This chapter focuses on the genes affecting three important tissues of the body, namely muscle, the nervous system and the skeleton. Each will be considered in turn.

Muscle

The muscles usually make up a large proportion of the body weight (c. 40%) and also about 40% of the body protein. Muscle development is very important in the production of broilers, since meat is often the main protein component of the average human diet in many countries. There are three basic types of muscle: skeletal or voluntary muscle, cardiac muscle, and smooth or involuntary muscle. Skeletal and cardiac muscle are striated in appearance, whereas smooth muscle is non-striated, reflecting its less regular structure. Smooth muscle is found particularly in the gut and the lining of blood vessels, whereas skeletal muscle is found in association with the skeleton.

Within skeletal muscle the constituent fibres may be subdivided into the two principal types, red fibres and white fibres. The difference in colour is dependent on the larger amount of myoglobin (see Chapter 10, section 10.2) and cytochromes in the red fibres. The white fibres have a poor supply of mitochondria and are often referred to as fast twitch muscles. They are able to undergo short, but not sustained bursts of activity.

Introduction

Feathers are probably the most complex derivatives of the integument to be found in any vertebrate and they are certainly one of the most striking anatomical features of birds. They are of great importance both to the poultry fancier and to the commercial poultryman. For the former much of the emphasis in breeding is to obtain a plumage pattern agreed upon by the ‘experts’ as the standard. For the commercial poultryman the feathers are important for two reasons: (i) since they are approximately 90% protein they represent a dietary protein input which will not be recovered at the end of the day as edible protein, (ii) they may also be a useful indicator of the growth rate and the sex of the bird. In this chapter both the structure and distribution of feathers are considered, and also the colours of the plumage. Although there has been quite a lot of research into the genes controlling feathering and plumage colour they are still, by general genetic standards of the 1990s, not well understood. There are are some instances where the genes controlling certain characters are well established, their alleles known, their dominance relations understood, and the genes in question have been mapped, but there are many other examples where it is not yet clear how many genes control a particular character and how they interact.

Introduction

Sexual reproduction ensures the combination of different genotypes, and thus generates progeny having new and varied genotypes. The combination of different genotypes is of greater importance than mutational events in its effect on the rate of evolution (see Chapter 1, section 1.2). In this chapter the current state of understanding of sex-determining mechanisms in the domestic fowl is summarised together with a description of sex-linked inheritance.

The nineteenth century poultry breeder was aware of the pattern of sex-linked inheritance, although the basis of it was not understood. Lancaster (1972) summarised the early reports of sex-linkage which included the inhibitor of dermal melanin in 1850, the silver locus in 1855, cuckoo barring in 1885 and slow feathering in 1885. By 1908 Bateson & Punnett (1908) and also others (see Hutt & Rasmusen, 1982) had shown from cytological studies that the hen is the heterogametic sex, but even by 1949 the nature of the sex chromosomes in the domestic fowl was not clear. Hutt (1949), in his book Genetics of the Fowl suggested that the cock has a pair of sex chromosomes (ZZ, equivalent to XX in mammals) and that the hen has a single sex chromosome (ZO, equivalent to XO).

Introduction

Much of the previous chapter dealt with the molecular basis of genetics; ultimately all genetic phenomena should be explicable in molecular terms. Historically, however, it is the branch of genetics now generally referred to as transmission genetics which originated the subject, and not until more than half a century after Mendel's work were the beginnings of a molecular explanation possible. In this chapter the phenotypic characters of an organism and their transmission are considered, but not the molecular events that underlie them. The essence of Mendel's findings is encompassed in his principles of inheritance, which are well documented in many biology and genetics textbooks (Strickberger, 1985; Suzuki et al., 1989; Weaver & Hedrick, 1989). The principles are therefore discussed briefly using examples from poultry genetics. This is followed by considering other important aspects of transmission genetics.

Monohybrid crosses

Mendel carried out his experiments using different strains of garden peas. He selected strains having contrasting characters, e.g. green/yellow, round/wrinkled, tall/dwarf, etc. In each case he first tested that the strains bred true. He then proceeded to cross strains having opposing characters, i.e. he made monohybrid crosses, and examined the first generation of the progeny (first filial generation, F1) which he then selfed to produce the F2 generation.

Introduction

Since the early 1970s it has become possible to isolate DNA and fragment it in a highly specific manner into pieces comparable in size to that of a gene, and then by joining such pieces to a suitable vector, which is normally viral DNA or a plasmid, to insert the chimaeras so formed into another species or organism. Over the last decade this technology, generally referred to as genetic engineering, has become refined and many of the initial technical difficulties overcome. This technology triggered what is generally regarded as the third rapid advance in the understanding of genetics (the first being the rediscovery of Mendel's work in 1901, and the second the advent of molecular genetics which began about 1940). It is now potentially possible to isolate a gene and transfer it either into another individual of the same species or into a different species. Further, by transferring it to a host with a short generation time, e.g. a bacterium such as E. coli with a generation time as short as 20 min, multiple copies or clones of the single gene may be produced. The much greater number of gene copies then available for isolation means that detailed structural studies can be carried out on the gene, including the determination of the sequence of its nucleotides.

The first sections of this chapter (2.1–2.3) form a résumé on the nature and functioning of genes, how they are organised and how they replicate. The second half (sections 2.4 and 2.5) then describes specifically the chromosomes in the domestic fowl, including chromosomal abnormalities.

The nature of the gene and its organisation on the chromosome

Since the turn of the century it has been apparent that genes are the units of inheritance and, since Watson and Crick's proposal in 1953 for the double helical structure of DNA, their molecular nature has been clear. However, there is still much to be learned about their organisation and also the details of replication and expression. Genes are comprised of DNA, a macromolecule having a double helical structure in which its two strands are arranged in antiparallel fashion. The information content of DNA arises from the specific order of the structural units attached to the backbone of the macromolecule; these structural units are known as bases. There are four different bases in DNA: adenine, thymine, guanine and cytosine, usually abbreviated to their first letters A, T, G, and C. Each gene may have as many as 1000 or more bases arranged in a unique sequence along the macromolecule.

The stages in genetic analysis

In the previous chapter sex-linked inheritance was discussed. In sex-linked inheritance the way in which certain characters are transmitted and expressed depends on the sex of the parents and offspring. The mechanisms involved depend on the genes for these characters being carried on one of the sex chromosomes, usually on the Z chromosome in the fowl since it is much larger than the W chromosome. In general, characters will show linked inheritance if the genes responsible are on the same chromosome, whether on the autosomes or sex chromosomes. The closer the genes are on the chromosome the stronger is the linkage. Linkage between two genes is a measure of the probability of them being transmitted together to offspring. An important goal of genetic analysis is to determine the positions of all the genes on the chromosomes and how their transmission and expression are controlled. This heightened understanding would enable genetic predictions to be made more accurately.

The process can be divided into a number of stages. (i) The first is to establish that a character is a genetically inherited character, and that it is inherited in Mendelian fashion. Some characters may be environmentally controlled. Others may be polygenetic, i.e. controlled by several genes (these are considered further in Chapter 9) and although each gene follows the normal Mendelian pattern, the overall analysis is rather complex.

One class of genes not described in this book is the oncogenes. It now seems fairly certain that many cancers are caused either by the malfunctioning of certain cellular genes or by a virus entering a host cell and so introducing additional genes able to transform normal cells into cancer cells. In recent years there have been great advances in understanding and defining these genes, which are termed oncogenes. Many of the oncogenes so far identified occur in the domestic fowl. Thus, in a review of oncogenes Bishop (1983) listed 25 of which nine were from the domestic fowl. At present more than 40 are known (Reddy, Skalka & Curran, 1988), and it is thought that the number may rise to the region of 100 (Watson et al., 1987), although the number of different classes appears to be less than 30. Since a number of the cellular oncogenes are present in normal uninfected cells they constitute part of the normal genome of the domestic fowl. Those oncogenes that are introduced on viral infection are related to their cellular counterparts. In this appendix the different types of oncogenes known to be present in the domestic fowl are listed, together with their protein products.

Introduction

The characters discussed in Chapters 3–8 are generally discrete in nature. There is a marked distinction between different alleles, and inheritance occurs in straightforward Mendelian fashion. The varieties of plumage, the type of comb, the feathering of the legs, polydactyly, and the colour of skin are all differences of kind. They are the types of character that both poultry fancier and geneticist are generally most interested in: the former because they represent many of the attractive features of the birds and they give them their individuality, and the latter because they are the more satisfactory traits to analyse in genetic terms.

However, most of the characters in which the commercial breeder is interested show continuous variation, e.g. body weight, proportion of body fat to muscle, size of egg, rate of growth and rate of egg laying. With these, there are not two alternative phenotypes which are easily distinguished, but continuous variations between two extremes. Most of these characters are quantitative and easily measured.

Characters that exhibit continuous variation are more difficult to analyse and, in fact, were a puzzle to early geneticists, until Nilsson-Ehle, a Swedish geneticist, showed in 1910 that it was possible to account for the colours of wheat kernels, which ranged from red, through medium-red, light red and very light red, to white, by assuming that two pairs of alleles were responsible for the colour, and that each allele had an additive effect.

It is often necessary in studies of Mendelian genetics to compare the results of particular crosses with those expected on the basis of a particular hypothesis. For example, if a homozygous dominant is crossed with a homozygous recessive and the progeny self-crossed, then we expect a 3:1 ratio of dominant: recessive phenotypes in the F2 generation (see Chapter 3, section 3.2). This ratio is dependent on the random segregation of homologous chromatids during meiosis. Being a chance event, the ratio will not be exactly 3:1 every time such a cross is performed. It is rather like tossing a coin ten times; on average we expect it to fall five times on heads and five times on tails. However, this will not be the case each time 10 tosses are carried out. We therefore need a method of assessing whether the results of a particular cross are close enough to fit our hypothesis. The statistical method used is the Chi squared (χ2) test. It enables us to assess whether or not a difference between an expected and observed result is significant.

A brief explanation of the test will now be given (for further details of this and other statistical tests, see Mead & Curnow, 1983) and the test will be applied to two sets of data given in Chapters 3 and 5.

Introduction

Genes may be transformed by spontaneous mutations, which occur at a low frequency in the range of 1 in every 2 × 10-4 to 4 × 10-10 meiotic divisions. Agents such as UV light, X-rays and certain chemicals known as mutagens increase the frequency of mutation. Mutations involve changes in the structure of DNA and hence the information coded in the DNA sequences. Different types of changes can occur such as the removal or addition of a base, or the inversion or transposition of a segment of DNA. Mutation is generally thought of as a random process, although certain positions in DNA may be more sensitive to change. Because of the random nature of any change most mutations are detrimental to the organism concerned. It is somewhat analogous to making a random replacement of a component in a computer; it is much more likely that the computer will perform less well, than that it will show additional capabilities. Very occasionally mutants may produce an improved genotype that will have a selective advantage in the environment. This is of great importance in the process of evolution.

Many mutations are pleiotropic, that is, they are wide ranging in their effects on the phenotype, and it is in most cases difficult to establish the nature of the primary effect.

The first linkage map for the domestic fowl was published by Hutt (1936); it consisted of 18 loci in five linkage groups. It has since been revised several times as new data became available, and the map given below is that published by Somes in 1988. For the complete details and references, see Somes (1988) and Bitgood & Somes (1990). All the earliest mapping was carried out by determining recombinant frequencies (see Chapter 5, section 5.2), thereby establishing the linkage groups that were given Roman numerals (I to X). Sex-linked characters can be assigned to the sex chromosomes, and apart from the H-W antigen that has been assigned to the small W chromosome, all other sex-linked characters have been assigned to the larger Z chromosome. Apart from the sex chromosomes it was not possible until 1973 to equate a particular linkage group with a particular chromosome. After the first chromosome translocations were studied by Zartman (1973), it became possible in some instances to link particular characters with particular translocations and hence identify the chromosome carrying a particular gene (Chapter 5, section 5.3). Once one gene has been located on a particular chromosome, linkage relations enable others to be linked. Chromosomes are given Arabic numerals in descending size order.

Introduction

Antibodies that make up part of the major defence system of the body, differ from the proteins discussed in the previous chapter in that the particular set of antibodies possessed by an individual is unique, and depends in part on the antigens with which the individual has been challenged during its lifetime. A process of selection occurs during the lifetime of the organism, but that does not imply that immunoglobulins (the antibodies) as a class have not evolved as with other proteins. The various types of immunoglobulins and their mechanisms of action have evolved over millions of years and collectively have the potential to combat a large range of antigens.

Before discussing the evolution and genetics of the immune system it will be necessary to outline the salient features of the system in general, and that of the fowl in particular. Immunogenetics is a subject that has developed greatly following the recent technical advances in the molecular biology of nucleic acids (see Chapter 12). Thus it has been possible to test the theories concerning the origin of antibody diversity proposed in the 1950s, since a number of gene sequences for immunoglobulins have become known (Porter, 1973).

Three separate areas are discussed in this chapter: (i) the genetics of antibody formation and the immune response, (ii) the Major Histocompatibility Complex (MHC), and (iii) the blood group antigens.

Introduction

Mutations alter the genotype by changing the nucleotide sequence in DNA, but natural selection operates on the phenotype, which is largely dependent on the particular proteins made by an organism. A study of the structure and sequence of individual proteins can therefore be useful in furthering the understanding of evolution in two important ways. Firstly, by comparing the structures of a specific protein, e.g. cytochrome c, that occur in different species, it is possible to establish or confirm phylogenetic relationships amongst organisms, and to build up phylogenetic trees involving phyla, classes, orders, etc. Secondly, a number of proteins are found to exist in more than one closely related form, e.g. ovalbumin A and B; these are known as polymorphisms. A study of the distribution of different polymorphic forms within a population of a given species, together with a knowledge of their dominance relationships, can be used to explain their more recent history. These two areas are interrelated, and in this chapter a number of proteins are examined, some of which have been primarily of importance in establishing and confirming phylogenetic relationships, e.g. the haem proteins, and others have been more useful in determining relationships between breeds of the domestic fowl, e.g. egg-white proteins.

Introduction

According to Seegeler (1983), 328 oil plant species are known to exist in Ethiopia. Of these, 15 are cultivated and the rest may have uses other than for oil and may be cultivated or wild. Oil-bearing plants having oil contents in excess of 10 per cent, but which are not yet cultivated commercially, have been catalogued by Goshe & Hamito (1983) (Table 1).

Ethiopia is known to be either a centre of origin or a centre of diversity for many cultivated oil crops. Several of the cultivated oilseed crops play an important role in the nutrition of the Ethiopian population and in foreign exchange earnings. The oil crops currently in production in the country are niger or noog, rapeseed, Ethiopian mustard or gomenzer, linseed, sunflower, sesame, groundnut, safflower and castor bean.

The overall objective of the research programme is to increase the production of oil seeds for food and to provide raw materials for agroindustrial development. This can be achieved by the development of high-yielding, stable cultivars with the necessary package of practices required for sustained high yields. The programme therefore falls into three sections:

1. – the improvement of noog, linseed, sesame and safflower which possess a wide range of variability and a wealth of unutilized indigenous germplasm;

2. – the improvement and popularization of oil seed Brassica and groundnut for which a wide range of indigenous germplasm is also available;

3. – the popularization of the introduced sunflower crop, for which probably no indigenous germplasm exists.