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

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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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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Population structure of Czech cold-blooded breeds of horses

Archives Animal Breeding ◽

10.5194/aab-54-1-2011 ◽

2011 ◽

Vol 54 (1) ◽

pp. 1-9

Author(s):

L. Vostrý ◽

Z. Čapková ◽

J. Přibyl ◽

B. Hofmanová ◽

H. Vostrá Vydrová ◽

...

Keyword(s):

Population Structure ◽

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Inbreeding Coefficient ◽

Effective Population ◽

The Czech Republic ◽

Generation Interval ◽

Average Value ◽

Inbreeding Coefficients

Abstract. In order to estimate effective population size, generation interval and the development of inbreeding coefficients (Fx) in three original breeds of cold-blooded horses kept in the Czech Republic: Silesian Noriker (SN), Noriker (N) and Czech-Moravian Belgian horse (CMB) all animals of the particular breeds born from 1990 to 2007 were analysed. The average values of generation interval between parents and their offspring were: 8.53 in SN, 8.88 in N and 8.56 in CMB. Average values of effective population size were estimated to be: 86.3 in SN, 162.3 in N and 104.4 in CMB. The average values of inbreeding coefficient were 3.13 % in SN stallions and 3.39 % in SN mares, in the N breed 1.76 % and 1.26 % and in the CMB breed 3.84 % and 3.26 % respectively. Overall averages of Fx were: 3.23 %, 1.51 % and 3.55 % for the breeds SN, N and CMB. The average value of inbreeding coefficient Fx increased by 1.22 % in SN, by 0.35 % in N and by 1.01 % in CMB, respectively. This may lead to a reduction in genetic variability. Reduction in genetic variability could be either controlled in cooperation with corresponding populations of cold-blooded breeds in other European countries or controlled by number of sires used in population

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Genetic diversity, viability and conservation value of the global captive population of the Moroccan Royal lions

PLoS ONE ◽

10.1371/journal.pone.0258714 ◽

2021 ◽

Vol 16 (12) ◽

pp. e0258714

Author(s):

Kristina Lehocká ◽

Simon A. Black ◽

Adrian Harland ◽

Ondrej Kadlečík ◽

Radovan Kasarda ◽

...

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

North Africa ◽

Reference Population ◽

Captive Population ◽

Effective Number ◽

Pedigree Data ◽

Effective Population ◽

Loss Of Diversity

This study evaluates the diversity of the so-called ‘Moroccan Royal lions’ using genealogical information. Lions are no longer extant in North Africa, but the previous wild population was an important element of the now-recognised northern subspecies (Panthera leo leo) that ranged across West Africa, North Africa and the Middle East into India. The remaining captive population of ‘Moroccan Royal lions’ seems to be significantly endangered by the loss of diversity due to the effective population size decrease. The pedigree file of this captive lion population consisted of 454 individuals, while the reference population included 98 animals (47 males and 51 females). The completeness of the pedigree data significantly decreased with an increasing number of generations. The highest percentage of pedigree completeness (over 70%) was achieved in the first generation of the reference population. Pedigree-based parameters derived from the common ancestor and gene origin were used to estimate the state of diversity. In the reference population, the average inbreeding coefficient was 2.14%, while the individual increase in inbreeding over generations was 2.31%. Overall, the reference population showed lower average inbreeding and average relatedness compared with the pedigree file. The number of founders (47), the effective number of founders (24) and the effective number of ancestors (22) were estimated in the reference population. The effective population size of 14.02 individuals confirms the critically endangered status of the population and rapid loss of diversity in the future. Thus, continuous monitoring of the genetic diversity of the ‘Moroccan Royal lion’ group is required, especially for long-term conservation management purposes, as it would be an important captive group should further DNA studies establish an affinity to P. leo leo.

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IDENTITY COEFFICIENTS IN FINITE POPULATIONS. I. EVOLUTION OF IDENTITY COEFFICIENTS IN A RANDOM MATING DIPLOID DIOECIOUS POPULATION

Genetics ◽

10.1093/genetics/86.3.697 ◽

1977 ◽

Vol 86 (3) ◽

pp. 697-713

Author(s):

C Chevalet ◽

M Gillois ◽

R F Nassar

Keyword(s):

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Random Mating ◽

Matrix Multiplication ◽

Inbred Lines ◽

Inbreeding Coefficient ◽

Effective Population ◽

The Mean ◽

Over Time

ABSTRACT Properties of identity relation between genes are discussed, and a derivation of recurrent equations of identity coefficients in a random mating, diploid dioecious population is presented. Computations are run by repeated matrix multiplication. Results show that for effective population size (Ne) larger than 16 and no mutation, a given identity coefficient at any time t can be expressed approximately as a function of (1—f), (1—f)3 and (1—f)6, where f is the mean inbreeding coefficient at time t. Tables are presented, for small Ne values and extreme sex ratios, showing the pattern of change in the identity coefficients over time. The pattern of evolution of identity coefficients is also presented and discussed with respect to N eu, where u is the mutation rate. Applications of these results to the evolution of genetic variability within and between inbred lines are discussed.

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The population genetics of haplo-diploids and X-linked genes

Genetics Research ◽

10.1017/s0016672300026550 ◽

1984 ◽

Vol 44 (3) ◽

pp. 321-341 ◽

Cited By ~ 48

Author(s):

P. J. Avery

Keyword(s):

Population Genetics ◽

Genetic Variability ◽

Population Size ◽

Effective Population Size ◽

Disease Genes ◽

Effective Population ◽

Random Drift ◽

Mutation Pressure ◽

Electrophoretic Data ◽

Fitness Parameters

SUMMARYFrom the available electrophoretic data, it is clear that haplodiploid insects have a much lower level of genetic variability than diploid insects, a difference that is only partially explained by the social structure of some haplodiploid species. The data comparing X-linked genes and autosomal genes in the same species is much more sparse and little can be inferred from it. This data is compared with theoretical analyses of X-linked genes and genes in haplodiploids. (The theoretical population genetics of X-linked genes and genes in haplodiploids are identical.) X-linked genes under directional selection will be lost or fixed more quickly than autosomal genes as selection acts more directly on X-linked genes and the effective population size is smaller. However, deleterious disease genes, maintained by mutation pressure, will give higher disease incidences at X-linked loci and hence rare mutants are easier to detect at X-linked loci. Considering the forces which can maintain balanced polymorphisms, there are much stronger restrictions on the fitness parameters at X-linked loci than at autosomal loci if genetic variability is to be maintained, and thus fewer polymorphic loci are to be expected on the X-chromosome and in haplodiploids. However, the mutation-random drift hypothesis also leads to the expectation of lower heterozygosity due to the decrease in effective population size. Thus the theoretical results fit in with the data but it is still subject to argument whether selection or mutation-random drift are maintaining most of the genetic variability at X-linked genes and genes in haplodiploids.

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Population structure of the Sahiwal breed in Pakistan

Animal Science ◽

10.1017/s1357729800008304 ◽

1995 ◽

Vol 60 (2) ◽

pp. 163-168 ◽

Cited By ~ 6

Author(s):

A. Dahlin ◽

U. N. Khan ◽

A. H. Zafar ◽

M. Saleem ◽

M. A. Chaudhry ◽

...

Keyword(s):

Population Structure ◽

Population Size ◽

Effective Population Size ◽

Breeding Population ◽

Effective Population ◽

Data Set ◽

Inbreeding Coefficients ◽

Sahiwal Cows ◽

The Mean ◽

Average Population Size

AbstractThe present study was undertaken to assist conservation and improvement schemes in the Sahiwal breed of cattle in Pakistan. A data set, consisting of records of 244 pure Sahiwal breeding bulls and 5247 cows, the latter representing about 80% of all recorded Sahiwal cows in Pakistan born during a period covering about 20 years, was analysed with regard to inbreeding, additive relationships, effective population size and generation intervals. Average inbreeding coefficients of 1224 cows and 49 bulls, for which at least the grandparents and great-grandsires were known, were 0·043 and 0·046, respectively. About two-thirds of the inbreeding was due to matings between animals with parents or grandparents in common. The mean additive relationship among the cows was 0·062, with within-herd averages ranging from 0·087 to 0·358. The average population size in a subdata set of recorded Sahiwal cattle from 1980 to 1984 was 1612, whereas the most likely estimate of the effective population size was about 30 animals for the same active breeding population. The study indicated the immediate need for an active conservation programme whereby the Sahiwal subpopulations of India and Kenya also should be involved.

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Analysis of genetic diversity in four Canadian swine breeds using pedigree data

Canadian Journal of Animal Science ◽

10.4141/cjas10002 ◽

2010 ◽

Vol 90 (3) ◽

pp. 331-340 ◽

Cited By ~ 11

Author(s):

M G Melka ◽

F. Schenkel

Keyword(s):

Genetic Diversity ◽

Population Size ◽

Effective Population Size ◽

Genetic Drift ◽

Relative Proportion ◽

Random Genetic Drift ◽

Pedigree Data ◽

Effective Population ◽

Animal Genetic Resources ◽

Loss Of Genetic Diversity

Conservation of animal genetic resources entails judicious assessment of genetic diversity as a first step. The objective of this study was to analyze the trend of within-breed genetic diversity and identify major causes of loss of genetic diversity in four swine breeds based on pedigree data. Pedigree files from Duroc (DC), Hampshire (HP), Lacombe (LC) and Landrace (LR) containing 480 191, 114 871, 51 397 and 1 080 144 records, respectively, were analyzed. Pedigree completeness, quality and depth were determined. Several parameters derived from the in-depth pedigree analyses were used to measure trends and current levels of genetic diversity. Pedigree completeness indexes of the four breeds were 90.4, 52.7, 89.6 and 96.1%, respectively. The estimated percentage of genetic diversity lost within each breed over the last three decades was approximately 3, 22, 12 and 2%, respectively. The relative proportion of genetic diversity lost due to random genetic drift in DC, HP, LC and LR was 74.5, 63.6, 72.9 and 60.0%, respectively. The estimated current effective population size for DC, HP, LC and LR was 72, 14, 36 and 125, respectively. Therefore, HP and LC have been found to have lost considerable genetic diversity, demanding priority for conservation. Key words: Genetic drift, effective population size

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On the prediction of simultaneous inbreeding coefficients at multiple loci

Genetics Research ◽

10.1017/s0016672303006633 ◽

2004 ◽

Vol 83 (2) ◽

pp. 113-120 ◽

Cited By ~ 8

Author(s):

JULES HERNÁNDEZ-SÁNCHEZ ◽

CHRIS S. HALEY ◽

JOHN A. WOOLLIAMS

Keyword(s):

Population Size ◽

Effective Population Size ◽

Conditional Probability ◽

Prior Probability ◽

Effective Population ◽

Infinite Population ◽

Inbreeding Coefficients ◽

Multiple Loci ◽

Monoecious Population ◽

Marker Spacing

A new deterministic method for predicting simultaneous inbreeding coefficients at three and four loci is presented. The method involves calculating the conditional probability of IBD (identical by descent) at one locus given IBD at other loci, and multiplying this probability by the prior probability of the latter loci being simultaneously IBD. The conditional probability is obtained applying a novel regression model, and the prior probability from the theory of digenic measures of Weir and Cockerham. The model was validated for a finite monoecious population mating at random, with a constant effective population size, and with or without selfing, and also for an infinite population with a constant intermediate proportion of selfing. We assumed discrete generations. Deterministic predictions were very accurate when compared with simulation results, and robust to alternative forms of implementation. These simultaneous inbreeding coefficients were more sensitive to changes in effective population size than in marker spacing. Extensions to predict simultaneous inbreeding coefficients at more than four loci are now possible.

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