scholarly journals Pedigree analysis of the racing line Quarter Horse: Genetic diversity and most influential ancestors

2021 ◽  
pp. 104484
Author(s):  
Ricardo António da Silva Faria ◽  
António Pedro Andrade Vicente ◽  
Alejandra Maria Toro Ospina ◽  
Josineudson Augusto II Vasconcelos Silva
Keyword(s):  
Genetic Diversity ◽  
Pedigree Analysis ◽  
Quarter Horse

scholarly journals Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

2019 ◽  
Vol 67 (6) ◽  
pp. 1457-1463 ◽  
Author(s):  
Radovan Kasarda ◽  
Nina Moravčíková ◽  
Ondrej Kadlečík ◽  
Anna Trakovická ◽  
Marko Halo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Quality Control ◽  
Genomic Analysis ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Snp Markers ◽  
Runs Of Homozygosity ◽  
Current Generation ◽  
Genomic Inbreeding

The objective of this study was to analyse the level of pedigree and genomic inbreeding in a herd of the Norik of Muran horses. The pedigree file included 1374 animals (603 stallions and 771 mares), while the reference population consisted of animals that were genotyped by using 70k SNP platform (n = 25). The trend of pedigree inbreeding was expressed as the probability that an animal has two identical alleles by descent according to classical formulas. The trend of genomic inbreeding was derived from the distribution of runs of homozygosity (ROHs) with various length in the genome based on the assumption that these regions reflect the autozygosity originated from past generations of ancestors. A maximum of 19 generations was found in pedigree file. As expected, the highest level of pedigree completeness was found in first five generations. Subsequent quality control of genomic data resulted in totally 54432 SNP markers covering 2.242 Mb of the autosomal genome. The pedigree analysis showed that in current generation can be expected the pedigree inbreeding at level 0.23% (ΔFPEDi = 0.19 ± 1.17%). Comparable results was obtained also by the genomic analysis, when the inbreeding in current generation reached level 0.11%. Thus, in term of genetic diversity both analyses reflected sufficient level of variability across analysed population of Norik of Muran horses.

scholarly journals Genetic diversity in the Lusitano horse breed assessed by pedigree analysis

2012 ◽  
Vol 148 (1-2) ◽  
pp. 16-25 ◽  
Author(s):  
A.A. Vicente ◽  
N. Carolino ◽  
L.T. Gama
Keyword(s):  
Genetic Diversity ◽  
Pedigree Analysis ◽  
Horse Breed

Genetic diversity in Polish hounds estimated by pedigree analysis

2008 ◽  
Vol 113 (2-3) ◽  
pp. 296-301 ◽  
Author(s):  
Iwona Głażewska
Keyword(s):  
Genetic Diversity ◽  
Pedigree Analysis

scholarly journals Diversity and effective population size of four horse breeds from microsatellite DNA markers in South-Central Mexico

2017 ◽  
Vol 60 (2) ◽  
pp. 137-143
Author(s):  
José Fernando Vázquez-Armijo ◽  
Gaspar Manuel Parra-Bracamonte ◽  
Miguel Abraham Velazquez ◽  
Ana María Sifuentes-Rincón ◽  
José Luis Tinoco-Jaramillo ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
The Other ◽  
Genetic Integrity ◽  
Effective Population ◽  
South Central ◽  
Microsatellite Dna Markers ◽  
Quarter Horse ◽  
Population Sizes

Abstract. The South-Central region of Mexico has experienced a sizeable introduction of purebred horses for recreational aims. A study was designed to assess effective population sizes and genetic diversity and to verify the genetic integrity of four horse breeds. Using a 12-microsatellite panel, Quarter Horse, Azteca, Thoroughbred and Creole (CRL) horses were sampled and analysed for diversity and genetic structure. Genetic diversity parameters showed high numbers of heterozygous horses but small effective population sizes in all breeds. Population structure results suggested some degree of admixture of CRL with the other reference breeds. The highly informative microsatellite panel allowed the verification of diversity in introduced horse populations and the confirmation of small effective population sizes, which suggests a risk for future breed integrity.

scholarly journals Evaluation of the Romosinuano cattle population structure in Mexico using pedigree analysis

2020 ◽  
Vol 33 (1) ◽  
pp. 44-59
Author(s):  
Rafael Núñez-Domínguez ◽  
Ricardo E Martínez-Rocha ◽  
Jorge A Hidalgo-Moreno ◽  
Rodolfo Ramírez-Valverde ◽  
José G García-Muñiz
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Gene Flow ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Drift ◽  
Pedigree Analysis ◽  
Effective Population ◽  
Genetic Management ◽  
Generation Interval

Background: Romosinuano cattle breed in Mexico has endured isolation and it is necessary to characterize it in order to facilitate sustainable genetic management. Objective: To assess the evolution of the structure and genetic diversity of the Romosinuano breed in Mexico, through pedigree analysis. Methods: Pedigree data was obtained from Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). The ENDOG program (4.8 version) was used to analyze two datasets, one that includes upgrading from F1 animals (UP) and the other with only straight-bred cattle (SP). For both datasets, three reference populations were defined: 1998-2003 (RP1), 2004-2009 (RP2), and 2010-2017 (RP3). The pedigree included 3,432 animals in UP and 1,518 in SP. Demographic parameters were: Generation interval (GI), equivalent number of generations (EG), pedigree completeness index (PCI), and gene flow among herds. Genetic parameters were: Inbreeding (F) and average relatedness (AR) coefficients, effective population size (Nec), effective number of founders and ancestors, and number of founder genome equivalents. Results: The GI varied from 6.10 to 6.54 for UP, and from 6.47 to 7.16 yr for SP. The EG of the UP and SP improved >63% from RP1 to RP3. The PCI increased over time. No nucleus or isolated herds were found. For RP3, F and AR reached 2.08 and 5.12% in the UP, and 2.55 and 5.94% in the SP. For RP3, Nec was 57 in the UP and 45 in the SP. Genetic diversity losses were attributed mainly (>66%) to genetic drift, except for RP3 in the SP (44%). Conclusions: A reduction of the genetic diversity has been occurring after the Romosinuano breed association was established in Mexico, and this is mainly due to random loss of genes.Keywords: effective population size; gene flow; genetic diversity; genetic drift; generation interval; inbreeding; pedigree; population structure; probability of gene origin; Romosinuano cattle. Resumen Antecedentes: La raza bovina Romosinuano ha estado prácticamente aislada en México y requiere ser caracterizada para un manejo genético sostenible. Objetivo: Evaluar la evolución de la estructura y diversidad genética de la raza Romosinuano en México, mediante el análisis del pedigrí. Métodos: Los datos genealógicos provinieron de la Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). Los análisis se realizaron con el programa ENDOG (versión 4.8) para dos bases de datos, una que incluyó animales en cruzamiento absorbente (UP) a partir de F1 y la otra con sólo animales puros (SP). Para ambas bases de datos se definieron tres poblaciones de referencia: 1998-2003 (RP1), 2004- 2009 (RP2), y 2010-2017 (RP3). El pedigrí incluyó 3.432 animales en la UP y 1.518 en la SP. Los parámetros demográficos fueron: intervalo generacional (GI), número de generaciones equivalentes (EG), índice de completitud del pedigrí (PCI), y flujo de genes entre hatos. Los parámetros genéticos fueron: coeficientes de consanguinidad (F) y de relación genética aditiva (AR), tamaño efectivo de la población (Nec), número efectivo de fundadores y ancestros, y número equivalente de genomas fundadores. Resultados: El GI varió de 6,10 a 6,54 para la UP, y de 6,47 a 7,16 años para la SP. El EG de la UP y la SP mejoró >63%, de RP1 a RP3. El PCI aumentó a través de los años, pero más para la SP que para la UP. No se encontraron hatos núcleo o aislados. Para RP3, F y AR alcanzaron 2,08 y 5,12% en la UP, y 2,55 y 5,94% en la SP. Para RP3, Nec fue 57 en la UP y 45 en la SP. Más de 66% de las pérdidas en diversidad genética se debieron a deriva genética, excepto para RP3 en la UP (44%). Conclusiones: una reducción de la diversidad genética ha estado ocurriendo después de que se formó la asociación de criadores de ganado Romosinuano en México, y es debida principalmente a pérdidas aleatorias de genes.Palabras clave: consanguinidad; deriva genética; diversidad genética; estructura poblacional; flujo de genes; ganado Romosinuano; intervalo generacional; pedigrí; probabilidad de origen del gen; tamaño efectivo de población. Resumo Antecedentes: A raça bovina Romosinuano tem estado praticamente isolada no México e precisa ser caracterizada para um manejo genético sustentável. Objetivo: Avaliar a evolução da estrutura e diversidade genética da raça Romosinuano no México, através da análise de pedigree. Métodos: Os dados genealógicos vieram da Asociación Mexicana de Criadores de Ganado Romosinuano y Lechero Tropical (AMCROLET). As análises foram feitas com o programa ENDOG (versão 4.8) para duas bases de dados, uma que incluiu animais em cruzamento absorvente (UP) a partir da F1 e a outra base de dados somente com animais puros (SP). Para ambas bases de dados foram definidas três populações de referência: 1998-2003 (RP1), 2004-2009 (RP2) e 2010-2017 (RP3). O pedigree incluiu 3.432 animais na UP e 1.518 na SP. Os parâmetros demográficos foram: intervalo entre gerações (GI), número de gerações equivalentes (EG), índice de completude do pedigree (PCI), e fluxo de genes entre rebanhos. Os parâmetros genéticos foram: coeficiente de consanguinidade (F) e da relação genética aditiva (AR), tamanho efetivo da população (Nec), número efetivo de fundadores e ancestrais, e número equivalente de genomas fundadores. Resultados: O GI variou de 6,10 a 6,54 para a UP, e de 6,47 a 7,16 anos para a SP. EG da UP e a SP melhorou >63%, de RP1 a RP3. O PCI aumentou ao longo dos anos, mas mais para a SP do que para o UP. Não se encontraram rebanhos núcleo ou isolados. Para RP3, F e AR alcançaram 2,08 e 5,12% na UP, e 2,55 e 5,94% na SP. Para RP3, Nec foi 57 na UP e 45 na SP. Mais de 66% das perdas em diversidade genética foram ocasionadas pela deriva genética, exceto para RP3 no UP (44%). Conclusões: Depois que a associação da raça Romosinuano foi estabelecida no México, tem ocorrido uma redução da diversidade genética, principalmente devido a perdas aleatórias de genes.Palavras-chave: consanguinidade; deriva genética; diversidade genética, estrutura populacional; fluxo de genes; intervalo entre gerações; pedigree; probabilidade de origem do gene; Romosinuano; tamanho efetivo da população.

Genetic diversity in Kermani sheep assessed from pedigree analysis

2013 ◽  
Vol 114 (2-3) ◽  
pp. 202-205 ◽  
Author(s):  
M.S. Mokhtari ◽  
M. Moradi Shahrbabak ◽  
A.K. Esmailizadeh ◽  
R. Abdollahi-Arpanahi ◽  
J.P. Gutierrez
Keyword(s):  
Genetic Diversity ◽  
Pedigree Analysis

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. 

Using pedigree analysis to determine the genetic diversity of the British dairy population over the last thirty years

1999 ◽  
Vol 1999 ◽  
pp. 123-123
Author(s):  
T. Roughsedge ◽  
S. Brotherstone ◽  
P.M. Visscher
Keyword(s):  
Genetic Diversity ◽  
Great Britain ◽  
North America ◽  
Pedigree Analysis ◽  
Base Population ◽  
Holstein Friesian ◽  
Random Samples ◽  
Friesian Cows

Over the last twenty years the British dairy population has undergone a large importation of Holstein genes, largely from North America and Canada. This study aimed to investigate what effect this importation has had on the genetic diversity of the population and also to look at the change in genetic diversity of the population over the last thirty years.As computing resources did not facilitate sampling of all cows born in the last thirty years, between 4 and 10 random samples of 2000 Holstein-Friesian cows, born every 5 years from 1967 to 1997 inclusive, were taken from the Holstein Friesian Society of Great Britain and Ireland's database. The base population of this database was born about 1960. The complete ancestry of these cows was traced on the database and these sample pedigrees were used for the various analyses.

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