scholarly journals Population structure of Brazilian Gyr dairy cattle

2010 ◽  
Vol 39 (12) ◽  
pp. 2640-2645 ◽  
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.

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

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 Estructura Genética de la Población de Llamas (Lama glama del Banco de Germoplasma del Instituto Nacional de Innovación Agraria -Perú

2016 ◽  
Vol 18 (1) ◽  
pp. 55
Author(s):  
Rubén Mamani Catoa ◽  
Roberto Gallegos Acero ◽  
Teodosio Huanca Mamani ◽  
Juan P Ablo Gutiérrez
Keyword(s):  
Genetic Structure ◽  
Reference Population ◽  
Critical Value ◽  
Inbreeding Coefficient ◽  
Gene Bank ◽  
Effective Number ◽  
Effective Population ◽  
Generation Interval ◽  
Average Ratio ◽  
Lama Glama

<p><strong>RESUMEN</strong></p><p>El objetivo del  estudio fue evaluar la estructura genética de la población de llamas, del Banco de Germoplasma  de  Quimsachata Estación Experimental Illpa-Puno del Instituto Nacional de Innovación Agraria, durante el año 2015<a href="#_msocom_1">[h1]</a> <a href="#_msocom_2">[h2]</a> . Se analizó el archivo de pedigrí de 4698 animales nacidos en el periodo 1993 al 2014, de los cuales 2075 fueron machos y 2623 hembras<a href="#_msocom_3">[h3]</a> . Para el cálculo de los coeficientes individuales de consanguinidad (<em>F</em>), coeficiente de relación media (<em>AR</em>), tamaño efectivo de la población (<em>N<sub>e</sub></em>), de fundadores (<em>f<sub>e</sub></em>)  de ancestros (<em>f<sub>a</sub></em>), intervalo generacional (IG) y la profundidad de pedigrí se ha utilizado el programa ENDOG v.4.8. Los resultados para coeficiente de consanguinidad media y el promedio de relación media de la población de llamas fueron 0.11 y 0.25% respectivamente. Del total de 906 ancestros que dieron origen a la población de referencia, 102 explican el 50% de la variabilidad genética de la población. El número efectivo de fundadores fue 508 y de ancestros 284. El intervalo generacional medio fue  5.65 años, siendo mayor en las vías gaméticas padre-hijo y padre-hija. Para el grado de profundidad de pedigrí fueron identificados 65.88% de animales con información sobre los padres y 83.95% sobre las madres. El tamaño efectivo de la población  fue de 281.81, este valor está por encima del valor crítico. En conclusión la consanguinidad en la población de llamas del banco de germoplasma fue de pequeña magnitud y que las prácticas de apareamiento fueron adecuadas durante el periodo evaluado.</p><p> </p><p><strong>ABSTRACT</strong></p><p>The objective of the study was to describe the genetic structure of the population of llama’s gene bank National Institute of Innovation Agrarian INIA-Puno. The pedigree file of 4698 animals born in the period 1993 to 2014, of which 2075 were males and 2623 females were analyzed. For the calculation of individual coefficients of inbreeding (<em>F</em>), coefficient average ratio (<em>AR</em>), effective population size (<em>N<sub>e</sub></em>), of founders (<em>f<sub>e</sub></em>)  of ancestors (<em>f<sub>a</sub></em>), generation interval (IG) and depth of pedigree has been used ENDOG v.4.8 program. The results for inbreeding coefficient average and average mean ratio of the population were 0.11 and 0.25 flames% respectively. Of the total of 906 ancestors that gave rise to the reference population, 102 account for 50% of the genetic variability of the population. The effective number of founders and ancestors was 508 284. The average generation interval was 5.65 years, being higher in the gametic roads father-son and father-daughter. For the degree of depth of pedigree they were identified 65.88% of animals with information about parents and 83.95% on mothers. The effective size of the population was 281.81, this value is above the critical value. In conclusion inbreeding in the population of llamas gene bank was small in magnitude and mating practices were adequate during the period evaluated.</p><div><hr align="left" size="1" width="33%" /><div><div><p> </p></div></div></div>

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

2010 ◽  
Vol 45 (10) ◽  
pp. 1109-1116 ◽  
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.

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.

scholarly journals Genetic Structure Analysis of the Pura Raza Español Horse Population through Partial Inbreeding Coefficient Estimation

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1360
Author(s):  
Davinia I. Perdomo-González ◽  
María J. Sánchez-Guerrero ◽  
Antonio Molina ◽  
Mercedes Valera
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Inbreeding Depression ◽  
Artificial Insemination ◽  
Genetic Parameters ◽  
Common Ancestor ◽  
Inbreeding Coefficient ◽  
Horse Population ◽  
Coefficient Estimation ◽  
Genealogical Information

The aim of this work was to analyze genetic parameters such as the inbreeding coefficient (F), relatedness coefficient (AR) and partial inbreeding coefficient (Fij) of the whole PRE population, and the ancestors which account for 50% of the total genetic variability of the current population, from genealogical information. The average F of the whole PRE population (328,706 animals) has decreased from 8.45% to 7.51% in the least 20 years. The Fij was estimated for the whole PRE population, resulting in a database of 58,772,533 records containing one record for each Fij that each animal receives from a certain common ancestor (CA). A total of 10,244 CAs contributed to the Fij with an average of 5370 descendants, with each descendant having an average of 170 CAs. Over the generations, the number of CAs has increased, while the proportion of Fij by each one has decreased. In addition, the contributions of the more influential ancestors have changed. The increased census, the limited use of artificial insemination and our increased knowledge about inbreeding depression and the animals’ breeding values allow breeders to select horses more for their functionality and conformation than for their pedigree reputation, which is the cause of all these changes.

scholarly journals Genetic Variability and Population Structure in the Sardinian Anglo-Arab Horse

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1018 ◽  
Author(s):  
Andrea Giontella ◽  
Francesca Maria Sarti ◽  
Irene Cardinali ◽  
Samira Giovannini ◽  
Raffaele Cherchi ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Variability ◽  
Iberian Peninsula ◽  
Inbreeding Coefficient ◽  
Historical Background ◽  
Effective Population ◽  
Horse Breed ◽  
Mitochondrial Data ◽  
The Last Glacial Maximum ◽  
The Last Glacial

The Sardinian Anglo Arab (SAA) is a famous horse breed in Italy, with a significant historical background in the island of Sardinia. The aim of the study is to perform an evaluation of genetic variability in SAA using pedigree and mitochondrial data. In the current population, pedigree completeness was observed to be close to 100%, while the inbreeding coefficient and the average relatedness were lower than 3%. The ratio of effective founders/numbers of ancestors was 3.68 for the whole pedigree. The effective population size (Ne) computed by an individual increase in inbreeding (Ne_1) was 456.86, the Ne on equivalent generations (Ne_2) was 184.75, and this value slightly increased to 209.31 when computed by log-regression on equivalent generations (Ne_3). These results suggest the presence of crossbreeding and bottleneck phenomena, and they were compared with other Italian horses (reported in bibliography) to present the SAA among the Italian horse breeds scenario. Furthermore, the noteworthy mitochondrial variability reflects the use of a considerable number of founder mares; the contribution of L lineage was very important, probably because of the re-colonization from the Iberian Peninsula after the Last Glacial Maximum.

scholarly journals Pedigree Analysis of Mangalica Pig Breeds

2016 ◽  
Vol 16 (3) ◽  
pp. 701-709 ◽  
Author(s):  
János Posta ◽  
Péter Szabó ◽  
István Komlósi
Keyword(s):  
Genetic Structure ◽  
Genetic Variability ◽  
Gene Pool ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Small Populations ◽  
Gene Conservation ◽  
Generation Interval ◽  
Pig Breeds ◽  
Gene Origin

AbstractAn effective gene conservation programme requires the knowledge of genetic variability of the population. The genetic structure of Mangalica pig breeds (Blonde, Red and Swallow-bellied) was studied from pedigree records. Herdbook data available up to 2011 of registered Mangalica pig breeds (Blonde, Red and Swallow-bellied) were analysed. The number of complete generations was 6 for Blonde and 5 for Red and Swallow-bellied Mangalica whereas the average complete generation equivalent was between 3.51 and 6.01. The average level of inbreeding of the reference population was low (4.07–5.87%). The investigated breeds could be considered as small populations based on the probability of gene origin. The most important ancestor contributed between 9 and 16% of the gene pool of the reference populations. The longest generation interval was found for the sire-to-son pathways whereas the shortest for dam-to-daughter pathways for each breed.

scholarly journals Pedigree analysis of 220 almond genotypes reveals two world mainstream breeding lines based on only three different cultivars

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Felipe Pérez de los Cobos ◽  
Pedro J. Martínez-García ◽  
Agustí Romero ◽  
Xavier Miarnau ◽  
Iban Eduardo ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Tree Breeding ◽  
Inbreeding Coefficient ◽  
Genetic Contribution ◽  
Pedigree Data ◽  
Breeding Programs ◽  
Breeding Lines ◽  
Inbreeding Coefficients ◽  
The Usa ◽  
The Mean

AbstractLoss of genetic variability is an increasing challenge in tree breeding programs due to the repeated use of a reduced number of founder genotypes. However, in almond, little is known about the genetic variability in current breeding stocks, although several cases of inbreeding depression have been reported. To gain insights into the genetic structure in modern breeding programs worldwide, marker-verified pedigree data of 220 almond cultivars and breeding selections were analyzed. Inbreeding coefficients, pairwise relatedness, and genetic contribution were calculated for these genotypes. The results reveal two mainstream breeding lines based on three cultivars: “Tuono”, “Cristomorto”, and “Nonpareil”. Descendants from “Tuono” or “Cristomorto” number 76 (sharing 34 descendants), while “Nonpareil” has 71 descendants. The mean inbreeding coefficient of the analyzed genotypes was 0.041, with 14 genotypes presenting a high inbreeding coefficient, over 0.250. Breeding programs from France, the USA, and Spain showed inbreeding coefficients of 0.075, 0.070, and 0.037, respectively. According to their genetic contribution, modern cultivars from Israel, France, the USA, Spain, and Australia trace back to a maximum of six main founding genotypes. Among the group of 65 genotypes carrying the Sf allele for self-compatibility, the mean relatedness coefficient was 0.125, with “Tuono” as the main founding genotype (24.7% of total genetic contribution). The results broaden our understanding about the tendencies followed in almond breeding over the last 50 years and will have a large impact into breeding decision-making process worldwide. Increasing current genetic variability is required in almond breeding programs to assure genetic gain and continuing breeding progress.

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

2021 ◽  
Vol 73 (1) ◽  
pp. 231-238
Author(s):  
N.L. Ribeiro ◽  
G.R. Medeiros ◽  
G.V. Nascimento ◽  
J.K.G. Arandas ◽  
M.N. Ribeiro
Keyword(s):  
Population Structure ◽  
Management Plan ◽  
Inbreeding Coefficient ◽  
Pedigree Information ◽  
Third Generation ◽  
Effective Number ◽  
Pedigree Data ◽  
Genetic Management ◽  
The Third ◽  
Genealogical Information

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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