of pneumococcal types: induction of transformation by a desoxyribonucleic acid fraction isolated from pneumococcus type III. Journal of Experimental Medicine 79: 137–158.
Bellone, R.B., Forsyth, G., Leeb, T. et al. (2010) Fine mapping and mutation analysis of TRPM1, a candidate gene for Leopard Complex (LP) spotting and congenital stationary night blindness (CNSB) in horses. Briefings in Functional Genomics and Proteomics 9: 193–207.
Brooks, S.A. and Bailey, E. (2005) Exon skipping in the KIT gene causes the sabino spotting pattern in horses. Mammalian Genome 16: 893–902.
Brooks, S.A., Lear, T.L., Adelson, D.A. and Bailey, E. (2008) A chromosome inversion near the KIT gene and the tobiano spotting pattern in horses. Cytogenetics and Genome Research 119: 225–230.
Brooks, S.A., Gabreski, N., Miller, D. et al. (2010) Whole-genome SNP association in the horse: identification of a deletion in myosin Va responsible for lavender foal syndrome. PLoS Genetics 6(4): e1000909, doi: 10.1371/journal.pgen.1000909.
Choi, Y., Sims, G.E., Murphy, S., Miller, J.R. and Chan, A.P. (2012) Predicting the functional effect of amino acid substitutions and indels. PLoS ONE 7, e46688.
Cook, D., Brooks, S.A., Bellone, R. and Bailey, E. (2008) Missense mutation in exon 2 of SLC36A1 responsible for champagne dilution in horses. PLoS Genetics 4(9): e1000195.
Franklin, R.E. and Gosling, R.G. (1953) Molecular configuration in sodium thymonucleate. Nature 171: 740–741.
Kumar, P., Henikoff, S. and Ng, P.C. (2009) Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nature Protocols 4: 1073–1081.
Mariat, D., Taourit, S. and Guérin, G. (2003) A mutation in the MATP gene causes the cream coat color in the horse. Genetics Selection Evolution 35: 119–133.
Marklund, L., Johansson, M.M., Sandberg, K. and Andersson, L. (1996) A missense mutation in the gene for melanocyte-stimulating hormone receptor (MC1R) is associated with the chestnut coat color in horses. Mammalian Genome 7: 895–899.
Shin, E.K., Perryman, L.E. and Meek, K. (1997) A kinase negative mutation of DNA-PK(CS) in equine SCID results in defective coding and signal joint formation. Journal of Immunology 158: 3565–3569.
Watson, J.D. and Crick, F.H. (1953) Molecular structure of nucleic acids; a structure for deoxyribose nucleic acid. Nature 171: 737–738.
Wilkins, M.H., Stokes, A.R. and Wilson, H.R. (1953) Molecular structure of deoxypentose nucleic acids. Nature 171: 738–740.
5 The Language and Patterns of Genetics
Terminology allows people to communicate entire concepts with a single word. We noted at the beginning of Chapter 4 that the term “gene” was initially used as an abstract concept. Later, the molecular basis of a gene was determined, and its meaning became, at once, more complex and less abstract. In this chapter we introduce additional genetic terms, conventions, and formats useful to discuss the patterns of inheritance for genetic traits.
Genes and alleles
When a gene at a particular “locus” (the position of a gene on a chromosome) has two alternative forms (variants) we call these “alleles.” For example, the Extension locus has two alleles, one for black hair (E) and one for red hair (e). We have learned the underlying molecular mechanism is a result of variation at the gene MC1R (Marklund et al., 1996). This gene was used as an example in the preceding chapter and is discussed further in Chapter 7.
Gray is another gene which influences coat color. The Gray locus has two alleles, G for gray and g for non-gray. The Gray locus is different from the Extension locus and is caused by a variation in an entirely different gene (discussed in Chapter 12). The allele responsible for gray is not allelic to the colors red or black. It comes from a different locus with a different gene action. Gray is an entirely different property of hair color. However, Gray (G) is an allele for non-Gray (g) at the Gray locus. Black (E) and red (e) are alleles of each other at the Extension locus.
Genotypes: Homozygous and Heterozygous
As noted in the previous chapter, each parent transmits one of its two chromosomes to its offspring. Every horse has two copies of every autosomal gene, one from its sire and one from its dam. If the two copies are identical, then the horse is said to be homozygous. If the two alleles are different, then the horse is said to be heterozygous for that trait. Homozygous and heterozygous are terms that refer to the genotype of the horse. Genotype describes the specific alleles present in the horse and is useful to predict what the parent will pass to offspring. Genotype could be called “the genetic recipe” of the individual for the locus. For Extension, the genotypes E/E and e/e would be homozygous genotypes because both alleles are the same. Horses that possess two different alleles at a locus, for example E and e, (genotype E/e) are heterozygotes. The symbols for each of the two alleles, one from the sire and one from the dam, are separated by a slash (/) by convention.
Dominant and recessive; phenotype and genotype
The phenotype of a horse is its measurable appearance. The Extension locus has three genotypes but only two phenotypes (Table 5.1). Why are there three genotypes and two phenotypes? Because the variant for black pigment is dominant over the variant for red pigment. It only takes a single allele for black to allow the horse to make black pigment. There is no difference in appearance between a horse homozygous for E or one that is heterozygous E/e; both will be equally able to make black pigment. In the absence of the gene for black pigment the horse will have the recessive phenotype, chestnut (genotype e/e). If you mate two chestnut horses, the offspring will always be chestnut because there is no way for their offspring to inherit the E allele. However, if you mate two black horses, you might produce a chestnut offspring. This will only happen if both parents are heterozygous (E/e) and can transmit the variant for e to the offspring resulting in a horse homozygous for the chestnut allele (e/e). The relationship of alleles, homozygous, heterozygous, phenotype, and genotype are summarized in Table 5.1 using Extension as an example.
Table 5.1. Chart showing the relationship of genotype to phenotype for the different combinations of the alleles E and e of the Extension gene for coat color.
| Genotype | Phenotype |
| E/E (homozygous for E) | Black and red pigment |
| E/e (heterozygous, both E and e) | Black and red pigment |
| e/e (homozygous for e) | Red pigment only |
A dominant allele is always expressed
