Plant Genetic Mapping Techniques

Abstract

Plant genetic maps are graphic representations of the organisation of chromosomes. These genetic maps are used in several applications to link a phenotype to a gene or a region on a chromosome. While genetic maps were classically dependent on morphological markers, recent advances in technology have allowed modern maps to be composed of hundreds to thousands of molecular markers. Since many plants have the ability to self‐fertilize, several different types of population structures can be created to facilitate genetic linkage map construction. Polyploidy and aneuploidy are also common in plants and require modified techniques that increase genetic mapping complexity or help facilitate marker placement onto chromosomes.

Key Concepts

  • Plant genetic maps are the foundation of many techniques used to map genes that contribute to plant traits.
  • Classical genetic maps provided the basis for determining the linkage order and distance between genes but were limited by the number of observable markers available.
  • Advances in modern molecular techniques have led to the ability to create genetic maps that contain thousands of markers.
  • The ability of plants to self‐fertilize allows for multiple population structures to be used for creating genetic maps.
  • Since polyploidy and aneuploidy are present in plants, modified techniques are required to create genetic maps.

Keywords: genetic maps; genetic variation; DNA markers; recombination; polyploid; aneuploid

Figure 1. Synapsed homologous chromosome pair of an AaCcSs female. The crossover observed produces new gene combinations between the A,a and C,c loci.
Figure 2. Crossovers between the C,c and S,s loci will occur less often because of the distance between these loci. Generating large numbers of offspring will reveal individuals with the Cs or cS recombinants.
Figure 3. (a) Depiction of chromosome 1 based on data from Emerson . (, Table 1). parent was in repulsion phase. Crossover depicted would produce only Xy and xY gametes, the parental combination. P locus was homozygous and thus could not be used to detect recombinants. (b) Depiction of chromosome 1 based on data from Emerson . (, Table 1). parent was in repulsion phase. Crossover depicted would produce Xy and xY gametes, the parental combination and also produce xy and XY recombinant gametes. P locus was homozygous and thus could not be used to detect recombinants.
Figure 4. (a) Depiction of chromosome 1 based on data from Emerson . (, Table 1). parent was in coupling phase. Crossover depicted would produce XY and xy gametes, the parental combination and also produce xY and Xy recombinant gametes. Gs1 locus was homozygous and thus could not be used to detect recombinants. (b) Depiction of chromosome 1 based on data from Emerson . (, Table 1). parent was in coupling phase. Crossover depicted would produce XY and xy gametes, the parental combination and also produce xY and Xy recombinant gametes. Gs1 locus was homozygous and thus could not be used to detect recombinants.
Figure 5. Linkage map for chromosome 1 showing the order and distance between seven loci controlling seed and plant phenotypes from Emerson . ().
Figure 6. An illustration of the logical approach to assembling a linkage map of seven loci based on the recombination frequency data assembled by Emerson . ().
Figure 7. Genetic variation between two plant individuals converted into molecular markers. (a) DNA sequence of two plants that have a difference in the number of AT repeats and a single nucleotide polymorphism (SNP). (b) The difference in AT repeats can be converted into a gel marker by designing PCR primers that flank the AT repeat, amplifying the DNA, and running the amplified DNA on an agarose gel to separate the size difference between the two individuals. (c) The SNP is converted into a DNA marker through direct sequencing. This trace shows a T/C polymorphism at basepair 168 in the sequence trace.
Figure 8. Development of mapping populations. Crossing strategies for developing both RILs (recombinant inbred lines) and backcrosses (BCs) are shown.
Figure 9. Mapping with monosomics. Panels (a) and (b) represent an array of DNA samples. P1, P2 diploid parents; F1, progeny of P1 × P2; 1, …, 7, progeny of P1× monosomic derivatives of P2, each of which was missing a single chromosome. DNAs in each panel were amplified with primers targeting different EST sequences with unknown chromosomal location. The results indicate that the primer used in panel (a) came from chromosome 3 while the one used in panel (b) came from chromosome 6.
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References

Burnham CR and Brink RA (1932) Linkage relations of a second brown midrib gene (bm2) in maize. Agronomy Journal, 24 (12): 960–963.

Emerson RA, Beadle GW and Fraser AC (1935) A Summary of Linkage Studies in Maize. Ithaca, NY: Cornell University.

Forster BP and Thomas WTB (2005) Doubled haploids in genetics and plant breeding. In: Janick J (ed) Plant Breeding Reviews, vol. 25. Oxford, UK: John Wiley & Sons, Inc. DOI: 10.1002/9780470650301.ch3.

Henry IM, Dilkes BP and Comai L (2006) Molecular karyotyping and aneuploidy detection in Arabidopsis thaliana using quantitative fluorescent polymerase chain reaction. The Plant Journal 48: 307–319.

Li X, Wei Y, Acharya A, et al. (2014) A saturated genetic linkage map of autotetraploid Alfalfa (Medicago sativa L.) developed using genotyping‐by‐sequencing is highly syntenous with the Medicago truncatula genome. G3 4: 1971–1979.

Further Reading

Grover A and Sharma PC (2014) Development and use of molecular markers: past and present. Critical Reviews in Biotechnology. DOI: 10.3109/0738851.2014.959891.

Lynch M and Walsh B (1998) Principles of marker‐based analysis. Genetics and Analysis of Quantitative Traits, Vol. 1 pp. 379–430. Sunderland, MA: Sinauer Associates, Inc.

Semagn K, Bjørnstad A and Ndjiondjop MN (2006) Principles, requirements and prospects of genetic mapping in plants. African Journal of Biotechnology 5: 2569–2587.

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How to Cite close
Hyten, David L, and Lee, Donald J(May 2016) Plant Genetic Mapping Techniques. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0002019.pub2]