Effects of Long-Term Selection in the Border Collie Dog Breed: Inbreeding Purge of Canine Hip and Elbow Dysplasia

Pedigree data of 13,339 border collie dog was collected along with canine hip dysplasia (CHD) and canine elbow dysplasia (CED) records (1352 CHD and 524 CED), and an inbreeding–purging (IP) model was created. Ancestral inbreeding coefficients were calculated by using a gene dropping simulation method with GRain 2.2 software. Cumulative logit models (CLM) for CHD and CED were fitted using a logit-link Poisson distribution and the classical (F_W), and ancestral inbreeding (F_BAL, F_KAL, and F_KAL_NEW) coefficients as linear regression coefficients. The effective population size was calculated from F_W and decreased in the examined period along with an increase of F_W; however, slight differences were found as a consequence of breeding dog imports. CHD values were lowered by the expansion of F_BAL, as the alleles had been inbred in the past. For CHD, signs of purging were obtained. There was a positive trend regarding the breeding activity (both sire and dam of the future litters should be screened and certified free from CHD and CED), as years of selection increased the frequency of alleles with favorable hip and elbow conformation. Division of the ancestral inbreeding coefficient showed that alleles that had been identical by descent (IBD) for the first time (F_KAL_NEW) had a negative effect on both traits, while F_KAL has shown favorable results for alleles IBD in past generations. Some authors had proven this phenomenon in captive populations or experimental conditions; however, no evidence of inbreeding purge has ever been described in dog populations. Despite the various breeding practices, it seems that alleles of these polygenic disorders could be successfully purged out of the population with long-term selection.

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Effects of Long Term Selection in the Border Collie Dog Breed: Inbreeding Purge of Canine Hip and Elbow Dysplasia

10.20944/preprints202008.0027.v1 ◽

2020 ◽

Author(s):

Virág Ács ◽

György Kövér ◽

János Farkas ◽

Árpád Bokor ◽

István Nagy

Keyword(s):

Simulation Method ◽

Inbreeding Coefficient ◽

Positive Trend ◽

Pedigree Data ◽

Effective Population ◽

Experimental Conditions ◽

Term Selection ◽

The Past ◽

Elbow Dysplasia

Pedigree data of 13 339 border collie dog was collected along with hip and elbow dysplasia records (1352 CHD and 524 CED), and an inbreeding-purging (IP) model was created to detect possible purging. Ancestral inbreeding coefficients were calculated by gene dropping simulation method (Ballou, 1997; Kalinowski, 2000) with GRain 2.0 (Baumung et al., 2015) software. GLMM models were created to the examined traits fitted with a log-link Poisson distribution, added to the estimated values of classical inbreeding coefficient (F_W), and the ancestral inbreeding (F_BAL, F_KAL, F_KAL_NEW) as covariates. The effective population size decreased in the examined period along with the increase of F_W however, slight differences were found as a consequence of breeding dog imports. CHD values were getting lower by the expansion of F_BAL as the alleles were inbred in the past. For CHD signs of purging were obtained. There was a positive trend regarding the breeding activity (both sire and dam of the future litters should be screened and certified free from CHD and CED), as years of selection increased the frequency of alleles with favorable hip and elbow conformation. Division of the ancestral inbreeding coefficient shows that alleles IBD for the first time (F_KAL_NEW) had a negative effect on both traits, while F_KAL shows favorable results for alleles IBD in the past generations. Some authors had proven this phenomenon in captive populations or experimental conditions however, no evidence of inbreeding purge has ever been described in dog populations. Despite the various breeding practices, it seems, that alleles of these polygenic disorders could be successfully purged out of the population with long term selection.

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Optimum selection intensities in artificial selection programmes: an experimental evaluation

Genetics Research ◽

10.1017/s0016672300017535 ◽

1977 ◽

Vol 30 (2) ◽

pp. 115-119 ◽

Cited By ~ 4

Author(s):

R. Frankham

Keyword(s):

Experimental Evaluation ◽

Selection Intensity ◽

Effective Population ◽

Term Selection ◽

Optimum Selection ◽

Selection For ◽

Selection Intensities ◽

Selection Of ◽

Better Than

SUMMARYAn experimental evaluation of Robertson's (1970) theory concerning optimum intensities of selection for selection of varying durations has been carried out using published results from a long term selection study in Drosophila. Agreement of predicted rankings of treatments with expectations was excellent for low values of t/T (generations/total number scored) but poor for larger values of t/T. This was due to the 20% selection intensity treatments responding worse than expected and the 40% treatments relatively better than expected. Several possible reasons for the discrepancies exist but the most likely explanation is considered to be the greater reduction in effective population size due to selection in treatments with more intense selection.

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Effect of heavy metals on the readaptive processes in the urinary bladder

Bangladesh Journal of Medical Science ◽

10.3329/bjms.v18i1.39558 ◽

2018 ◽

Vol 18 (1) ◽

pp. 100-106

Author(s):

Anatolii Romaniuk ◽

Vladyslav Sikora ◽

Yulia Lуndіna ◽

Mykola Lуndіn ◽

Natalia Hyriavenko ◽

...

Keyword(s):

Heavy Metals ◽

Vitamin E ◽

Urinary Bladder ◽

Medical Science ◽

Adaptation Period ◽

Experimental Conditions ◽

Laboratory Rats ◽

Negative Effect ◽

High Concentrations

Introduction: Heavy metals (HM) are dangerous elements due to their toxicity and prevalence play an important role in the environmental pollution and hazards to health risk. Impact of HM at high concentrations may lead to the failures of urinary bladder (UB) structure and functions. The aim of our study was to determine the readaptive changes in the UB of the rats and effectiveness of vitamin E using after the long-term intake of the HMS mixtures. Materials and Methods: We used mature male laboratory rats which were divided into three series with special experimental conditions after the influence of HM. The detailed analysis of the UB state was performed by using morphometric, spectrophotometric, histological and electron microscopy methods. Results: We had determined that the long-term intake of HM caused the significant increase of their accumulation in the tissue and morphometric changes of UB. Obtained results after the cancelation of the HM effect demonstrate smooth morphological restructuring of the UB wall with the reduction of difference of accumulation and morphometric indicators with control. The adjustment of vitamin E during there adaptation period showed better result recovery and optimization of all parameters, but they haven’t completely returned to normal state. Conclusions: The influence of HMS mixture led to significant negative effect on the UB at all stages of research. However, under the conditions of readaptation the tendency towards a certain stabilization of all indicators was observed, but they didn’t completely pass to the end of the study. The vitamin E using has caused the acceleration and improved the development of readaptive change after HM exposure. Bangladesh Journal of Medical Science Vol.18(1) 2019 p.100-106

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Genetic Variability in Polish Lowland Sheepdogs Assessed by Pedigree and Genomic Data

Animals ◽

10.3390/ani10091520 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1520

Author(s):

Paula Wiebke Michels ◽

Ottmar Distl

Keyword(s):

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Ductus Arteriosus ◽

Genomic Data ◽

Reference Population ◽

Pedigree Data ◽

Effective Population ◽

Inbreeding Coefficients ◽

Candidate Loci

Genetic variability of Polish Lowland Sheepdog (PON) population was evaluated using both pedigree and genomic data. The analyzed pedigree encompassed 8628 PONs, including 153 individuals genotyped on the Illumina CanineHD BeadChip. Runs of homozygosity (ROH) were defined for homozygous stretches extending over 60 to 4300 kb. The inbreeding coefficients FPed based on pedigree data and FROH50 based on ROHs were at 0.18 and 0.31. The correlation between both was 0.41 but 0.52 when excluding animals with less than seven complete generations. The realized effective population size (Ne¯) was 22.2 with an increasing trend over years. Five PONs explained 79% of the genetic diversity of the reference population. The effective population size derived from linkage disequilibrium measured by r² was 36. PANTHER analysis of genes in ROHs shared by ≥50% of the PONs revealed four highly over- or underrepresented biological processes. One among those is the 7.35 fold enriched “forelimb morphogenesis”. Candidate loci for hip dysplasia and patent ductus arteriosus were discovered in frequently shared ROHs. In conclusion, the inbreeding measures of the PONs were high and the genetic variability small compared to various dog breeds. Regarding Ne¯, PON population was minimally endangered according to the European Association for Animal Production.

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Models of long-term artificial selection in finite population with recurrent mutation

Genetics Research ◽

10.1017/s001667230002485x ◽

1986 ◽

Vol 48 (2) ◽

pp. 125-131 ◽

Cited By ~ 27

Author(s):

William G. Hill ◽

Jonathan Rasbash

Keyword(s):

Population Size ◽

First Generation ◽

Finite Population ◽

Effective Population ◽

Term Selection ◽

Cumulative Response ◽

Mean And Variance ◽

The Mean ◽

Selection For

SummaryThe effects of mutation on mean and variance of response to selection for quantitative traits are investigated. The mutants are assumed to be unlinked, to be additive, and to have their effects symmetrically distributed about zero, with absolute values of effects having a gamma distribution. It is shown that the ratio of expected cumulative response to generation t from mutants, , and expected response over one generation from one generation of mutants, , is a function of t/N, where t is generations and N is effective population size. Similarly, , is a function of t/N, where is the increment in genetic variance from one generation of mutants. The mean and standard deviation of response from mutations relative to that from initial variation in the population, in the first generation, are functions of . Evaluation of these formulae for a range of parameters quantifies the important role that population size can play in response to long-term selection.

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Long-term selection for protein amount over 70 generations in mice

Genetics Research ◽

10.1017/s0016672398003401 ◽

1998 ◽

Vol 72 (2) ◽

pp. 93-109 ◽

Cited By ~ 15

Author(s):

LUTZ BÜNGER ◽

ULLA RENNE ◽

GERHARD DIETL ◽

SIEGFRIED KUHLA

Keyword(s):

Body Weight ◽

Selection Response ◽

Direct Selection ◽

Control Line ◽

Phenotypic Variance ◽

Effective Population ◽

Term Selection ◽

General Importance ◽

Selection For

Based on the outbred mouse strain Fzt: Du, which has been obtained by systematic crossing of four inbred and four outbred lines, a long-term selection experiment was carried out for total protein amount (PA) in the carcass, starting in 1975. An unselected control line (CO) was kept under the same management but without continuous protein analysis. The protein amount of male carcasses at 42 days of age (P42) increased from 2·9 g in generation 0 to 5·2 g at generation 70, representing 97% of a theoretical selection limit. The total selection response amounts to 2·3 g, which is about 80% above the initial value and corresponds to 9σp or 12σA . The estimated realized heritability of protein amount decreased from 0·56 to 0·03 at generation 70, which was due to an increase in phenotypic variance from 0·065 to 0·24 g2 and a reduction in genetic variance from 0·04 to 0·01 g2. Half the selection response was obtained after about 18 to 23 generations, a half-life of 0·25 to 0·3 Ne. The maximum selection response was 0·094 g/generation and the response was 0·01 g/generation at generation 70. The measurements of body weights at 0, 10, 21, 42 and 63 days throughout the experiment showed a strong correlated effect for all weights. The PA mice are one of the heaviest lines of mice ever reported, and do not differ significantly in their body composition from control mice at 42 days. The direct selection response was due primarily to increased general growth. Body weight and protein amount are phenotypically and genetically highly correlated (rp=0·82, rA≈1); however, selection for body weight led to fatter animals, whereas selection for protein opposed increased fatness (at least until selection age). This may be of general importance in animal breeding. The comparatively high selection response in this experiment seems due to the heterogeneity of the base population, the relatively high effective population size, and the duration of the experiment.

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Estimation of Additive and Non-Additive Genetic Variances of Body Weight, Egg Weight and Egg Production for Quails (Coturnix coturnix japonica) with an Animal Model Analysis

Archives Animal Breeding ◽

10.5194/aab-49-300-2006 ◽

2006 ◽

Vol 49 (3) ◽

pp. 300-307 ◽

Cited By ~ 3

Author(s):

N. Mielenz ◽

R. R. Noor ◽

L. Schüler

Keyword(s):

Animal Model ◽

Body Weight ◽

Egg Production ◽

Additive Model ◽

The Body ◽

Phenotypic Variance ◽

Egg Weight ◽

Term Selection ◽

Inbreeding Coefficients

Abstract. This study estimates the additive and non-additive variances for egg production and body weight traits of two lines of quails from a long-term selection with the help of the REML method. For the body weight of 42-day-old females (BW42f) and males (BW42m), a total of 7,934 records for line 1 and 7,214 records for line 2 from 21 generations were used in our analyses. Additionally, 1,717 records of females from line 1 and 1,671 records of females from line 2 contained information on their egg production at an age of 42 to 200 days (EN200), on the average egg weight for the first 11 weeks of their laying season (EW1), on the average egg weight from weeks 12 to 23 (EW2), and on their body weight at an age of 200 days (BW200f). A multivariate additive animal model and one-trait dominance models, which include the inbreeding coefficients as covariates, were fitted to the data. The estimates of the heritability gained from our dominance models were smaller than those from the additive model. For line 1, the heritability values decreased for EN200 from 0.35 to 0.32, for EW1 from 0.66 to 0.56, for BW200f from 0.42 to 0.38, and for BW200m from 0.51 to 0.49, respectively. For the first line, the respective ratio (d2) of the dominance variance to the phenotypic variance for EN200, EW1, BW200f and BW200m was 0.08, 0.22, 0.09 and 0.21, and the values for the second line were 0.12, 0.06, 0.001 and 0.23.

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Population Structure Analysis of the Border Collie Dog Breed in Hungary

Animals ◽

10.3390/ani9050250 ◽

2019 ◽

Vol 9 (5) ◽

pp. 250 ◽

Cited By ~ 5

Author(s):

Virág Ács ◽

Árpád Bokor ◽

István Nagy

Keyword(s):

Genetic Diversity ◽

Reference Population ◽

Inbreeding Coefficient ◽

Pedigree Data ◽

Effective Population ◽

Inbreeding Coefficients ◽

Population Structure Analysis ◽

Dog Breed ◽

Fixation Indices ◽

Mixed Line

Pedigree data of the Border Collie dog breed were collected in Hungary to examine genetic diversity within the breed and its different lines. The database was based on available herd books dating from the development of the breed (in the late 1800s) to the present day. The constructed pedigree file consisted of 13,339 individuals, of which 1566 dogs (born between 2010 and 2016) composed the alive reference population which was active from breeding perspective. The breed is subdivided by phenotype, showing a thicker coat, harmonic movement, a wide skull, and heavier bones for the show type, and a thinner or sometimes short coat and smaller body for the working line, while the mixed line is quite heterogeneous (a combination of the above). Thus, the reference population was dissected according to the existing lines. The number of founders was 894, but eight individuals were responsible for contributing 50% of the genetic variability. The reference population had a pedigree completeness of 99.6% up to 15 generations and an inbreeding coefficient of 9.86%. Due to the changing breed standards and the requirements of the potential buyers, the effective population size substantially decreased between 2010 and 2016. Generation intervals varied between 4.09 and 4.71 years, where the sire paths were longer due to the later initial age of breeding in males compared to females. Genetic differences among the existing lines calculated by fixation indices are not significant; nonetheless ancestral inbreeding coefficients are able to show contrasts.

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Genetic Diversity and the Impact of the Breed Proportions of US Brown Swiss in German Brown Cattle

Animals ◽

10.3390/ani11010152 ◽

2021 ◽

Vol 11 (1) ◽

pp. 152

Author(s):

Anna Wirth ◽

Jürgen Duda ◽

Ottmar Distl

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Reference Population ◽

Pedigree Data ◽

Effective Population ◽

Brown Swiss ◽

Inbreeding Coefficients ◽

Loss Of Genetic Diversity ◽

The Impact

Increase of inbreeding and loss of genetic diversity have large impact on farm animal genetic resources. Therefore, the aims of the present study were to analyse measures of genetic diversity as well as recent and ancestral inbreeding using pedigree data of the German Brown population, and to identify causes for loss of genetic diversity. The reference population included 922,333 German Brown animals born from 1990 to 2014. Pedigree depth and completeness reached an average number of complete equivalent generations of 6.24. Estimated effective population size for the German Brown reference population was about 112 with a declining trend from 141 to 95 for the birth years. Individual inbreeding coefficients increased from 0.013 to 0.036. Effective number of founders, ancestors and founder genomes of 63.6, 36.23 and 20.34 indicated unequal contributions to the reference population. Thirteen ancestors explained 50% of the genetic diversity. Higher breed proportions of US Brown Swiss were associated with higher levels of individual inbreeding. Ancestral inbreeding coefficients, which are indicative for exposure of ancestors to identical-by-descent alleles, increased with birth years but recent individual inbreeding was higher than ancestral inbreeding. Given the increase of inbreeding and decline of effective population size, measures to decrease rate of inbreeding and increase effective population size through employment of a larger number of sires are advisable.

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Assessment of the Genetic Diversity of a Local Pig Breed Using Pedigree and SNP Data

Genes ◽

10.3390/genes12121972 ◽

2021 ◽

Vol 12 (12) ◽

pp. 1972

Author(s):

Emil Krupa ◽

Nina Moravčíková ◽

Zuzana Krupová ◽

Eliška Žáková

Keyword(s):

Genetic Diversity ◽

Correlation Coefficients ◽

Pedigree Analysis ◽

Minimum Size ◽

Snp Analysis ◽

Effective Population ◽

Inbreeding Coefficients ◽

Snp Data ◽

Inbreeding Rate

Herein, the genetic diversity of the local Přeštice Black-Pied pig breed was assessed by the simultaneous analysis of the pedigree and single nucleotide polymorphism (SNP) data. The information about sire line, dam, date of birth, sex, breeding line, and herd for 1971 individuals was considered in the pedigree analysis. The SNP analysis (n = 181) was performed using the Illumina PorcineSNP60 BeadChip kit. The quality of pedigree and SNPs and the inbreeding coefficients (F) and effective population size (Ne) were evaluated. The correlations between inbreeding based on the runs of homozygosity (FROH) and pedigree (FPED) were also calculated. The average FPED for all animals was 3.44%, while the FROH varied from 10.81% for a minimum size of 1 Mbp to 3.98% for a minimum size of 16 Mbp. The average minor allele frequency was 0.28 ± 0.11. The observed and expected within breed heterozygosities were 0.38 ± 0.13 and 0.37 ± 0.12, respectively. The Ne, obtained using both the data sources, reached values around 50 animals. Moderate correlation coefficients (0.49–0.54) were observed between FPED and FROH. It is necessary to make decisions that stabilize the inbreeding rate in the long-term using optimal contribution selection based on the available SNP data.

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