scholarly journals The genomic structure of isolation across breed, country and strain for important South African and Australian sheep populations

BMC Genomics ◽  
2022 ◽  
Vol 23 (1) ◽  
Author(s):  
Cornelius Nel ◽  
Phillip Gurman ◽  
Andrew Swan ◽  
Julius van der Werf ◽  
Margaretha Snyman ◽  
...  
Keyword(s):  
South Africa ◽  
South African ◽  
Genomic Structure ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Effective Population ◽  
Absolute Level ◽  
Genomic Resources ◽  
Sheep Breeds ◽  
Population Structures

Abstract Background South Africa and Australia shares multiple important sheep breeds. For some of these breeds, genomic breeding values are provided to breeders in Australia, but not yet in South Africa. Combining genomic resources could facilitate development for across country selection, but the influence of population structures could be important to the compatability of genomic data from varying origins. The genetic structure within and across breeds, countries and strains was evaluated in this study by population genomic parameters derived from SNP-marker data. Populations were first analysed by breed and country of origin and then by subpopulations of South African and Australian Merinos. Results Mean estimated relatedness according to the genomic relationship matrix varied by breed (-0.11 to 0.16) and bloodline (-0.08 to 0.06) groups and depended on co-ancestry as well as recent genetic links. Measures of divergence across bloodlines (FST: 0.04–0.12) were sometimes more distant than across some breeds (FST: 0.05–0.24), but the divergence of common breeds from their across-country equivalents was weak (FST: 0.01–0.04). According to mean relatedness, FST, PCA and Admixture, the Australian Ultrafine line was better connected to the SA Cradock Fine Wool flock than with other AUS bloodlines. Levels of linkage disequilibrium (LD) between adjacent markers was generally low, but also varied across breeds (r2: 0.14–0.22) as well as bloodlines (r2: 0.15–0.19). Patterns of LD decay was also unique to breeds, but bloodlines differed only at the absolute level. Estimates of effective population size (Ne) showed genetic diversity to be high for the majority of breeds (Ne: 128–418) but also for bloodlines (Ne: 137–369). Conclusions This study reinforced the genetic complexity and diversity of important sheep breeds, especially the Merino breed. The results also showed that implications of isolation can be highly variable and extended beyond breed structures. However, knowledge of useful links across these population substructures allows for a fine-tuned approach in the combination of genomic resources. Isolation across country rarely proved restricting compared to other structures considered. Consequently, research into the accuracy of across-country genomic prediction is recommended.

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

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.

scholarly journals 335 Genomic predictions with a multi-breed genomic relationship matrix

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 49-50
Author(s):  
Yvette Steyn ◽  
Daniela Lourenco ◽  
Ignacy Misztal
Keyword(s):  
Prediction Accuracy ◽  
Negative Impact ◽  
Reference Population ◽  
Single Step ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Genomic Relationship ◽  
Effective Population ◽  
Specific Allele ◽  
Missing Genotypes

Abstract Multi-breed evaluations have the advantage of increasing the size of the reference population for genomic evaluations and are quite simple; however, combining breeds usually have a negative impact on prediction accuracy. The aim of this study was to evaluate the use of a multi-breed genomic relationship matrix (G), where SNP for each breed are non-shared. The multi-breed G is set assuming known genotypes for one breed and missing genotypes for the remaining breeds. This setup may avoid spurious IBS relationships between breeds and considers breed-specific allele frequencies. This scenario was contrasted to multi-breed evaluations where all SNP are shared, i.e., the same SNP, and to single-breed evaluations. Different SNP densities, namely 9k and 45k, and different effective population sizes (Ne) were tested. Five breeds mimicking recent beef cattle populations that diverged from the same historical population were simulated using different selection criteria. It was assumed that QTL effects were the same over all breeds. For the recent population, generations 1 to 9 had approximately half of the animals genotyped, whereas all 1200 animals were genotyped in generation 10. Genotyped animals in generation 10 were set as validation; therefore, each breed had a validation set. Analysis were performed using single-step GBLUP (ssGBLUP). Prediction accuracy was calculated as correlation between true (T) and genomic estimated (GE) BV. Accuracies of GEBV were lower for the larger Ne and low SNP density. All three scenarios using 45K resulted in similar accuracies, suggesting that the marker density is high enough to account for relationships and linkage disequilibrium with QTL. A shared multi-breed evaluation using 9K resulted in a decrease of accuracy of 0.08 for a smaller Ne and 0.11 for a larger Ne. This loss was mostly avoided when markers were treated as non-shared within the same genomic relationship matrix.

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

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.

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

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.

scholarly journals Impact of genotypic errors with equal and unequal family contribution on accuracy of genomic prediction in aquaculture using simulation

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
N. Khalilisamani ◽  
P. C. Thomson ◽  
H. W. Raadsma ◽  
M. S. Khatkar
Keyword(s):  
Genomic Structure ◽  
Penaeus Monodon ◽  
Error Rates ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Substantial Impact ◽  
Lower Accuracy ◽  
Black Tiger Prawn ◽  
Genomic Predictions ◽  
Family Contribution

AbstractGenotypic errors, conflict between recorded genotype and the true genotype, can lead to false or biased population genetic parameters. Here, the effect of genotypic errors on accuracy of genomic predictions and genomic relationship matrix are investigated using a simulation study based on population and genomic structure comparable to black tiger prawn, Penaeus monodon. Fifty full-sib families across five generations with phenotypic and genotypic information on 53 K SNPs were simulated. Ten replicates of different scenarios with three heritability estimates, equal and unequal family contributions were generated. Within each scenario, four SNP densities and three genotypic error rates in each SNP density were implemented. Results showed that family contribution did not have a substantial impact on accuracy of predictions across different datasets. In the absence of genotypic errors, 3 K SNP density was found to be efficient in estimating the accuracy, whilst increasing the SNP density from 3 to 20 K resulted in a marginal increase in accuracy of genomic predictions using the current population and genomic parameters. In addition, results showed that the presence of even 10% errors in a 10 and 20 K SNP panel might not have a severe impact on accuracy of predictions. However, below 10 K marker density, even a 5% error can result in lower accuracy of predictions.

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

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.

scholarly journals Genomic predictions in purebreds with a multibreed genomic relationship matrix1

2019 ◽  
Vol 97 (11) ◽  
pp. 4418-4427 ◽  
Author(s):  
Yvette Steyn ◽  
Daniela A L Lourenco ◽  
Ignacy Misztal
Keyword(s):  
Prediction Accuracy ◽  
Negative Impact ◽  
Single Step ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
Limited Information ◽  
Genomic Relationship ◽  
Effective Population ◽  
Specific Allele ◽  
Trait Locus

Abstract Combining breeds in a multibreed evaluation can have a negative impact on prediction accuracy, especially if single nucleotide polymorphism (SNP) effects differ among breeds. The aim of this study was to evaluate the use of a multibreed genomic relationship matrix (G), where SNP effects are considered to be unique to each breed, that is, nonshared. This multibreed G was created by treating SNP of different breeds as if they were on nonoverlapping positions on the chromosome, although, in reality, they were not. This simple setup may avoid spurious Identity by state (IBS) relationships between breeds and automatically considers breed-specific allele frequencies. This scenario was contrasted to a regular multibreed evaluation where all SNPs were shared, that is, the same position, and to single-breed evaluations. Different SNP densities (9k and 45k) and different effective population sizes (Ne) were tested. Five breeds mimicking recent beef cattle populations that diverged from the same historical population were simulated using different selection criteria. It was assumed that quantitative trait locus (QTL) effects were the same over all breeds. For the recent population, generations 1–9 had approximately half of the animals genotyped, whereas all animals in generation 10 were genotyped. Generation 10 animals were set for validation; therefore, each breed had a validation group. Analyses were performed using single-step genomic best linear unbiased prediction. Prediction accuracy was calculated as the correlation between true (T) and genomic estimated breeding values (GEBV). Accuracies of GEBV were lower for the larger Ne and low SNP density. All three evaluation scenarios using 45k resulted in similar accuracies, suggesting that the marker density is high enough to account for relationships and linkage disequilibrium with QTL. A shared multibreed evaluation using 9k resulted in a decrease of accuracy of 0.08 for a smaller Ne and 0.12 for a larger Ne. This loss was mostly avoided when markers were treated as nonshared within the same G matrix. A G matrix with nonshared SNP enables multibreed evaluations without considerably changing accuracy, especially with limited information per breed.

scholarly journals Female Fertility and Single Nucleotide Polymorphism Comparisons in Cylindrocladium pauciramosum

Plant Disease ◽  
2001 ◽  
Vol 85 (9) ◽  
pp. 941-946 ◽  
Author(s):  
Conrad L. Schoch ◽  
Pedro W. Crous ◽  
Giancarlo Polizzi ◽  
Steven T. Koike
Keyword(s):  
United States ◽  
South Africa ◽  
South African ◽  
Mating Type ◽  
Dna Sequences ◽  
The United States ◽  
South American ◽  
Effective Population ◽  
Single Nucleotide ◽  
Β Tubulin

Cylindrocladium pauciramosum is well established in South America, and has recently been collected from nurseries in South Africa, Italy, and the United States. Isolates were compared with respect to the percentages of hermaphrodites and the respective mating types in the different samples. Based on these data, the effective population size could be determined for the different areas studied. All nurseries had mating type ratios significantly different from an idealized 1:1 ratio. In the South African nursery, the MAT-1 mating type was dominant, while the MAT-2 mating type dominated in other samplings. This is consistent with an introduction of a small starter population. High percentages of hermaphrodites also agreed with recent introductions into nurseries in Italy and the United States. Variability of DNA sequences of the 5′ end of the β-tubulin gene from a set of C. pauciramosum isolates from different geographic regions was low to high. Isolates from South Africa, the United States, and Australia had identical β-tubulin DNA sequences; this sequence was also found in the Italian sample, along with another unique group. Finally, a group of isolates obtained from South and Central America had the highest variation of all isolates investigated, and also included isolates that shared single nucleotide variations with another species, C. candelabrum. These findings suggest that C. pauciramosum most likely has a Central or South American center of origin.

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.

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