Synthetic tma12 Gene and Codon Optimization
The coding sequence of the tma12 gene was retrieved from the National Center for Biotechnology Information (GenBank accession code: JQ438776.1). To get enhanced expression in the transgenic cotton, the sequence was codon optimized by using the Gossypium spp. codon usage table and Geneious V8.0 software [23]. After codon optimization, the protein sequence remained the same but the DNA sequence has 70% identity of the original gene sequence. This codon-optimized gene sequence of tma12 was commercially synthesized by ATUM, Newark, CA, USA. The supplier provided the synthetic gene cloned in the plasmid pJIT201 (Figure S1 in Additional file 1).
Cloning of tma12 Gene under CaMV-2X35S Promoter and NSP Promoter
Two different promoters were used for the expression of TMA12 protein: 1) constitutive promoter CaMV-2X35S and 2) phloem-specific promoter-NSP). Plasmid pJ201 with the gene of interest was restricted with HindIII and EcoRI and the fragments were checked on the agarose gel. The desired band of the gene of interest (651bp) was eluted from the gel by Wizard SV Gel and PCR Clean-Up System (Promega). Then the gene of interest was cloned in the pJIT163 at HindIII and EcoRI sites under the 35S promoter. Then the expression cassette (CaMV-2X35S promoter, GOI, and CaMV terminator) was restricted from the pJIT163 with SacI and EcoRV and then ligated in the pCambia 2300 at SacI and SmaI sites. To clone the gene under the NSP promoter, the pJIT163 (with the gene of interest) was restricted with SacI and HindIII to remove the CaMV-2X35S promoter and at the same sites, NSP promoter was ligated. The ligation mixture was transformed into E. coli top 10. The recombinant plasmids having tma12 under CaMV-2X35S promoter and NSP promoter are shown in Figure S2 (Additional file 1).
Transformation into Agrobacterium LBA14404
To transform the recombinant plasmid DNA pCambia 2300 (tma12 constructs under CaMV-2X35S promoter and NSP promoter) into Agrobacterium tumefaciens with electroporation method, DNA was diluted to 15-20 ng/µL concentration. About 5 µL of DNA was mixed with 100 µL of agrobacterium cells in a 1.5 mL tube and incubated on ice for 30 min. The mixture was transferred to the cuvette (1mm gap) and the electroporator was adjusted at voltage: 1440 volts, resistance: 200 W, capacitance: 250 μFD. After passing an electric pulse through the cuvette, 1 mL LB medium was poured into the electroporation cuvette and after mixing well was transferred to a 2 mL tube. Then the tube was incubated at 28 ºC and 180 rpm for 2-3 hours. Then 150 µL of cells were spread on the LB agar plate supplemented with kanamycin and rifampicin. The LB agar plates were incubated at 28ºC to get the single colonies. These single colonies were cultured into the LB broth. The transformation was confirmed with colony PCR. Agrobacterium LBA4404 50 mL cultures (one transformed with tma12 construct under CaMV-2X35S promoter and the other under NSP promoter) were prepared to transform the N. tabacum.
Transformation into N. tabacum
To get the stable expression of tma12 gene, N. tabacum was transformed with the agrobacterium transformation method described by Horsch et al. [24]. N. tabacum seeds were sterilized by immersing in the 10 % bleach for 10 min and followed by rinsing (2-3 times) with autoclaved distilled water. After completely drying, the seeds were sprinkled over MS medium plates. MS0 medium contained 4.34 g/L of Murashige and Skoog salt, 3 % sucrose, and 2 % agar; and pH was adjusted to 5.7. Then for seed germination, MS agar plates were placed in a growth chamber with controlled conditions (28 + 2 ºC temperature and 16:8 daylight cycle). After germination, each seedling was shifted to an isolated container cast with MS agar medium and allowed to grow for at least 4 weeks to get the explants. After cutting the explants, these were pre-cultured on the solidified MS1 medium supplemented with hormones BAP (1 mg/L) and NAA (1 mg/L) under dark conditions for 2-3 days.
Overnight cultures of LBA4404 transformed with pCambia 2300 plasmids having GOI cassettes (tma12 under CaMV-2X35S promoter and NSP promoter) (Figure S2, Additional file 1) were diluted by 10 times in liquid MS1 medium. For inoculation, pre-cultured explants were dipped in these Agrobacterium diluted cultures for 20-30 min. Explants were removed from the cultures and dried in the aseptic condition. To co-cultivate, these explants were grown over solidified MS1 medium for 2-3 days in growth chamber under dark conditions. After co-cultivation these explants were rinsed with cefotaxime (250 mg/mL) to kill the excessive Agrobacterium cells. After drying these explants were shifted to the shooting medium (MS1 medium supplemented with kanamycin 50 mg/mL). Shoots initiation started after 3-4 weeks. These expected transgenic shoots were cut off and shifted to the rooting medium (recipe described in Table S1-Additional file 1). After the development of roots, plantlets were shifted to the soil in pots for further growth in a controlled environment. These transgenic lines (T0) were subjected to molecular characterization and bioassays. Seeds from the T0 lines were also collected to get the T1 lines. T1 lines were also subjected to the molecular characterization and whitefly bioassays to check the efficacy of tma12.
Molecular Characterization of Tobacco Transgenic Lines
The T0 and T1 lines of tobacco plants expressing tma12 under 35S promoter and NSP promoter were molecularly characterized. For preliminary screening of the transgenic lines, samples were collected from the plants and subjected to the direct PCR without extracting the DNA using the commercial kit Phire Plant Direct PCR (Thermo Scientific). In this protocol, a small piece of the young leaves about 2 mm in size was taken and crushed in the 20 µL of the dilution buffer with a pipette tip. Then this sample mixture was briefly centrifuged and 0.5 µL of the supernatant was taken as the template for the 20 µL reaction. The reaction mixture contained 10 µL of the 2X Phire plant PCR buffer, 0.5 µM of each of the forward and reverse primers (tm12F: 5’-ATGCATGGCTCTATGGAAGATCCT-3’/tm12R: 5’-TCATGTAGTAGAATGAAGTGACAA-3’), 0.5 µL of the template sample, 0.4 µL of the Phire Hot Start II DNA Polymerase and water to make up volume 20 µL. Thermocycling profile was set as 1 cycle of initial denaturation at 94 ºC followed by 35 cycles of 94 ºC for 30 sec, 55 ºC for 30 sec, 72 ºC for 30 sec, and then 1 cycle of final extension at 72 ºC for 5 min. After completing the polymerase chain reaction, samples were electrophoresed through the agarose gel for the confirmation of required band size (651 bp).
Bioassays: Evaluation of Tobacco Transgenic Lines
The confirmed lines were subjected to bioassays to find the efficacy of the transgenic lines against the whitefly. For the bioassays, whiteflies were reared in a controlled environment on the tobacco wild type plants for at least 2 months. Transgenic plants (when reached the 4-6 leaves stage) were exposed to the whiteflies in the random block design along with the control plants (wild-type Coker312) of the same stage in the closed containment with the controlled condition described above. The mortality data of the whiteflies were collected after 14 days of exposure to the whiteflies.
Transformation into Cotton
After checking the efficacy (against the whitefly) of the tma12 gene expressed under both promoters in model plant N. tabacum, cotton transgenic lines expressing TMA12 under 2X35S promoter and under NSP promoter were also developed in this study. To develop transgenic cotton lines Agrobacterium transformation method was used as described by Umbeck et al. [25]. G. hirsutum var. Coker 312 was used to transform with LBA4404 having tma12 construct under 2X35S promoter and NSP promoter.
Seeds of Coker 312 were delineated with H2SO4 and then sterilized by immersing the seeds in the mixture of HgCl2 (0.2%) and SDS (1%) for 15-20 min. After washing with distilled water 4-5 times, seeds were dried and then grown in the glass jars in the growth chamber with controlled conditions (described in the previous section). After about a week, seeds germinated into the hypocotyls which were dissected to prepare the explants. These explants were immersed in the Agrobacterium LBA4404 culture for 20-30 min. After inoculation, these explants were dried and grown over the cotton callus induction (CCI) medium in the petri plates incubated in the dark at 28 ºC for 2 days. Then explants were sub-cultured to the CCI medium supplemented with kanamycin (50 mg/mL) and cefotaxime (250 mg/mL). Sub-culturing had been done to fresh medium after every 2 weeks until the callus emerged from the explants (hypocotyls). These calli were removed and sub-cultured further in the medium as described above.
After 8-10 weeks, the matured calli were sub-cultured to the embryo maturation medium (Table S1). Then after 4-6 weeks, embryos were separated from the calli under aseptic conditions and grown in the embryo germination selection medium until development of complete plantlets. These plantlets were grown in the same medium for root development in the glass jars. After development of roots these putative transgenic plants were shifted to the soil in the pots in the growth chamber.
Molecular Characterization of Transgenic Cotton Lines
PCR Confirmation
DNA was extracted from all the putative transgenic lines of cotton by the CTAB method described above. Integration of the tma12 sequence in the putative transgenic lines was confirmed by the PCR using specific primers. For PCR, DreamTaq Green PCR Master Mix 2X was used, which is ready to use solution, contained optimized DreamTaq DNA Green buffer, DreamTaq Polymerase, MgCl2, and dNTPs. This master mix is optimized to amplify up to 6 kb of the DNA in length. The 20 µL of the total reaction mixture contained the 10 µL of DreamTaq Green PCR Master Mix, 0.5 µM of each of the forward and reverse primers (Ptm12F: 5’-CATGGCTCTATGGAAGATCCT-3’/Ptm12R: 5’-TCATGTAGTAGAATGAAGTGACAA-3’), 25-50 ng of DNA and water to make volume 20 µL. The PCR profile was 98 °C for 3 mins, followed by 35 cycles of 95 °C for 30 sec, 60 °C for 30 sec, and 72 °C for 1 min, with a final step of 72 °C for 5 mins. After completing the PCR, the product was analyzed by running the agarose gel.
Expression Analysis
To estimate the relative expression of the TMA12 in the cotton transgenic plants, real-time quantitative PCR (qPCR) from the cDNA was performed. In the qPCR, sadI gene was used as a reference gene to normalize the Ct value. Each reaction mixture contained 5 µL PowerUpTM SYBRTM Green PCR master mix (Applied Bioscience, USA), 1 µL (10 ng) cDNA, 0.25 µL of each of the forward and reverse primer (qtm12F: 5’-ATGGCAGTATGGAGGATCCTATAAG-3’/qtm12R: 5’-GCGTTTGGGATATTAACTTCGTTCC-3’) and 3.75 µL of water. PCR reactions were initiated with an incubation at 95 °C for 30 sec, followed by a 40 times cycle of 95 °C for 5 sec, 60 °C for 1 min followed by a melting curve was collected analysis. The Ct values were used to quantify and analyze gene expression according to the 2-DDCT method [26]. The RT-qPCR was performed including all positive and negative controls in triplicates. In these experiments, QuantStudioTM 6 Flex System (ThermoScientific, USA) was used with 384 well plates. Changes in the expression level of the gene of interest was calculated by comparing the DDCT values of samples of transgenic plants to those collected from wild type plants.
Copy Number Estimation
To estimate the number of copies of the tma12 that was integrated into the genome of each of the transgenic lines of cotton plants qPCR was performed using DNA as template and sad1 as a reference gene. Each reaction mixture contained 5 µL PowerUpTM SYBRTM Green PCR master mix (Applied Bioscience, USA), 1 µL (25 ng) DNA, 0.25 µL of each of the forward and reverse primer (qtm12F: 5’-ATGGCAGTATGGAGGATCCTATAAG-3’/qtm12R: 5’-GCGTTTGGGATATTAACTTCGTTCC-3’) and 3.75 µL of water. PCR reactions were initiated with an incubation at 95 °C for 30 sec, followed by a 40 times cycle of 95 °C for 5 sec, 60 °C for 1 min, followed by melt curve analysis. The 2-DDCT method [27] was used to estimate the copy number of tma12 with relation to the internal control in each of the transgenic plant.
Bioassays: Evaluation of Cotton Transgenic Lines
Whiteflies (Asia II 1) populations were reared on the cotton plants (wild type: Coker 312) in the closed containment with conditions described above. After estimating expression level of tma12 by qPCR, two plants of each transgenic event were exposed to whiteflies in the closed containment with controlled condition. The eggs and nymphs were counted from 1-inch square area of the three upper leaves and adults were counted from the upper 3 leaves of each plant (transgenic lines and as well as the controlled plants). Thus, each transgenic line had six data points. Then data was tested using ANOVA followed by the Tukey’s HSD test [28].