Effect of inbreeding and individual increase in inbreeding on growth in Nilagiri and Sandyno breeds of sheep

2016 ◽  
Vol 58 ◽  
pp. 63-71 ◽  
Author(s):  
R. Venkataramanan ◽  
A. Subramanian ◽  
S.N. Sivaselvam ◽  
T. Sivakumar ◽  
C. Sreekumar ◽  
...  
Keyword(s):  
Growth Traits ◽  
Inbreeding Coefficient ◽  
Pedigree Information ◽  
Research Station ◽  
Sheep Breeding ◽  
Inbreeding Coefficients ◽  
Equivalent Number ◽  
Breeding Research ◽  
Percent Increase ◽  
Two Populations

SummaryIndividual increase in inbreeding coefficients (ΔFi) has been recommended as an alternate measure of inbreeding. It can account for the differences in pedigree knowledge of individual animals and avoids overestimation due to increased number of known generations. The effect of inbreeding (F) and equivalent inbreeding (EF) calculated fromΔFi, on growth traits were studied in Nilagiri and Sandyno flocks of sheep. The study was based on data maintained at the Sheep Breeding Research Station, Sandynallah. The pedigree information and equivalent number of generations were less in Sandyno compared with Nilagiri sheep. The average F and EF for the Nilagiri population were 2.17 and 2.44, respectively and the corresponding values for Sandyno sheep were 0.83 and 0.84, respectively. The trend of inbreeding over years in both the populations indicated that EF was higher during earlier generations when pedigree information was shallow. Among the significant effects of inbreeding, the depression in growth per 1 percent increase in inbreeding ranged from 0.04 kg in weaning weight to 0.10 kg in yearling weight. In general, more traits were affected by inbreeding in Nilagiri sheep, in which greater regression of growth traits was noticed with F compared with EF. Higher values of EF than F in earlier generations in both the populations indicate that EF avoided the potential overestimation of inbreeding coefficient during recent generations. In the Sandyno population, the magnitude of depression noticed among growth traits with significant effects of inbreeding was higher. The differences in response to F and EF noticed in the two populations and possible causes for the trait wise differences in response to F and EF are appropriately discussed.

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< Fi ≤ 6.25, 6.25< 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 Evaluation of selection program by assessing the genetic diversity and inbreeding effects on Nellore sheep growth through pedigree analysis

2020 ◽  
Vol 33 (9) ◽  
pp. 1369-1377
Author(s):  
Satish Kumar Illa ◽  
Gangaraju Gollamoori ◽  
Sapna Nath
Keyword(s):  
Genetic Diversity ◽  
Growth Traits ◽  
Selection Process ◽  
Reference Population ◽  
Inbreeding Coefficient ◽  
Research Station ◽  
Effective Population ◽  
Generation Interval ◽  
Nellore Sheep ◽  
Reference Cohort

Objective: The main objectives of the present study were to assess the genetic diversity,population structure and to appraise the efficiency of ongoing selective breeding program in the closed nucleus herd of Nellore sheep through pedigree analysis.Methods: Information utilized in the study was collected from the pedigree records of Livestock Research Station, Palamaner during the period from 1989 to 2016. Genealogical parameters like generation interval, pedigree completeness, inbreeding level, average relatedness among the animals and genetic conservation index were estimated based on gene origin probabilities. Lambs born during 2012 and 2016 were considered as reference population. Two animal models either with the use of Fi or ∆Fi as linear co-variables were evaluated to know the effects of inbreeding on the growth traits of Nellore sheep.Results: Average generation interval and realized effective population size for the reference cohort were estimated as 3.38±0.10 and 91.56±1.58, respectively and the average inbreeding coefficient for reference population was 3.32%. Similarly, the effective number of founders, ancestors and founder genome equivalent of the reference population were observed as 47, 37, and 22.48, respectively. Fifty per cent of the genetic variability was explained by 14 influential ancestors in the reference cohort. The ratio fe/fa obtained in the study was 1.21, which is an indicator of bottlenecks in the population. The number of equivalent generations obtained in the study was 4.23 and this estimate suggested the fair depth of the pedigree.Conclusion: Study suggested that the population had decent levels of genetic diversity and a non-significant influence of inbreeding coefficient on growth traits of Nellore lambs. However, small portion of genetic diversity was lost due to a disproportionate contribution of founders and bottlenecks. Hence, breeding strategies which improve the genetic gain, widens the selection process and with optimum levels of inbreeding are recommended for the herd.

scholarly journals Survivability in Nilagiri and Nilagiri Synthetic Sheep: Genetic and Non-Genetic Effects

2017 ◽  
Vol 12 (4) ◽  
Author(s):  
Arth B. Chaudhari ◽  
R. Rajendran ◽  
R. Venkataramanan ◽  
S. N. Sivaselvam
Keyword(s):  
Birth Weight ◽  
Significant Influence ◽  
Tamil Nadu ◽  
Genetic Factors ◽  
Research Station ◽  
Sheep Breeding ◽  
Contemporary Group ◽  
Genetic Groups ◽  
Breeding Research ◽  
Birth Type

Data on 9333 records of Sheep Breeding Research Station, Sandynallah, The Nilagiris (Tamil Nadu) available for 25 years (1989 to 2015) were analyzed for pre- and post-weaning survivability (0- 3 months, 3-6 months, 6-9 months and 9-12 months of age). The effect of various genetic and non-genetic factors, viz., breed, contemporary group of birth, birth type, inbreeding, sex and birth weight on survivability were analyzed. The least squares means for survivability during 0-3, 3-6, 6-9 and 9-12 months were 92.8 ± 0.8, 95.3 ± 0.8, 98.6 ± 0.6 and 98.2 ± 0.7 % for Nilagiri sheep and 89.9 ± 1.0, 92.9 ± 1.0, 96.9 ± 0.7 and 97.0 ± 0.8 % for Nilagiri synthetic sheep, respectively. Breed and contemporary group of birth had significant (P less than 0.01) effects on pre-weaning survivability. Post-weaning survivability was significantly different in the two genetic groups. Contemporary groups and sex of lamb had a significant effect on all the survivability traits, except that for the period from 9-12 months. Birth weight of lambs had a significant influence on early survivability traits of preweaning and 3-6 months group.

scholarly journals Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3234
Author(s):  
José Cortes-Hernández ◽  
Adriana García-Ruiz ◽  
Carlos Gustavo Vásquez-Peláez ◽  
Felipe de Jesus Ruiz-Lopez
Keyword(s):  
Inbreeding Coefficient ◽  
Pedigree Information ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Genomic Relationship ◽  
Runs Of Homozygosity ◽  
Inbreeding Coefficients ◽  
Improvement Programs ◽  
Genomic Inbreeding ◽  
Holstein Population

This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.

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 Grid search approach to discriminate between old and recent inbreeding using phenotypic, pedigree and genomic information

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Pattarapol Sumreddee ◽  
El Hamidi Hay ◽  
Sajjad Toghiani ◽  
Andrew Roberts ◽  
Samuel E. Aggrey ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Growth Traits ◽  
Average Daily Gain ◽  
Recent Common Ancestor ◽  
Pedigree Information ◽  
Grid Search ◽  
Genomic Information ◽  
The Impact ◽  
Daily Gain ◽  
Harmful Effects

Abstract Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes were trait-specific and varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration.

scholarly journals Population structure of Czech cold-blooded breeds of horses

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

scholarly journals Effects of the MHS locus on growth, carcass and meat quality traits in F<sub>2</sub> crosses between Mangalitza and Piétrain breeds

2000 ◽  
Vol 43 (3) ◽  
pp. 263-276 ◽  
Author(s):  
G. Thaller ◽  
L. Dempfle ◽  
A. Schlecht ◽  
S. Wiedemann ◽  
H. Eichinger ◽  
...  
Keyword(s):  
Meat Quality ◽  
Growth Traits ◽  
Live Weight ◽  
Negative Influence ◽  
Carcass Composition ◽  
Research Station ◽  
Dna Test ◽  
Whole Genome Scan ◽  
Group Sex ◽  
High Level

Abstract. A total of 345 F2 animals from a crossbred design Mangalitza (homozygous NN) x Piétrain (homozygous nn) were fed ad libitum at the institute's Thalhausen Research Station and slaughtered at a live weight of approximately 100 kg. MHS genotypes (67 nn, 192 Nn and 86 NN) were determined directly in a DNA test targeting the ryanodine reeeptor locus. Models for analysis of variance included sire, dam, pen, slaughter group, sex and MHS effects. Growth Performance was generally lower and carcass composition minor compared to other breeds and crosses. No significant differences were found between MHS genotypes for growth traits but NN animals tended to be less eflicient with respect to food conversion. However, nearly all measurements of the carcass showed significant differences between nn and NN which were especially pronounced for sidefat thickness (−7 1mm) fat over the musculus longissimus dorsi (−8.8 mm) and loin eye area (+8.7 cm2) as well as fat area (−5.1 cm2) We found Nn animals performing similar to NN animals due to incomplete dominance of the N allele. As expected nn had a substantial negative influence on meat quality compared to NN and Nn (e.g. −0.61 and −0.15 for pH 45 min, respectively). Intramuscular fat content was at a high level and nn had significantly lower values with differences of −0.40% and −0.25% relative to NN and Nn, respectively. A whole genome scan is currently underway with emphasis on fat measurements which showed promising Variation in this study.

scholarly journals Response to Inbreeding of Seedling Traits in a Prunus domestica L. Breeding Population

2005 ◽  
Vol 130 (6) ◽  
pp. 904-911 ◽  
Author(s):  
Carolyn J. DeBuse ◽  
Douglas V. Shaw ◽  
Theodore M. DeJong
Keyword(s):  
Growth Traits ◽  
Random Mating ◽  
Growth Trait ◽  
Breeding Population ◽  
Prunus Domestica ◽  
Selfed Progeny ◽  
Seedling Traits ◽  
Inbreeding Coefficients ◽  
Control Set ◽  
Percent Decrease

Controlled pollinations were made using 20 elite selections from the University of California, Davis, Prunus domestica (european plum) breeding program as parents. These parents were used to generate 11 self-pollinated progenies with an inbreeding coefficient (F) of 0.5, 10 full-sibling progenies (F = 0.25), and 11 progenies from among nonrelated parents (F = 0). Seven additional progenies were chosen as a random-mating control set within the parental group; progenies in the control set had accumulated a range of current inbreeding coefficients (average F = 0.23) over two to five generations with intervening cycles of selection. Survival percentages were 85, 82, and 74 for the full-sib progeny, control set progeny, and selfed progeny, respectively, relative to nonrelated progeny. Two months after germination the percent decrease in the growth trait means for the selfed progeny compared to the nonrelated progeny ranged from 14% to 30% whereas growth trait means for full-sib progeny decreased from 1% to 9% compared to nonrelated progeny. The percent decrease for growth trait means of the selfed progeny after completing one season of growth in the field (10 months) was similar to that observed after 2 months, ranging from 14% to 28% compared to nonrelated progeny, whereas the decrease in full-sib progeny trait means was somewhat greater, ranging from 6% to 20%. Regression analysis of all growth traits on current-generation rates of inbreeding indicated a significant negative linear relationship (P = 0.0011 to 0.0232). No significant relationships were found between accumulated Fs and growth trait means of the control set progenies and the nonrelated progenies after 2 months in the greenhouse or one season growing in the field, suggesting that selection between breeding cycles decreased inbreeding depression.

scholarly journals Effects of inbreeding on number of piglets born total, born alive and weaned in Austrian Large White and Landrace pigs

2009 ◽  
Vol 52 (1) ◽  
pp. 51-64 ◽  
Author(s):  
A. Köck ◽  
B. Fürst-Waltl ◽  
R. Baumung
Keyword(s):  
Inbreeding Depression ◽  
Reproductive Performance ◽  
Regression Models ◽  
Inbreeding Coefficient ◽  
Significant Positive Effect ◽  
Weaned Piglets ◽  
Large White ◽  
Inbreeding Coefficients ◽  
Negative Effect ◽  
Positive Effect

Abstract. In this study records of 58 925 litters of Austrian Large White and 17 846 litters of Austrian Landrace pigs were analysed. Regression models were used to determine the effects of litter, dam and sire inbreeding on total number of born, born alive and weaned piglets in Large White and Landrace. In both populations, litter and dam inbreeding showed a negative effect on all traits. Sire inbreeding had no effect in Large White, whereas a significant positive effect was observed in Landrace. On average, inbred sires with an inbreeding coefficient of 10 % had 0.45 more piglets born total and 0.43 more piglets born alive in comparison to non-inbred sires. In a further analysis the total inbreeding coefficients of the animals were divided into two parts: »new« and »old« inbreeding. »New« inbreeding was defined as the period of the first five generations. It was shown that the observed inbreeding effects were not only caused by recent inbreeding. Reproductive performance was also affected by »old« inbreeding. Finally partial inbreeding coefficients of four important ancestors in each population were calculated to investigate if inbreeding effects are similar among these ancestors. The results revealed a varation of inbreeding effects among the four ancestors. Alleles contibuting to inbreeding depression were descendent from specific ancestors.

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