Assessing the contribution of breeds to genetic diversity in conservation schemes

Eding, Herwin; Crooijmans, R.P.M.A.; Groenen, M.A.M.; Meuwissen, Theo H. E.

doi:10.1186/1297-9686-34-5-613

Cited by 108 publications

(113 citation statements)

References 7 publications

(7 reference statements)

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“…In contrast, the WEL originated from the single comb White Leghorn breed which is of European origin [25-27]. Our PCA results are thus in agreement with the existing knowledge of the origin of the lines/breeds and are also in agreement with the previous studies such as by Eding et al [28] and Elferink et al [27] which showed phylogenetic relationship among different poultry breeds.…”

Section: Resultssupporting

confidence: 92%

Development of a high density 600K SNP genotyping array for chicken

et al. 2013

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BackgroundHigh density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.ResultsWe report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10–15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P < 0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses.ConclusionsThis Affymetrix® Axiom® array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants.

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Section: Resultssupporting

confidence: 92%

Development of a high density 600K SNP genotyping array for chicken

et al. 2013

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“…Alternatively, the contribution of a breed to within-breed diversity was evaluated by its partial contribution to expected heterozygosity. In an attempt to combine both perspectives, the method of Eding et al [30] was applied, to analyze the contribution of a breed to a core set using molecular information to estimate the within- and between-breed kinships. After investigating different alternatives to account for molecular coancestries, the weighted log-linear mixed model (WLMM) of Eding and Meuwissen [31] was chosen.…”

Section: Methodsmentioning

confidence: 99%

Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

Gama¹,

Martínez²,

Carolino

et al. 2013

Genet Sel Evol

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BackgroundNative pig breeds in the Iberian Peninsula are broadly classified as belonging to either the Celtic or the Mediterranean breed groups, but there are other local populations that do not fit into any of these groups. Most of the native pig breeds in Iberia are in danger of extinction, and the assessment of their genetic diversity and population structure, relationships and possible admixture between breeds, and the appraisal of conservation alternatives are crucial to adopt appropriate management strategies.MethodsA panel of 24 microsatellite markers was used to genotype 844 animals representing the 17 most important native swine breeds and wild populations existing in Portugal and Spain and various statistical tools were applied to analyze the results.ResultsGenetic diversity was high in the breeds studied, with an overall mean of 13.6 alleles per locus and an average expected heterozygosity of 0.80. Signs of genetic bottlenecks were observed in breeds with a small census size, and population substructure was present in some of the breeds with larger census sizes. Variability among breeds accounted for about 20% of the total genetic diversity, and was explained mostly by differences among the Celtic, Mediterranean and Basque breed groups, rather than by differences between domestic and wild pigs. Breeds clustered closely according to group, and proximity was detected between wild pigs and the Mediterranean cluster of breeds. Most breeds had their own structure and identity, with very little evidence of admixture, except for the Retinto and Entrepelado varieties of the Mediterranean group, which are very similar. Genetic influence of the identified breed clusters extends beyond the specific geographical areas across borders throughout the Iberian Peninsula, with a very sharp transition from one breed group to another. Analysis of conservation priorities confirms that the ranking of a breed for conservation depends on the emphasis placed on its contribution to the between- and within-breed components of genetic diversity.ConclusionsNative pig breeds in Iberia reveal high levels of genetic diversity, a solid breed structure and a clear organization in well-defined clusters.

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“…[15,44]). In the present study, the core set refers to the smallest set of sheep breeds that still encompasses the neutral genetic diversity in the species using the co-ancestry measure detailed above.…”

Section: Methodsmentioning

confidence: 99%

Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia

et al. 2010

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BackgroundIdentification of global livestock diversity hotspots and their importance in diversity maintenance is essential for making global conservation efforts. We screened 52 sheep breeds from the Eurasian subcontinent with 20 microsatellite markers. By estimating and weighting differently within- and between-breed genetic variation our aims were to identify genetic diversity hotspots and prioritize the importance of each breed for conservation, respectively. In addition we estimated how important within-species diversity hotspots are in livestock conservation.ResultsBayesian clustering analysis revealed three genetic clusters, termed Nordic, Composite and Fat-tailed. Southern breeds from close to the region of sheep domestication were more variable, but less genetically differentiated compared with more northern populations. Decreasing weight for within-breed diversity component led to very high representation of genetic clusters or regions containing more diverged breeds, but did not increase phenotypic diversity among the high ranked breeds. Sampling populations throughout 14 regional groups was suggested for maximized total genetic diversity.ConclusionsDuring initial steps of establishing a livestock conservation program populations from the diversity hot-spot area are the most important ones, but for the full design our results suggested that approximately equal population presentation across environments should be considered. Even in this case, higher per population emphasis in areas of high diversity is appropriate. The analysis was based on neutral data, but we have no reason to think the general trend is limited to this type of data. However, a comprehensive valuation of populations should balance production systems, phenotypic traits and available genetic information, and include consideration of probability of success.

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Assessing the contribution of breeds to genetic diversity in conservation schemes

Cited by 108 publications

References 7 publications

Development of a high density 600K SNP genotyping array for chicken

Development of a high density 600K SNP genotyping array for chicken

Genetic structure, relationships and admixture with wild relatives in native pig breeds from Iberia and its islands

Microsatellite-based genetic diversity and population structure of domestic sheep in northern Eurasia

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