies. Currently, a number of basic techniques are being used to determine the zygosity of transgenic plants in T1 generation. For successful application of any technique, precision and simplicity of approach combined with the power of resolution are important parameters. On the basis of simplicity, resolution and cost involved, the available techniques have been classified into three major classes which are conventional methods, current methods and next generation methods. Conventional methods include antibiotic marker-based selection and the highly labor intensive Southern blot analysis. In contrast, methods such as real time PCR, TAIL PCR and competitive PCR are not only cost effective but rapid as well. Moreover, methods such as NGS, digital PCR and loop-mediated isothermal amplification also provide a cost effective, fast and not so labor intensive substitute of current methods. In this review, we have attempted to compare and contrast all the available efficient methods to distinguish homozygous plants in progeny of transgenics. This review also provides information of various techniques available for determining zygosity in plants so as to permit researchers to make informed choices of techniques that best suit their analyses. More importantly, detection and subsequent selection of homozygous individuals is central for facilitating the movement of transgenic plants from the laboratory to the field.
Collapse
Affiliation(s)
- Nishat Passricha
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shabnam Saifi
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Surender Khatodia
- Amity Institute of Biotechnology, Amity University, Gurgaon 122413, India
| | - Narendra Tuteja
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi 110067, India
- Amity Institute of Microbial Technology, Amity University, Noida 201313, India
| |
Collapse
|
11
|
Shekhar S, Agrawal L, Mishra D, Buragohain AK, Unnikrishnan M, Mohan C, Chakraborty S, Chakraborty N. Ectopic expression of amaranth seed storage albumin modulates photoassimilate transport and nutrient acquisition in sweetpotato. Sci Rep 2016; 6:25384. [PMID: 27147459 PMCID: PMC4857128 DOI: 10.1038/srep25384] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 04/18/2016] [Indexed: 11/22/2022] Open
Abstract
Storage proteins in plants, because of high nutrient value, have been a subject of intensive investigation. These proteins are synthesized de novo in the cytoplasm and transported to the storage organelles where they serve as reservoir of energy and supplement of nitrogen during rapid growth and development. Sweetpotato is the seventh most important food crop worldwide, and has a significant contribution to the source of nutrition, albeit with low protein content. To determine the behaviour of seed storage proteins in non-native system, a seed albumin, AmA1, was overexpressed in sweetpotato with an additional aim of improving nutritional quality of tuber proteins. Introduction of AmA1 imparted an increase in protein and amino acid contents as well as the phytophenols. The proteometabolomics analysis revealed a rebalancing of the proteome, with no significant effects on the global metabolome profile of the transgenic tubers. Additionally, the slower degradation of starch and cellulose in transgenic tubers, led to increased post-harvest durability. Present study provides a new insight into the role of a seed storage protein in the modulation of photoassimilate movement and nutrient acquisition.
Collapse
Affiliation(s)
- Shubhendu Shekhar
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India.,Department of Molecular Biology and Biotechnology, Tezpur University, Assam, India
| | - Lalit Agrawal
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Divya Mishra
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| | | | | | - Chokkappan Mohan
- Central Tuber Crops Research Institute, Thiruvananthapuram, Kerala, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Jawaharlal Nehru University Campus, Aruna Asaf Ali Marg, New Delhi-110067, India
| |
Collapse
|
12
|
Nahampun HN, López-Arredondo D, Xu X, Herrera-Estrella L, Wang K. Assessment of ptxD gene as an alternative selectable marker for Agrobacterium-mediated maize transformation. PLANT CELL REPORTS 2016; 35:1121-32. [PMID: 26883223 DOI: 10.1007/s00299-016-1942-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 01/24/2016] [Indexed: 05/21/2023]
Abstract
Bacterial phosphite oxidoreductase gene and chemical phosphite can be used as a selection system for Agrobacterium -mediated maize transformation. Application of phosphite (Phi) on plants can interfere the plant metabolic system leading to stunted growth and lethality. On the other hand, ectopic expression of the ptxD gene in tobacco and Arabidopsis allowed plants to grow in media with Phi as the sole phosphorous source. The phosphite oxidoreductase (PTXD) enzyme catalyzes the conversion of Phi into phosphate (Pi) that can then be metabolized by plants and utilized as their essential phosphorous source. Here we assess an alternative selectable marker based on a bacterial ptxD gene for Agrobacterium-mediated maize transformation. We compared the transformation frequencies of maize using either the ptxD/Phi selection system or a standard herbicide bar/bialaphos selection system. Two maize genotypes, a transformation amenable hybrid Hi II and an inbred B104, were tested. Transgene presence, insertion copy numbers, and ptxD transcript levels were analyzed and compared. This work demonstrates that the ptxD/Phi selection system can be used for Agrobacterium-mediated maize transformation of both type I and type II callus culture and achieve a comparable frequency as that of the herbicide bar/bialaphos selection system.
Collapse
Affiliation(s)
- Hartinio N Nahampun
- Interdepartmental Plant Biology Major, Iowa State University, Ames, IA, 50011-1010, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA
- PT.BISI International, Tbk., Jl. Raya Pare-Wates Km 9, Ds. Sumberagung, Kab, Kediri, East Java, 64175, Indonesia
| | - Damar López-Arredondo
- StelaGenomics México, S de RL de CV, Av. Camino Real de Guanajuato s/n, 36821, Irapuato, Guanajuato, Mexico
| | - Xing Xu
- Interdepartmental Plant Biology Major, Iowa State University, Ames, IA, 50011-1010, USA
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA
- Zhejiang University, Hangzhou, China
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada del Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Km 9.6 carretera Irapuato-León, 36500, Irapuato, Guanajuato, Mexico
| | - Kan Wang
- Department of Agronomy, Iowa State University, Ames, IA, 50011-1010, USA.
| |
Collapse
|
13
|
Evaluation and Selection of Appropriate Reference Genes for Real-Time Quantitative PCR Analysis of Gene Expression in Nile Tilapia (Oreochromis niloticus) during Vaccination and Infection. Int J Mol Sci 2015; 16:9998-10015. [PMID: 25941937 PMCID: PMC4463629 DOI: 10.3390/ijms16059998] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 04/23/2015] [Accepted: 04/24/2015] [Indexed: 01/09/2023] Open
Abstract
qPCR as a powerful and attractive methodology has been widely applied to aquaculture researches for gene expression analyses. However, the suitable reference selection is critical for normalizing target genes expression in qPCR. In the present study, six commonly used endogenous controls were selected as candidate reference genes to evaluate and analyze their expression levels, stabilities and normalization to immune-related gene IgM expression during vaccination and infection in spleen of tilapia with RefFinder and GeNorm programs. The results showed that all of these candidate reference genes exhibited transcriptional variations to some extent at different periods. Among them, EF1A was the most stable reference with RefFinder, followed by 18S rRNA, ACTB, UBCE, TUBA and GAPDH respectively and the optimal number of reference genes for IgM normalization under different experiment sets was two with GeNorm. Meanwhile, combination the Cq (quantification cycle) value and the recommended comprehensive ranking of reference genes, EF1A and ACTB, the two optimal reference genes, were used together as reference genes for accurate analysis of immune-related gene expression during vaccination and infection in Nile tilapia with qPCR. Moreover, the highest IgM expression level was at two weeks post-vaccination when normalized to EF1A, 18S rRNA, ACTB, and EF1A together with ACTB compared to one week post-vaccination before normalizing, which was also consistent with the IgM antibody titers detection by ELISA.
Collapse
|
14
|
Fritsch L, Fischer R, Wambach C, Dudek M, Schillberg S, Schröper F. Next-generation sequencing is a robust strategy for the high-throughput detection of zygosity in transgenic maize. Transgenic Res 2015; 24:615-23. [PMID: 25648956 DOI: 10.1007/s11248-015-9864-x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 01/22/2015] [Indexed: 01/05/2023]
Abstract
Simple and reliable, high-throughput techniques to detect the zygosity of transgenic events in plants are valuable for biotechnology and plant breeding companies seeking robust genotyping data for the assessment of new lines and the monitoring of breeding programs. We show that next-generation sequencing (NGS) applied to short PCR products spanning the transgene integration site provides accurate zygosity data that are more robust and reliable than those generated by PCR-based methods. The NGS reads covered the 5' border of the transgenic events (incorporating part of the transgene and the flanking genomic DNA), or the genomic sequences flanking the unfilled transgene integration site at the wild-type locus. We compared the NGS method to competitive real-time PCR with transgene-specific and wild-type-specific primer/probe pairs, one pair matching the 5' genomic flanking sequence and 5' part of the transgene and the other matching the unfilled transgene integration site. Although both NGS and real-time PCR provided useful zygosity data, the NGS technique was favorable because it needed fewer optimization steps. It also provided statistically more-reliable evidence for the presence of each allele because each product was often covered by more than 100 reads. The NGS method is also more suitable for the genotyping of large panels of plants because up to 80 million reads can be produced in one sequencing run. Our novel method is therefore ideal for the rapid and accurate genotyping of large numbers of samples.
Collapse
Affiliation(s)
- Leonie Fritsch
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Forckenbeckstrasse 6, 52074, Aachen, Germany
| | | | | | | | | | | |
Collapse
|
15
|
Cardoso AM, Morais CM, Cruz AR, Cardoso AL, Silva SG, do Vale ML, Marques EF, Pedroso de Lima MC, Jurado AS. Gemini surfactants mediate efficient mitochondrial gene delivery and expression. Mol Pharm 2015; 12:716-30. [PMID: 25634573 DOI: 10.1021/mp5005349] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Gene delivery targeting mitochondria has the potential to transform the therapeutic landscape of mitochondrial genetic diseases. Taking advantage of the nonuniversal genetic code used by mitochondria, a plasmid DNA construct able to be specifically expressed in these organelles was designed by including a codon, which codes for an amino acid only if read by the mitochondrial ribosomes. In the present work, gemini surfactants were shown to successfully deliver plasmid DNA to mitochondria. Gemini surfactant-based DNA complexes were taken up by cells through a variety of routes, including endocytic pathways, and showed propensity for inducing membrane destabilization under acidic conditions, thus facilitating cytoplasmic release of DNA. Furthermore, the complexes interacted extensively with lipid membrane models mimicking the composition of the mitochondrial membrane, which predicts a favored interaction of the complexes with mitochondria in the intracellular environment. This work unravels new possibilities for gene therapy toward mitochondrial diseases.
Collapse
Affiliation(s)
- Ana M Cardoso
- CNC-Center for Neuroscience and Cell Biology, ‡Department of Life Sciences, and §Faculty of Pharmacy, University of Coimbra , Coimbra, Portugal
| | | | | | | | | | | | | | | | | |
Collapse
|
16
|
Veerappan V, Chen N, Reichert AI, Allen RD. HSI2/VAL1 PHD-like domain promotes H3K27 trimethylation to repress the expression of seed maturation genes and complex transgenes in Arabidopsis seedlings. BMC PLANT BIOLOGY 2014; 14:293. [PMID: 25367506 PMCID: PMC4232687 DOI: 10.1186/s12870-014-0293-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2014] [Accepted: 10/17/2014] [Indexed: 05/22/2023]
Abstract
BACKGROUND The novel mutant allele hsi2-4 was isolated in a genetic screen to identify Arabidopsis mutants with constitutively elevated expression of a glutathione S-transferase F8::luciferase (GSTF8::LUC) reporter gene in Arabidopsis. The hsi2-4 mutant harbors a point mutation that affects the plant homeodomain (PHD)-like domain in HIGH-LEVEL EXPRESSION OF SUGAR-INDUCIBLE GENE2 (HSI2)/VIVIPAROUS1/ABI3-LIKE1 (VAL1). In hsi2-4 seedlings, expression of this LUC transgene and certain endogenous seed-maturation genes is constitutively enhanced. The parental reporter line (WT LUC ) that was used for mutagenesis harbors two independent transgene loci, Kan R and Kan S . Both loci express luciferase whereas only the Kan R locus confers resistance to kanamycin. RESULTS Here we show that both transgene loci harbor multiple tandem insertions at single sites. Luciferase expression from these sites is regulated by the HSI2 PHD-like domain, which is required for the deposition of repressive histone methylation marks (H3K27me3) at both Kan R and Kan S loci. Expression of LUC and Neomycin Phosphotransferase II transgenes is associated with dynamic changes in H3K27me3 levels, and the activation marks H3K4me3 and H3K36me3 but does not appear to involve repressive H3K9me2 marks, DNA methylation or histone deacetylation. However, hsi2-2 and hsi2-4 mutants are partially resistant to growth inhibition associated with exposure to the DNA methylation inhibitor 5-aza-2'-deoxycytidine. HSI2 is also required for the repression of a subset of regulatory and structural seed maturation genes in vegetative tissues and H3K27me3 marks associated with most of these genes are also HSI2-dependent. CONCLUSIONS These data implicate HSI2 PHD-like domain in the regulation of gene expression involving histone modifications and DNA methylation-mediated epigenetic mechanisms.
Collapse
Affiliation(s)
- Vijaykumar Veerappan
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
- />Current address: Department of Biological Sciences, University of North Texas, Denton, TX 76203-5017 USA
| | - Naichong Chen
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Angelika I Reichert
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
| | - Randy D Allen
- />Institute for Agricultural Biosciences, Oklahoma State University, 3210 Sam Noble Parkway, Ardmore, OK 73401 USA
| |
Collapse
|
17
|
Mierziak J, Wojtasik W, Kostyn K, Czuj T, Szopa J, Kulma A. Crossbreeding of transgenic flax plants overproducing flavonoids and glucosyltransferase results in progeny with improved antifungal and antioxidative properties. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:1917-1932. [PMID: 25506258 PMCID: PMC4257994 DOI: 10.1007/s11032-014-0149-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2014] [Accepted: 07/04/2014] [Indexed: 05/12/2023]
Abstract
Flavonoids are a large group of secondary plant metabolites with many important functions; they play a role in fruit, flower and seed pigmentation and are involved in multiple protective mechanisms. They are very active natural antioxidants, acting as antimicrobial compounds in defense against pathogens, and they protect the plant against various stress factors, including excessive solar radiation and temperature. They are also an animal deterrent. Flax is already a very useful crop plant with nutritional and biomedical applications. With increased phenylpropanoid content, flax plants could be used in the production of improved dietary supplements and antimicrobial agents. The main aim of this study was to engineer a flax variety with increased flavonoid content by crossing two transgenic flax varieties that have heightened flavonoid levels. A mother plant that over expresses genes encoding the flavonoid biosynthesis pathway enzymes chalcone synthase, chalcone isomerase and dihydroflavonol reductase was crossed with plants overexpressing the glucosyltransferase (GT) gene. It was expected that the progeny would display better properties thanks to the simultaneous increases in flavonoid synthesis and stability. In comparison to the control and parental plants, plants of the selected flax lines were found to have increased contents of flavonoids and other phenylpropanoids, including phenolic acids, in their stems and seeds. A significant increase in the secoisolariciresinol diglucoside content was found in the seeds. The antioxidative properties of extracts from W92 × GT crossbreed plants were higher than the control (non-transgenic) and parental plants. These results correlated with the increase in the susceptibility of the crossbreeds to Fusarium infection. The increased flavonoid content did not cause any negative phenotypic changes or reduce the yield of seeds.
Collapse
Affiliation(s)
- Justyna Mierziak
- Faculty of Biotechnology, Wroclaw University, Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| | - Wioleta Wojtasik
- Faculty of Biotechnology, Wroclaw University, Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| | - Kamil Kostyn
- Faculty of Biotechnology, Wroclaw University, Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| | - Tadeusz Czuj
- Faculty of Biotechnology, Wroclaw University, Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| | - Jan Szopa
- Faculty of Biotechnology, Wroclaw University, Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| | - Anna Kulma
- Faculty of Biotechnology, Wroclaw University, Przybyszewskiego 63/77, 51-148 Wrocław, Poland
| |
Collapse
|
18
|
Evaluation of reference genes for quantitative real-time RT-PCR analysis of gene expression in Nile tilapia (Oreochromis niloticus). Gene 2013; 527:183-92. [PMID: 23792389 DOI: 10.1016/j.gene.2013.06.013] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Revised: 05/29/2013] [Accepted: 06/07/2013] [Indexed: 11/20/2022]
Abstract
Quantitative real-time reverse-transcriptase polymerase chain reaction (RT-qPCR) has been used frequently to study gene expression related to fish immunology. In such studies, a stable reference gene should be selected to correct the expression of the target gene. In this study, seven candidate reference genes (glyceraldehyde-3-phosphate dehydrogenase (GADPH), ubiquitin-conjugating enzyme (UBCE), 18S ribosomal RNA (18S rRNA), beta-2-microglobulin (B2M), elongation factor 1 alpha (EF1A), tubulin alpha chain-like (TUBA) and beta actin (ACTB)), were selected to analyze their stability and normalization in seven tissues (liver, spleen, kidney, brain, heart, muscle and intestine) of Nile tilapia (Oreochromis niloticus) challenged with Streptococcus agalactiae or Streptococcus iniae, respectively. The results showed that all the candidate reference genes exhibited tissue-dependent transcriptional variations. With PBS injection as a control, UBCE was the most stable and suitable single reference gene in the intestine, liver, brain, kidney, and spleen after S. iniae infection, and in the liver, kidney, and spleen after S. agalactiae infection. EF1A was the most suitable in heart and muscle after S. iniae or S. agalactiae infection. GADPH was the most suitable gene in intestine and brain after S. agalactiae infection. In normal conditions, UBCE and 18S rRNA were the most stably expressed genes across the various tissues. These results showed that for RT-qPCR analysis of tilapia, selecting two or more reference genes may be more suitable for cross-tissue analysis of gene expression.
Collapse
|
19
|
Mieog JC, Howitt CA, Ral JP. Fast-tracking development of homozygous transgenic cereal lines using a simple and highly flexible real-time PCR assay. BMC PLANT BIOLOGY 2013; 13:71. [PMID: 23627847 PMCID: PMC3668147 DOI: 10.1186/1471-2229-13-71] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 04/23/2013] [Indexed: 05/22/2023]
Abstract
BACKGROUND A crucial step in the evaluation of newly produced transgenic plants is the selection of homozygous plants. Here we describe an efficient and highly flexible real-time PCR-based method for the development of homozygous lines in plant models with complex (multiple) genomes and/or relatively long generation times (>3 months) using direct copy number determinations. RESULTS An existing DNA extraction method was converted into a high-throughput plant leaf DNA extraction procedure yielding DNA suitable for real-time PCR analyses. Highly specific and efficient primer pairs were developed for a bread wheat reference gene (Epsilon Cyclase) and for standard sequence elements in the gene cassette routinely used for cereal transformations (an intron bridge and the Nopaline Synthase terminator). The real-time PCR assay reliably distinguished wheat plants with a single copy of the transgene from individuals with multiple copies or those lacking the transgene. To obtain homozygous lines carrying a unique insertion event as efficiently as possible, T0 plants (plants raised from transformed callus) with a single copy of the transgene were selected and their progeny screened for homozygous plants. Finally, the assay was adapted to work on rice. CONCLUSIONS The ability to quickly, easily and accurately quantify the construct copy numbers, as provided by the real-time PCR assay, greatly improved the efficiency and reliability of the selection of homozygous transgenic plants in our case study. We were able to select homozygous plants in early generations, avoiding time-consuming methods such as large scale analysis of segregation patterns of descendants and/or Southern blotting. Additionally, the ability to specifically develop homozygous lines carrying a unique insertion event could be important in avoiding gene silencing due to co-suppression, and if needed assist in the selection of lines suitable for future deregulation. The same primer pairs can be used to quantify many different wheat transgenic events because the construct-specific primer pairs are targeted to standard sequence elements of the cereal gene cassettes, making the method widely applicable in wheat GM research. Moreover, because all procedures described here are standardized, the method may easily be adapted to vectors lacking the target regions used here and/or to other plant models.
Collapse
Affiliation(s)
- Jos C Mieog
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601, Australia
| | - Crispin A Howitt
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601, Australia
| | - Jean-Philippe Ral
- CSIRO Food Futures National Research Flagship, GPO Box 1600, Canberra ACT 2601, Australia
| |
Collapse
|