**1. Introduction**

In recent years, genetic studies on dog genomics have multiplied worldwide. Currently, there are over 50 international laboratories which are involved in canine genome projects and several applications will be available in the near future from these studies. These new findings will improve our understanding of the selection process of the dogs and provide useful information for the study and control of genetic diseases.

### **2. Basic genetics**

The single-control characters are influenced by genes located in a locus on one of the pairs of the chromosomes (78 in the dog) and have a binomial distribution. For example, the hair length in dogs is coded by two genes present at an autosomal locus. Short-haired animals have genotype LL (dominant homozygotes), while, long-haired animals have genotype ll (recessive homozygotes). From their mating originates short-haired animals with genotype Ll (heterozygotes), indistinguishable from short-haired parents. Even those characters that express different degrees of dominance, different from the Mendelian inheritance, are considered simple characters (e.g. incomplete or partial dominance). The simple characters are not influenced by the environment and, therefore, to each genotype corresponds a certain phenotype (P = G, where P = phenotype and G = genotype). The study of simple characters includes also multiple alleles (several alleles present in a population), pleitropy, association or linkage and incomplete penetrance. For characters

with simple inheritance, it is easier to make selection than for multiple control characters. The multiple control characters are also called quantitative or polygenic characters. These characters are influenced by many genes distributed on several loci and they are influenced by environmental factors. The strong artificial selection exercised by man during the domestication process and during the creation of the different breeds has led to the setting of several characters. Color inheritance illustrates the case of separate loci that control the expression of the phenotype. The coat of dogs consists of two parts: top coat (protective function) and undercoat (heat-insulating function). Some breeds have no undercoat (e.g. Yorkshire). The color of the coat depends on the characteristics of the pigments contained in the medullary and cortical layers of the hair [1]. According to Willis [1], it is possible to explain all the colors by means of two chemical pigments: hemoglobin and melanin. More specifically, melanin is differentiated into eumelanin (black-brown) and pheomelanin (yellow-reddish). The synthesis of pigments in the hair of mammals depends on the interaction between the Agouti protein and the Melanocortin 1 receptor [2]. The coat colors in the dog are linked to the presence/absence of two types of melanin and their possible combinations. It is important to underline that melanin do not show a precise time of formation and they develop during the different phases of the fetal development and after birth [1]. The knowledge of the genetic inheritance of the morphological traits is very important in order to establish suitable selection objectives in the different breeds.

#### **3. Relationship and inbreeding**

Measurement of F coefficient (consanguinity) in a population can be considered as a measure of the increase in the proportion of homozygous individuals following an inbreeding mating (between relatives) [3]. The coefficient of consanguinity F can be calculated with the following methods: 1) pedigree 2) run of homozigosity (ROH); 3) genomic kinship matrix; 4) SNP genotyping [4, 5]. Inbreeding can occur in small closed populations due to mating between related animals. In a closed population, the decrease in the fraction of heterozygotes from one generation to the next may be referred to as ΔF. This value varies in relation to the size of the population: ΔF = 1 / 2Ne where Ne is the effective number or effective size of the population. In a population, Ne depends on the number of males (Nm), and on the number of females (Nf), in the following relationship:

$$\mathbf{1}/N\mathbf{e} = \mathbf{1}/4\mathbf{N}\mathbf{f} + \mathbf{1}/4\ \mathbf{N}m; \Delta F = \mathbf{1}/8\mathbf{N}\mathbf{f} + \mathbf{1}/8\ \mathbf{N}m\tag{1}$$

The inbreeding coefficient, at a given t generation, can be calculated as a function of ΔF and t as:

$$\mathbf{F}\_{\mathbf{t}} = \mathbf{1} - \left(\mathbf{1} - \Delta F\right)^{\mathbf{t}} \tag{2}$$

**5**

*Canine Genetics and Genomics*

*DOI: http://dx.doi.org/10.5772/intechopen.95781*

an optimal genetic diversity in the population.

The general actions to be taken in a program for the genetic improvement within a breed should include: 1) genomic identification and characterization of individuals, highlighting their potential in terms of their contribution to maintaining biodiversity, aptitude and use 2) monitoring of demographic parameters and assessment of the risk of reduced genetic variability 3) characterization and evaluation of the intra-breed genetic variability for proper management activities. Modern molecular techniques can be helpful for the improvement of management strategies, even for small breeds and for qualitative traits. The current hypothesis is to add molecular data to classical schemes (assisted selection) to improve their accuracy. The first step in planning an improvement program consists of: 1) a clear definition of the objectives 2) identification of the traits to be recorded 3) evaluation of the gene effect of the characters to be selected 4) estimate of the effect of the environment

**4. Breeding programs and strategies**

resistance to diseases, longevity, etc.). These findings are based on the results of experiments carried out on different breeds and for several generations. Leroy *et al.* [8] showed that the increase in inbreeding in the population has an effect on individual survival and litter size of different breeds. Deleterious effects begin to occur when the value of F is about 0.375. Lower values are not to be considered dangerous. It is worth noting that this is the level of inbreeding that is achieved in only two generations of full sibling mating. For this reason, it is recommended to avoid mating between close relatives. Consanguinity is influenced by the number of individuals used per generation [9]. As a general rule, individuals whose numbers are lower in the breeding population they exert a proportionately greater effect on consanguinity. This is true both in relation to the male/female ratio (depend more on the number of males) and the different numbers of breeders in the various generations. The actual number of breeding animals is the parameter used in small populations to determine the expected inbreeding coefficient. Since the less numerous sex is the most important, the actual number of the population can be calculated even if the number of the larger sex is not known (e.g. 2 males and the number of females is assumed to be infinite: 1/Ne = 1/ 4Nf = 1/4 (2) =1/8 \* F = 1/16 = 0.0625). The family size is the number of offspring in each family who become parents in the next generation. In ideal conditions, the size of the population will remain constant in subsequent generations if each parent is replaced by another individual. In this case, the average number of offspring per parent is equal to 1 with an average family size of 2 (two parents). The Ne is also function of the variance of the family size. If males mate with more than one female, the number of offspring and thus the variance of the family size will differ between the two sexes. Several measures can be implemented to keep consanguinity within acceptable limits in the population: increase the number of breeders; mating of one male with a female (since the number within the sexes is the same, Ne will be maximized), reduce the variance size of the family (for a constant number of offspring for each family, the variance is equal to 0 and the Ne is double); avoid mating between siblings or cousins; avoid mating individuals in generations that overlap as inbreeding increases. If the management program includes the genetic improvement of one or more characters, selection must be carried out using selection indices that take into account of the level of relationship. The goal is to find the optimal number of offspring for each breeding animal and determine if a young animal (a candidate for selection) should be selected for breeding or not. This is done in an optimal way using the software EVA [10] that guarantees the achievement of the genetic progress and the maintenance

which shows the decrease (ΔF) of heterozygotes that occurs at each generation following inbreeding [6]. Lewis *et al.* [7] reported for 221 breeds of the UK Kennel Club a Ne that varies between 23.8 of the Manchester terrier breed to 918 of the Borzoi breed and an average value of F equal to 0.06. The deleterious effects of inbreeding are universally known. They can be summarized briefly in the increase in the frequency of all genetic defects and abnormalities (reproductive sphere,

#### *Canine Genetics and Genomics DOI: http://dx.doi.org/10.5772/intechopen.95781*

*Canine Genetics, Health and Medicine*

with simple inheritance, it is easier to make selection than for multiple control characters. The multiple control characters are also called quantitative or polygenic characters. These characters are influenced by many genes distributed on several loci and they are influenced by environmental factors. The strong artificial selection exercised by man during the domestication process and during the creation of the different breeds has led to the setting of several characters. Color inheritance illustrates the case of separate loci that control the expression of the phenotype. The coat of dogs consists of two parts: top coat (protective function) and undercoat (heat-insulating function). Some breeds have no undercoat (e.g. Yorkshire). The color of the coat depends on the characteristics of the pigments contained in the medullary and cortical layers of the hair [1]. According to Willis [1], it is possible to explain all the colors by means of two chemical pigments: hemoglobin and melanin. More specifically, melanin is differentiated into eumelanin (black-brown) and pheomelanin (yellow-reddish). The synthesis of pigments in the hair of mammals depends on the interaction between the Agouti protein and the Melanocortin 1 receptor [2]. The coat colors in the dog are linked to the presence/absence of two types of melanin and their possible combinations. It is important to underline that melanin do not show a precise time of formation and they develop during the different phases of the fetal development and after birth [1]. The knowledge of the genetic inheritance of the morphological traits is very important in order to estab-

Measurement of F coefficient (consanguinity) in a population can be considered as a measure of the increase in the proportion of homozygous individuals following an inbreeding mating (between relatives) [3]. The coefficient of consanguinity F can be calculated with the following methods: 1) pedigree 2) run of homozigosity (ROH); 3) genomic kinship matrix; 4) SNP genotyping [4, 5]. Inbreeding can occur in small closed populations due to mating between related animals. In a closed population, the decrease in the fraction of heterozygotes from one generation to the next may be referred to as ΔF. This value varies in relation to the size of the population: ΔF = 1 / 2Ne where Ne is the effective number or effective size of the population. In a population, Ne depends on the number of males (Nm), and on

1 / 1 / 4Nf 1 / 4 ; 1 /8Nf 1 /8 *Ne* = + ∆= + *Nm F Nm* (1)

F11 <sup>t</sup> = − −∆*F* (2)

The inbreeding coefficient, at a given t generation, can be calculated as a func-

( ) t

which shows the decrease (ΔF) of heterozygotes that occurs at each generation following inbreeding [6]. Lewis *et al.* [7] reported for 221 breeds of the UK Kennel Club a Ne that varies between 23.8 of the Manchester terrier breed to 918 of the Borzoi breed and an average value of F equal to 0.06. The deleterious effects of inbreeding are universally known. They can be summarized briefly in the increase in the frequency of all genetic defects and abnormalities (reproductive sphere,

lish suitable selection objectives in the different breeds.

the number of females (Nf), in the following relationship:

**3. Relationship and inbreeding**

**4**

tion of ΔF and t as:

resistance to diseases, longevity, etc.). These findings are based on the results of experiments carried out on different breeds and for several generations. Leroy *et al.* [8] showed that the increase in inbreeding in the population has an effect on individual survival and litter size of different breeds. Deleterious effects begin to occur when the value of F is about 0.375. Lower values are not to be considered dangerous. It is worth noting that this is the level of inbreeding that is achieved in only two generations of full sibling mating. For this reason, it is recommended to avoid mating between close relatives. Consanguinity is influenced by the number of individuals used per generation [9]. As a general rule, individuals whose numbers are lower in the breeding population they exert a proportionately greater effect on consanguinity. This is true both in relation to the male/female ratio (depend more on the number of males) and the different numbers of breeders in the various generations. The actual number of breeding animals is the parameter used in small populations to determine the expected inbreeding coefficient. Since the less numerous sex is the most important, the actual number of the population can be calculated even if the number of the larger sex is not known (e.g. 2 males and the number of females is assumed to be infinite: 1/Ne = 1/ 4Nf = 1/4 (2) =1/8 \* F = 1/16 = 0.0625). The family size is the number of offspring in each family who become parents in the next generation. In ideal conditions, the size of the population will remain constant in subsequent generations if each parent is replaced by another individual. In this case, the average number of offspring per parent is equal to 1 with an average family size of 2 (two parents). The Ne is also function of the variance of the family size. If males mate with more than one female, the number of offspring and thus the variance of the family size will differ between the two sexes. Several measures can be implemented to keep consanguinity within acceptable limits in the population: increase the number of breeders; mating of one male with a female (since the number within the sexes is the same, Ne will be maximized), reduce the variance size of the family (for a constant number of offspring for each family, the variance is equal to 0 and the Ne is double); avoid mating between siblings or cousins; avoid mating individuals in generations that overlap as inbreeding increases. If the management program includes the genetic improvement of one or more characters, selection must be carried out using selection indices that take into account of the level of relationship. The goal is to find the optimal number of offspring for each breeding animal and determine if a young animal (a candidate for selection) should be selected for breeding or not. This is done in an optimal way using the software EVA [10] that guarantees the achievement of the genetic progress and the maintenance an optimal genetic diversity in the population.
