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

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.

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GENOMIC AND PEDIGREE-BASED INBREEDING IN SLOVAK SPOTTED CATTLE

AGROFOR ◽

10.7251/agreng1901102k ◽

2019 ◽

Vol 4 (1) ◽

Cited By ~ 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.

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Level of Inbreeding in Norik of Muran Horse: Pedigree vs. Genomic Data

Acta Universitatis Agriculturae et Silviculturae Mendelianae Brunensis ◽

10.11118/actaun201967061457 ◽

2019 ◽

Vol 67 (6) ◽

pp. 1457-1463 ◽

Cited By ~ 2

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.

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Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations

Animals ◽

10.3390/ani11113234 ◽

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.

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

Genomics ◽

10.1016/j.ygeno.2021.03.005 ◽

2021 ◽

Author(s):

Maryam Nosrati ◽

Hojjat Asadollahpour Nanaei ◽

Arash Javanmard ◽

Ali Esmailizadeh

Keyword(s):

World Wide ◽

Runs Of Homozygosity ◽

Genomic Inbreeding

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Genetic variability and population structure based on pedigree information for Muzaffarnagari sheep in India

Small Ruminant Research ◽

10.1016/j.smallrumres.2020.106182 ◽

2020 ◽

Vol 191 ◽

pp. 106182

Author(s):

Ajoy Mandal ◽

Hasan Baneh ◽

B.V. Subramanyam ◽

D.R. Notter

Keyword(s):

Population Structure ◽

Genetic Variability ◽

Pedigree Information

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Pedigree analysis of the Turkish Arab horse population: structure, inbreeding and genetic variability

animal ◽

10.1017/s175173111700009x ◽

2017 ◽

Vol 11 (9) ◽

pp. 1449-1456 ◽

Cited By ~ 7

Author(s):

S. Duru

Keyword(s):

Population Structure ◽

Genetic Variability ◽

Pedigree Analysis ◽

Horse Population

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Analysis of diversity and population structure in the Lipizzan horse breed based on pedigree information

Livestock Production Science ◽

10.1016/s0301-6226(02)00079-9 ◽

2002 ◽

Vol 77 (2-3) ◽

pp. 137-146 ◽

Cited By ~ 59

Author(s):

P Zechner ◽

J Sölkner ◽

I Bodo ◽

T Druml ◽

R Baumung ◽

...

Keyword(s):

Population Structure ◽

Pedigree Information ◽

Horse Breed

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

PLoS ONE ◽

10.1371/journal.pone.0232436 ◽

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.

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205 Runs of homozygosity and analysis of inbreeding depression

Journal of Animal Science ◽

10.1093/jas/skz258.078 ◽

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.

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