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Results for “nondestructive genotyping”

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PubMed2025

Nondestructive Larval Genotyping of Danio rerio for Mitochondrial and Nuclear DNA Genetics.

The rapid advancement of nuclear and mitochondrial genomic editing tools has created an urgent need for efficient, nonlethal larval genotyping methods in zebrafish (Danio rerio) research. This study optimizes and validates a nondestructive proteinase K digestion method for mitochondrial and nuclear DNA genotyping while characterizing its impact on larval survival and gene expression. Using optimized protocol parameters, we demonstrate successful amplification of different mitochondrial and nuclear genetic loci with consistently high sensitivity. Molecular validation through PCR, restriction fragment length polymorphism analysis, and Sanger sequencing confirmed the specificity and reliability of the extracted DNA. The method successfully detected C-to-T base edits in the mt-tl1 gene introduced using the FusX TALE Base editor system, demonstrating its applicability to gene editing studies. Both 48-well and optimized 96-well formats were used, enabling this approach to be deployed at scale. This optimized method enables researchers to correlate genotypes with phenotypes in longitudinal studies while maintaining specimen viability, particularly valuable for investigating early-onset mitochondrial diseases, and utilizes standard laboratory equipment and reagents, facilitating widespread adoption in zebrafish research while adhering to ethical principles in reducing animal mortality.

Animals↗

PubMed2004

Ice-cap. A high-throughput method for capturing plant tissue samples for genotype analysis.

High-throughput genotype screening is rapidly becoming a standard research tool in the post-genomic era. A major bottleneck currently exists, however, that limits the utility of this approach in the plant sciences. The rate-limiting step in current high-throughput pipelines is that tissue samples from living plants must be collected manually, one plant at a time. In this article I describe a novel method for harvesting tissue samples from living seedlings that eliminates this bottleneck. The method has been named Ice-Cap to reflect the fact that ice is used to capture the tissue samples. The planting of seeds, growth of seedlings, and harvesting of tissue are all performed in a 96-well format. I demonstrate the utility of this system by using tissue harvested by Ice-Cap to genotype a population of Arabidopsis seedlings that is segregating a previously characterized mutation. Because the harvesting of tissue is performed in a nondestructive manner, plants with the desired genotype can be transferred to soil and grown to maturity. I also show that Ice-Cap can be used to analyze genomic DNA from rice (Oryza sativa) seedlings. It is expected that this method will be applicable to high-throughput screening with many different plant species, making it a useful technology for performing marker assisted selection.

Genetic Techniques↗

PubMed2006

Perennial Ryegrass (Lolium perenne L.).

A protocol that facilitates rapid establishment of Agrobacterium-mediated transformation for perennial ryegrass is described. The synthetic green fluorescent protein (sgfpS65T) reporter gene is introduced in combination with the nptII selectable marker gene into axillary bud derived embryogenic calli of perennial ryegrass (Lolium perenne L.) by co-cultivation with Agrobacterium tumefaciens strain AGL0 harboring binary vector pYF132. Following the co-cultivation calli are cultured for 48 h in liquid callus medium containing timentin at 10 degrees C and 70 rpm, which reduces Agrobacterium overgrowth. Using green fluorescent protein (GFP) as a nondestructive visual marker allows identification of responsive genotypes and transgenic cell clusters at an early stage. GFP screening is combined with paromomycin selection to suppress wild type cells. Transgenic plantlets ready to transfer to soil are obtained within 4 mo of explant culture. Between 8 and 16% of the Agrobacterium-inoculated calli regenerate independent, Southern positive transgenic plants. Reproducibility and efficiency in this perennial ryegrass transformation protocols is controlled by multiple factors including genotype dependent tissue culture and gene transfer response, a short tissue culture-and-selection period and the efficient suppression of Agrobacterium following Agrobacterium-mediated gene transfer.

Agrobacterium tumefaciens↗

PubMed1975

Potential for nitrogen fixation in maize genotypes in Brazil.

N(2) fixation in field-grown maize (Zea mays L.) plants was estimated by a nondestructive acetylene reduction method which permitted the plants to continue growing and produce seeds. Samples from six areas revealed mean nitrogenase activities of 74-2167 nmol of C(2)H(4)/(g of dry roots x hr) for 10 plants. Among 276 S(1) lines planted in two field experiments, 17 lines were selected for further nitrogenase activity assays after prescreening. Variability within lines was high but significant differences among lines were obtained in one experiment. The best lines showed mean nitrogenase activities of 2026, 2315, and 7124 nmol of C(2)H(4)/(g of dry roots x hr), whereas the original cultivar reduced only 313 nmol. The highest value approaches the nitrogenase activity of soybean. If the theoretical 3:1 (C(2)H(4)/N(2) reduced) conversion factor is used, a potential daily N(2) fixation of 2 kg of N(2)/hectare can be calculated. Periodic sampling within a brachytic maize cultivar revealed that maximum nitrogenase activity occurred at about the 75% silking stage. Soil effects also were pronounced. N(2)-fixing Spirillum sp. could be isolated from all active root pieces when they were surface sterilized. These organisms appear to be primarily responsible for root nitrogenase activity in maize.

Journal Article↗