scholarly journals Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information

Animals ◽  
2020 ◽  
Vol 10 (8) ◽  
pp. 1310
Author(s):  
Enrico Mancin ◽  
Michela Ablondi ◽  
Roberto Mantovani ◽  
Giuseppe Pigozzi ◽  
Alberto Sabbioni ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Genomic Structure ◽  
Population Level ◽  
Snp Markers ◽  
Pedigree Information ◽  
Pedigree Data ◽  
Selection Signatures ◽  
Effective Population ◽  
Genomic Inbreeding ◽  
Inbreeding Level

This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (fa/fe). Genotypic information from SNP markers were available for 267 individuals of both sexes, and it allowed estimating genomic inbreeding in two methods (observed versus expected homozygosity and from ROH) to study the breed genomic structure and possible selection signatures. Pedigree and genomic inbreeding were greatly correlated (0.65 on average). The inbreeding trend increased over time, apart from periods in which the base population enlarged, when Ne increased also. Recent bottlenecks did not occur in the genome, as fa/fe have shown. The observed homozygosity results were on average lower than expected, which was probably due to the use of French Breton stallions to support the breed genetic variability. High homozygous regions suggested that inbreeding increased in different periods. Two subpopulations were distinguished, which was probably due to the different inclusion of French animals by breeders. Few selection signatures were found at the population level, with possible associations to disease resistance. The almost low inbreeding rate suggested that despite the small breed size, conservation actions are not yet required.

scholarly journals 331 Efficient quality control methods for genomic and pedigree data used in routine genomic evaluation

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 50-51
Author(s):  
Yutaka Masuda ◽  
Andres Legarra ◽  
Ignacio Aguilar ◽  
Ignacy Misztal
Keyword(s):  
Quality Control ◽  
Large Scale ◽  
Computing Time ◽  
Academic Research ◽  
Snp Markers ◽  
Pedigree Information ◽  
Memory Usage ◽  
Pedigree Data ◽  
Genomic Evaluation ◽  
Data Set

Abstract Quality control and consistency tests on genotypes and historical pedigree data are applied in a routine genomic evaluation and academic research. The quality control takes more time to finish as more genotypes become available, and this step is a bottleneck in a pipeline of routine evaluation. For the efficient quality control, we have developed several algorithms and a computer program to support for large-scale, biallelic, single nucleotide polymorphisms (SNPs). The program is designed to detect unsatisfactory genomic markers and individuals in terms of call rate, marker allele frequencies, duplicate samples, and Mendelian inconsistency in the large genomic data with the pedigree including millions of individuals. Duplicated genotypes can be detected using a set of markers. An SNP genotype is packed into a 2-bit representation in memory that enables bitwise operations with parallel computing to efficiently perform the quality control. The software optionally checks the inconsistency of pedigree information. We compared QCF90 with preGSf90, a preceding program, in terms of memory usage and computing time using a data set including 200,000 genotyped individuals, 50,000 SNP markers per individual, and 216,500 pedigree individuals. In total running time, QCF90 was approximately 6 times faster than PREGSF90 (307 s vs 2075 s) while the memory usage was 30 times less (2 GB vs 75 GB) using only 1 thread. The QCF90 program performed better in speed as more threads were used. A check for genomic duplications took 159 s with 16 threads when 5,000 genotypes were compared with 200,000 genotypes using 2500 SNP markers. The new tool is useful in the routine genomic evaluation and the academic research in which both the genotypes and the pedigree information are used. The QCF90 executable is available at http://nce.ads.uga.edu with a user manual.

scholarly journals Genetic Variability in Polish Lowland Sheepdogs Assessed by Pedigree and Genomic Data

Animals ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1520
Author(s):  
Paula Wiebke Michels ◽  
Ottmar Distl
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Ductus Arteriosus ◽  
Genomic Data ◽  
Reference Population ◽  
Pedigree Data ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Candidate Loci

Genetic variability of Polish Lowland Sheepdog (PON) population was evaluated using both pedigree and genomic data. The analyzed pedigree encompassed 8628 PONs, including 153 individuals genotyped on the Illumina CanineHD BeadChip. Runs of homozygosity (ROH) were defined for homozygous stretches extending over 60 to 4300 kb. The inbreeding coefficients FPed based on pedigree data and FROH50 based on ROHs were at 0.18 and 0.31. The correlation between both was 0.41 but 0.52 when excluding animals with less than seven complete generations. The realized effective population size (Ne¯) was 22.2 with an increasing trend over years. Five PONs explained 79% of the genetic diversity of the reference population. The effective population size derived from linkage disequilibrium measured by r² was 36. PANTHER analysis of genes in ROHs shared by ≥50% of the PONs revealed four highly over- or underrepresented biological processes. One among those is the 7.35 fold enriched “forelimb morphogenesis”. Candidate loci for hip dysplasia and patent ductus arteriosus were discovered in frequently shared ROHs. In conclusion, the inbreeding measures of the PONs were high and the genetic variability small compared to various dog breeds. Regarding Ne¯, PON population was minimally endangered according to the European Association for Animal Production.

scholarly journals Joint inference of demography and mutation rates from polymorphism data and pedigrees

2016 ◽  
Author(s):  
Florence Parat ◽  
Sándor Miklós Szilágyi ◽  
Daniel Wegmann ◽  
Aurélien Tellier
Keyword(s):  
Mutation Rate ◽  
Overlapping Generations ◽  
Genetic Data ◽  
Mutation Rates ◽  
Pedigree Information ◽  
Pedigree Data ◽  
Computationally Efficient ◽  
Effective Population ◽  
Joint Inference ◽  
Major Interest

ABSTRACTInference of demography and mutation rates is of major interest but difficult because genetic data is only informative about the population mutation rate, the product of the effective population size times the mutation rate, and not about these quantities individually. Here we show that this limitation can be overcome by combining genetic data with pedigree information. To successfully use pedigree data, however, important aspects of real populations such as the presence of two sexes, unbalanced sex ratios and overlapping generations have to be taken into account. We present here an extension of the classic Wright-Fisher model accounting for these effects and show that the coalescent process under this model reduces to the classic Kingman coalescent with specific scaling parameters. We further derive the probability of a pedigree under that model and show how pedigree data can thus be used to infer demographic parameters. Finally, we present a computationally efficient inference approach combining pedigree information and genetic data summarized by the site frequency spectrum (SFS) that allows for the joint inference of the mutation rate, sex-specific population sizes and the fraction of overlapping generations. Using simulations we then show that these parameters can be accurately inferred from pedigrees spanning just a few generations, as are available for many species. We finally discuss future possible extensions of the model and inference framework necessary for applications to wild and domesticated species, namely the account for more complex demographies and the uncertainty in assigning pedigree individuals to specific generations.

scholarly journals Genetic Variability of Cold-Blooded Horses Participating in Genetic Resources Conservation Programs, Using Pedigree Analysis

2019 ◽  
Vol 19 (1) ◽  
pp. 49-60 ◽  
Author(s):  
Grażyna Polak
Keyword(s):  
Genetic Variability ◽  
Genetic Resources ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Pedigree Information ◽  
Effective Population ◽  
Conservation Programs ◽  
Data Set ◽  
Genetic Resources Conservation ◽  
Resources Conservation

AbstractTwo types of Polish local cold-blooded horses – Sztumski and Sokólski, covered by genetic resources conservation programs, were analyzed for founder’s contribution, genetic structure and inbreeding. In both populations, created in the early twentieth century, were used the same stallions, mainly Ardennes, Belgians and Bretons. The aim of the study was to analyze the genetic variability of Sztumski and Sokólski cold-blooded horses, using pedigree information. The reference population contained 2359 horses: 1129 Sztumski and 1230 Sokólski included in conservation programs in 2014. The data set consisted of a total of 12,821 ancestor pedigrees. The results showed that in the analyzed population the number of founders was 1139 for Sztumski and 1118 for Sokólski horses; effective population size and effective number of founders were 688.8; 156.9 and 704.5; 111.4, respectively. The mean coefficient of inbreeding was 1.54 for Sztumski and 1.56 for Sokólski horses. In the gene pool the most important contribution was of Ardennes horses (43.67% in Sztumski and 46.82% in Sokólski horses), followed by Belgian horses (18.32% and 9.3%, respectively). The most important ancestors in both populations were Ardennes sires Roll-tan 699 and Gustaw 2807, and German cold-blooded sires Elbgang 1504 and Bär.

scholarly journals Pedigree structure of American bison (Bison bison) population

2018 ◽  
Vol 63 (No. 12) ◽  
pp. 507-517 ◽  
Author(s):  
E. Skotarczak ◽  
P. Ćwiertnia ◽  
T. Szwaczkowski
Keyword(s):  
Mean Value ◽  
Bison Bison ◽  
Pedigree Information ◽  
Effective Population ◽  
Pedigree Structure ◽  
Breeding Programs ◽  
Inbreeding Coefficients ◽  
Animal Populations ◽  
The Mean ◽  
Inbreeding Level

An effective realization of breeding programs in zoos is strongly determined by completeness of animal pedigree information. The knowledge of pedigree structure allows to maintain optimal genetic variability of a given population. The aim of this study was to estimate the parameters describing the pedigree structure of American bison housed in zoos in the context of further management of the population. Finally, 4269 American bison were analysed (1883 males, 2217 females, and 169 with unknown sex). The registered animals were born between years 1874 and 2013. The following pedigree parameters were estimated: number of fully traced generations, number of complete generations equivalent, index of pedigree completeness, individual inbreeding coefficients, increase of inbreeding for each individual, effective population size, and genetic diversity. The maximum number of fully traced generations was 3 (the mean value is 0.693). The mean inbreeding coefficient for the population studied was 3.26%, whereas individual increase in inbreeding ranged from 0 to 25.12%. Although the pedigree parameters (including the inbreeding level) in the American bison obtained in the present study seem to be acceptable (from the perspective of other wild animal populations), they can be over/underestimated due to incomplete pedigree.

scholarly journals Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 321
Author(s):  
Jorge Hidalgo ◽  
Alberto Cesarani ◽  
Andre Garcia ◽  
Pattarapol Sumreddee ◽  
Neon Larios ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Background ◽  
Cattle Breed ◽  
Pedigree Information ◽  
Runs Of Homozygosity ◽  
Genomic Information ◽  
Effective Population ◽  
Genetic Progress

The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.

scholarly journals Evaluation of runs of homozygosity and genomic inbreeding in Holstein cattle from Colombia

2020 ◽  
Vol 41 (6supl2) ◽  
pp. 3397-3418
Author(s):  
Maria Fernanda Betancur Zambrano ◽  
◽  
Juan Carlos Rincón Flórez ◽  
Ana Cristina Herrera Rios ◽  
Carlos Eugenio Solarte Portilla ◽  
...  
Keyword(s):  
Snp Markers ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Holstein Cattle ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Selection Processes ◽  
Starting Point ◽  
Genomic Markers ◽  
Genomic Inbreeding

Traditional selection programs for dairy cattle, based on quantitative principles, have worked well and allowed strong selection processes in the world over many decades. The objectives of this work were to estimate linkage disequilibrium (LD) levels at varying SNPs densities, to evaluate the effective population size of Holstein cattle, to characterize runs of homozygosity (ROH) distribution through Holstein cattle from Nariño and, to estimate and compare inbreeding coefficient (F) based on genomic markers information, runs of homozygosity (FROH), genomic relationship matrix (FGRM), and excess of homozygous (FSNP). After quality control, the dataset used was composed of 606 Holstein animals and 22200 SNP markers. PLINK program was used to identify LD, Ne, ROH segment and FROH and FSNP, FGRM was calculated with BLUPF90 family of programs. The average of r2 in all chromosomes was 0.011, the highest r2 was found in BTA3 (0.0323), and the lowest in BTA12 (0.0039). 533 ROH segments were identified in 319 animals; findings obtained in this study suggest that on average 0,28% of Holstein genome is autozygous. Total length of ROH was composed mostly of small segments (ROH1-4Mb and ROH4-8Mb). These segments accounted for approximately 96%, while larger ROH (ROH>8Mb) were 3.37% of all ROH detected. Inbreeding averages FROH, FSNP and FGRM methodologies were 0.28%, 3.11% and 3.36% respectively. The Pearson’s correlation among these different F values was: 0.49 (FROH-FSNP), 0.25 (FROH-FGRM), 0.22 (FSNP-FGRM). The distribution of ROH shared regions identified on 19 autosome chromosomes, cover a relevant number of genes inside these ROH. Our result evidenced lowest LD extension levels compared with other Holstein populations; inbreeding results suggest that FGRM and FSNP may be useful estimators of individual autozygosity in Holstein from Colombia. Genes related with production and reproduction were found, but the most important are the two that may be related to adaptation to Colombian high tropics. This work is a pioneer and be the starting point for programs of genetic improvement and genomic population studies in the country and mainly in high tropic areas where the dairy breeds have an important production.

scholarly journals Population and genetic features, genomic inbriding and homozy-gosity level for black-and-white and holstein breeds by STR and SNP markers in Russia

2021 ◽  
pp. 295-306
Author(s):  
Igor S. Nedashkovsky ◽  
◽  
Alexander A. Sermyagin ◽  
Olga V. Kostyunina ◽  
Valeria V. Volkova ◽  
...  
Keyword(s):  
Pairwise Comparison ◽  
Snp Markers ◽  
Pedigree Data ◽  
Subsequent Increase ◽  
Group V ◽  
Genetic Characteristics ◽  
Black And White ◽  
Group I ◽  
Significant Difference ◽  
Genomic Inbreeding

The object of the study was sires of the Black-and-White and Holstein breeds, which had STR profiles and passed the genotyping procedure for SNP markers. The subject of the study was the level of genomic inbreeding and homozygosity, as well as population-genetic characteristics based on them. With an increase in Fx based on pedigree data, an increase in the level of genomic inbreeding (FROH) calculated from SNP markers was also noted. The results for 9 STR markers record a wavelike increase in homozygosity from group I to group IV with a subsequent increase from group V to group VII inclusive. During the study of the average FROH values in accordance with the years of birth of sires, a significant difference was found between the last two groups (2009-2011; 2012-2014) from all the others in a pairwise comparison. The results of calculating the FROHand Ca9 of bulls from different countries of origin indicate a statistically significant differentiation of the group of animals from Russia (RF) from animals, born in German and Canadian. A significant difference was noted for the highest FROH level in the samples in the Holstein Black-and-White breed from the Red-and-White Holstein and Black-and-White breeds. The Fst values between the SNP and STR species of the animals had insignificant differentiation (0.008-0.027). Differences in STR calculation between the Black-and-White Holstein and Red-and-White Holstein breeds were insignificant, less than 20%, while the rest of the values differed many times. Fst between RF and Germany, RF and the Netherlands according to STR data is 0.006 and 0.008, according to SNP data 0.005 and 0.006, respectively. A mutual increase in the value of Fst and the year of birth of the sires was noted, emphasizing the greatest remoteness of the population of 1983-1997 from the populations of recent years, when new genotypes of bulls were obtained. The similarity of Fst values between genealogical lines is replaced by a significant scatter in the indicators when they are compared in pairs.

scholarly journals Pedigree analysis in White Shorthaired goat: First results

2013 ◽  
Vol 56 (1) ◽  
pp. 547-554
Author(s):  
M. Oravcová
Keyword(s):  
Genetic Variability ◽  
Information Needs ◽  
Reference Population ◽  
Pedigree Analysis ◽  
Pedigree Information ◽  
Effective Population ◽  
Mean Values ◽  
First Results ◽  
Marginal Contributions ◽  
The Individual

Abstract. Pedigree records of 1 682 animals of the White Shorthaired goat in Slovakia were investigated. The reference population was defined as the animals born from 2008 to 2011 with at least one ancestor known in the second ancestral generation (670 animals kept in eight flocks). The numbers of founders (286), ancestors (256), effective founders (73), effective ancestors (45) and founder genome equivalents (32) were assessed. Fifteen ancestors were needed to explain 50 % of genetic variability. Marginal contributions of the ten most influential ancestors varied between 5.45 % and 2.47 % and accounted for 39.8 % of genetic variability. The mean values of inbreeding and co-ancestry were 0.69 % and 1.55 %, respectively. The effective population size was assessed to consist of 182 and 142 individuals, depending whether it was calculated from the individual increase in inbreeding or the individual increase in co-ancestry. The number of maximum generations traced, fully traced generations and equivalent complete generations traced were 5.62, 1.97 and 3.04, respectively. The first, second and third ancestral generation were 100 %, 83 % and 71 % complete, respectively. The completeness decreased to as low as 35 % and 11 % in the fourth and fifth generation. To be able to keep genetic links across generations in touch, the amount of pedigree information needs to be increased. This is a serious requirement for appropriate monitoring and management of genetic relations within the population.

scholarly journals Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Emmanuel A. Lozada-Soto ◽  
Christian Maltecca ◽  
Duc Lu ◽  
Stephen Miller ◽  
John B. Cole ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Inbreeding Depression ◽  
Growth Traits ◽  
Effective Population ◽  
Angus Cattle ◽  
Genomic Inbreeding ◽  
Chromosome Segments ◽  
The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

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