Genetic Linkage in Humans





When the loci of two genes are on the same chromosome, they are said to be syntenic. When they are on the same chromosome, and are close enough together that they do not segregate independently, they are said to be linked. Linkage is a powerful tool in modern genetic counseling. In many families it allows predictions of an outcome rather than probabilities of an outcome.

The human genome project now occupies a major effort of the human genetics community. Its first goal is to establish the precise chromosomal locus for each known Mendelian genetic trait, as well as any other “marker” loci. These “marker” loci may help to understand the inheritance of multifactorial traits, or they may be helpful in refining recurrence risk estimates in some families. This first goal is to be completed in two steps: first establish a genetic map and second convert the genetic map into a physical map of precise chromosomal position for each gene. This goal is supported by a vast majority of human geneticists. The second, and more controversial goal of the human genome project is to establish a complete DNA sequence for each chromosome.

Linkage studies in experimental organisms quickly led to the accumulation of rather complete maps of loci on individual chromosomes. The constraints of small family size, the lack of available polymorphic loci for normal variation, and random mating patterns has delayed the establishment of linkage maps in humans until new techniques beyond those of classical Mendelian genetics were developed. These techniques are now available.

However, human linkage studies, no matter how complex, like those in experimental organisms are based upon the consequences of the chromosomal movement and recombination in meiosis. The student would do well to review the events of the first meiotic division and their consequences.


Mendelian inheritance patterns are sufficiently powerful to establish the fact that a gene lies on the X chromosome. We discussed X-linked dominant and X-linked recessive inheritance in Mendelian genetics. It is not difficult to establish that two traits are syntenic, that is, both traits show X-linked inheritance. In developing chromosomal maps the genetic distance between the various loci is the first thing that needs to be established.

If the two loci are far apart, so that a chiasma always occurs between them during first meiotic division, the genetic distance between them cannot be established even though they are syntenic. If, however, the two loci are sufficiently close together that recombination occurs, but not all the time, the genetic distance can be estimated. Figure 19 reviews the chromosomal movements and recombination of the two X chromosomes of the female in first meiotic division.

First meiotic division

Figure 19. Recombination of hemophilia A and glucose 6-phosphate dehydrogenase deficiency during first meiotic division of oogenesis, showing the four possible resulting gametes.

In A, the female is a double heterozygote for hemophilia B and glucose 6-phosphate dehydrogenase deficiency, two X-linked recessive traits. Only one pair of homologous chromosomes is shown. In B, the chromosomes have paired and two of the chromatids have exchanged parts, the result of a chiasma between the two loci. Only one chiasma is shown. At anaphase of first meiotic division the two centromeres will move to opposite poles. In C, the four resulting possible gametes of second meiotic division are shown. Gametes 2 and 3 are recombinants, gametes 1 and 4 are nonrecombinants, sometimes called parental types. Linkage distances are assigned on the basis that chiasma formation is random, that is, the farther apart the two loci, the more likely a chiasma will occur between them. With this assumption, which has proven to be approximately true, the ratio of recombinants to nonrecombinants gives an indication of the genetic distance between the two loci. If 5% of the gametes are like chromosome 2 and 5% are like chromosome 3, then there is 10% recombination. The two loci are said to be linked at a distance of 10 centimorgans. (1% recombination equals 1 centimorgan, named for T.H. Morgan, the first to discover linkage.) The theoretical maximum distance that can be measured in genetic studies is 50 centimorgans, or 50% recombination. At this distance all four of the gametic products of a double heterozygote would have an equal chance of appearing, just as they would have if they were on different chromosomes with independent assortment. In actual practice, with the relatively small size of human families, greater distances than 25 centimorgans are extremely difficult to measure.

When the two recessive alleles are on different homologs in the double heterozygote, as they are in Figure 19, linkage is said to be in repulsion, or trans. When they are on the same homologous chromosome in the double heterozygote, linkage is said to be in coupling, or cis. Unless the two loci are extremely close together, linkage in cis is equally likely as linkage in trans in the general population. There is no a priori reason to choose one over the other.

X-linkage distances in a pedigree are most easily estimated when a grandfather expresses both recessive genes. Since he has only one X chromosome, linkage must be in coupling. His daughters’ sons should be doubly affected or normal. Any grandson expressing only one trait must be a recombinant resulting from crossing over. A pedigree demonstrating the grandfather method of mapping is shown in Pedigree 10.

Grandfather method of mapping

Pedigree 10. The grandfather method of estimating linkage distances for X-linked traits. I-1 has hemophilia B and is color blind.

In Pedigree 10, I-1 is a color blind hemophiliac. He has the recessive allele for each trait. His sons will all be normal, since they receive his Y chromosome and their mother’s X chromosome. However, all of his daughters will be obligate carriers for both recessive alleles, hemophilia and color blindness. By chance, half of their sons should be normal and half should be doubly affected, if there is no recombination. I-1 has 8 grandsons through his daughters, two are normal, 5 are doubly affected, and one is color blind. III-4, the color blind child, is a recombinant. In this pedigree the best estimate of linkage distance is 12.5 centimorgans. Of course, several other families will have to be added to this sample for meaningfully accurate estimates to be made.


X-linkage is greatly simplified because there can be no recombination in the male. He has only one X chromosome and it is passed on intact to his daughters. In autosomal linkage studies, this does not hold. Recombination can, and does, occur in both oogenesis and spermatogenesis. Useful pedigrees for linkage studies using classical methods are quite limited. Other methods must be employed. These are discussed quite well in Gelehrter, Collins, and Ginsburg, 2nd ed., Chapters 9 and 10, and need not be replicated here. The student is referred to these chapters and is responsible for all of the material they contain. Sample questions from this material are included.

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