Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

Flury, Christine; Tapio, Miika; Sonstegard, Tad S.; Drögemüller, Cord; Leeb, Tosso; Simianer, Henner; Hanotte, Olivier; Rieder, Stefan

doi:10.1111/j.1439-0388.2010.00862.x

Cited by 68 publications

(89 citation statements)

References 24 publications

(38 reference statements)

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“…Differences in LD among chromosomes have already been reported in Holstein cattle, and these can be attributed to the recombination rate, heterozygosity, genetic drift, and the effect of selection (Qanbari et al, 2010). Other authors reported similar average LD at University of Edinburgh on November 6, 2014 www.journalofanimalscience.org Downloaded from values between adjacent SNP pairs among the 29 different autosomes (Bohmanova et al, 2010;Flury et al, 2010;Beghain et al, 2013). The comparison of LD levels in different studies is not straightforward because of differences in several factors, such as sample size, type of LD measure (D´ or r 2 ), marker types (microsatellites or SNP), marker density and distribution, and population demography (Qanbari et al, 2010).…”

Section: Linkage Disequilibriumsupporting

confidence: 58%

“…So far, studies of the extent of LD have been reported mostly for dairy and beef cattle breeds under selection, but there is little information about the degree of genome-wide LD in local cattle breeds and populations. Considering the LD levels between adjacent markers, the average r 2 in the MOD breed was comparable to those reported for] indigenous Swiss Eringer (r 2 = 0.24; Flury et al, 2010), Blonde d'Aquitaine (r 2 = 0.20; Beghain et al, 2013), and Chinese and Nordic Holsteins (r 2 = 0.20 and 0.21, respectively; Zhou et al, 2013), whereas the CIN breed had lower values. The results may be explained by considering the influence of selection on LD; in fact, the CIN breed is not subject to breeding programs, whereas the MOD breed is characterized by low selection pressure.…”

Section: Linkage Disequilibriumsupporting

confidence: 56%

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The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

Mastrangelo

Saura

Tolone

et al. 2014

Journal of Animal Science

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ABSTRACT:Genomic technologies, such as highthroughput genotyping based on SNP arrays, provided background information concerning genome structure in domestic animals. The aim of this work was to investigate the genetic structure, the genome-wide estimates of inbreeding, coancestry, effective population size (N e ), and the patterns of linkage disequilibrium (LD) in 2 economically important Sicilian local cattle breeds, Cinisara (CIN) and Modicana (MOD), using the Illumina Bovine SNP50K v2 BeadChip. To understand the genetic relationship and to place both Sicilian breeds in a global context, genotypes from 134 other domesticated bovid breeds were used. Principal component analysis showed that the Sicilian cattle breeds were closer to individuals of Bos taurus taurus from Eurasia and formed nonoverlapping clusters with other breeds. Between the Sicilian cattle breeds, MOD was the most differentiated, whereas the animals belonging to the CIN breed showed a lower value of assignment, the presence of substructure, and genetic links with the MOD breed. The average molecular inbreeding and coancestry coefficients were moderately high, and the current estimates of N e were low in both breeds. These values indicated a low genetic variability. Considering levels of LD between adjacent markers, the average r 2 in the MOD breed was comparable to those reported for others cattle breeds, whereas CIN showed a lower value. Therefore, these results support the need of more dense SNP arrays for a high-power association mapping and genomic selection efficiency, particularly for the CIN cattle breed. Controlling molecular inbreeding and coancestry would restrict inbreeding depression, the probability of losing beneficial rare alleles, and therefore the risk of extinction. The results generated from this study have important implications for the development of conservation and/or selection breeding programs in these 2 local cattle breeds.

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Section: Linkage Disequilibriumsupporting

confidence: 58%

Section: Linkage Disequilibriumsupporting

confidence: 56%

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

Mastrangelo

Saura

Tolone

et al. 2014

Journal of Animal Science

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“…Some earlier studies (e.g. Flury et al, 2010;Hasler et al, 2011;Uimari and Tapio, 2011; with cattle, horses and pigs, respectively) presented N e (LD) that were lower than N e (DF) for the same breeds. However, in some studies (e.g.…”

Section: Discussionmentioning

confidence: 99%

“…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%

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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“…With the wider use of genomic technologies in animal breeding and animal genetics, it is worthwhile revising and improving the current knowledge and understanding of cattle LD (Pérez O'Brien et al, 2014). Flury et al (2010) used this method for the estimation of LD and effective population size of a local cattle breed of Switzerland. Among livestock species, this technology has been applied most successfully in cattle, because factors such as evolutionary history, genetic structure and economics make cattle particularly suitable for the application of genome assisted selection (Nicolazzi et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Extent of genome-wide linkage disequilibrium in Pinzgau cattle

Šidlová¹,

Kasarda²,

Moravčíková³

et al. 2016

JCEA

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The aim of this study was to describe the extent of linkage disequilibrium (LD) based on genotyping data in Pinzgau cattle population. DNA samples were obtained from 19 bulls of active Pinzgau cattle population in Slovakia. Genotyping was carried out in commercial lab using an Illumina BovineSNP50 BeadChip. The genotyping array contained 54,609 single nucleotide polymorphisms (SNPs). After quality control SNPs localized on sex chromosomes were excluded. A total of 42,248 (79.97%) SNPs were found to be polymorphic. The distribution of SNPs over entire genomes of all chromosomes was not uniform. The minor allele frequencies across autosomal loci ranged from 0.266 (BTA4) to 0.280 (BTA23) with average value 0.273±0.133. Only adjacent SNPs with distance less than 5 Mb and LD (r 2 ) values from 0.01 to 0.99 were used in the characterization of LD extent. After filtering, the genome coordinates of 31,063 SNP markers covered all regions of autosomes on the length 2519232 kb. The spacing across genome between adjacent SNPs was in average 46.89±47.48 kb and within autosomes ranged from 43.65 kb (BTA25) to 52.59 kb (BTA5). The distribution of SNPs on different chromosomes ranged from 633 (79.13%) on BTA29 to 1123 (83.62%) on BTA14. The average LD between adjacent markers within autosomes reached values from 0.189 to 0.234 for chromosomes BTA 29 and 21, respectively. Division of r 2 -values over all 29 autosomes were performed according to their physical intermarker distances and averaged within the groups for analysis of distance effect on LD. The results of our study indicated the rapid decay of LD with increasing distance between markers. Further investigation will be oriented on evaluation of effective population size based on LD data. This could allow improvement of our knowledge about genetic diversity and its use for breed preservation of original phenotype supported by the current selection schemes and breeding programmes. . Na základe fyzickej vzdialenosti medzi markérmi boli r 2 rozdelené do skupín a priemerné hodnoty za každú skupinu použité pre analýzu vplyvu vzdialenosti na LD. Výsledky našej práce ukázali rýchly pokles LD s rastúcou vzdialenosťou medzi markérmi. Ďalšie výskumy budú zamerané na odhad efektívnej veľkosti populácie odvodenej z LD, čo môže zlepšiť naše vedomosti o genetickej diverzite a jej použití pre zachovanie plemena v jeho originálnej podobe s podporou selekčných systémov a šľachtiteľských programov.

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Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

Cited by 68 publications

References 24 publications

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

The genome-wide structure of two economically important indigenous Sicilian cattle breeds1

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

Extent of genome-wide linkage disequilibrium in Pinzgau cattle

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