Pedigree analysis of Polish warmblood horses participating in riding performance tests

2015 ◽  
Vol 95 (1) ◽  
pp. 21-29 ◽  
Author(s):  
Alicja Borowska ◽  
Tomasz Szwaczkowski
Keyword(s):  
Genetic Diversity ◽  
Performance Test ◽  
Pedigree Analysis ◽  
Pedigree Information ◽  
Performance Tests ◽  
Effective Number ◽  
Horse Population ◽  
Inbreeding Coefficients ◽  
Discrete Generation ◽  
Inbreeding Rate

Borowska, A. and Szwaczkowski, T. 2015. Pedigree analysis of Polish warmblood horses participating in riding performance tests. Can. J. Anim. Sci. 95: 21–29. The aim of this study was to describe the population structure and genetic diversity in Polish warmblood horse population participating in the performance test. The reference population consisted of 596 stallions and 866 mares that participated in stationary performance tests conducted between 2002 and 2011 in Poland. The pedigree data contained 15 452 individuals. Completeness of pedigree information was assessed by two measures: percentage of animals with both parents known and discrete generation equivalent. Individual inbreeding coefficients, coancestry coefficient, individual increase in inbreeding, founder equivalent, founder genome equivalent, effective number of non-founders and genetic diversity loss were estimated to characterize the genetic diversity of the population. The average number of discrete generation equivalents reached 4.50 for observed stallions and 5.04 for mares, which shows good pedigree completeness. Pedigree analysis showed that 34% of the stallions and 44% of mares had inbreeding coefficients above zero. The average coancestry was 0.39% in the whole tested population. Average inbreeding rate of studied populations was very low (0.46%). The effective number of founders was 560. Generally, the inbreeding rate was low; genetic diversity was observed at a constant level for mares and only a small decrease was noticed for stallion. However, further studies are needed in this area.

scholarly journals Genetic diversity of Brazilian Brahman cattle by pedigree analysis

2018 ◽  
Vol 53 (1) ◽  
pp. 74-79 ◽  
Author(s):  
Ligia Cavani ◽  
Rafael Medeiros de Oliveira Silva ◽  
Luis Orlando Duitama Carreño ◽  
Rafael Keith Ono ◽  
Tássia Souza Bertipaglia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Drift ◽  
Pedigree Analysis ◽  
Genetic Bottleneck ◽  
Brazilian Population ◽  
Pedigree Information ◽  
Effective Number ◽  
Inbreeding Coefficients ◽  
Brahman Cattle

Abstract: The objective of this work was to evaluate the genetic diversity of Brahman cattle in Brazil with pedigree analysis. Genealogical records of a subpopulation were used considering all pedigree information (Pt) and the pedigree information divided into two periods (P1, from 1994 to 2004; and P2, from 2005 to 2012) or according to the raising system (Ppt, animals on pasture; or Pst, on stable). Estimates were obtained for average inbreeding coefficients, generation intervals (GI), number of equivalent known generation (CGE), number of founders (Nf), effective number of founders (fe), effective number of ancestors (fa), and founder genome equivalents (fg). The average inbreeding coefficients were 11.97, 7.79, 11.95, 11.74, and 11.31% for Pt, P1, P2, Ppt, and Pst, respectively. Average GI was 4.4 years, whereas CGE was 3.18. The fe values were similar to those of fa, which were greater than those of fg. The fe/fa and fg/fe ratios were close to 1, which indicates no genetic bottleneck and small losses by genetic drift. The genetic diversity in the Brazilian population of Brahman breed is not significantly reduced.

Analysis of population structure and genetic variability in Iranian buffaloes (Bubalus bubalis) using pedigree information

2016 ◽  
Vol 56 (7) ◽  
pp. 1130 ◽  
Author(s):  
Navid Ghavi Hossein-Zadeh
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Genetic Variability ◽  
Bubalus Bubalis ◽  
Pedigree Analysis ◽  
Inbreeding Coefficient ◽  
Pedigree Information ◽  
Genome Equivalent ◽  
Effective Number ◽  
Inbreeding Coefficients

The objective of this study was to use pedigree analysis to evaluate the population structure, genetic variability and inbreeding in Iranian buffaloes. The analysis was based on the pedigree information of 42 285 buffaloes born from 549 sires and 6376 dams within 1697 herds. Pedigree information used in this study was collected during 1976 to 2012 by the Animal Breeding Centre of Iran. The CFC program was applied to calculate pedigree statistics and genetic structure analysis of the Iranian buffaloes. Also, the INBUPGF90 program was used for calculating regular inbreeding coefficients for individuals in the pedigree. The analysis of pedigree indicated that inbreeding coefficient ranged from 0% to 31% with an average of 3.42% and the trend of inbreeding was significantly positive over the years (P < 0.0001). Average coancestry was increased in recent years and overall generation interval was 6.62 years in Iranian buffaloes. Founder genome equivalent, founder equivalent, effective number of founders and effective number of non-founders were increased from 1976 to 2002, but their values decreased from 2002 onwards. A designed mating system to avoid inbreeding may be applied to this population of buffalo to maintain genetic diversity.

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

Genes ◽  
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.

scholarly journals Using pedigree information to study genetic diversity and re-evaluating a selection program in an experimental flock of Afshari sheep

2012 ◽  
Vol 55 (4) ◽  
pp. 375-384 ◽  
Author(s):  
F. Ghafouri-Kesbi
Keyword(s):  
Genetic Diversity ◽  
Phenotypic Selection ◽  
Reference Population ◽  
Pedigree Information ◽  
Selection Experiment ◽  
Founder Population ◽  
Effective Number ◽  
Effective Population ◽  
Breeding Values ◽  
Closed Population

Abstract. The purpose of this paper was to evaluate the inbreeding consequences of a short-term selection experiment which was initiated in 1998 in an Afshari sheep flock. Moreover, the conducted selection experiment was re-evaluated through assessing change in ranking of the first 10 influential ancestors when their genetic contributions were replaced with their breeding values. A total of 1714 animals were registered in the herdbook with a founder population comprised of 243 animals. The average coancestry (f) and inbreeding (F) in the reference population were 2.1% and 1.2%, respectively. Estimated value of the effective population size (Ne) was 50. The effective number of founders (fe) was estimated to be 40 and the effective number of ancestors (fa) was 34. Estimates of breeding values revealed that owing to phenotypic selection some ancestors with lower breeding values had greater contribution to the reference genome than those with greater breeding values and, for this reason, the population has been deprived from the maximum genetic improvement that could be achieved if selection was based on breeding values. The effective number of founder genomes (fg) was computed to be 23 and the effective number of non-founder genomes (fne) was 55. The index of genetic diversity decreased by almost 2.2% over the period studied. In general, decrease in genetic variability was low and Ne was not very low for a small-closed population under selection, indicating even in populations which undergo selection, besides achieving genetic gain, the rate of inbreeding is controllable if matings carefully planned.

scholarly journals Genetic Diversity of 17 Autochthonous Italian Chicken Breeds and Their Extinction Risk Status

2021 ◽  
Vol 12 ◽  
Author(s):  
Dominga Soglia ◽  
Stefano Sartore ◽  
Emiliano Lasagna ◽  
Cesare Castellini ◽  
Filippo Cendron ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Extinction Risk ◽  
Low Frequency ◽  
Effective Number ◽  
Risk Of Extinction ◽  
Chicken Breeds ◽  
Inbreeding Rate ◽  
The Mean ◽  
Endangered Status

The preservation of genetic variability of autochthonous poultry breeds is crucial in global biodiversity. A recent report revealed small breed size and potential risk of extinction of all native Italian poultry breeds; therefore, a correct assessment of their genetic diversity is necessary for a suitable management of their preservation. In this work, we provided an overview of the contribution to poultry biodiversity of some Italian autochthonous breeds reared in conservation centers devoted to local biodiversity preservation. The level of genetic diversity, molecular kinship, inbreeding, contribution to overall genetic diversity, and rate of extinction of each breed were analyzed with a set of 14 microsatellite loci in 17 autochthonous chicken breeds. To evaluate genetic variability, total number (Na), and effective number (Ne) of alleles, observed (Ho) and expected (He) heterozygosity, and F (Wright’s inbreeding coefficient) index were surveyed. The contribution of each analyzed breed to genetic diversity of the whole dataset was assessed using MolKin3.0; global genetic diversity and allelic richness contributions were evaluated. All the investigated loci were polymorphic; 209 alleles were identified (94 of which private alleles). The average number of alleles per locus was 3.62, and the effective number of alleles was 2.27. The Ne resulted lower in all breeds due to the presence of low-frequency alleles that can be easily lost by genetic drift, thus reducing the genetic variability of the breeds, and increasing their risk of extinction. The global molecular kinship was 27%, the average breed molecular kinship was 53%, and the mean inbreeding rate 43%, with a self-coancestry of 78%. Wright’s statistical analysis showed a 41% excess of homozygous due to breed genetic differences (34%) and to inbreeding within the breed (9%). Genetic variability analysis showed that 11 breeds were in endangered status. The contribution to Italian poultry genetic diversity, estimated as global genetic diversity, and ranged from 30.2 to 98.5%. In conclusion, the investigated breeds maintain a unique genetic pattern and play an important role in global Italian poultry biodiversity, providing a remarkable contribution to genetic variability.

In-depth Pedigree Analysis and Inbreeding Effect on Reproduction Traits in Sahiwal Nucleus Herd 

2021 ◽  
Author(s):  
Shabahat Mumtaz ◽  
Anupama Mukherjee ◽  
Prajwalita Pathak ◽  
Kaiser Parveen
Keyword(s):  
Genetic Diversity ◽  
Pregnancy Rate ◽  
Future Generation ◽  
Selection Response ◽  
Pedigree Analysis ◽  
Mating Strategies ◽  
Pedigree Information ◽  
Sustainable Improvement ◽  
Reproduction Traits ◽  
Negative Effect

Background: Loss of genetic diversity is allied with adverse incidents such as inbreeding depression in fitness related traits, addiction of favorable alleles and enhances fluctuation on selection response. Therefore, the study aims to monitor population structure and avoid unfavorable effects of inbreeding for sustainable improvement in breeding programme.Methods: Pedigree information on 3449 animals born from 1955-2018 was analyzed. The effect on inbreeding on Age at first calving (AFC), Service period (SP), Daughter pregnancy rate (DPR), Calving interval (CI) and pregnancy rate was seen by regression analysis.Result: The pedigree completeness index (PCI) were found to be (%) 92.32, 80.26, 65.22, 49.43% and 32.54 respectively from first to fifth generations. The estimated average inbreeding rate was 2.30% and average genetic diversity loss was 2.64%. Study also revealed significant effect of inbreeding on (AFC, CI and SP) with slightly increasing trends. Hence, it is suggested that more precise pedigree recording and planned mating strategies should be adopted to avoid negative effect of inbreeding in future generation. 

scholarly journals Pedigree analysis in four Slovak endangered horse breeds

2012 ◽  
Vol 57 (No. 2) ◽  
pp. 54-64 ◽  
Author(s):  
J. Pjontek ◽  
O. Kadlečík ◽  
R. Kasarda ◽  
M. Horný
Keyword(s):  
Genetic Diversity ◽  
Pedigree Analysis ◽  
Effective Number ◽  
Identity By Descent ◽  
Average Value ◽  
The Mean ◽  
Gene Origin

The aim of this study was to perform an analysis of genetic diversity in four endangered horse populations bred in Slovakia, describing parameters on the probability of identity by descent and gene origin. The analysed populations consisted of (reference populations in brackets) 656 (158) Hucul horses, 2052 (162) Lipizzan horses, 1951 (171) Shagya Arabian horses, and 220 (42) Slovak Sport Ponies. The equivalent complete generations ranged from 4.93 for the Slovak Sport Pony to 10.25 for the Lipizzan horses. The average value of inbreeding ranged from 2.67% for the Slovak Sport Pony to 6.26% for the Hucul. The mean average relationship coefficients varied from 3.08% for the Shagya Arabian to 9.34% for the Hucul. Individual increases in inbreeding ranged from 0.43% for the Lipizzan to 1.06% for the Hucul, while the realized effective sizes were from 117.14 to 47.67 animals. The evaluated populations were derived from 80 to 499 founders. The effective number of founders ranged from 26 to 160, while the effective number of ancestors from 7 to 32. &nbsp;

scholarly journals Inbreeding effects on body weight traits of Iranian Moghani sheep

2012 ◽  
Vol 55 (2) ◽  
pp. 171-178 ◽  
Author(s):  
N. G. Hossein-Zadeh
Keyword(s):  
Body Weight ◽  
Birth Weight ◽  
Mating System ◽  
Pedigree Information ◽  
The Third ◽  
Inbreeding Coefficients ◽  
Breeding Station ◽  
Different Ages ◽  
Inbreeding Rate

Abstract. The objective of the present study was to evaluate the effects of inbreeding on body weight at different ages in Moghani sheep. Traits included were birth weight (BW), 3-month weight (3MW), 6-month weight (6MW), 9-month weight (9MW), and yearling weight (YW). Data and pedigree information used in this study were collected at the Breeding Station of Moghani sheep, Iran during 1987-2005. All the animals were grouped into three classes according to the inbreeding coefficients obtained by their pedigree: the first class included non-inbred animals (F=0 %); and the second and third classes included inbred animals (00.10, respectively). Average inbreeding rate was 2.93 % in the pedigree of Moghani sheep. The BW of animals within second class of inbreeding was significantly higher than those of lambs belonging to the third class (P<0.05). The 3MW of animals within third class of inbreeding was significantly (P<0.05) higher than those of lambs belonging to the first and second classes. The 6MW of animals within third class of inbreeding was significantly (P<0.05) lower than those of lambs belonging to the first and second classes. Animals within third class of inbreeding had greater mean of 9MW than two other groups (P<0.05). Also, the YW of animals within second class of inbreeding was significantly (P<0.05) lower than those of lambs belonging to the first and third classes. The utilization of designed mating system could be a suitable approach to maintain the level of inbreeding under control.

scholarly journals Assessing Genetic Diversity and Estimating the Inbreeding Effect on Economic Traits of Inner Mongolia White Cashmere Goats Through Pedigree Analysis

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhiying Wang ◽  
Bohan Zhou ◽  
Tao Zhang ◽  
Xiaochun Yan ◽  
Yongsheng Yu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Inbreeding Depression ◽  
Inner Mongolia ◽  
Inbreeding Coefficient ◽  
Production Performance ◽  
Pedigree Information ◽  
Economic Traits ◽  
Inbreeding Coefficients ◽  
Cashmere Goats

Objective: The purpose of this study was to discover the population structure and genetic diversity of Inner Mongolia White Cashmere goats (IMCGs) and demonstrate the effect of inbreeding on the live body weight (LBW), cashmere yield (CY), fiber length (FL), and fiber diameter (FD) of IMCGs.Materials and Methods: All data were collected from pedigree information and production performance records of IMCGs from 1983 to 2019. The population structure and genetic diversity were analyzed by Endog 4.8 software. Inbreeding coefficients were obtained by the pedigree package in R. Then, a linear regression model was used to analyze how inbreeding influences economic traits in IMCGs. Four levels of inbreeding coefficients (Fi) were classified in this study, including Fi = 0, 0&lt; Fi ≤ 6.25, 6.25&lt; Fi ≤ 12.5 and Fi≥12.5. Variance analysis was performed to determine whether inbreeding levels had a significant effect on economic traits in IMCGs.Results: The proportions of rams and dams in IMCGs for breeding were relatively small, with values of 0.8 and 20.5%, respectively. The proportion of inbred animals in the entire population was high, with values up to 68.6%; however, the average inbreeding coefficient and relatedness coefficient were 4.50 and 8.48%, respectively. To date, the population has experienced 12 generations. The average generation interval obtained in the present study was 4.11 ± 0.01 years. The ram-to-son pathway was lowest (3.97 years), and the ewe-to-daughter pathway was highest (4.24 years). It was discovered that the LBW, CY, and FL increased by 3.88 kg, 208.7 g, and 1.151 cm, respectively, with every 1% increase in the inbreeding coefficient, and the FD decreased by 0.819 μm with every 1% increase in the inbreeding coefficient. Additionally, multiple comparison analysis indicated that when the inbreeding coefficient was higher than 6.25%, the LBW showed an obvious decreasing trend. The threshold value of inbreeding depression in the CY is 12.5%. However, inbreeding depression has not been observed in the FL and FD.Conclusion: Pedigree completeness needs to be further strengthened. The degree of inbreeding in this flock should be properly controlled when designing breeding programs.

scholarly journals Management of genetic diversity using gene dropping method based on pedigree information

2013 ◽  
Vol 56 (1) ◽  
pp. 518-526
Author(s):  
M. Khaldari ◽  
A. N. Javaremi ◽  
A. Pakdel ◽  
H. M. Yeganeh ◽  
P. Berg
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Low Frequency ◽  
Pedigree Analysis ◽  
Simulation Software ◽  
Pedigree Information ◽  
Genetic Contribution ◽  
Effective Population ◽  
Management Plans

Abstract. Preservation of genetic diversity in populations is an important task to ensure a possible longterm response to selection in animal breeding. The purpose of this study was to consider how pedigree analysis and gene dropping method could be used for management plans in order to maintain genetic variation in a population under selection of Japanese quail. Therefore, the distributions of alleles frequencies originated from founders were estimated on an actual pedigree using gene dropping simulation software. Then, genetic contribution of founders to the current population, components such as the F-statistics and effective population size were estimated. The results show that from 156 founders there are only 64 of them (22 males and 42 females) in the last generation. The average genetic contribution of a founder male and female contributing to the last generation were 1.87 and 1.40 %, respectively. A total of 87 and 95 % of the genome in the last generation were constituted by 34 and 42 founders, respectively. The effective population size decreased as inbreeding increases. The allele frequency averaged over replicates agreed with the genetic contribution. Some useful information regarding the management of genetic diversity such as the probability of allele extinction, the probability of alleles surviving at a critically low frequency and risk of future allele extinction were derived by using these distributions. Results show that pedigree analysis and gene dropping are valuable tools in optimizing decisions to preserve genetic variability.

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