Analysis of the population structure of a cattle conservation nucleus Curraleiro Pé Duro

ABSTRACT The objective of this research was to study the population structure of the Cattle Conservation Nucleos Curraleiro Pé Duro of the Instituto Nacional do Semiárido (NCP_INSA) based on pedigree data. Genealogical information from 338 animals registered in the period from 1991 to 2019 was used. The number of founding animals (Nf), the effective number of founders (fe), effective number of ancestors (fa), inbreeding coefficient (F), and average relatedness coefficient (AR), in addition to Fis, Fit and Fst were estimated. It was possible to identify ancestors up to the third generation, with an increase in information over the generations. Of the total pedigree information evaluated, 90.53% had the identification of the father and mother. The effective size of the population was smaller than those proposed by FAO, suggesting the need to redefine the herd management and genetic management plan strategies, promoting gene flow and breed expansion.

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

Animal Production Science ◽

10.1071/an14738 ◽

2016 ◽

Vol 56 (7) ◽

pp. 1130 ◽

Cited By ~ 6

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.

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Genetic improvement and population structure of the Nelore breed in Northern Brazil

Pesquisa Agropecuária Brasileira ◽

10.1590/s0100-204x2010001000009 ◽

2010 ◽

Vol 45 (10) ◽

pp. 1109-1116 ◽

Cited By ~ 8

Author(s):

Carlos Henrique Mendes Malhado ◽

Paulo Luiz Souza Carneiro ◽

Ana Claudia Mendes Malhado ◽

Raimundo Martins Filho ◽

Riccardo Bozzi ◽

...

Keyword(s):

Population Structure ◽

Genetic Variability ◽

Genetic Improvement ◽

Selective Breeding ◽

Growth Traits ◽

Management Strategies ◽

Pedigree Information ◽

Effective Number ◽

Northern Brazil ◽

Nelore Cattle

The objective of this work was to evaluate the population structure and the genetic and phenotypic progress of Nelore cattle in Northern Brazil. Pedigree information concerning animals born between 1942 and 2006 were analyzed. Population structure was performed using the Endog program. Out of the 140,628 animals studied, 67.7, 14.52 and 3.18% had complete pedigree record of the first, second and third parental generation, respectively. Inbreeding and average relatedness coefficients were low: 0.2 and 0.13%, respectively. However, these parameters may have been underestimated, since information on pedigree was incomplete. The effective number of founders was 370 and the genetic contribution of 10, 50 and 448 most influent ancestors explained 13.2, 28 and 50% of the genetic variability in the population, respectively. The genetic variability for growth traits and population structure demonstrates high probability of increasing productivity through selective breeding. Moreover, management strategies to reduce the currently observed age at first calving and generation intervals are important for Nelore cattle genetic improvement.

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Retriever and Pointer: Software to Evaluate Inbreeding and Genetic Management in Captive Populations

Animals ◽

10.3390/ani11051332 ◽

2021 ◽

Vol 11 (5) ◽

pp. 1332

Author(s):

Jack J. Windig ◽

Ina Hulsegge

Keyword(s):

Population Structure ◽

Allelic Diversity ◽

Captive Population ◽

Pedigree Data ◽

Effective Population ◽

Genetic Management ◽

Captive Populations ◽

Population Structures ◽

Population Sizes ◽

Well Data

The Retriever and Pointer software has been developed for genetic management of (small) captive populations The Retriever program uses as input pedigree data and extracts data on population structure that determine inbreeding rates such as skewness of sire contributions. Levels and rates of inbreeding and kinship and effective population sizes are determined as well. Data on population structure can be used as input for the Pointer program. This program uses stochastic simulation to evaluate a population and provides expected levels and rates of inbreeding and kinship, and optionally allelic diversity. The user can simulate different options for genetic management such as sire restrictions, restrictions on inbreeding levels, mean kinships and breeding circles. Both Retriever and Pointer can analyze populations with subpopulations and different rates of exchange between them. Although originally devised for dogs, the software can be, and has been, used for any captive population including livestock and zoo populations, and a number of examples are provided. The pointer software is also suitable in education where students may generate their own populations and evaluate effects of different population structures and genetic management on genetic diversity. Input is provided via a graphical user interface. The software can be downloaded for free.

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

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.665872 ◽

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.

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Analyse der Populationsstruktur des Bunten Bentheimer Schweins

Archives Animal Breeding ◽

10.5194/aab-49-447-2006 ◽

2006 ◽

Vol 49 (5) ◽

pp. 447-461 ◽

Cited By ~ 1

Author(s):

C. Kolk gen. Sundag ◽

J. Wrede ◽

O. Distl

Keyword(s):

Population Structure ◽

Present State ◽

Paper Analysis ◽

Inbreeding Coefficient ◽

Pedigree Data ◽

Coancestry Coefficient ◽

Black And White ◽

The Mean

Abstract. Title of the paper: Analysis of the population structure of the Black and White Bentheim pig The assessment of the present state of the Black-and-White Bentheim pig (Buntes Bentheimer Schwein) is based on an analysis of the inbreeding and coancestry coefficients of 112 breeding animals registered in the year 2003. Pedigree data included 575 individuals from five generations. Pedigrees reached a completeness of about 76%. The average inbreeding coefficient in the actual population was 8.01%. The mean coancestry coefficient was 14.54%. The mean coancestry coefficient within boar and sow lines was higher.

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Genetic Variability of Bharat Merino Sheep Derived from Pedigree Information

Indian Journal of Animal Research ◽

10.18805/ijar.b-3847 ◽

2020 ◽

Author(s):

P. K. Mallick ◽

I. Chauhan ◽

S. M.K. Thirumaran ◽

R. Pourouchttamane ◽

Arun Kumar

Keyword(s):

Genetic Diversity ◽

Body Weight ◽

Genetic Variability ◽

Pedigree Analysis ◽

Inbreeding Coefficient ◽

Production Performance ◽

Effective Number ◽

Pedigree Data ◽

Breeding Values ◽

Merino Sheep

Background: The genetic variability in a population is the raw material for selection, because the estimation of genetic parameters depends on the variability present within the population. The pedigree analysis is a method to assess population genetic variability. An increase in the level of inbreeding disturbs the production performance of the animals. Hence, it is essential to assess the effect of inbreeding on production performance of the animals at regular intervals. The present study was conducted on data of Bharat Merino (BM) sheep with twin objectives of evaluating the population structure by pedigree analysis and possible effect of inbreeding on lamb growth and heritability estimates. Methods: The study was conducted on data consisting of a total of 9688 pedigree records of BM sheep born from 1975 to 2018 (43 years), out of which 9050 formed population reference (with both the parents known). ENDOG ver 4.8 program was used to generate different measures of genetic diversity. General Linear Model of SPSS 25.0 was used to ascertain the effect of inbreeding (Fi) or change in inbreeding (ÄFi) on the lamb live weights. Using animal model with software WOMBAT, single trait linear mixed model analyses were performed. The heritability estimates and breeding values were obtained by including or excluding the inbreeding coefficient in the model to observe how the estimates of heritability varied with inclusion or exclusion of the inbreeding coefficient. Result: Effective number of founders (fe) was 56, constituting 11.39% founders in the population reference, while the effective number of ancestors (fa) was 43.The genetic contribution of the 15 most influent ancestors explained 50% of the genetic variability in the dataset. The ratio fe/fa, representing the effect of population bottleneck, was 1.302. The average inbreeding coefficients for the whole pedigree was 2.36%, while it was 3.84% for inbred animals. It was found that the inbreeding coefficient (Fi) increased with the addition of each generation to the pedigree. The average relatedness coefficient was 4.53% between members of the population.The effect of individual inbreeding (Fi) or the change in inbreeding (DFi) was not significant on the lamb live weights, except the effect of individual inbreeding (Fi) on three-month body weight and average daily gain (0-3month) and of change in inbreeding (DFi) on three-month body weight. From the analysis of the pedigree data of Bharat Merino sheep, it was found that the most of the measures of genetic diversity were within acceptable limits and the pedigree data was reasonably well maintained. When inbreeding was accounted for in the model, there were reductions in h2 estimates as well as the estimates of breeding values for both 3WT and ADG1 and consequently there were changes in ranking of animals for both 3WT and ADG1.

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Population structure of Brazilian Gyr dairy cattle

Revista Brasileira de Zootecnia ◽

10.1590/s1516-35982010001200012 ◽

2010 ◽

Vol 39 (12) ◽

pp. 2640-2645 ◽

Cited By ~ 12

Author(s):

João Cruz Reis Filho ◽

Paulo Sávio Lopes ◽

Rui da Silva Verneque ◽

Robledo de Almeida Torres ◽

Roberto Luiz Teodoro ◽

...

Keyword(s):

Population Structure ◽

Genetic Structure ◽

Genetic Variability ◽

Inbreeding Coefficient ◽

Mating Strategies ◽

Future Generations ◽

Breeding Value ◽

Effective Number ◽

Generation Interval ◽

Inbreeding Coefficients

The objective of the present study was to evaluate the genetic structure of Gyr cattle selected for milk production. Files of pedigree and production were composed of 27,610 animals. The ENDOG program was used for the calculation of individual inbreeding coefficient (F) and coefficient of average relatedness (AR), effective number of animals(Ne), effective number of founders (f e) and ancestors (f a), and generation interval (GI). Individual inbreeding coefficients and average relatedness in the population were 2.82% and 2.10%, respectively. It was observed a reduction in the effective number of animals, especially after publication of the results of the first progeny test. The estimated effective number of founders was 146 and 75 for the ancestrals. Out of those, only 28 ancestors accounted for the origin of 50% of the population genes. The average generation interval was 8.41 years and it was longer for males than for females. For maintaining genetic variability in future generations, it should be invested mating strategies that reduce inbreeding and which do not use massively only some high breeding value sires.

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