scholarly journals Genetic Diversity in the Portuguese Mertolenga Cattle Breed Assessed by Pedigree Analysis

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 1990
Author(s):  
Nuno Carolino ◽  
Andreia Vitorino ◽  
Inês Carolino ◽  
José Pais ◽  
Nuno Henriques ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Erosion ◽  
Cattle Breed ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Effective Population ◽  
Factors Affecting ◽  
Native Breed ◽  
The Mean ◽  
Major Factors

The Mertolenga beef cattle, currently with 27,000 breeding females in Portugal, is the largest Portuguese native breed, despite some variation in the breeding stock over the last years. The purpose of this study was to estimate parameters related to the population structure and genetic diversity and to investigate the major factors affecting genetic erosion in the breed, based on the pedigree herdbook information collected since the 1950s, including records on 221,567 animals from 425 herds. The mean generation intervals were 6.4 years for sires and 7.1 years for dams, respectively. The rate of inbreeding per year was 0.183% ± 0.020% and the correspondent effective population size was 38.83. In the reference population (35,017 calves born between 2015 and 2019), the average inbreeding and relatedness were 8.82% ± 10% and 2.05% ± 1.26%, respectively. The mean relationship among animals from the same and from different herds was 29.25% ± 9.36% and 1.87% ± 1.53%, respectively. The estimates for the effective number of founders, ancestors, founding herds and herds supplying sires were 87.9, 59.4, 21.4 and 73.5, respectively. Although the situation of the Mertolenga breed is not alarming, these results indicate the need to adopt measures to maintain the genetic variability of the population.

scholarly journals Analysis of Genetic Diversity in the Czech Spotted Dog

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1416
Author(s):  
Karolína Machová ◽  
Anita Kranjčevičová ◽  
Luboš Vostrý ◽  
Emil Krupa
Keyword(s):  
Genetic Diversity ◽  
Population Size ◽  
Effective Population Size ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Inbreeding Coefficient ◽  
Random Genetic Drift ◽  
Effective Population ◽  
Founding Population ◽  
The Mean

Loss off genetic diversity negatively affects most of the modern dog breeds. However, no breed created strictly for laboratory purposes has been analyzed so far. In this paper, we sought to explore by pedigree analysis exactly such a breed—the Czech Spotted Dog (CSD). The pedigree contained a total of 2010 individuals registered since the second half of the 20th century. Parameters such as the mean average relatedness, coefficient of inbreeding, effective population size, effective number of founders, ancestors and founder genomes and loss of genetic diversity—which was calculated based on the reference population and pedigree completeness—were used to assess genetic variability. Compared to the founding population, the reference population lost 38.2% of its genetic diversity, of which 26% is due to random genetic drift and 12.2% is due to the uneven contribution of the founders. The reference population is highly inbred and related. The average inbreeding coefficient is 36.45%, and the mean average relatedness is 74.83%. The effective population size calculated based on the increase of inbreeding coefficient is 10.28. Thus, the Czech Spotted Dog suffered significant losses of genetic diversity that threaten its future existence.

The prediction of voluntary intake of grazing dairy cows

1986 ◽  
Vol 107 (1) ◽  
pp. 43-54 ◽  
Author(s):  
Lindsey Caird ◽  
W. Holmes
Keyword(s):  
Organic Matter ◽  
Measurement Techniques ◽  
Live Weight ◽  
Simple Equation ◽  
Factors Affecting ◽  
Farm Planning ◽  
Sward Height ◽  
The Mean ◽  
Major Factors ◽  
Grazing Dairy Cows

SUMMARYInformation on the total organic matter intake, concentrates supplied (C), live weight (LW), week of lactation (WL), milk yield (MY), herbage organic matter digestibility (HOMD), herbage mass, sward height (SHT) or herbage allowance (HAL) measured individually for 357 cows at one of three sites was assembled. Observed intake was compared with intakes predicted by existing intake equations and new prediction equations based on regression models or regression and least-squares constants were developed. Major factors affecting intake were MY, LW, WL, C and HAL or SHT. Although HOMD was correlated with intake, better predictions were obtained when HOMD was omitted. There were differences between sites possibly associated with differences in measurement techniques.The predictive value of some existing equations and new equations were tested against independent sets of data. A simple equation (A) based on MY and LW (Ministry of Agriculture, Fisheries and Food, 1975) gave satisfactory average predictions but the mean square prediction error (MSPE) was high. The equations of Vadiveloo & Holmes (1979) adjusted for bias gave a relatively low MSPE. The preferred new equations for grazing cattle included MY, LW, WL, C and HAL or SHT, and their MSPE were similar to or lower than for indoor equations.The discussion indicates that a simple equation (A) would give adequate predictions for farm planning. The more detailed equations illustrate the inter-relations of animal with sward conditions and concentrate allowances. Predicted intakes may deviate from actual intakes because of short-term changes in body reserves.

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 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 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.

Pedigree-based analysis of genetic variability in the registered Normande cattle breed in Colombia

2017 ◽  
Vol 57 (3) ◽  
pp. 422
Author(s):  
Derly Rodríguez Sarmiento ◽  
Emanuela Tullo ◽  
Rita Rizzi
Keyword(s):  
Genetic Diversity ◽  
Genetic Variability ◽  
Population Size ◽  
Cattle Breed ◽  
Inbreeding Coefficient ◽  
Mating Strategies ◽  
Effective Population ◽  
Significant Difference ◽  
Genealogical Information ◽  
Over Time

Genetic variability and structure of the population were studied in 7949 registered Normande cattle in Colombia. The pedigree was deep with 18 traced generations, but there were some incomplete genealogical information for the cattle born in the more distant past. The average number of complete and equivalent complete generations was 2.42 and 5.21, respectively. The average pedigree completeness index for five generations was 0.62, which increased over time, and a significant difference between sexes was found (males: 0.82 ± 0.11; females: 0.62 ± 0.38). The average generation interval was 7.57 years. The number of founders, effective founders, ancestors, and founder genomes were 575, 115, 47, and 22.22, respectively, which suggests that an unequal use of founders and a random loss of alleles from founders occurred over time. The level of inbreeding was 0.019 and increased to 0.023, when the inbreeding coefficient was calculated by assigning inbreeding of contemporaries to founders. These levels of inbreeding lead to an effective population size of 138.5 and 117.9 and to a 0.36% and 0.42% rate of inbreeding, respectively. Out of 267 herds with more than five registered breeding animals, only one nucleus herd was present, whereas 117 and 119 were classified as multiplier and commercial herds, respectively. About 92% of calves were sired by French bulls; but the use of Colombian bulls for breeding is increasing. The Colombian Normande breed is at an acceptable level of genetic variability, although some losses of founder alleles have occurred. As the level of inbreeding has been increasing, inbreeding and mating strategies should be monitored in order to maintain the genetic diversity of the breed.

Studies on some of the physical and biological factors affecting the abundance of the Aedes simpsoni (Diptera: Culicidae) complex-larvae and pupae in plant axils

1994 ◽  
Vol 84 (2) ◽  
pp. 255-263 ◽  
Author(s):  
J. J. Lutwama ◽  
L. G. Mukwaya
Keyword(s):  
Water Content ◽  
Habitat Segregation ◽  
Biological Factors ◽  
Factors Affecting ◽  
Developmental Rates ◽  
Dry Seasons ◽  
The Mean ◽  
Major Factors ◽  
Aedes Simpsoni ◽  
Indices Of Association

AbstractSome physical and biological factors affecting the abundance of larvae and pupae of the Aedes simpsoni (Theobald) complex, in leaf axils of different plants at several locations in Uganda, were investigated during the rainy and dry seasons. The mean number of axils per plant, axils containing larvae and pupae, and the mean number of larvae and pupae per ml of axil water all varied between seasons and locations. The percentage of axils containing larvae and pupae increased with volume of water in the axils of the different plants. The mean number of larvae and pupae per axil containing water also increased with water content of the axils. There was more water in the axils during the rainy than during the dry seasons. The mean temperature of water was lower in Xanthosorna sagittifoliurn (20.4°C) and Colocasia esculentum (22.1°–22.7°C) than in those of banana (25.0°–27.2°C) and this affected developmental rates of larvae and pupae. The indices of association between larvae and pupae of the A. simpsoni complex and Malaya taeniarostris (Theobald) did not indicate competition and there was some habitat segregation between them. The volume and temperature of water in the axils appeared to be the major factors affecting larval and pupal abundance of A. simpsoni in the axils.

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.  

Pedigree analysis of the Afrikaner cattle breed

2015 ◽  
Vol 57 ◽  
pp. 51-56 ◽  
Author(s):  
L. Pienaar ◽  
F.W.C. Neser ◽  
J.P. Grobler ◽  
M.M. Scholtz ◽  
M.D. MacNeil
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Cattle Breed ◽  
Pedigree Analysis ◽  
Rate Of Change ◽  
Full Potential ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Sanga Cattle

SummaryThe reduction of genetic variability in beef cattle has been extensively researched on a global scale. However, the genetic variability and inbreeding of indigenous cattle breeds of Southern Africa, referred to as Sanga cattle, has been less well characterized. Breeds of Sanga cattle include Afrikaner, Drakensberger and Nguni breeds. In recent years, the number of Afrikaner cattle and herds has decreased. Our objective was to determine the mean level of inbreeding (F), effective population size (Ne) and generation intervals of Afrikaner cattle using their recorded pedigree. A total of 244 718 records extending from 1940 until 2011 were analysed. The average inbreeding coefficient was 1.83 percent and the effective population size was 167.54. The average generation interval was calculated as 6.6 ± 3.9 years. Pedigree analysis on the Afrikaner cattle population yielded levels of inbreeding that appear to be both acceptable and manageable. By implication, the largeNeresults in a low rate of change inF. Current results study can be utilized by farmers and the breeders’ society to conserve the Afrikaner and utilize the breed to its full potential in the era of climate change.

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

PLoS ONE ◽  
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.

Sign in / Sign up

Export Citation Format

Share Document