Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population

Rodríguez‐Ramilo, Silvia Teresa; Fernández, Jesús; Toro, M. Á.; Hernández, Delfino; Villanueva, Beatriz

doi:10.1371/journal.pone.0124157

Cited by 46 publications

(49 citation statements)

References 51 publications

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“…The very close matches between N e (DF), N e (LD) and N e (ROH) (79.4, 74.4 and 70.0, respectively) calculated by Rodriguez-Ramilo et al (2014) for Spanish Holstein cattle may reflect the use of Holstein in designing the 50 K SNP chip that was used. Similarly, the first formal study of congruence of methodologies in pigs (Saura et al, 2015) gave N e (LD) 20.8 ±3.7 and N e (DF) 21.…”

Section: Discussionmentioning

confidence: 76%

“…There have been relatively few studies giving direct comparisons, within specific breeds, of genealogy-and LD-based estimates of N e (but see, e.g. Flury et al, 2010;Rodriguez-Ramilo et al, 2014;Bohmanova et al, 2015 with cattle;Hasler et al, 2011, horses;Saura et al, 2015, pigs). Although some studies show a close convergence, in others there are large disparities.…”

Section: Introductionmentioning

confidence: 99%

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Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

Hall¹

2016

Animal

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Accurate measures of effective population sizes ( N e ) in livestock require good quality data and specialized skills for their computation and analysis. N e can be estimated by Wright's equation N e = 4MF/( M + F) (M, F being sires and dams, respectively), but this requires assumptions which are often not met. Total census sizes N c of livestock breeds are collated globally. This paper investigates whether estimates of N e can be made from N c ; this would facilitate conservation monitoring. Some N e methodologies avoid the assumptions of Wright's equation and permit measurement, rather than estimation, of N e . Those considered here employ, respectively, linkage disequilibrium (LD) of single-nucleotide polymorphisms (yielding N e ( LD)), and genealogical analysis (rate of increase of inbreeding, DF), yielding N e (DF). Considering breeds of cattle, sheep, horses, pigs and goats for which N c and either N e ( LD) or N e ( DF) are known (totals of 203 breeds and 321 breeds, respectively), proportionality has been investigated between N c and these measures of N e . N e ( LD) was found to increase with N c , significantly in sheep and horses, less so in cattle, but not at all in pigs. N e ( DF) was correlated with log 10 ( N c ) in cattle, sheep and horses (53, 56, 43 breeds, respectively). N e ( LD) was correlated in cattle (73 breeds) and pigs (31 breeds) with the log 10 transformation of N e as calculated by Wright's equation.Further verification and refinement are needed, particularly of census data, but credible predictions of N e are obtainable by applying the following multipliers to log 10 ( N c ): cattle 17.61, sheep 97.72, horse 70.78. For cattle and pigs, multiplying log 10 ( N e (Wright)) by, respectively, 40.69 and 60.09, also gives credible predictions. Such census-based estimates of N e could in principle be generated by non-specialists and are likely to be suited to audits of conservation activity when financial resources or availability of data are limiting. The ratio N e /N c varied among species with an overall median value of 0.03, less than a tenth of that typically observed in wild mammals. Characteristics were also investigated of a distinct herdbook-based methodology, namely the development of Wright's equation to take into account variances of progeny numbers to yield what has been termed here N e (Hill). Comparison of these values with N e (Wright) could help to identify breeds with breeding structures conducive or inimical to genetic conservation. However, N e (Hill) requires breed-specific values for these variances, and this restricts its applicability.

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Section: Discussionmentioning

confidence: 76%

Section: Introductionmentioning

confidence: 99%

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

Hall¹

2016

Animal

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“…In fact, F coefficients estimated using allele frequencies (F HOM ) showed Genome structure in Barbaresca sheep breed considerable variation within the breed with respect to the other estimates (F ROH and F i ) and had the highest CV. Molecular inbreeding (F i ) and molecular coancestry (f ij ) coefficient values were much higher than the other coefficients because these two methods (which are obtained on a SNP-by-SNP basis) do not discriminate between alleles that are identical by descent (IBD) or IBS (Rodríguez-Ramilo et al, 2015). Moreover, the strong correlation between the pedigree inbreeding coefficient and the sum of ROH reported by several authors (Purfield et al, 2012) indicates that the estimates of F ROH are a good reflection of IBD and suggests that, in the absence of an animal's pedigree data, as may be the case for local endangered breeds, the extent of a genome under ROH may be used to infer aspects of recent population history, even from relatively few samples.…”

Section: Discussionmentioning

confidence: 95%

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Mastrangelo

Portolano

Gerlando

et al. 2017

Animal

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Analysis of genomic data is becoming increasingly common in the livestock industry and the findings have been an invaluable resource for effective management of breeding programs in small and endangered populations. In this paper, with the goal of highlighting the potential of genomic analysis for small and endangered populations, genome-wide levels of linkage disequilibrium, measured as the squared correlation coefficient of allele frequencies at a pair of loci, effective population size, runs of homozygosity (ROH) and genetic diversity parameters, were estimated in Barbaresca sheep using Illumina OvineSNP50K array data. Moreover, the breed's genetic structure and its relationship with other breeds were investigated. Levels of pairwise linkage disequilibrium decreased with increasing distance between single nucleotide polymorphisms. An average correlation coefficient <0.25 was found for markers located up to 50 kb apart. Therefore, these results support the need to use denser single nucleotide polymorphism panels for high power association mapping and genomic selection efficiency in future breeding programs. The estimate of past effective population size ranged from 747 animals 250 generations ago to 28 animals five generations ago, whereas the contemporary effective population size was 25 animals. A total of 637 ROH were identified, most of which were short (67%) and ranged from 1 to 10 Mb. The genetic analyses revealed that the Barbaresca breed tended to display lower variability than other Sicilian breeds. Recent inbreeding was evident, according to the ROH analysis. All the investigated parameters showed a comparatively narrow genetic base and indicated an endangered status for Barbaresca. Multidimensional scaling, model-based clustering, measurement of population differentiation, neighbor networks and haplotype sharing distinguished Barbaresca from other breeds, showed a low level of admixture with the other breeds considered in this study, and indicated clear genetic differences compared with other breeds. Attention should be given to the conservation of Barbaresca due to its critical conservation status. In this context, genomic information may have a crucial role in management of small and endangered populations.

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“…Leroy et al [29] demonstrated variation in N e estimates using different approaches. For Holsteins, N e estimates range from 50 [30] to 150 [31], with many intermediate estimates in between [32–35]. Estimates for Jerseys range from 73 [34] to 135 [33].…”

Section: Resultsmentioning

confidence: 99%

Dimensionality of genomic information and performance of the Algorithm for Proven and Young for different livestock species

et al. 2016

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BackgroundA genomic relationship matrix (GRM) can be inverted efficiently with the Algorithm for Proven and Young (APY) through recursion on a small number of core animals. The number of core animals is theoretically linked to effective population size (N e). In a simulation study, the optimal number of core animals was equal to the number of largest eigenvalues of GRM that explained 98% of its variation. The purpose of this study was to find the optimal number of core animals and estimate N e for different species.MethodsDatasets included phenotypes, pedigrees, and genotypes for populations of Holstein, Jersey, and Angus cattle, pigs, and broiler chickens. The number of genotyped animals varied from 15,000 for broiler chickens to 77,000 for Holsteins, and the number of single-nucleotide polymorphisms used for genomic prediction varied from 37,000 to 61,000. Eigenvalue decomposition of the GRM for each population determined numbers of largest eigenvalues corresponding to 90, 95, 98, and 99% of variation.ResultsThe number of eigenvalues corresponding to 90% (98%) of variation was 4527 (14,026) for Holstein, 3325 (11,500) for Jersey, 3654 (10,605) for Angus, 1239 (4103) for pig, and 1655 (4171) for broiler chicken. Each trait in each species was analyzed using the APY inverse of the GRM with randomly selected core animals, and their number was equal to the number of largest eigenvalues. Realized accuracies peaked with the number of core animals corresponding to 98% of variation for Holstein and Jersey and closer to 99% for other breed/species. N e was estimated based on comparisons of eigenvalue decomposition in a simulation study. Assuming a genome length of 30 Morgan, N e was equal to 149 for Holsteins, 101 for Jerseys, 113 for Angus, 32 for pigs, and 44 for broilers.ConclusionsEigenvalue profiles of GRM for common species are similar to those in simulation studies although they are affected by number of genotyped animals and genotyping quality. For all investigated species, the APY required less than 15,000 core animals. Realized accuracies were equal or greater with the APY inverse than with regular inversion. Eigenvalue analysis of GRM can provide a realistic estimate of N e.

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Genome-Wide Estimates of Coancestry, Inbreeding and Effective Population Size in the Spanish Holstein Population

Cited by 46 publications

References 51 publications

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

Genome-wide analysis in endangered populations: a case study in Barbaresca sheep

Dimensionality of genomic information and performance of the Algorithm for Proven and Young for different livestock species

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