Horse Genetics. Ernest Bailey

the DNA sequence into the protein (Chapter 15).

      Changes in gene expression (alternate splicing)

      A single nucleotide base change in the intronic splice site of the KIT gene causes an unusual transcript causing the sabino1 phenotype. For this variant, an entire exon is absent from the resulting protein. In this case the variant is a SNP that destroys the signal for creating the splice. However, since it is not in an exon, it is neither synonymous nor non-synonymous (Brooks and Bailey, 2005; Chapter 9).

      Chromosome inversions

      The Tobiano mutation, which causes white spotting (Brooks et al., 2008; Chapter 9), occurs well outside the gene thought to be responsible for the tobiano color pattern. In this case, the mutation is a large chromosome rearrangement; approximately 50 megabases (50,000,000 bases) of DNA near the gene have an inverted order when compared with that of other horses. The precise effect of this mutation is not known but thought to affect the function of DNA sequences outside the gene that regulates expression of the gene during development.

      Changes affecting gene expression

      Mutation can alter splice sites for excision of introns or DNA sequences that serve as binding sites for regulatory molecules determining time and amount of expression. The variant affecting the gene for appaloosa (leopard spotting) is an insertion outside the coding portion of the gene that alters the amount of transcription by the TRPM1 gene (Bellone et al., 2010).

      Where Are Genes Found?

      Genes in the nucleus

      Horse genes are packaged into 64 DNA molecules called chromosomes that are found in the nucleus of nearly every cell. Chromosomes can be seen with the aid of a microscope and dyes that bind to DNA or to the proteins associated with DNA. The genetic information of all domesticated horses is nearly identical and, not surprisingly, horses of all breeds have the same number, size, and shape of chromosomes.

      Before a cell divides, chromosomal DNA is in an extended form and the areas active in transcription are exposed for action by polymerases. Electron micrographs show an image not unlike tangled spaghetti. When a cell starts the process of division into two daughter cells, chromosomes condense by supercoiling about chromatin proteins to form discrete rod-shaped bodies we recognize as the classical image of chromosomes. Careful cutting and matching of stained chromosome images obtained from microscopic examination of a cell in the process of division shows that the 64 chromosomes can be arranged as a series of 32 pairs of chromosome structures (Fig. 4.4). This array of paired and condensed chromosomes is visualized as a karyotype. The only distinguishing feature between most horse karyotypes is a difference between males and females seen in a single pair of chromosomes (the sex chromosomes), which are discussed in a later section.

Fig. 4.4. Microscopic images of dye-stained nuclei from horse lymphocytes (white blood cells) undergoing cell division (image: T.L. Lear).

      Genes in mitochondria

      In addition to the DNA in chromosomes, each cell has a pair of small, circular DNA molecules in their mitochondria. Mitochondria are small organelles in the cell important for oxidative metabolism. Horses have 37 mitochondrial genes, all of which are dedicated to the function of mitochondria. The mitochondria in an offspring usually originate from the eggs of the dam. The mitochondria in sperm are almost always lost. Consequently, the inheritance of mitochondrial DNA and mitochondrial genes follows the maternal line of inheritance (Chapter 21 has more information about mitochondria genetics)

      Behavior of Chromosomes

      The behavior of chromosomes through cell life cycles is the key to the principles of Mendelian inheritance. Two types of division cycles are characteristic of vertebrates. The first process (mitosis) occurs in all cells of the body. The second chromosome process (meiosis) is directly involved in the formation of the gametes (sperm and eggs) and occurs only in the reproductive organs or gonads (testes in males and ovaries in females).

      In Fig. 4.4, the large mass to the right of the image is a large, intact nucleus. The smaller, dark staining bodies are chromosomes which have burst from another cell’s nucleus. Each contains tightly coiled DNA from one of the 64 horse chromosomes. All chromosomes participate in mitosis and meiosis. Two of the chromosomes are called “sex chromosomes” and are involved in gender determination. The remaining chromosomes are called autosomes. Chromosome (Cytogenetic) studies are described further in Chapter 17.

      Mitosis

      When body cells divide, the chromosomes first replicate, then condense by tight coiling (as already described) to become the discrete chromosome elements shown in a karyotype. At cell partition, the duplicated strands separate so that each daughter cell has an exact replica of the genetic material of the original cell. This process assures that all cells of the body are genetically identical and have the normal chromosome number (the diploid number). For domestic horses, this diploid chromosome number is 64, a collection of 32 pairs of chromosomes. One chromosome of each pair has a maternal origin, the other a paternal origin.

       Meiosis

      Meiosis generates gametes (sperm in males and ova in females) with only 32 chromosomes (the haploid number)—only one copy from each of the chromosome pairs found in normal diploid cells. When a sperm and an ovum combine during fertilization to form a zygote, the chromosome number in the resulting cell is 64, reconstituting the diploid chromosome number and gene composition appropriate for the animal we know as the horse.

      Integral to meiosis are two aspects directly responsible for the characteristics of gene inheritance.

      • Reduction division, which results in the gamete receiving only one chromosome of each pair. Thus, chromosomes derived from each parent are randomly distributed through the children and on to the grandchildren. This process reassorts chromosome pairs in each generation and generates characteristic trait ratios and segregation of alleles. Mendel did not know about chromosomes, but he hypothesized this kind of process to explain inheritance.

      • Recombination, which allows homologous maternal- and paternal-derived chromosomes to exchange sections. This crossing-over process was not part of the genetic theory hypothesized by Mendel but is the basis for the important concept of linkage genetics.

      An animal has only two copies of each gene despite the genetic input from many pedigree elements. For example, all four grandparents will provide material to the overall genetic makeup of a grandchild, although for each specific gene only two grandparents, one from the paternal side and one from the maternal side, will be represented. Certain groups of genes are likely to be co-contributed because genes are closely strung together on linear chromosomes. Meiosis ensures that genes on different chromosomes, or far apart on one chromosome, are unlikely to stay together beyond a few generations.

      This summary of the cell division processes is by necessity brief. Consult a basic text on genetics for a more detailed review. For this topic, it would make very little difference for understanding the fundamental process whether a mouse, a fly, or a horse was the example. From the description of the