### INTRODUCTION

### MATERIAL AND METHODS

### Pedigree data

### Pedigree completeness measures

*C*and

_{sire}*C*are the indexes for paternal and maternal contribution, respectively, and where,

_{dam}*a*is the percentage of ancestors known in generation

_{i}*i*and

*d*is a preset number of generations traced back in pedigree.

### Measures of genetic diversity

#### Inbreeding coefficient:

*F*is the inbreeding coefficient of individual

_{i}*i*,

*a*is the additive genetic relationship between individual

_{ii}*i*and itself.

#### Coefficient of coancestry:

*f*and

_{xy}*a*are the coancestry coefficient and additive genetic relationship between individual

_{xy}*x*and

*y*, respectively.

#### Effective population size:

*F*) in a given reference subpopulation. The Δ

_{i}*F*was computed as: where

_{i}*F*is the individual coefficient of inbreeding and

_{i}*t*is the ‘equivalent complete generations’ (Maignel et al., 1996).

#### Effective number of founders:

*f*) is a measure of founder contributions to the population and is defined as the number of founders with equal contribution, which would give the same amount of genetic diversity that is present in the current population. The

_{e}*f*was calculated based on the method described by Lacy (1989) using the formula below: where

_{e}*q*is the genetic contribution of the ith founder to the reference population and

_{i}*f*is the total number of founders. It is usually much smaller than the actual number of founders in pedigree (animals with both parents unknown). This reflects the unequal contribution of founders to the current population due to selection rates (probability of becoming a parent and variation of family size).

#### Effective number of founder genomes:

*f*), therefore, is defined as the number of equally contributing founders with no loss of founder alleles that would give the same amount of genetic diversity as is presented in the reference population. The

_{ge}*f*was calculated using the method proposed by Caballero and Toro (2000), and calculated as: where

_{ge}*f̅*

_{g}is the average coancestry for the group considered.

#### Effective number of nonfounders:

*nf*) was calculated as: where,

_{e}*nf*accounts for the contributions of nonfounders and, therefore, for loss of genetic diversity due to drift accumulated over nonfounder generations (Caballero and Toro, 2000).

_{e}#### Genetic diversity loss:

*f*,

_{e}*f*, and

_{ge}*nf*. The amount of genetic diversity (GD) in the reference population accounting for loss of diversity due to genetic drift and unequal founder contribution was calculated as (Lacy, 1995): when expressed as 1-GD, it measures the genetic diversity lost in the population due to bottlenecks and genetic drift since the founder generation. It is assumed that the number of founders in the base population is large enough so that GD in the base population is close to 1 (Melka and Schenkel, 2010).

_{e}### Software used

### RESULTS

### Completeness of pedigree

### Demographic parameters

### Probabilities of gene origin

*f*/

_{e}*f*ratio in CD was larger than in CY and CL. This might mean that the selection intensities of interesting traits (such as days to 100 kg, backfat to 100 kg, litter size, etc.) in CY and CL were higher than in CD. The

*f*/

_{ge}*f*ratios of CD, CL and CY were 0.56, 0.32 and 0.31, respectively.

_{e}### Inbreeding and coancestry

### Genetic diversity loss

### DISCUSSION

### Pedigree completeness

### Effective population size, inbreeding and generation interval

### Probabilities of gene origin

*f*was one of those parameters that was used to assess whether or not there was a balanced contribution of founders (Lacy, 1989). If all founders were to contribute equally, the effective number of founders is equal to the total number of founders, however, the effective number is usually lower than total number of founders because of unequal contributions of founders due to selection. The comparison between

_{e}*f*and

_{e}*f*demonstrates a loss in genetic diversity due to unequal contributions of founders, which could happen as a consequence of the excessive use of some animals as parents of subsequent generations (Melka and Schenkel, 2010). Moreover, the unequal contributions of founders will directly cause an increase of average inbreeding and coancestry in the reference population. The smaller the

*f*/

_{e}*f*ratio, the greater the amount of loss of genetic diversity caused by the unequal contribution of founders. The

*f*is another very important parameter for measuring genetic diversity (Lacy, 1995). The

_{ge}*f*indicates the loss of genetic diversity due to both unequal founder contribution and random genetic drift. The

_{ge}*f*/

_{ge}*f*ratio measures the impact of genetic drift excluding the effect of founder contribution on genetic diversity, so that lower ratios are associated with a higher impact of genetic drift. Melka and Schenkel (2010) reported the

_{e}*f*/

_{ge}*f*ratio of Canadian Duroc, Lacombe, Hampshire and Landrace were 0.07, 0.07, 0.36 and 0.33, respectively. They concluded that the effect of random genetic drift was substantial in Canadian Duroc and Lacombe populations. In this study, CY and CL showed a high

_{e}*f*/

_{ge}*f*ratio (0.31 and 0.32, respectively), which was close to the ratios of Canadian Hampshire and Landrace. This implies random genetic drift has smaller effect on genetic diversity loss than unequal founder contribution. Whereas in CD, both

_{e}*f*/

_{e}*f*and

*f*/

_{ge}*f*ratios were high (0.3 and 0.56, respectively), which showed the percentage of diversity loss caused by unequal founder contribution was larger in CD than in CY and CL.

_{e}