Founder representation and effective population size in old versus young breeds—genetic diversity of Finnish and Nordic Spitz

Finnish Spitz is 130‐year‐old breed and has been highly popular in Finland throughout its history. Nordic Spitz is very similar to Finnish Spitz by origin and use, but is a relatively recent breed with much smaller population size. To see how breed age and breeding history have influenced the current population, we performed comprehensive population genetic analysis using pedigree data of 28,119 Finnish and 9,009 Nordic Spitzes combined with genomewide single nucleotide polymorphism (SNP) data from 135 Finnish and 110 Nordic Spitzes. We found that the Finnish Spitz has undergone repeated male bottlenecks resulting in dramatic loss of genetic diversity, reflected by 20 effective founders (f_a) and mean heterozygosity (Hz) of 0.313. The realized effective population size in the breed based on pedigree analysis () is 168, whereas the genetic effective population size (N_eg) computed the decay of linkage disequilibrium (r²) is only 57 individuals. Nordic Spitz, although once been near extinction, has not been exposed to similar repeated bottlenecks than Finnish Spitz and had f_a of 27 individuals. However, due to the smaller total population size, the breed has also smaller effective population size than Finnish Spitz ( = 98 and N_eg = 49). Interestingly, the r² data show that the effective population size has contracted dramatically since the establishment of the breed, emphasizing the role of breed standards as constrains for the breeding population. Despite the small population size, Nordic Spitz still maintains SNP heterozygosity levels similar to mixed breed dogs (mean Hz = 0.409). Our study demonstrates that although pedigree analyses cannot provide estimates of the present diversity within a breed, the effective population sizes inferred from them correlate with the genotyping results. The genetic relationships of the northern Spitz breeds and the benefits of the open breed registry are discussed.     

The assessment of genetic diversity within and among the eight subpopulations of Japanese Black cattle using 52 microsatellite markers

Japanese Black cattle are at risk for genetic homogeneity due to intensive use of a few sires. Therefore, assessment of the actual genetic diversity of this breed is important for future breeding plans. In the present study, we investigated the genetic diversity within and among eight subpopulations of Japanese Black cattle using 52 microsatellite markers. The parameters for genetic diversity of Japanese Black cattle were comparable to those of other cattle breeds, suggesting that the relatively high genetic diversity of the breed. However, upon comparison among the eight subpopulations, the Hyogo subpopulation showed markedly low genetic diversity. The results of the pairwise F_ST values, phylogenetic network and structure analysis indicated that the Hyogo population has remarkably high level of genetic differentiation from other populations, while Yamagata, Niigata, Hiroshima and Kagawa populations have low levels of genetic differentiation. Furthermore, multidimensional scaling plots indicated that individuals in some subpopulations were separated from individuals in the other subpopulations. We conclude that while the overall genetic diversity of Japanese Black cattle is still maintained at a relatively high level, that of a particular subpopulation is significantly reduced, and therefore the effective population size of the breed needs to be controlled by correct mating strategies.     

Heritage Finnish Landrace chickens are genetically diverse and geographically structured

ABSTRACT

The Finnish Landrace breed of chickens (in Finnish suomalainen maatiaiskana) traces its origins to almost 1,000 years ago. Today, remnant populations of phenotypically distinct lineages are maintained by a network of volunteer hobbyists in Finland, managed by Natural Resources Institute Finland (Luke). Guided by a prior Major Histocompatibility Complex B-locus haplotype study, we sought now to characterize genetically Finnish Landrace chickens using denser genomic sampling. A new panel of 101 selectively neutral SNP sites was used to interrogate genetic variation in 192 individuals sampled from 13 putatively distinctive population units. Individuals partitioned into K?=?11 genetic clusters characterized by high levels of genetic diversity, strong patterns of genetic structure and low levels of inbreeding. Evidence of an undocumented genetic lineage was also discovered. Facilitated by an inexpensive SNP assay, this study shows that the genetic integrity of the Finnish Landrace persists and represents a rich resource of natural (adaptive) genomic variation.     

Evaluation of genetic diversity in Japanese Brown cattle population by pedigree analysis

The Japanese Brown is the second most common domestic beef breed in Japan. However, nowadays this breed is facing reduction in numbers because of pressure from a profitable domestic breed. This breed is uniformly characterized by its brown coat colour, but is comprised of two isolated sub‐breeds, Kumamoto and Kouchi, each possessing a different gene pool. Pedigree analyses were carried out for the two sub‐breeds using the pedigree records of animals born from 1970 to 2000. The effective population size has been found to be consistently reducing during the last three decades in both sub‐breeds. The current effective sizes were estimated to be 25.5 and 6.0 for the Kumamoto and Kouchi sub‐breeds, respectively. The estimate of the effective number of founders (N_ef) in the Kumamoto sub‐breed decreased from 152.1 to 74.4; that of non‐founders (N_enf), from 41.7 to 5.3; and that of founder genome equivalents (N_ge), from 32.7 to 4.9. The corresponding changes in the Kouchi sub‐breed were from 108.2 to 79.4, 16.2 to 4.1, and 14.1 to 3.9. Increasing differences between the two genetic diversity indices in the sub‐breeds indicate that the greater part of the reduction of genetic diversity can be attributed to genetic drift that accumulated in the non‐founder generations. A comparison with published estimates for several cattle breeds suggests the extremely limited genetic diversity of Japanese Brown. In addition to the avoidance of further reduction of genetic diversity, it will be important to counteract the process of breed decline by establishing a production system to efficiently utilize the unique characteristics of this breed and by developing links between the breed and products with market value.     

Genetic diversity decreases as population density declines: Implications of temporal variation in mitochondrial haplotype frequencies in a natural population of Tscherskia triton

Although the spatial genetic differentiation that occurs in animal populations has been extensively studied, information on temporal variations in genetic structure and diversity is still lacking, especially for animals with oscillating populations. In the present study, we used the mtDNA D‐loop sequence to assess the temporal genetic variation in samples from six successive years for the greater long‐tailed hamster, Tscherskia triton. Sampling was carried out between 1998 and 2003 in cropland on the North China Plain, China. A total of 108 individuals were analyzed. The temporal samples showed a high level of genetic diversity. Substantial genetic changes in haplotype frequencies over time were detected for the hamster population. Random genetic drift and migration are likely to be the major factors responsible for the observed temporal pattern. The genetic diversity of the hamster population was higher in years with higher population density, and lower in years with lower population density. The result supports our hypothesis that genetic diversity decreases when population density declines in animals whose population oscillates greatly between years. The combined effects of inbreeding and genetic drift caused by reproduction, dispersal and population size might play important roles in the observed changes in genetic structure and diversity between years.     

Diversity of the Icelandic goat breed assessed using population data

Abstract

The Icelandic goat breed is a closed population consisting of around 700 animals kept in 45 herds. Several population bottlenecks are known to have occurred and the population has at least twice declined below 100 animals. Here the genetic diversity of the breed was estimated using pedigree information, D-loop sequencing and microsatellite markers. The annual rate of inbreeding was estimated as 3% and the effective population size as 5.1 animals. The effective population size based on molecular markers was estimated in the range of 4.1–8.8 individuals and mtDNA D-loop sequencing identified only three haplotypes. The results presented here show the population to be highly inbred, fragmented and the level of genetic variation among the lowest found in livestock. The results will be an important input into conservation planning for the Icelandic goat.     

Identification and characterization of hierarchical structures in dog breeding schemes, a novel method applied to the Norfolk Terrier

Popular sires, a limited population size, and the founder event are widely considered the main reasons for the low genetic diversity observed in many dog breeds. However, these factors have had only a small role in the historic decrease in diversity observed in the Norfolk Terrier breed. We show that the decrease in this breed has been mainly due to large, popular kennels. Dogs from these kennels have, on average, larger genetic contributions to subsequent generations than others. A test for the presence of a popular kennel effect is proposed and applied (P < 0.001). These kennels were found to be the same as nuclei of selection existing in other livestock species. This result revealed a hierarchical structure of dog breeding schemes, with an asymmetric gene flow predominantly from the nuclei toward the main population. Possible reasons for this structure and implications for future population management are discussed. The main reason is probably that the breed type was established by large, popular kennels and that small kennel breeders used their stud dogs to benefit from the achievements of the popular kennels. Many kennels, however, were unable to make their own substantial genetic contributions to the breed.     

Microsatellite marker analysis of the genetic variability in Hanoverian Hounds

Genetic variability of the dog breed Hanoverian Hound was analysed using a set of 16 microsatellites. The sample of 92 dogs was representative for the total current population [n = 334, inbreeding coefficient 9.2%, relationship coefficient 11.2%] with respect to the level and distribution of the inbreeding and relationship coefficients. All microsatellites used were in Hardy–Weinberg equilibrium. The average number of alleles was 6.4. The average observed heterozygosity (H_O) was slightly higher than the expected heterozygosity (H_E). Dinucleotide microsatellites exhibited lower polymorphism information content (PIC) than tetranucleotide microsatellites (0.52 versus 0.66). The average PIC was 0.61. The individual inbreeding coefficient was negatively related to the average H_O of all microsatellites, whereas the proportion of genes from introducing of Hanoverian Hounds from abroad showed no relationships to H_O. We found that the genetic variability in the Hanoverian Hounds analysed here was unexpectedly higher than that previously published for dog breeds of similar population size. Even in dog breeds of larger population size heterogyzosity was seldom higher than that observed here. The rather high genetic variability as quantified by polymorphic microsatellites in Hanoverian Hounds may be due to a large genetic variation in the founder animals of this breed and to the fact that this genetic diversity could be maintained despite genetic bottlenecks experienced by this breed in the 1920s and 1950s and despite the presence of high inbreeding and relationship coefficients for more than 50 years.     

Genetic structure and recent population demographic history of Taihangshan macaque (Macaca mulatta tcheliensis), North China

Massive actions have been and are being taken into protecting the world's primates from extinction, while the study of the properties of genetic diversity, demographic history, and ecological relationships will benefit the understanding of the long-term survival of a species. The Taihangshan macaque (Macaca mulatta tcheliensis), a subspecies of rhesus macaque (Macaca mulatta), is endemic to China and currently restricted to southern Mt. Taihangshan area. Herein, we evaluated the genetic diversity, population structure, and demographic history of this subspecies using mitochondrial (Cytb and high variable region I: HVR I) and nuclear markers (microsatellite loci) of 131 individuals collected from 9 localities covering the distribution range of this subspecies. Both phylogenetic analyses and genetic assignment revealed that the wild populations of Taihangshan macaques could be divided into 2 major highly divergent clades, THS-east and THS-west. Low genetic diversity (π: 0.00266 ± 0.00016) but high haplotype diversity (H_d: 0.80352 ± 0.015) were detected in the Taihangshan macaques, particularly in THS-east. Analyses of demographic history suggested that the Taihangshan macaques experienced first a stable historical population size from Holocene to early 19th century but a subtle decline and then slight growth in the recent 200 years. We suggest that bridging the neighbor populations (i.e. setting corridors) would facilitate the male-mediated gene flow and subsequently increase the genetic diversity of the Taihangshan macaque populations.     

Genetic diversity of Indian native cattle breeds as analysed with 20 microsatellite loci

The aim of the present study was to assess the genetic variation and establish the relationship amongst the three Indian zebu cattle breeds using 20 bovine‐specific microsatellite markers. A total of 136 unrelated DNA samples from Sahiwal (SC), Hariana (HC) and Deoni (DC) breeds of cattle were genotyped to estimate within and between breed genetic diversity indices. The estimated mean allelic diversity was 5.2, 6.5 and 5.9 in SC, HC and DC, respectively, with a total of 167 alleles. The average observed and expected heterozygosity for the population varied from 0.42 (SC) to 0.59 (DC), and from 0.61 (SC) to 0.70 (DC), respectively. Low values of genetic variability estimates were observed in SC when compared with DC and HC, indicating some loss of variability because of its relatively small population size. From global F‐statistics a significant deficit of heterozygotes of 24.2% (p < 0.05) was observed for each one of the analysed breeds whereas the total population had a 32.8% (p < 0.05) deficit of heterozygotes. The F_ST estimates demonstrated that approximately 88.7% of the total genetic variation was because of the genetic differentiation within each breed. Pair‐wise breed differentiation, Nei's standard and D_A genetic distance estimates revealed relatively close genetic similarity between HC and DC in comparison with SC. In the UPGMA‐based phylogenetic tree constructed from the genetic distances, HC and DC were grouped together in one cluster and SC in the other. The estimated time of divergence suggested a separation time of approximately 776 years between DC and HC, and a comparatively longer period (1296 years) between DC and SC.     

Genetic structure of the oriental white stork (Ciconia boyciana): implications for a breeding colony in a non‐breeding area

The oriental white stork (Ciconia boyciana) is a threatened species, and their numbers are still in decline due to habitat loss and poaching. China is a breeding and main wintering area for this animal and in recent years some individuals have been found breeding in wintering areas and at some stopover sites. These new breeding colonies are an exciting sign, however, little is understood of the genetic structure of this species. Based on the analysis of a 463‐bp mitochondrial DNA (mtDNA) control region, we investigated the genetic structure and genetic diversity of 66 wild oriental white storks from a Chinese population. We analyzed the sequences of 66 storks obtained in this study and the data of 17 storks from a Japanese population. Thirty‐seven different haplotypes were detected among the 83 samples. An analysis of molecular variance showed a significant population subdivision between the two populations (F_ST= 0.316, P < 0.05). However, the phylogenetic analysis revealed that the samples from the different populations did not form separate clusters and that there were genetic exchanges between the two populations. Compared with the Japanese population, the Chinese population had a relatively higher genetic diversity with a haplotype diversity (hπ SD) of 0.953 ± 0.013 and a nucleotide diversity (π± SD) of 0.013 ± 0.007. The high haplotype diversity and low nucleotide diversity indicate that this population might be in a rapidly increasing period from a small effective population. A neighbor‐joining tree analysis indicated that genetic exchange had occurred between the newly arisen southern breeding colony and the northern breeding colony wintering in the middle and lower Yangtze River floodplain. These results have important implications for the conservation of the oriental white stork population in China.     

Using genetic tools to inform conservation of fragmented populations of Asian elephants (Elephas maximus) across their range in China

A herd of 15 Chinese elephants attracted international attention during their 2021 northward trek, motivating the government to propose establishment of an Asian elephant national park. However, planning is hampered by a lack of genetic information on the remaining populations in China. We collected DNA from 497 dung samples from all 5 populations encompassing the entire range of elephants in China and used mitochondrial and microsatellite markers to investigate their genetic and demographic structure. We identified 237 unique genotypes (153 females, 84 males), representing 81% of the known population. However, the effective population size was small (28, range 25–32). Historic demographic contraction appeared to account for low haplotype diversity (H_d = 0.235), but moderate nucleotide and nuclear diversity (π = 0.6%, H_e = 0.55) was attributable to post-bottleneck recovery involving recent population expansion plus historical gene exchange with elephants in Myanmar, Lao PDR, and Vietnam. The 5 populations fell into 3 clusters, with Nangunhe elephants differing consistently from the other 4 populations (F_ST = 0.23); elephants from Mengyang, Simao, and Jiangcheng belonged to a single population (henceforth, MSJ), and differed from the Shangyong population (F_ST = 0.11). Interpopulation genetic variation reflected isolation by distance and female-biased dispersal. Chinese elephants should be managed as 2 distinct units: Nangunhe and another combining Shangyong and MSJ; their long-term viability will require restoring gene flow between Shangyong and MSJ, and between elephants in China and neighboring countries. Our results have the potential to inform conservation planning for an iconic megafaunal species.     

湘西黄牛Y-SNPs遗传多样性研究

[目的]通过Y-SNP分子标记方法研究湘西黄牛的遗传多样性、群体遗传结构及父系起源。[方法]采用PCR扩增、测序与生物信息学方法,对24头湘西黄牛的2个Y-SNPs(UTY-19和ZFY-10)标记进行多态性分析。[结果]结果表明,湘西黄牛有Y1和Y3两种单倍型组,频率分别为12.5%和87.5%,表明湘西黄牛可能有普通牛和瘤牛2个父系起源。湘西黄牛的Y-SNP遗传多样度为0.2283±0.0978,表明湘西黄牛具有较低的父系遗传多样性,品种纯度较高。[结论]湘西黄牛的父系起源为瘤牛Y3单倍型组,其Y1单倍型组为国外肉牛杂交所致。     

Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis

The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (N_ge) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on N_ge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non-founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.     

Population structure of Reyna Creole cattle in Nicaragua

Reyna Creole cattle originated from Bos taurus cattle brought to Latin America during the Spanish colonization in the fifteenth century and are the only remaining local breed in Nicaragua. However, the current genetic status of this breed is unknown. Therefore, the population structure of three recorded Reyna Creole herds in Nicaragua was studied to estimate their level of inbreeding, effective population size, and generation intervals. Data from 2,609 animals born between 1958 and 2007 were analyzed. A pedigree completeness index higher than 0.8 was required to obtain reliable estimates of the level of inbreeding, and this criterion was met for 367 animals (14%) in two herds. The average level of inbreeding was 13.0%, with values ranging from 0% to 43.8% for individual animals. One of the herds had an average inbreeding level of 21.6%, primarily due to long periods in which the same bulls were used for mating, leading to excessive frequencies of matings between closely related animals. The effective population size differed between years and ranged from 28 to 46 animals, showing that the Reyna Creole cattle breed is endangered, close to critical status. The average generation interval was 6.9 years with values as high as 19.1 years for some sires that were used for artificial insemination over a long period of time. Due to the high level of inbreeding and small population size, urgent actions are required for the development of a breeding program to protect the breed and support its sustainable utilization.     

Extinction probabilities of Jordan indigenous cattle using population viability analysis

Estimation of expected loss of genetic diversity in a population or breed within a defined future time horizon requires initially population viability analysis (PVA). The PVA needs estimates of probability of extinction (PE). In this study, the PE of Jordan indigenous cattle breed was simulated by PVA using Vortex^® modeling program. The annual numbers of recorded cows, bulls and their progeny were used as census data. Using the census data, effective population size (N_e) was calculated and found to be almost half (N_e = 40) of what is recommended (N_e = 82) by FAO [FAO, 1995. World Watch List for Domestic Animal Diversity. 2nd Ed. Rome, Italy] to escape endangerment. Furthermore, the EP, growth rate, heterozigosity and inbreeding rate were simulated using the PVA for a past and future time horizon. The estimates of EPs were sensible and depended heavily on the time horizon, physiological parameters and catastrophic events considered. The catastrophes were exotic breed competition and drought of 25% severity each on the population living. The model concludes that, while perhaps more or less variation in simulated population dynamic compared to real population dynamic in the past, the simulation was a fairly simulation of the likely fate under assumed living conditions. Further, the future simulated model concluded that the population is currently expected to decline rapidly toward extinction within the coming 10 years considering the same assumed conditions and absence of conserving genetic program. In such situation, it is recommended that an ex-situ live conservation program can only be a successful tool to conserve this endangered breed.     

Genetic characterization of a small closed island population of Norwegian coastal goat

ABSTRACT

The Norwegian coastal goat is a national and endangered breed. Coastal goat populations are mainly divided with a large mainland and two small island populations. The objective of this study is to describe genetic diversity in the feral Skorpa island population and its relationship to the mainland coastal goat population (Selje) using the Norwegian milk goat population as a reference. Analyses were based on 96 samples genotyped by the CaprineSNP50 Beadchip from three populations; 7 Skorpa (SK), 37 Selje (SE) and 52 Norwegian milk goats (MG). The SK population had significantly less genetic variation and higher levels of inbreeding than the two other populations. It was more distant from the two mainland populations than they were from each other. The marginal contribution of the SK population to genetic diversity was small. Means of introducing genetic diversity into the SK population should be considered if the population is prioritized for conservation.     

Diversity analysis of sheep breeds from Southern peninsular and Eastern regions of India

Information is presented on the genetic diversity and relationship among six Indian sheep breeds/populations belonging to the Southern peninsular and Eastern agroecological zones, based on microsatellite markers. Parameters of genetic variation, viz., allele diversity, observed heterozygosity, gene diversity and population inbreeding estimates, were calculated for the six breeds. The allele diversity ranged from 6.40 to 7.92, whereas the gene diversity varied from 0.617 to 0.727. The highest allele and gene diversity was observed for Nellore sheep, while the lowest was exhibited by Garole breed. Within population inbreeding estimate (F _IS) revealed a significant deficit of heterozygotes in Deccani, Madgyal, Nellore and Garole, whereas Ganjam and Chhotanagpuri sheep showed an excess of heterozygotes. The contribution of each breed to the total diversity of the breeds was quantified by the Weitzman approach. The marginal loss of diversity incurred with removal of Nellore and Garole breeds was higher (>27%), whereas removal of Deccani breed resulted in lowest loss of diversity (3.84%) from the set. Estimation of the genetic differentiation (F _ST) and genetic distance (D _A) between the pairs of breeds revealed a close relationship between Deccani and Madgyal sheep (F _ST = 0.017; D _A = 0.080) and greatest demarcation between Madgyal and Garole breeds (F _ST = 0.110; D _A = 0.622). The information generated would help in shaping genetic management and conservation programs for the sheep breeds under consideration.     

Genetic diversity and population structure analysis of eight local chicken breeds of Southern Xinjiang

ABSTRACT

1. The genetic diversity and population structure were studied for eight local chicken breeds, including Anjiyan (AN), Hetian Black (HH), Hetian Ma (HM), Aheqi (AH), Baicheng You (BC), Hejing (HJ), Tashkurghan (TS) and Ruoqiang (RQ), in the Southern Xinjiang region of China, using 20 microsatellite markers.

2. Total 336 alleles were obtained from all chicken breeds, with a mean of 16.8 alleles per locus. The polymorphism information content ranged from 0.444 to 0.911, with a mean of 0.729 and almost all of the loci showed significant deviation from Hardy-Weinberg standards. The observed and expected heterozygosity of the eight breeds ranged from 0.5 to 0.677 and from 0.656 to 0.774, with the lowest observed in the AN and the highest in BC breed. The average breed genetic diversity was 0.655 for AN and 0.766 for BC chickens.

3. According to the neighbour-joining (NJ) method, three main clusters were identified in the NJ phylogenetic tree with AN and RQ breeds in one clade, HH and HM breeds in the second clade and TS, HJ, AH and BC breeds in the third clade.

4. Based on STRUCTURE analysis, the most likely cluster number of all breeds was K = 4, whereby HH and HM breeds formed one cluster and AH, BC, HJ and TS formed another, and RQ, AN chicken formed their own distinct cluster. These results indicated that HH and HM breeds had similar genetic background, as did the breeds of AH, BC, HJ and TS. RQ, AN breed had unique genetic backgrounds, distinct from the other breeds. Genetic introgression was detected from AN to HH and HM.

5. The results of the current study can be used as baseline genetic information to implement effective conservation programs and to make better use of these local chicken breeds, especially for the AN, RQ and TS breeds.     

Implementation of genetic evaluation and mating designs for the endangered local pig breed ‘Bunte Bentheimer’

A pedigree including 1538 individuals of the endangered pig breed ‘Bunte Bentheimer’ and 3008 records of the fertility traits ‘number of piglets born alive’ (NBA) and ‘number of piglets weaned’ (NW) were used to i) characterize the population structure, ii) to estimate genetic (co)variance components and estimated breeding values (EBVs) and iii) to use EBVs for the application of the concept of optimal genetic contributions. The average coefficient of inbreeding increased from F = 0.103 to F = 0.121 within the two recent cohorts. Average rate of inbreeding amounted to 1.66%, which resulted in an effective population size of N_e = 30 animals in the recent cohort. Average generation interval was 3.07 years considering the whole pedigree, and in total, only 612 sows and boars generated offspring. Estimated heritabilities for both traits NBA and NW were 0.12, and the estimated genetic correlation between both traits was 0.96. The variance component due to the service sire was higher than in commercial pig breeds, presumably due to the widespread use of natural service boars. The EBVs for NBA from 333 selection candidates (63 boars and 270 sows) were used to determine optimal genetic contributions. Based on selected animals and their optimal genetic contributions, specific mating designs were evaluated to minimize inbreeding in the next generation. Best results were achieved when using a simulated annealing algorithm and allowing artificial insemination.