LAISHA Explains
Genetics and plant breeding

Mutation and mutation breeding

Gene and chromosome mutations, physical and chemical mutagens, the M1 to M3 steps of mutation breeding, famous mutant varieties, and a population sum.

Exam essential5 min readUpdated
On this page
  1. What a mutation is
  2. Kinds of mutation
  3. Mutagens
  4. How mutation breeding works
  5. Notable mutant varieties
  6. Strengths and limits
  7. Key points
  8. What the exams ask
  9. Questions people ask
  10. Sources
  11. Related on Laisha
  12. Discussion

All genetic variation, the raw material of evolution and of plant breeding, ultimately comes from mutation: a heritable change in DNA. Most mutations are harmful or neutral, but a few create useful traits, such as a shorter stem, a new grain quality or tolerance of a herbicide. Since the 1920s, breeders have deliberately increased the mutation rate with radiation and chemicals, and then searched the treated populations for useful changes. More than 3,000 crop varieties bred this way have been released worldwide.

Mutation and mutation breeding are standard topics in genetics and plant breeding exams.

What a mutation is

A mutation is any heritable change in the DNA sequence or in chromosome structure or number. Mutations can be:

  • Spontaneous, from errors in DNA replication or natural damage; typical rates are about one in 100,000 to one in a million per gene per generation.
  • Induced, by mutagens such as radiation or chemicals.
  • Somatic (in body cells, inherited only through vegetative propagation, which is how many bud sports of fruit trees arise) or germinal (in cells that form gametes, passed to seed progeny).

Hugo de Vries coined the term in 1901. H. J. Muller showed in 1927 that X-rays cause mutations in fruit flies, and L. J. Stadler showed the same in barley and maize in 1928.

Kinds of mutation

Gene (point) mutations

  • Substitutions: one base replaced by another. A transition swaps a purine for a purine or a pyrimidine for a pyrimidine (A↔G, C↔T); a transversion swaps a purine with a pyrimidine.
  • Silent: the codon still codes for the same amino acid.
  • Missense: a different amino acid.
  • Nonsense: a stop codon, truncating the protein.
  • Insertions and deletions (indels): unless they involve multiples of three bases, they shift the reading frame and usually destroy the protein.

Chromosomal mutations

  • Deletion (loss of a segment), duplication, inversion (a segment reversed), and translocation (a segment moved to another chromosome).
  • Changes in number: aneuploidy (gain or loss of single chromosomes) and polyploidy (whole extra sets), covered in a separate article.

Mutagens

TypeExamplesTypical effects
Ionising radiationgamma rays (from cobalt-60 or caesium-137), X-rays, fast neutrons, ion beamsDNA breaks; deletions and chromosomal rearrangements as well as point mutations
Non-ionising radiationultraviolet lightpyrimidine dimers; used for pollen and microbes, as it penetrates poorly
Alkylating chemicalsethyl methanesulfonate (EMS), methyl nitrosoureamainly point mutations; EMS causes mostly G/C to A/T transitions
Azidessodium azidepoint mutations, very effective in barley
Base analogues and others5-bromouracil, acridine dyessubstitutions and frameshifts; used mainly in microbes

The dose is set so that enough mutations occur without killing too many plants, often by finding the dose that reduces seedling growth or survival by about 30 to 50 per cent in a pilot test (the GR30–GR50 or LD50 range).

How mutation breeding works

Steps in mutation breeding of a seed crop: seed is treated with radiation or a chemical mutagen; the M1 plants grown from it are chimeric and partly sterile; in the M2 generation recessive mutations appear as homozygous plants and are screened for; desirable mutants are confirmed and made pure in M3 to M5, then tested in yield trials and released Treat seedgamma rays, X-rays,EMS, sodium azide M1plants are chimeric;some sterility M2mutations segregate;screen for the trait M3–M5confirm andmake pure lines Trialsyield, quality,release a variety Why screen in M2, not M1? A new mutation is usually recessive and present in only one copy (Aa) in part of an M1 plant. Its selfed M2 offspring segregate, and about a quarter of the progeny from the mutated sector are aa, so the new trait can be seen. Because M1 plants are chimeric, the overall fraction in M2 is usually lower than a quarter.
Mutation breeding of a seed-propagated crop, from treated seed to a released variety.Diagram: Laisha, original.
  1. Treat seed, pollen, buds or tissue cultures with a mutagen.
  2. M1 generation: plants grown from treated seed are chimeric, made of mutated and unmutated cell lineages, and often show reduced fertility and growth; mutations are mostly recessive and heterozygous, so few new traits appear.
  3. M2 generation: progeny of self-pollinated M1 plants. Recessive mutations now appear in homozygous form. This is where most screening happens, often among thousands to hundreds of thousands of plants.
  4. M3 to M5: confirm that selected mutants breed true, remove unwanted background mutations by selection or backcrossing, and evaluate them.
  5. Trials and release, or use of the mutant as a parent in crossing programmes.

For vegetatively propagated crops, such as banana, citrus, apple and ornamentals, buds or cuttings are treated and mutated sectors are separated by repeated propagation until stable mutant plants are obtained.

Modern refinements

  • TILLING (Targeting Induced Local Lesions in Genomes), developed around 2000, screens mutagenised populations with DNA methods to find mutations in a chosen gene.
  • Whole-genome sequencing of mutants speeds up finding the causal mutation.
  • Gene editing now creates targeted mutations, complementing random mutagenesis.

Notable mutant varieties

The FAO/IAEA Mutant Variety Database lists more than 3,300 officially released mutant varieties in over 200 species. Examples:

  • Calrose 76 rice (USA, 1976), a semi-dwarf from gamma-ray treatment, parent of many later Californian rice varieties.
  • Golden Promise barley (Scotland, 1966), a gamma-ray semi-dwarf important for malting and for barley research.
  • Rio Red and Star Ruby grapefruits (Texas), deep red-fleshed mutants from irradiated buds.
  • High-oleic sunflower (Pervenets, USSR, 1970s), from a chemical mutant, the origin of most high-oleic sunflower oil.
  • Imidazolinone-tolerant crops (Clearfield rice, wheat, canola and sunflower), from mutations in the ALS gene.
  • Many durum wheat, chickpea, mungbean, groundnut, jute and ornamental varieties in Europe and Asia.
Worked example

How many M2 plants should be screened?

A breeder wants a mutant that occurs on average in one of every 2,000 M2 plants, and wants a 95 per cent chance of finding at least one.

The chance of not finding it in n plants is (1 − 1⁄2,000)n. Setting this to 0.05:

  • n = ln(0.05) ÷ ln(1 − 0.0005) = −2.996 ÷ −0.0005001 ≈ 5,990 plants.

For a 99 per cent chance: n = ln(0.01) ÷ −0.0005001 ≈ 9,210 plants. Large M2 populations, and efficient screening methods, are the key to success.

Strengths and limits

Strengths:

  • Creates new alleles not found in existing germplasm.
  • Can improve one trait in an otherwise excellent variety.
  • Mutant varieties are not regulated as genetically modified organisms in most countries, and many are accepted in organic production.

Limits:

  • Most mutations are harmful; useful ones are rare.
  • Many unwanted background mutations must be removed.
  • Recessive mutations in polyploids such as wheat are masked by duplicate genes, so screening is harder.
  • Large populations and careful screening are costly.

Key points

  • Mutation is a heritable change in DNA; spontaneous rates are about 10−5 to 10−6 per gene per generation.
  • Gene mutations: substitutions (silent, missense, nonsense; transitions and transversions) and frameshift indels; chromosomal: deletion, duplication, inversion, translocation, and changes in number.
  • Mutagens: gamma rays, X-rays, fast neutrons, EMS, sodium azide.
  • M1 plants are chimeric; screening for recessive mutants starts in M2.
  • Over 3,300 mutant varieties are listed, including Calrose 76 rice, Golden Promise barley and Rio Red grapefruit.
  • Population size for finding a mutant: n = ln(1 − P) ÷ ln(1 − f).

What the exams ask

  • School-leaving and entrance papers: types of mutation and mutagens, and examples of mutant varieties.
  • Degree and research-fellowship entrances: molecular basis of mutation, M1–M3 handling, chimeras, dose selection, mutation breeding in seed and vegetatively propagated crops, and TILLING.
  • Research and professional examinations: mutation breeding versus gene editing, regulation of mutant varieties, and screening strategies.

Described in general terms: the kind of examination, not a past paper. Laisha never reproduces exam questions.

Questions people ask

Are crops bred with radiation radioactive?

No. The seeds or buds are exposed to radiation briefly, which changes their DNA, but they do not become radioactive, and the food from them is the same as from any other variety.

Why are most mutations recessive?

Most mutations damage a gene's function. One working copy usually makes enough product, so the effect only shows when both copies are damaged.

How is mutation breeding different from gene editing?

Mutation breeding makes many random changes across the genome and screens for useful ones. Gene editing makes a targeted change in a chosen gene, with far fewer other changes.

Sources

  1. FAO/IAEA. Mutant Variety Database (MVD). Joint FAO/IAEA Centre of Nuclear Techniques in Food and Agriculture, online.
  2. Spencer-Lopes, M. M., Forster, B. P. and Jankuloski, L. (eds) Manual on Mutation Breeding, 3rd edition. FAO, 2018.
  3. Muller, H. J. "Artificial transmutation of the gene." Science 66, 84–87 (1927).
  4. McCallum, C. M., Comai, L., Greene, E. A. and Henikoff, S. "Targeted screening for induced mutations." Nature Biotechnology 18, 455–457 (2000).
  5. Ahloowalia, B. S., Maluszynski, M. and Nichterlein, K. "Global impact of mutation-derived varieties." Euphytica 135, 187–204 (2004).

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Discussion

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