Genetic variability in Colombian Creole cattle populations estimated by pedigree information

Genealogical structure of the Colombian Romosinuano Creole cattle

The Romosinuano cattle breed is one of the most important Creole genetic resources in Colombia, and interesting traits like adaptation or reproductive efficiency have promoted its use in different countries in America. To consolidate the genealogical historical records, the review of very first yield records in this population was used to reconstruct the genealogy of the breed since the first animals incorporated to the in vivo germplasm bank and estimate different demographic parameters. The complete genealogy comprises 17,136 animals with 5.8 years of generation interval for two pathways. The estimated average inbreeding for the population and inbred animals was 2.53% and 6.32% respectively, with a progressive increase of inbred animals across the generations. Almost 48% of the total animals presented some level of consanguinity. Effective population size (Ne) based on the inbreeding rate estimated by regression in all generations was 120 animals whereas Ne estimated by equivalent generations was 69 animals. Effective number of founders (Fe), effective number of ancestors (Fa), and ancestors explaining 50% of variability were 75, 48, and 22, respectively. The relation between Fa/Fe of 64% indicates a genetic bottleneck effect in the population studied.

Genetic structure of a small closed population of the New Zealand white rabbit through pedigree analyses

The genetic structure of a small population of New Zealand White rabbits maintained at the Sheep Breeding and Research Station, Sandynallah, The Nilgiris, India, was evaluated through pedigree analyses. Data on pedigree information (n=2503) for 18 yr (1995-2012) were used for the study. Pedigree analysis and the estimates of population genetic parameters based on the gene origin probabilities were performed. The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.49 yr, 13.23 and 17.59%, respectively. The proportion of population inbred was 100%. The estimated mean values of average relatedness and individual increase in inbreeding were 22.73 and 3.00%, respectively. The percentage increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations and complete generations, respectively. The number of ancestors contributing the majority of 50% genes (f_a50) to the gene pool of reference population was only 4, which might have led to reduction in genetic variability and increased the amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (f_e) and the effective number of ancestors (f_a), as expressed by the f_e/f_a ratio was 1.1, which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29% pedigree was complete, reflecting the well maintained pedigree records. The maximum known generations were 15, with an average of 7.9, and the average equivalent generations traced were 5.6, indicating a fairly good depth in pedigree. The realized effective population size was 14.93, which is very critical, and with the increasing trend of inbreeding the situation has been assessed as likely to become worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10%, which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred, with a very high inbreeding coefficient, and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.

Marginal ancestral contributions to atrial fibrillation in the Standardbred racehorse: Comparison of cases and controls

Admissions of Standardbred racehorses (Std) to the Ontario Veterinary College Teaching Hospital (OVCTH) for treatment of atrial fibrillation (AF) began to increase in the early 1990s. The arrhythmia has been shown to have a modest heritability (h² ≃ 0.15), with some stallions appearing as sires or sires of mares used in breeding (broodmares) of affected horses more frequently than others. The objective of this study was to determine the marginal genetic contributions of ancestors to cohorts of Std affected with AF and their contemporary control groups, and whether these ancestors contribute significantly more to the affected cohorts than to controls. All Std admitted to OVCTH for treatment of AF that were born between 1993 and 2007 comprised the affected case group (n = 168). Five randomly selected racing contemporaries for each Std admitted, assumed to not suffer from the arrhythmia, comprised the control group (n = 840). Three-year overlapping cohorts were created for case and control horses, determined according to year of birth, for a total of 26 cohorts. Marginal genetic contributions of ancestors to each cohort were determined and differences analyzed for statistical significance using a two-tailed paired t-test, with P ≤ 0.05 considered significant. The marginal contributions of 26 ancestors were significant, with 11 contributing significantly more to affected cohorts than the corresponding controls, and 15 contributing significantly more to controls than the corresponding affected cohorts. One stallion and one broodmare were very highly significant to affected cohorts at P ≤ 0.001, and nine stallions and three broodmares were very highly significant to control cohorts at P ≤ 0.001. Therefore, a number of stallions have statistically significant contributions to the genetics of Std affected with AF, while many others have statistically significant contributions to healthy Std. The arrhythmia appears to be particularly prevalent in the descendants of one sire family.

Population structure of Mazandaran native fowls using pedigree analysis

The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability of the Mazandaran native fowls in Iran by quantifying the pedigree completeness index, effective population size, genetic diversity, inbreeding level, and individual increase in inbreeding. The pedigree completeness analysis showed 3.31 full, 10.19 maximum, and 6.30 equivalent generations. The effective number of founders (f _e) was 131, representing 5% of the potential number of founders. The effective number of ancestors (f _a) was 81, and the genetic contribution of the 37 most influent ancestors explained 50% of the genetic variability in the population. The ratio f _e/f _a (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.62. The inbreeding coefficient increased over generations and the average was 1.93%. The average relatedness coefficient between individuals of the population was estimated to be 2.59%. The effective population size, based on the number of full generations, was 56. Family size analysis showed that fewer males than females were used, resulting in the observed levels of inbreeding. Average inbreeding coefficient in the Mazandaran native fowls can be regarded to be below critical levels. However, considering the relationship coefficients of individuals is recommended to aid maintaining genetic diversity of Mazandaran native fowls.

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

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.

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

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.

Analysis of conservation priorities of Iberoamerican cattle based on autosomal microsatellite markers

Background

Determining the value of livestock breeds is essential to define conservation priorities, manage genetic diversity and allocate funds. Within- and between-breed genetic diversity need to be assessed to preserve the highest intra-specific variability. Information on genetic diversity and risk status is still lacking for many Creole cattle breeds from the Americas, despite their distinct evolutionary trajectories and adaptation to extreme environmental conditions.

Methods

A comprehensive genetic analysis of 67 Iberoamerican cattle breeds was carried out with 19 FAO-recommended microsatellites to assess conservation priorities. Contributions to global diversity were investigated using alternative methods, with different weights given to the within- and between-breed components of genetic diversity. Information on Iberoamerican plus 15 worldwide cattle breeds was used to investigate the contribution of geographical breed groups to global genetic diversity.

Results

Overall, Creole cattle breeds showed a high level of genetic diversity with the highest level found in breeds admixed with zebu cattle, which were clearly differentiated from all other breeds. Within-breed kinships revealed seven highly inbred Creole breeds for which measures are needed to avoid further genetic erosion. However, if contribution to heterozygosity was the only criterion considered, some of these breeds had the lowest priority for conservation decisions. The Weitzman approach prioritized highly differentiated breeds, such as Guabalá, Romosinuano, Cr. Patagonico, Siboney and Caracú, while kinship-based methods prioritized mainly zebu-related breeds. With the combined approaches, breed ranking depended on the weights given to the within- and between-breed components of diversity. Overall, the Creole groups of breeds were generally assigned a higher priority for conservation than the European groups of breeds.

Conclusions

Conservation priorities differed significantly according to the weight given to within- and between-breed genetic diversity. Thus, when establishing conservation programs, it is necessary to also take into account other features. Creole cattle and local isolated breeds retain a high level of genetic diversity. The development of sustainable breeding and crossbreeding programs for Creole breeds, and the added value resulting from their products should be taken into consideration to ensure their long-term survival.

A raça Gir Mocha na região Nordeste do Brasil: estrutura genética populacional via análise de pedigree

Foram utilizados dados de pedigree de 2.558 bovinos da raça Gir Mocha nascidos no período de 1954 a 2005. As análises foram realizadas utilizando-se o programa Endog. Do total de animais estudados, 61,9%; 10,6% e 0,1% possuíam pedigree na primeira, segunda e terceira gerações, respectivamente.O número efetivo de rebanhos que forneceram machos reprodutores foi de 10,25 para pais e 3,87 para avôs, confirmando a baixa integralidade do pedigree. O número de animais fundadores foi de 975,5, e o número efetivo de fundadores de 141,34. O número de ancestrais na população referência foi de 924 animas, dos quais apenas 39 explicaram 50% da variabilidade genética da população.O coeficiente médio de relação foi estimado em 0,75%, sendo o maior coeficiente individual de 25%. O coeficiente de endogamia foi igual a zero de 1954 a 1984. Vale salientar que, neste período, estão incluídos os animais sem ascendência conhecida. A endogamia e o coeficiente médio de relação da população foram baixos, contudo podem estar subestimados em razão da pequena integralidade do pedigree.

Population structure and genetic variability in the Murrah dairy breed of water buffalo in Brazil accessed via pedigree analysis

The objective of this study was to use pedigree analysis to evaluate the population structure and genetic variability in the Murrah dairy breed of water buffalo (Bubalus bubalis) in Brazil. Pedigree analysis was performed on 5,061 animals born between 1972 and 2002. The effective number of founders (fe) was 60, representing 6.32 % of the potential number of founders. The effective number of ancestors (fa) was 36 and the genetic contribution of the 17 most influent ancestors explained 50 % of the genetic variability in the population. The ratio fe/fa (effective number of founders/effective number of ancestors), which expresses the effect of population bottlenecks, was 1.66. Completeness level for the whole pedigree was 76.8, 49.2, 27.7, and 12.8 % for, respectively, the first, second, third, and fourth known parental generations. The average inbreeding values for the whole analyzed pedigree and for inbreed animals were, respectively, 1.28 and 7.64 %. The average relatedness coefficient between individuals of the population was estimated to be 2.05 %-the highest individual coefficient was 10.31 %. The actual inbreeding and average relatedness coefficient are probably higher than estimated due to low levels of pedigree completeness. Moreover, the inbreeding coefficient increased with the addition of each generation to the pedigree, indicating that incomplete pedigrees tend to underestimate the level of inbreeding. Introduction of new sires with the lowest possible average relatedness coefficient and the use of appropriate mating strategies are recommended to keep inbreeding at acceptable levels and increase the genetic variability in this economically important species, which has relatively low numbers compared to other commercial cattle breeds. The inclusion of additional parameters, such as effective number of founders, effective number of ancestors, and fe/fa ratio, provides better resolution as compared to the inclusion of inbreeding coefficient and may help breeders and farmers adopt better precautionary measures against inbreeding depression and other deleterious genetic effects.

Assessment of inbreeding depression in a Guzerat dairy herd: effects of individual increase in inbreeding coefficients on production and reproduction

Influences of inbreeding on daily milk yield (DMY), age at first calving (AFC), and calving intervals (CI) were determined on a highly inbred zebu dairy subpopulation of the Guzerat breed. Variance components were estimated using animal models in single-trait analyses. Two approaches were employed to estimate inbreeding depression: using individual increase in inbreeding coefficients or using inbreeding coefficients as possible covariates included in the statistical models. The pedigree file included 9,915 animals, of which 9,055 were inbred, with an average inbreeding coefficient of 15.2%. The maximum inbreeding coefficient observed was 49.45%, and the average inbreeding for the females still in the herd during the analysis was 26.42%. Heritability estimates were 0.27 for DMY and 0.38 for AFC. The genetic variance ratio estimated with the random regression model for CI ranged around 0.10. Increased inbreeding caused poorer performance in DMY, AFC, and CI. However, some of the cows with the highest milk yield were among the highly inbred animals in this subpopulation. Individual increase in inbreeding used as a covariate in the statistical models accounted for inbreeding depression while avoiding overestimation that may result when fitting inbreeding coefficients.

Variabilidade genética de búfalos em rebanho-núcleo com base na análise de pedigree

Parâmetros baseados na probabilidade de origem do gene foram usados para descrever a variabilidade em uma população de búfalos da Embrapa Amazônia Oriental. A magnitude dos resultados foi de média a baixa (por volta de 20 animais), sugerindo que poucos fundadores contribuiriam para a formação da população. Dentre os 20 ancestrais que mais aportam genes aos machos - representando ao todo 71% dos alelos -, 39%, 26% e 5%, respectivamente, são as contribuições marginais das raças Murrah e Mediterrâneo e seus mestiços. Para as fêmeas, em que os 20 ancestrais aportam 67,5% dos genes, 42% e 26%, respectivamente, são as contribuições marginais das raças Murrah e Mediterrâneo.

Population structure of Reyna Creole cattle in Nicaragua

Reyna Creole cattle originated from Bos taurus cattle brought to Latin America during the Spanish colonization in the fifteenth century and are the only remaining local breed in Nicaragua. However, the current genetic status of this breed is unknown. Therefore, the population structure of three recorded Reyna Creole herds in Nicaragua was studied to estimate their level of inbreeding, effective population size, and generation intervals. Data from 2,609 animals born between 1958 and 2007 were analyzed. A pedigree completeness index higher than 0.8 was required to obtain reliable estimates of the level of inbreeding, and this criterion was met for 367 animals (14%) in two herds. The average level of inbreeding was 13.0%, with values ranging from 0% to 43.8% for individual animals. One of the herds had an average inbreeding level of 21.6%, primarily due to long periods in which the same bulls were used for mating, leading to excessive frequencies of matings between closely related animals. The effective population size differed between years and ranged from 28 to 46 animals, showing that the Reyna Creole cattle breed is endangered, close to critical status. The average generation interval was 6.9 years with values as high as 19.1 years for some sires that were used for artificial insemination over a long period of time. Due to the high level of inbreeding and small population size, urgent actions are required for the development of a breeding program to protect the breed and support its sustainable utilization.