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8.4: Genetic linkage and Genetic Maps

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    Figure 8.4.1 Dihybrid Cross

    Mendel then crossed these dihybrids. If it is inevitable that round seeds must always be yellow and wrinkled seeds must be green, then he would have expected that this would produce a typical monohybrid cross: 75% round-yellow; 25% wrinkled-green. But, in fact, his mating generated seeds that showed all possible combinations of the color and texture traits.

    • 9/16 of the offspring were round-yellow
    • 3/16 were round-green
    • 3/16 were wrinkled-yellow, and
    • 1/16 were wrinkled-green

    Rule of Independent Assortment

    Finding in every case that each of his seven traits was inherited independently of the others, he formed his "second rule" the Rule of Independent Assortment:

    The inheritance of one pair of factors (genes) is independent of the inheritance of the other pair.

    Today we know that this rule holds only if two conditions are met:

    • the genes are on separate chromosomes or
    • the genes are widely separated on the same chromosome.

    Mendel was lucky in that every pair of genes he studied met one requirement or the other. The table shows the chromosome assignments of the seven pairs of alleles that Mendel studied. Although all of these genes showed independent assortment, several were, in fact, syntenic with three loci occurring on chromosome 4 and two on chromosome 1. However, the distance separating the syntenic loci was sufficiently great that the genes were inherited as though they were on separate chromosomes.

    Trait Phenotype Alleles Chromosome
    Seed form round-wrinkled R-r 7
    Seed color yellow-green I-i 1
    Pod color green-yellow Gp-gp 5
    Pod texture smooth-wrinkled V-v 4
    Flower color purple-white A-a 1
    Flower location axial-terminal Fa-fa 4
    Plant height tall-dwarf Le-le 4
    Figure 8.4.2. Linkage in corn

    Start with two different strains of corn (maize).

    • one that is homozygous for two traits
      • yellow kernels (C,C) which are filled with endosperm causing the kernels to be
      • smooth (Sh,Sh).
    • a second that is homozygous for
      • colorless kernels (c,c) that are wrinkled because their endosperm is
      • shrunken (sh,sh)

    When the pollen of the first strain is dusted on the silks of the second (or vice versa), the kernels produced (F1) are all yellow and smooth. So the alleles for yellow color (C) and smoothness (Sh) are dominant over those for colorlessness (c) and shrunken endosperm (sh).

    To simplify the analysis, mate the dihybrid with a homozygous recessive strain (ccshsh). Such a mating is called a test cross because it exposes the genotype of all the gametes of the strain being evaluated.

    According to Mendel's second rule, the genes determining color of the endosperm should be inherited independently of the genes determining texture. The F1 should thus produce gametes in approximately equal numbers.

    • CSh, as inherited from one parent.
    • csh, as inherited from the other parent
    • Csh, a recombinant
    • cSh, the other recombinant.
    Figure 8.4.4 Plot Linkage

    In fact, the recombination frequency is 2.0%, telling us that the actual order of loci is

    Mapping by linkage analysis is best done with loci that are relatively close together; that is, within a few centimorgans of each other. Why? Because as the distance between two loci increases, the probability of a second crossover occurring between them also increases.

    But a second crossover would undo the effect of the first and restore the parental combination of alleles. These would show up as nonrecombinants. Thus as the distance between two loci increases, the percentage of recombinants that forms understates the actual distance in centimorgans that separates them. And, in fact, that has happened in this example. Using a three-point cross reveals the existence of a small number of double recombinants and tells us that the actual distance c—bz is indeed 5 cM as we would expect by summing

    • c—sh = 3 cM
    • sh—bz = 2 cM

    and not the 4.6 cM revealed by the dihybrid cross.

    A three-point cross also tells us the gene order in a single cross rather than the three we needed here.

    There are other problems with preparing genetic maps of chromosomes.

    • The probability of a crossover is not uniform along the entire length of the chromosome.
      • Crossing over is inhibited in some regions (e.g., near the centromere).
      • Some regions are "hot spots" for recombination (for reasons that are not clear). Approximately 80% of genetic recombination in humans is confined to just one-quarter of our genome.
    • In humans, the frequency of recombination of loci on most chromosomes is higher in females than in males. Therefore, genetic maps of female chromosomes are longer than those for males.
    Figure 8.4.5 Genetic Map of Chromosome 9

    A genetic map of chromosome 9 (the one that carries the C, Sh, and bz loci) of the corn plant (Zea mays) is shown above. If one maps in small intervals from one end of a chromosome to the other, the total number of centimorgans often exceeds 100 (as you can see for chromosome 9). However, even for widely-separated loci, the maximum frequency of recombinants that can form is 50%. And this is also the frequency of recombinants that we see for genes independently assorting on separate chromosomes. So we cannot tell by simply counting recombinants whether a pair of gene loci is located far apart on the same chromosome or are on different chromosomes. As we saw above, several of Mendel's independently assorting traits are controlled by genes on the same chromosome but located so far apart that they are inherited as if they were located on different chromosomes.

    Genes that are present on the same chromosome are called syntenic.

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