Chapter 4 - Mapping Eukaryote Chromosomes by Recombination

• Gene position is crucial information needed to build complex genotypes required for experimental purposes or for commercial applications.
• Knowing the position occupied by a gene provides a way of isolating it and discovering its structure and function.
• The DNA sequence of a wild-type gene or its mutant allele is a necessary part of deducing its underlying function.
• The genes present and their arrangement on chromosomes are often slightly different in related species.
• Chromosome maps are useful in interpreting mechanisms of evolution.
• The arrangement of genes on chromosomes is represented diagrammatically as a unidimensional chromosome map, showing gene positions known as loci (sing., locus), and the distances between the loci based on some kind of scale.
• Two basic types of chromosome maps are currently used in genetics; they are assembled by quite different procedures yet are used in a complementary way.
• Recombination-based maps map the loci of genes that have been identified by mutant phenotypes showing single-gene inheritance.
• Physical maps show the genes as segments arranged along the long DNA molecule that constitutes a chromosome.
• These maps show different views of the genome, but, just like the maps of London, they can be used together to arrive at an understanding of what a gene’s function is at the molecular level and how that function influences phenotype.
• Genetic maps are useful for strain building, for interpreting evolutionary mechanisms, and for discovering a gene’s unknown function.
• Linkage is suggested by a F 1 dihybrid with female parental type pr + / pr + and male parental type vg / vg ×.
• Dihybrid testcross results follow the general pattern: when two genes are close together on the same chromosome pair, they do not assort independently but produce a recombinant frequency of less than 50 percent, indicating linkage.
• The linkage hypothesis explains why allele combinations from the parental generations remain together: the genes are physically attached by the segment of chromosome between them.
• Morgan suggested that, when homologous chromosomes pair at meiosis, the chromosomes occasionally break and exchange parts in a process called crossing over.
• Crossing over produces new allelic combinations.
• Chiasmata are the visible manifestations of crossovers.
• For linked genes, recombinants are produced by crossovers between nonsister chromatids during meiosis.
• Chiasmata are located where the chromosomes are physically attached to one another.
• The work of Morgan showed that linked genes in a dihybrid may be present in one of two basic conformations: cis conformation, where the two dominant, or wild-type, alleles are present on the same homolog, and trans conformation, where they are on different homologs.
• Alleles on the same homolog have no punctuation between them.
• A slash symbolically separates the two homologs.
• Alleles are always written in the same order on each homolog.
• Dihydrid selfed (independent assortment), 9 to 3 to 3 to 1.
• Trihybrid testcrossed (independent assortment), 1 to 1 to 1 to 1 to 1 to 1 to 1 to 1.
• Single gene inheritance and two-gene inheritance (linked and unlinked) can be inferred from diagnostic phenotypic ratios in both selfing and testcrossing.
• Phenotypic markers mark certain points on the chromosome that can produce visibly different phenotypes in the outward appearance of progeny.
• Molecular markers are loci showing neutral simple DNA sequence differences, perhaps a G-C base pair replaced by a T-A base pair, or loci showing variable numbers of tandem (adjacent) repeats of short, simple DNA sequences.
• Both simple sequence differences and repeated DNA differences are highly polymorphic; there are often many “alleles” of each marker in the population.
• Molecular markers can be mapped by recombinant frequency in exactly the same way as phenotypic markers.
• The location of the gene for the human disease cystic fibrosis was originally discovered through its linkage to molecular markers known to be located on chromosome 7.
• The gene for Huntington disease was also located in this way, leading to the discovery that it encodes a muscle protein now called huntingtin.
• The general experimental procedure for mapping genes with molecular markers involves assuming that the cross is A / a ⋅ M1/M2 × a / a ⋅ M1/M1, a kind of testcross.
• Discovering a gene’s function is facilitated by integrating information on recombination-based and physical maps.
• In 1911, Sturtevant suggested that the variations in strength of linkage, already attributed by Morgan to differences in the spatial separation of genes, offered the possibility of determining sequences in the linear dimension of a chromosome.
• The recombinant frequency would be (37 + 41)/200 = 78/200 = 39 percent, or 39 m.u.
• Sturtevant spent most of the night producing the first chromosome map after realizing the potential of Morgan's testcross results with the pr and vg genes.
• The probability of a chance deviation of this magnitude from a 1:1:1:1 ratio can be calculated using the χ (chi-square) test.
• Sturtevant defined one genetic map unit (m.u.) as that distance between genes for which 1 product of meiosis in 100 is recombinant.
• The recombinant frequency (RF) of 10.7 percent obtained by Morgan is defined as 10.7 m.u.