Genome Editing: the smartest toolbox for genetic modification of plants

Vocabulary flashcards covering key terms, concepts, and individuals from the lecture notes on genome editing, CRISPR technologies, wheat blast, and related regulatory and agricultural applications.

Genome editing

Deliberate modification of an organism’s DNA at specific locations using tools like CRISPR, ZFN, or TALENs.

CRISPR-Cas9

A programmable genome editing system using the Cas9 nuclease guided by RNA to cut DNA at a target site near a PAM.

Cas9

The nuclease protein that cleaves DNA at a site specified by a guide RNA and PAM.

crRNA

CRISPR RNA containing the sequence that guides Cas9 to the target DNA.

tracrRNA

RNA that pairs with crRNA and is required for Cas9 activity.

sgRNA

Single guide RNA combining crRNA and tracrRNA into one molecule to guide Cas9.

PAM

Protospacer Adjacent Motif; a short DNA sequence required next to the target for Cas9 binding.

NGG PAM

A PAM sequence (N = any base; GG) recognized by SpCas9.

Double-strand break

A break in both strands of DNA created by Cas9 at the target site.

NHEJ

Non-Homologous End Joining, a quick repair pathway often creating insertions/deletions at breaks.

HDR

Homology-Directed Repair, a precise repair pathway using a donor template to introduce edits.

ZFN

Zinc Finger Nuclease; an early programmable nuclease platform for genome editing.

TALENs

Transcription Activator-Like Effector Nucleases; programmable DNA-cutting enzymes.

Base editing

Editing single bases without creating a double-strand break.

Cytidine deaminase (CBE)

Enzyme used in cytidine base editors to convert C to T (on the opposite strand, G to A).

TadA

A deaminase used in ABEs to convert A to G.

TadA*

Engineered TadA variant that improves A-to-G editing efficiency.

ABE

Adenine Base Editor; converts A to G without DNA breaks.

nCas9

Cas9 nickase that cuts only one DNA strand, reducing double-strand breaks.

Prime editing

Editing method using a Cas9 nickase fused to reverse transcriptase and a pegRNA to install precise edits without DSBs.

pegRNA

Prime editing guide RNA that directs reverse transcription for the edit.

Cas12a (Cpf1)

Alternative CRISPR nuclease with different PAMs and staggered cuts.

Cas9 nuclease

Enzyme in CRISPR-Cas9 that cleaves DNA at a targeted site.

Magnaporthe oryzae

Fungal pathogen that causes wheat blast.

Wheat blast

Devastating fungal disease of wheat that can spread globally.

First wheat blast outbreak in Bangladesh 2016

Initial major outbreak in BD causing extensive yield loss.

SHMA gene

Small heavy metal-associated gene studied in wheat blast resistance work.

S-gene (susceptibility gene)

Gene whose alteration can modify plant susceptibility or resistance to disease.

MLO locus

Genetic locus linked to disease susceptibility; mutations can confer resistance.

Doubled Haploids (DH)

Plants produced from a single gamete to create fully homozygous lines in one generation.

Speed breeding

Accelerating plant generation time using extended light periods and controlled conditions.

Speed breeding 2.0

Advanced speed breeding with LEDs and optimized conditions for faster cycles.

Doubled Haploid production

Process to generate doubled haploids for rapid pure-line development.

Genomic selection

Prediction of breeding values using genome-wide marker data to speed improvement.

High-throughput sequencing

Rapid sequencing technologies enabling analysis of many samples quickly.

PlotVision

Digital field imaging and remote sensing platform for phenotyping in breeding.

Marker-assisted selection

Breeding using DNA markers linked to desirable traits.

CRISPR advantages over ZFN/TALEN

Cheaper, easier to design, multiplexable, and enabling heritable edits.

Multiplexed genome editing

Editing multiple genomic sites simultaneously in a single step.

Cpf1 (Cas12a) vs Cas9

Cas12a is an alternative nuclease with different PAMs and cut patterns.

Transgene-free CRISPR crops

CRISPR-edited crops that do not carry foreign DNA and may escape GM regulation.

CRISPR-based diagnostics

Using CRISPR systems to detect pathogens via nucleic acid recognition.

Lateral Flow Assay (LFA)

Paper-based strip test used for rapid CRISPR diagnostics at the point of care.

RPA (Recombinase Polymerase Amplification)

Isothermal DNA amplification method used in rapid diagnostics.

CRISPR-Cas9 in plant breeding

Application of CRISPR to accelerate crop improvement and trait development.

Casgevy

FDA-approved CRISPR-based therapy for sickle cell disease.

Lyfgenia

FDA-approved gene therapy for sickle cell disease employing gene-editing concepts.

FDA approval 2023

First cell-based gene therapies for sickle cell disease approved by FDA.

Doudna

Emmanuelle Doudna, co-discoverer of CRISPR-Cas9; Nobel Prize 2020 co-winner.

Charpentier

Emmanuelle Charpentier, co-discoverer of CRISPR-Cas9; Nobel Prize 2020 co-winner.

Jinek et al. 2012 Science

Paper showing programmable Cas9 endonuclease guided by RNA.

Holley

Robert W. Holley; Nobel Prize 1968 for work on the genetic code.

Khorana

Har Gobind Khorana; Nobel Prize 1968 for decoding the genetic code.

Nirenberg

Marshall W. Nirenberg; Nobel Prize 1968 for deciphering the code.

Codon

Three-nucleotide DNA (or RNA) unit that encodes an amino acid.

DNA bases A, T, G, C

The four nucleotides that make up DNA: adenine, thymine, guanine, cytosine.

DNA double helix (1953)

Discovery of the helical structure of DNA by Watson, Crick, and Wilkins.

Rosalind Franklin

Scientist whose X-ray work contributed to solving DNA structure.

Beadle-Tatum-Lederberg (1958)

Founders describing DNA as containing information to build proteins and govern function.

Transcriptomic analyses

Study of RNA transcripts to understand gene expression patterns.

South American lineage of Magnaporthe oryzae

Origin of the wheat blast pathogen introduced to Asia and Africa.

Open Wheat Blast website

Platform for rapid sharing of data on wheat blast outbreaks.

DRR Rice 100 Kamala

India’s genome-edited rice variety released for cultivation.

Pusa DST Rice 1

India’s genome-edited rice variety released for cultivation.

DS Faraday

Australia’s first high-protein milling wheat developed via speed breeding.

BSMRAU

Bangabandhu Sheikh Mujibur Rahman Agricultural University.

GAU/IBGE

Gazipur Agricultural University; Institute of Biotechnology and Genetic Engineering.

Codon (reiteration)

Triplet in DNA/RNA that specifies an amino acid during translation.

DNA base pairing (A–T, G–C)

Complementary base pairing rules underpin DNA structure and replication.

1953 DNA discovery

Identification of the DNA double helix structure by Crick, Watson, and Wilkins.

Nobel Prize 1962 (DNA structure)

Award recognizing the discovery of the DNA double-helix model.

CRISPR immune system

Bacterial adaptive immune system that protects against viruses using RNA-guided interference.

DRR Rice 100 Kamala (summary)

See DRR Rice 100 Kamala above.

Pusa DST Rice 1 (summary)

See Pusa DST Rice 1 above.

SCD (sickle cell disease) therapy

Cell-based gene therapies aiming to correct the sickle cell mutation.

Open data sharing in plant pathology

Encourages rapid data exchange to combat outbreaks like wheat blast.

CRISPR in human therapy

Clinical use of CRISPR-based edits to treat human diseases.

Glyph of Nobel prize names (Holley, Khorana, Nirenberg)

Pioneers associated with deciphering the genetic code.

Nature Plants 2018 (context)

Reference to CRISPR and speed-breeding research presented in high-profile journals.

Silencing of invading nucleic acids

CRISPR mechanism by which bacteria deactivate foreign DNA.

Hub: IBGE GAU collaboration

Joint program between IBGE and GAU focusing on genome editing in crops.

Genomic editing in crops

Use of CRISPR-based tools to improve crop traits like yield and disease resistance.

Genome editing and climate resilience

Applying editing to develop crops tolerant to drought, heat, and pests.

CRISPR-Cas9 market relevance

Emerging industry applications in agriculture and medicine.

DNA repair templates

Templates used in HDR to introduce precise edits.

CRISPR off-target effects

Unintended edits at sites similar to the intended target (a consideration in editing).

Ethical/regulatory landscape for gene editing

Policies governing use of gene-editing in crops and medicines.

CRISPR in Bangladesh (GAU/IBGE activity)

Local research activity applying CRISPR to crops in BD.