Correlation of Genomic and Pedigree Inbreeding Coefficients in Small Cattle Populations

Abstract Background Genomic relationship matrices are used to obtain genomic inbreeding coefficients. However, there are several methodologies to compute these matrices and there is still an unresolved debate on which one provides the best estimate of inbreeding. In this study, we investigated measures of inbreeding obtained from five genomic matrices, including the Nejati-Javaremi allelic relationship matrix (FNEJ), the Li and Horvitz matrix based on excess of homozygosity (FL&H), and the VanRaden (methods 1, FVR1, and 2, FVR2) and Yang (FYAN) genomic relationship matrices. We derived expectations for each inbreeding coefficient, assuming a single locus model, and used these expectations to explain the patterns of the coefficients that were computed from thousands of single nucleotide polymorphism genotypes in a population of Iberian pigs. Results Except for FNEJ, the evaluated measures of inbreeding do not match with the original definitions of inbreeding coefficient of Wright (correlation) or Malécot (probability). When inbreeding coefficients are interpreted as indicators of variability (heterozygosity) that was gained or lost relative to a base population, both FNEJ and FL&H led to sensible results but this was not the case for FVR1, FVR2 and FYAN. When variability has increased relative to the base, FVR1, FVR2 and FYAN can indicate that it decreased. In fact, based on FYAN, variability is not expected to increase. When variability has decreased, FVR1 and FVR2 can indicate that it has increased. Finally, these three coefficients can indicate that more variability than that present in the base population can be lost, which is also unreasonable. The patterns for these coefficients observed in the pig population were very different, following the derived expectations. As a consequence, the rate of inbreeding depression estimated based on these inbreeding coefficients differed not only in magnitude but also in sign. Conclusions Genomic inbreeding coefficients obtained from the diagonal elements of genomic matrices can lead to inconsistent results in terms of gain and loss of genetic variability and inbreeding depression estimates, and thus to misleading interpretations. Although these matrices have proven to be very efficient in increasing the accuracy of genomic predictions, they do not always provide a useful measure of inbreeding.

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Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

10.21203/rs.2.17561/v3 ◽

2020 ◽

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil Sarghale ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Muscle Development ◽

Bone Development ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Effective Population ◽

A Genome ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P≤0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

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Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

10.21203/rs.2.17561/v5 ◽

2020 ◽

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil Sarghale ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Muscle Development ◽

Bone Development ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Effective Population ◽

A Genome ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P≤0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

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Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

10.21203/rs.2.17561/v1 ◽

2019 ◽

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil-Sarghaleh ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Muscle Development ◽

Bone Development ◽

Coat Colour ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Effective Population ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background: Consecutive homozygous fragments of the genome inherited from a common ancestor to offspring are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identifying genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P<0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial and/or natural selection.

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Application of single-step GBLUP in New Zealand Romney sheep

Animal Production Science ◽

10.1071/an19315 ◽

2020 ◽

Vol 60 (9) ◽

pp. 1136

Author(s):

M. A. Nilforooshan

Keyword(s):

New Zealand ◽

Single Step ◽

Pedigree Information ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

Genomic Relationship ◽

Genetic Trend ◽

Weaning Weight ◽

Sheep Population ◽

Pedigree Relationship

Context In New Zealand, Romney is the most predominant breed and is reared as a dual-purpose sheep. The number of genotypes is rapidly increasing in the sheep population, and making use of both genotypes and pedigree information is of importance for genetic evaluations. Single-step genomic best linear unbiased prediction (ssGBLUP) is a method for simultaneous prediction of genetic merits for genotyped and non-genotyped animals. The combination and the compatibility of the genomic relationship matrix (G) and the pedigree relationship matrix for genotyped animals (A22) is important for unbiased ssGBLUP. Aims The aim of the present study was to find an optimum genetic relationship matrix for ssGBLUP weaning-weight evaluation of Romney sheep in New Zealand. Methods Data consisted of adjusted weaning weights for 2422011 sheep, 50K single-nucleotide polymorphism genotypes for 13304 animals and 3028688 animals in the pedigree. Blending of G and A22 was tested with weights (k) ranging from 0.2 to 0.99 (kG + (1 – k)A22), followed by none or one of the three methods of tuning G to A22. Key results The averages of G and A22 were close to each other for overall, diagonal and off-diagonal elements. Therefore, differently tuned G performed similarly. However, elements of G showed larger variation than did the elements of A22 and, on average, genotyped animals were less related in G than in A22. Correlations between genomic estimated breeding values (GEBV) for the top 500 genotyped animals, as well as the rank correlations, were almost 1 among ssGBLUP evaluations using tuned G. The corresponding correlations with BLUP evaluations were increased by blending G with a larger proportion of A22, and were further increased by tuning G, indicating improved compatibility between G and A22. Blending and tuning G suppressed the inflation of GEBV and bias and it moved the genetic trend closer to the genetic trend obtained from BLUP. Conclusions A combination of blending and tuning G to A22, with a blending rate of 0.5 at most, is recommended for weaning weight of Romney sheep in New Zealand. Failure to do that resulted in inflated GEBV that can reduce the accuracy of selection, especially for genotyped animals. Implications There is a growing interest in the single-step GBLUP method for simultaneous genetic evaluation of genotyped and non-genotyped animals, in which genomic and pedigree relationship matrices are admixed. Using data from New Zealand Romney sheep, we have shown that adjustment of the genomic relationship matrix on the basis of the pedigree relationship matrix is necessary to avoid inflated evaluations. Improving the compatibility between genomic and pedigree relationship matrices is important for obtaining accurate and unbiased single-step GBLUP evaluations.

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Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

10.21203/rs.2.17561/v2 ◽

2020 ◽

Author(s):

Seyed Mohammad Ghoreishifar ◽

Hossein Moradi-Shahrbabak ◽

Mohammad Hossein Fallahi ◽

Ali Jalil Sarghale ◽

Mohammad Moradi-Shahrbabak ◽

...

Keyword(s):

Muscle Development ◽

Bone Development ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

River Buffalo ◽

Runs Of Homozygosity ◽

Effective Population ◽

A Genome ◽

Genomic Inbreeding ◽

Genomic Regions

Abstract Background: Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P≤0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial or natural selection.

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Estimating inbreeding using dense marker panels and pedigree information

Suomen Maataloustieteellisen Seuran Tiedote ◽

10.33354/smst.75434 ◽

2012 ◽

pp. 1-6

Author(s):

Alban Bouquet ◽

Mikko Sillanpää ◽

Jarmo Juga

Keyword(s):

Estimation Accuracy ◽

Ancestral Population ◽

Pedigree Information ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

Genomic Relationship ◽

Trends Over Time ◽

Level Of Selection ◽

Dense Marker ◽

Selection Of

The aim of this simulation study was to compare the accuracy and bias of different inbreeding (F) estimators exploiting dense panels of diallelic markers and pedigree information. All genotype simulations were started by generating an ancestral population at mutation-drift equilibrium considering an effective size of 1000 and a mutation rate (µ) of 5.10-4. Two types of subpopulation were derived from the ancestral population for 10 discrete generations. They differed by the level of selection applied both on males and females: no selection or a structure close to a breeding program with selection of the best 40 males and 500 females on EBV with accuracy of 0.85 and 0.71, respectively, on a trait with heritability of 0.3. Marker panels were made up of 36 000 biallelic markers (18 per cM) and were available for animals in the last 4 generations. Pedigrees were recorded on the last 8 generations. For each scenario, 30 replicates were carried out. Analysed estimators were the correlation (VR1) and regression (VR3) estimators described to build the genomic relationship matrix by VanRaden in 2008. Other estimators included the weighted corrected similarity (WCS) estimator published by Ritland in 1996 and a modified WCS estimator accounting for pedigree information (WPCS). Pedigree-based inbreeding (PED) was also estimated using exhaustive pedigree information. Inbreeding estimates were correlated and regressed to the true simulated genomic F values to assess the precision and bias of estimators, respectively. Main results show that use of dense marker information improves the estimation of F, whatever the scenario. The accuracy of F estimates and the bias were increased in presence of selection, except for PED. Across scenarios, VR3, WCS and WPCS were the most correlated with true F values. In the situation where pedigree was exhaustive, VR3 performed as well as WCS and WPCS but had a larger variability over replicates. Although less biased on average, VR1 was less accurate than other estimators especially when allele frequencies were not properly defined. Accounting for pedigree information into WCS did not increase its estimation accuracy and did not reduce bias in the tested scenarios. Finally, error in estimating inbreeding trends over time in selected populations was greater for some marker-based estimators (VR3, VR1) than PED estimator. WCS and WPCS rendered the most accurate estimations of inbreeding trends. Thus, results indicate that WCS, which can be also used with multiallelic markers, is a promising estimator both to build the genomic relationship matrix for genomic evaluations and to better assess genetic diversity in selected populations.

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PSIII-2 Assessment of runs of homozygosity and estimates of inbreeding in three purebred turkey (Meleagris gallopavo) lines

Journal of Animal Science ◽

10.1093/jas/skaa278.421 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 229-229

Author(s):

Sarah M Adams ◽

Martijn F Derks ◽

Bayode Makanjuola ◽

Benjamin Wood ◽

Christine F Baes

Keyword(s):

Single Nucleotide Polymorphism Array ◽

Meleagris Gallopavo ◽

Genomic Relationship Matrix ◽

Relationship Matrix ◽

Runs Of Homozygosity ◽

Single Nucleotide ◽

Breeding Programs ◽

Inbreeding Coefficients ◽

Fitness And Health ◽

Dense Single Nucleotide Polymorphism

Abstract Runs of homozygosity (ROH) are continuous stretches of homozygous genotypes in an individual that have been passed down from a common ancestor and can be used to accurately characterize genomic data. These ROH are correlated with other measures of inbreeding and have been applied to quantify individual autozygosity. The aim of this study was to detect and describe ROH in the turkey genome and estimate and compare measures of pedigree-based inbreeding coefficients (FPED) and genomic-based inbreeding coefficients estimated from ROH (FROH) and the genomic relationship matrix (FGRM). Pedigree records (n = 2,616,890) and genotypic records (n = 6,371) were available from three purebred turkey (Meleagris gallopavo) lines. Genotypic records were collected between 2013 and 2019 and were obtained using a dense single nucleotide polymorphism array (56,452 SNP). The overall mean length of detected ROH per animal was 2.87±0.29 Mb and mean number of ROH per animal was 84.87±8.79. Short ROH with lengths of 1–2 Mb long were the most abundant throughout the genome, accounting for approximately 45% of the identified segments. Mean ROH coverage differed greatly between chromosomes and lines. Across all lines, genomic derived inbreeding coefficients (FROH=0.27; FGRM=0.32) were higher than coefficients estimated from pedigree records (FPED=0.14). Ranges of correlations between FROH and FPED (0.19–0.31), FROH and FGRM (0.68–0.73), and FPED and FGRM (0.17–0.30) were estimated. Results from the current research provide a fundamental description of inbreeding in the turkey genome which is critical considering the growing concerns of the detrimental effects of increased inbreeding on fitness and health in livestock production. The knowledge gained from this study may subsequently be used to evaluate and maintain genetic diversity that is necessary for genetic improvement and minimizing inbreeding in turkey breeding programs.

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Genome-Wide Assessment of Runs of Homozygosity and Estimates of Genomic Inbreeding in a Chinese Composite Pig Breed

Frontiers in Genetics ◽

10.3389/fgene.2021.720081 ◽

2021 ◽

Vol 12 ◽

Author(s):

Zhong Xu ◽

Shuqi Mei ◽

Jiawei Zhou ◽

Yu Zhang ◽

Mu Qiao ◽

...

Keyword(s):

Genetic Diversity ◽

Genomic Selection ◽

Artificial Selection ◽

Sus Scrofa ◽

Genome Structure ◽

Inbreeding Coefficient ◽

Runs Of Homozygosity ◽

Inbreeding Coefficients ◽

Genome Wide ◽

Genomic Inbreeding

The primary purpose of the current study was to assess the genetic diversity, runs of homozygosity (ROH) and ROH islands in a Chinese composite pig and explore hotspot regions for traces of selection. First, we estimated the length, number, and frequency of ROH in 262 Xidu black pigs using the Porcine SNP50 BeadChip and compared the estimates of inbreeding coefficients, which were calculated based on ROHs (FROH) and homozygosity (FHOM). Our result shows that a total of 7,248 ROH exceeding 1Mb were detected in 262 pigs. In addition, Sus scrofa chromosome (SSC) 8 and SSC10, respectively, has the highest and lowest chromosome coverage by ROH. These results suggest that inbreeding estimation based on total ROH may be a useful method, especially for crossbreed or composite populations. We also calculated an inbreeding coefficient of 0.077 from the total ROH. Eight ROH islands were found in this study. These ROH islands harbored genes associated with fat deposition, muscular development, reproduction, ear shape, and adaptation, such as TRAF7, IGFBP7, XPO1, SLC26A8, PPARD, and OR1F1. These findings may help to understand the effects of environmental and artificial selection on the genome structure of composite pigs. Our results provide a basis for subsequent genomic selection (GS), and provides a reference for the hybrid utilization of other pig breeds.

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

Semina Ciências Agrárias ◽

10.5433/1679-0359.2020v41n6supl2p3397 ◽

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.

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