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Isolate 2 plant dna kit

Manufactured by Meridian Bioscience
Sourced in United States, Australia, United Kingdom

The ISOLATE II Plant DNA Kit is a laboratory product designed for the extraction and purification of high-quality genomic DNA from a variety of plant species. The kit utilizes a silica-based membrane technology to efficiently capture and purify DNA, enabling users to obtain DNA samples suitable for downstream applications such as PCR, sequencing, and other molecular biology techniques.

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21 protocols using isolate 2 plant dna kit

1

Barley Landrace and Wild Accession Preparation

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The study material was 200 barley landraces (H. vulgare L.) and 220 wild barley accessions (H. spontaneum [K. Koch] Thell.) (S1 Table) obtained from the United States Department of Agriculture–Agricultural Research Service (USDA-ARS) Small Grains Collection (NSGC). Seeds were germinated at room temperature (c.22°C) in Petri dishes in hydroponic conditions. When coleoptiles emerged, the seeds were transferred to moist filter paper and seedlings grown until 21 days old. Fresh leaf material was then collected and DNA extracted using the ISOLATE II Plant DNA kit (Bioline).
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2

Barley Landrace and Wild Accession DNA Extraction

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Seeds of 228 barley landraces and 216 wild barley accessions (S1 Table, S2 Table) were obtained from the United States Department of Agriculture–Agricultural Research Service (USDA-ARS) Small Grains Collection (NSGC). Seeds were germinated and seedlings grown in Petri dishes in hydroponic conditions at room temperature (c.22°C). Once the coleoptiles emerged, the seeds were placed on moist filter paper. Fresh leaf material was collected when the seedlings were 21 days old and DNA extracted using the ISOLATE II Plant DNA kit (Bioline).
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3

Estimating Wild Region Size in IL R182

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SCAR and CAPS markers were designed in order to estimate the size of the wild region present in the IL sub-line R182. Genomic DNA was extracted from young leaves collected from M82, IL7-3, and R182 using the ISOLATE II Plant DNA Kit (Bioline). Primers for the PCR amplification were designed based on polymorphisms detected in the IL7-3 introgression region between the S. lycopersicum (SL3.0 assembly and iTAG3.2 annotation) and the S. pennellii (v2 Assembly) genomes, by investigating the Genome Browser available in the Sol Genomics Network database2. PCR amplification was carried out in 50 μl reaction volume containing 50 ng DNA, 1X of My Taq reaction buffer, 1.0 mM primer and 1 U My Taq DNA polymerase (Bioline). For designing CAPS markers, restriction enzymes suitable to detect polymorphic SNPs between the fragments amplified were found using the tool CAPS Designer available at the Sol Genomics Network2. Amplified and restricted fragments were visualized on agarose gel at different concentrations depending on their expected size.
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4

Molecular Techniques for Liberibacter DNA

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Standard methods were used for chromosomal DNA isolation, restriction enzyme digestion, agarose gel electrophoresis, ligation and transformation (Sambrook et al., 1989). Plasmids were isolated using QIAprep® Spin Miniprep Kit (Qiagen, Valencia, CA, USA), and PCR products were purified using QIAquick® purification kits (Qiagen). The primers utilized are described in Table 4. Liberibacter asiaticus DNA was isolated from leaf tissues of infected plants using the Isolate II Plant DNA kit (Bioline, Taunton, Massachusetts, USA).
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5

Extraction and Quantification of Grain DNA

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This study used dried maize and cowpea grains obtained from commercial outlets (maize from Afrikan Continental, 391B Prospect Rd, Blair Athol SA 5084, Australia Lat:-34.8596168 Lon: 138.59248680; cowpea from Adelaide Central Market, 44–60 Gouger St., Adelaide SA5000, Australia Lat: -34.9295219 Lon: 138.572832) to best represent the condition of grains in the supply chain. DNA was extracted from the ground seeds (flour), from seed mixes (based on weight) and aerosol samples using ISOLATE II Plant DNA Kit (Bioline, Australia) following the manufacturer’s instructions and quantified using a NanoDrop spectrophotometer (Thermo Fisher Scientific, USA).
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6

Prolonged DNA Extraction from Fructose-Positive Samples

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DNA was extracted from the aliquot of homogenate (above) of fructose–positive samples using the ISOLATE II Plant DNA Kit (Bioline, London, UK) according to the manufacturer’s instructions with a slight modification. This included extension of the incubation period with the lysis buffer PA1 and RNase by 4–6 hr and elution with Buffer PG by 10 min. The extracted DNA was stored at -20°C until further processing.
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7

Wheat Genotyping-by-Sequencing Protocol

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Seeds were vernalized for 2 days at 4°C and grown for two weeks at room temperature in petri dishes covered with filter paper. DNA was extracted from first leaves using the Bioline Isolate II Plant DNA Kit. In a few cases where germination did not occur DNA was extracted from pulverized seeds with the Roche HighPure PCR Product Purification Kit. DNA was quantified by a Qubit dsDNA HS assay with a Qubit 2.0 Fluorometer and DNA integrity was checked by electrophoresis in 1% agarose gels. The resulting samples had DNA concentrations between 30–100 ng μl–1.
Genotyping-by-sequencing (Genomic Diversity Facility, Cornell University) was carried out as described by Elshire et al. [35 (link)]. Optimization was attempted with PstI and EcoT221 and the former chosen for genome complexity reduction. Unique sequence tags were identified from the FASTQ files and aligned to release 31 of the T. aestivum genome using BWA v.0.7.8-r455 [36 (link)]. SNP calling was carried out with the TASSEL-GBS pipeline [37 (link)] and the vcf files were handled with VCFtools v.0.1.13 [38 (link)] and TASSEL [39 (link)]. Different filters for coverage, missing data, biallelic SNPs, indels and minimum allele frequency were applied as described in Results. The GBS data are available at the European Nucleotide Archive, study PRJEB42105.
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8

Plant DNA Extraction from Seeds

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Unless stated otherwise, genomic DNA was extracted from approximately 30 mg of seeds using the Isolate II plant DNA kit (Bioline, UK), according to the manufacturer’s instructions. Seeds were first hydrated overnight in sterile distilled water at room temperature and then crushed in 400 µl lysis buffer PA1 using 5 mm stainless steel beads (Qiagen, USA) in 2 ml microcentrifuge tubes on a mixer mill MM400 (Retsch, Germany) at 30 Hz for 40 s, repeated twice. DNA was eluted in 100 µl buffer PG and stored at −20 °C until required. For DNA extraction from single seeds, steps were as described above with the following exceptions: individual seeds were crushed in 150 µl lysis buffer PA1 in 0.2 ml PCR tubes using 1 ml pipette tips and DNA eluted in 30 µl buffer PG. Where required, genomic DNA was quantified using the NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific, USA) according to the manufacturer’s instructions. DNA concentrations (ng/µl) were adjusted in sterile distilled water to concentrations specific to each experiment.
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9

Comprehensive DNA Isolation of Rumex and Outgroup Species

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DNA was isolated from 109 accessions, representing 67 Rumex species. Of the 109 included accessions, a total of 99 Rumex accessions, six Rheum L. species, three Emex L. accessions and one species of Persicaria L. (Mill.) are represented. Persicariavirginiana (L.) Gaertn., Rheumalexandrae Batalin, Rheumemodii Wall., Rheumnobile Hook. f. & Thomson, Rheumofficinale Baill., Rheumpalmatum L. and Rheumrhabarbarum L. were included as outgroup species. Additional plant samples were obtained through the GenBank sequence database (Appendix A1). Samples were taken from a combination of herbarium specimens (K, NY, OSC, RAB, US), field collections and cultivated samples from collaborators. Herbarium acronyms follow the Index Herbariorum (Thiers 2019 ).
All fresh leaf samples were dried using silica gel. Plant tissue was homogenised using the FastPrep-24 5G Sample Preparation System (M. P. Biomedicals, LLC Santa Ana CA, USA). Total genomic DNA was extracted from herbarium specimen-sampled and silica-dried leaf tissues using a BIOLINE ISOLATE II Plant DNA Kit (Cat No. BIO-52070). Modification for herbarium material proceeded as follows: Cell lysis was carried out using 300 µl of buffer (PA1 or PA2) and 30 µl of proteinase K (20 µg/ml) and incubated for 18 hours at 65 °C on an orbital shaker.
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10

Caecal DNA Extraction with Slight Modification

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Caecal DNA was extracted following the protocol of ISOLATE II Plant DNA Kit (Bioline, NSW, Australia) with slightly modification. Approximately 200 mg of freshly defrosted caecal content were placed in a 2-mL Eppendorf tube contained 300 mg of glass beads. An aliquot of 450 μL Lysis Buffer PA1 was added to the samples and thoroughly mixed with a vortex mixer. The samples were transferred to a block bead mill (Retsch GmbH & Co, Haan, Germany) to disrupt at a frequency of 30/s for 5 min prior to being heated at 95 °C for 5 min. The digesta was lysed and homogenised after adding 200 μL and then 100 μL of Extraction Buffer with vortex-mixing following each addition. An aliquot of 10 μL of RNase was added to 600 μL of the lysate in a 1.5-mL microcentrifuge tube in order to remove RNA. The solution was incubated at 65 °C for 10 min. The incubated mixture was centrifuged for 1 min at 11,000 × g to pellet potential impurities. An aliquot of 450 μL of Binding Buffer was used to capture DNA by vortexing thoroughly and then centrifuging for 1 min at 11,000 × g. Then 400 and 700 μL of Wash Buffer PAW1 and PAW2 respectively were added at independent steps to purify DNA, centrifuged for 1 min at 11,000 × g to remove the wash buffer and to dry the silica membrane completely. An aliquot of 50 μL of Elution Buffer was used to elute DNA into a 1.5-mL Eppendorf tube.
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