scholarly journals GENOMIC AND PEDIGREE-BASED INBREEDING IN SLOVAK SPOTTED CATTLE

AGROFOR ◽  
2019 ◽  
Vol 4 (1) ◽  
Author(s):  
Radovan KASARDA ◽  
Ondrej KADLEČÍK ◽  
Anna TRAKOVICKÁ ◽  
Nina MORAVČÍKOVÁ
Keyword(s):  
Slovak Republic ◽  
Genomic Data ◽  
Pedigree Information ◽  
Runs Of Homozygosity ◽  
Total Length ◽  
Identical By Descent ◽  
Genomic Inbreeding ◽  
Genealogical Information

The objective of this study was to evaluate the level of inbreeding in population ofSlovak Spotted cattle and to compare its genomic and pedigree-based estimates.The genomic data have been obtained from in total of 37 AI sires and 50 sire damsgenotyped by using Illumina BovineSNP50v2 BeadChip and ICBF InternationalDairy and Beef v3, respectively. The genealogical information have been obtainedfrom the database of Breeding Services of the Slovak Republic, s. e. The pedigreefile consisted of 109,686 individuals (105,229 dams and 4,457 sires), while thereference population included only living animals, AI sires (129) and dams(36,949). The genomic inbreeding (FROH) was computed as the length of thegenome present in runs of homozygosity (ROH) divided by the total length of theautosomal genome covered by SNPs on the chip and the pedigree-based inbreeding(FPED) was calculated based on assumption that inbreeding of an individual reflectsthe probability that both alleles in one locus are derived from the same ancestor orare identical by descent. The ROH segments greater than 4 Mb (FROH > 4Mb) coveredin average 2.09 % of the genome, while the ROH segments greater than 16 Mb(FROH > 16Mb) achieved 0.43 % which indicated in analysed population recentinbreeding. Similarly, the increase of inbreeding across generation signalized theaverage ΔFPED computed from pedigree information (0.094%). However, thepedigree-based and genomic estimates of inbreeding differ from each other (inaverage FROH>4=0.02; FPED=0.004). In recent generation, the obtained values ofFROH indicated considerably higher degree of inbreeding.

scholarly journals Suitability of Pedigree Information and Genomic Methods for Analyzing Inbreeding of Polish Cold-Blooded Horses Covered by Conservation Programs

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 429
Author(s):  
Grażyna Polak ◽  
Artur Gurgul ◽  
Igor Jasielczuk ◽  
Tomasz Szmatoła ◽  
Jędrzej Krupiński ◽  
...  
Keyword(s):  
Population Structure ◽  
Genomic Data ◽  
Pedigree Information ◽  
Runs Of Homozygosity ◽  
Q Value ◽  
Horse Population ◽  
Livestock Breeding ◽  
Genomic Inbreeding ◽  
And Control ◽  
Shared Alleles

Traditionally, pedigree-based relationship coefficients were used to manage inbreeding and control inbreeding depression that occurs within populations. The extensive incorporation of genomic data in livestock breeding creates the opportunity to develop and implement methods to manage populations at the genomic level. Consequently, the realized proportion of the genome that two individuals share can be more accurately estimated instead of using pedigree information to estimate the expected proportion of shared alleles. To make use of this improvement, in this study we evaluated the genomic inbreeding measures in the Polish conserved cold-blooded horse population and compared the data with the traditional measures of inbreeding. Additionally, an ancestry fractions/proportions from Admixture software were tested as an estimate of lineage (ancestry coefficient) used for horses qualifying for the conservation program. The highest correlation of pedigree-based (FPED) and genomic inbreeding estimates was found for FROH (runs of homozygosity-based F coefficient) and FUNI (F coefficient based on the correlation between uniting gametes). FROH correlation with FPED tended to increase as the number of generations registered as pedigree increased. While lineage and gene contributions (Q) from Admixture software correlated, they showed poor direct compliance; hence, Q-value cannot be recommended as the estimate of pedigree-based lineage. All these findings suggest that the methods of genomics should be considered as an alternative or support in the analysis of population structure in conservative breeding that can help control inbreeding in rare horse populations.

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 The German Shorthair Pointer Dog Breed (Canis lupus familiaris): Genomic Inbreeding and Variability

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 498 ◽  
Author(s):  
Antonio Boccardo ◽  
Stefano Paolo Marelli ◽  
Davide Pravettoni ◽  
Alessandro Bagnato ◽  
Giuseppe Achille Busca ◽  
...  
Keyword(s):  
Canis Lupus ◽  
Inbreeding Coefficient ◽  
Nucleotide Polymorphisms ◽  
Canis Lupus Familiaris ◽  
Runs Of Homozygosity ◽  
Single Nucleotide ◽  
The Mean ◽  
Dog Breed ◽  
Genomic Inbreeding ◽  
Genealogical Information

The German Shorthaired Pointer (GSHP) is a breed worldwide known for its hunting versatility. Dogs of this breed are appreciated as valuable companions, effective trackers, field trailers and obedience athletes. The aim of the present work is to describe the genomic architecture of the GSHP breed and to analyze inbreeding levels under a genomic and a genealogic perspective. A total of 34 samples were collected (24 Italian, 10 USA), and the genomic and pedigree coefficients of inbreeding have been calculated. A total of 3183 runs of homozygosity (ROH) across all 34 dogs have been identified. The minimum and maximum number of Single Nucleotide Polymorphisms (SNPs) defining all ROH are 40 and 3060. The mean number of ROH for the sample was 93.6. ROH were found on all chromosomes. A total of 854 SNPs (TOP_SNPs) defined 11 ROH island regions (TOP_ROH), in which some gene already associated with behavioral and morphological canine traits was annotated. The proportion of averaged observed homozygotes estimated on total number of SNPs was 0.70. The genomic inbreeding coefficient based on ROH was 0.17. The mean inbreeding based on genealogical information resulted 0.023. The results describe a low inbred population with quite a good level of genetic variability.

scholarly journals Differences in the level of inbreeding in populations of Dagestan: analysis of runs of homozygosity

2020 ◽  
pp. 21-22
Author(s):  
Н.А. Колесников ◽  
В.Н. Харьков ◽  
М.О. Раджабов ◽  
А.А. Зарубин ◽  
С.С. Литвинов ◽  
...  
Keyword(s):  
Data Analysis ◽  
Genomic Data ◽  
Inbreeding Coefficient ◽  
The Other ◽  
Runs Of Homozygosity ◽  
Autosomal Snps ◽  
Total Length ◽  
Genomic Data Analysis ◽  
Other World ◽  
Inbreeding Level

Анализ геномных данных (~ 907 750 аутосомных SNP) позволил оценить уровень инбридинга на основе идентификации регионов высокой гомозиготности (FROH) в выборке из 518 человек 23 коренных народов Дагестана. В результате, в популяциях коренного населения Дагестана количество и суммарная длина ROH, а также коэффициент FROH показывают значительное разнообразие как внутри, так и между исследованными популяциями. У гинухцев, гунзибцев, ахвахцев, бежтинцев и цезов наблюдаются одни из самых высоких значений коэффициента инбридинга (FROH>1,5 млн п.н.) по сравнению с остальными мировыми популяциями. The genomic data analysis (~907750 autosomal SNPs) allowed us to estimate the inbreeding level based on the analysis of runs of homozygosity (Froh) in the group of 518 people from 23 indigenous Dagestan peoples. As a result, the number and total length of ROH, as well as the FROH coefficient, show a significant diversity in the indigenous Dagestan populations both inside and between them. One of the highest values of the inbreeding coefficient (FROH> 1.5Mb) is observed for the Ginukhs, Gunzibians, Akhvakhs, Bezhtins, and Tsez, as compared with the other world populations.

scholarly journals Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations

Animals ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 3234
Author(s):  
José Cortes-Hernández ◽  
Adriana García-Ruiz ◽  
Carlos Gustavo Vásquez-Peláez ◽  
Felipe de Jesus Ruiz-Lopez
Keyword(s):  
Inbreeding Coefficient ◽  
Pedigree Information ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Genomic Relationship ◽  
Runs Of Homozygosity ◽  
Inbreeding Coefficients ◽  
Improvement Programs ◽  
Genomic Inbreeding ◽  
Holstein Population

This study aimed to identify inbreeding coefficient (F) estimators useful for improvement programs in a small Holstein population through the evaluation of different methodologies in the Mexican Holstein population. F was estimated as follows: (a) from pedigree information (Fped); (b) through runs of homozygosity (Froh); (c) from the number of observed and expected homozygotic SNP in the individuals (Fgeno); (d) through the genomic relationship matrix (Fmg). The study included information from 4277 animals with pedigree records and 100,806 SNP. The average and standard deviation values of F were 3.11 ± 2.30 for Fped, −0.02 ± 3.55 for Fgeno, 2.77 ± 0.71 for Froh and 3.03 ± 3.05 for Fmg. The correlations between coefficients varied from 0.30 between Fped and Froh, to 0.96 between Fgeno and Fmg. Differences in the level of inbreeding among the parent’s country of origin were found regardless of the method used. The correlations among genomic inbreeding coefficients were high; however, they were low with Fped, so further research on this topic is required.

The pattern of runs of homozygosity and genomic inbreeding in world-wide sheep populations

Genomics ◽  
2021 ◽  
Author(s):  
Maryam Nosrati ◽  
Hojjat Asadollahpour Nanaei ◽  
Arash Javanmard ◽  
Ali Esmailizadeh
Keyword(s):  
World Wide ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding

scholarly journals Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0232436
Author(s):  
Christos Dadousis ◽  
Francesca Cecchi ◽  
Michela Ablondi ◽  
Maria Chiara Fabbri ◽  
Alessandra Stella ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Cross Validation ◽  
Small Region ◽  
Economic Factors ◽  
Admixture Analysis ◽  
Goat Breed ◽  
Runs Of Homozygosity ◽  
Genomic Inbreeding ◽  
Assignment Success ◽  
Integrated Study

The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell’Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. ROH analyses was used to assess the genetic diversity of GRF, while admixture and DAPC to evaluate its relationship to the other breeds. For GRF, common ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25–50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of common ROH was also present in DIT, while a broader region (~49.25–51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRF shared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.

scholarly journals Runs of homozygosity for autozygosity estimation and genomic analysis in production animals

2018 ◽  
Vol 53 (9) ◽  
pp. 975-984 ◽  
Author(s):  
Arnaldo Basso Rebelato ◽  
Alexandre Rodrigues Caetano
Keyword(s):  
Evolutionary History ◽  
Genomic Analysis ◽  
Runs Of Homozygosity ◽  
Demographic Information ◽  
Genomic Information ◽  
Selection Signatures ◽  
Effective Population ◽  
High Frequencies ◽  
Production Animals ◽  
Genealogical Information

Abstract: Runs of homozygosity (ROHs) are long stretches of homozygous genomic segments, identifiable by molecular markers, which can provide genomic information for accurate estimates to characterize populations, determine evolutionary history and demographic information, estimate levels of consanguinity, and identify selection signatures in production animals. This review paper aims to perform a survey of the works on the efficiency of ROHs for these purposes. Factors such as genetic drift, natural or artificial selection, founder effect, and effective population size directly influence the size and distribution of ROHs along the genome. Individually, genome estimates of consanguinity based on ROHs can be obtained using the FROH index, which is generally considered more accurate than indexes based on other types of genomic or genealogical information. High frequencies of specific ROHs in a population can be used to identify selection signatures. The results of recent studies with ROHs in domestic animals have shown the efficiency of their use to characterize herds in a reliable and accessible way, using genomic information.

scholarly journals 205 Runs of homozygosity and analysis of inbreeding depression

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 39-40
Author(s):  
Pattarapol Sumreddee ◽  
Sajjad Toghiani ◽  
Andrew J Roberts ◽  
El H Hay ◽  
Samuel E Aggrey ◽  
...  
Keyword(s):  
Inbreeding Depression ◽  
Clustering Algorithm ◽  
Search Algorithm ◽  
Pedigree Information ◽  
Minimum Length ◽  
Runs Of Homozygosity ◽  
Model Based Clustering ◽  
Genome Wide ◽  
Hereford Cattle ◽  
Density Marker

Abstract Pedigree information was traditionally used to assess inbreeding. Availability of high-density marker panels provides an alternative to assess inbreeding, particularly in the presence of incomplete and error-prone pedigrees. Assessment of autozygosity across chromosomal segments using runs of homozygosity (ROH) is emerging as a valuable tool to estimate inbreeding due to its general flexibility and ability to quantify chromosomal contribution to genome-wide inbreeding. Unfortunately, identifying ROH segments is sensitive to the parameters used during the search process. These parameters are heuristically set, leading to significant variation in the results. The minimum length required to identify a ROH segment has major effects on the estimation of inbreeding, yet it is arbitrarily set. Understanding the rise, purging, and the effects of deleterious mutations requires the ability to discriminate between ancient and recent inbreeding. However, thresholds to discriminate between short and long ROH segments are largely unknown. To address these questions, an inbred Hereford cattle population of 785 animals genotyped for 30,220 SNPs was used. A search algorithm to approximate mutation loads was used to determine the minimum length of ROH segments. It consisted of finding genome segments with significant differences in trait means between animals with high and low autozygosity intervals at certain threshold values. The minimum length was around 1 Mb for weaning and yearling weights and ADG, and 2.5 Mb for birth weight. Using a model-based clustering algorithm, a mixture of three Gaussian distributions was clearly separable, resulting in three classes of short (< 6.16 Mb), medium (6.16–12.57 Mb), and long (>12.27 Mb) ROH segments, representing ancient, intermediate, and recent inbreeding. Contribution of ancient, intermediate and recent to genome-wide inbreeding was 37.4%, 40.1% and 22.5%, respectively. Inbreeding depression analyses showed a greater damaging effect of recent inbreeding, likely due to purging of old highly deleterious haplotypes.

scholarly journals A Comprehensive Analysis of Runs of Homozygosity of Eleven Cattle Breeds Representing Different Production Types

Animals ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 1024 ◽  
Author(s):  
Tomasz Szmatoła ◽  
Artur Gurgul ◽  
Igor Jasielczuk ◽  
Tomasz Ząbek ◽  
Katarzyna Ropka-Molik ◽  
...  
Keyword(s):  
High Frequency ◽  
Production Traits ◽  
Runs Of Homozygosity ◽  
White Variety ◽  
Black And White ◽  
Cattle Breeds ◽  
Hereford Cattle ◽  
Holstein Friesian ◽  
Genomic Inbreeding ◽  
The Impact

In the presented research, BovineSNP50 microarrays (Illumina) were applied to determine runs of homozygosity in the genomes of 11 cattle breeds maintained in Poland. These cattle breeds represent three basic utility types: milk, meat and dual purpose. Analysis of runs of homozygosity allowed the evaluation of the level of autozygosity within each breed in order to calculate the genomic inbreeding coefficient (FROH), as well as to identify regions of the genome with a high frequency of ROH occurrence, which may reflect traces of directional selectin left in their genomes. Visible differences in the length and distribution of runs of homozygosity in the genomes of the analyzed cattle breeds have been observed. The highest mean number and mean sums of lengths of runs of homozygosity were characteristic for Hereford cattle and intermediate for the Holstein-Friesian Black-and-White variety, Holstein-Friesian Red-and-White variety, Simmental, Limousin, Montbeliarde and Charolais breeds. However, lower values were observed for cattle of conserved breeds. Moreover, the selected livestock differed in the level of inbreeding estimated using the FROH coefficient. In regions of the genome with a high frequency of ROH occurrence, which may reflect the impact of directional selection, a number of genes were observed that can be potentially related to the production traits which are under selection pressure for specific production types. The most important detected genes were GHR, MSTN, DGAT1, FABP4, and TRH, with a known influence on the milk and meat traits of the studied cattle breeds.

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