Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

Herrero-Medrano, J.M.; Megens, Hendrik‐Jan; Groenen, Martien A. M.; Ramis, G.; Bosse, Mirte; Pérez‐Enciso, Miguel; Crooijmans, R.P.M.A.

doi:10.1186/1471-2156-14-106

Cited by 99 publications

(104 citation statements)

References 61 publications

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“…Landrace and Yorkshire presented a higher proportion of longer ROH segments compared to the other populations, suggesting higher levels of recent inbreeding in these breeds and thus lower individual genetic diversity. A characterization of ROH in pigs has also been previously reported by Herrero-Medrano et al [35] for pig populations from the Iberian Peninsula. The authors reported a mean of the total number of ROH per population between 24 and 34, which are slightly higher than the values reported in the present study, however, consistent with the breeds’ history.…”

Section: Discussionsupporting

confidence: 63%

Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

et al. 2017

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BackgroundKnowledge on the levels of linkage disequilibrium (LD) across the genome, persistence of gametic phase between breed pairs, genetic diversity and population structure are important parameters for the successful implementation of genomic selection. Therefore, the objectives of this study were to investigate these parameters in order to assess the feasibility of a multi-herd and multi-breed training population for genomic selection in important purebred and crossbred pig populations in Canada. A total of 3,057 animals, representative of the national populations, were genotyped with the Illumina Porcine SNP60 BeadChip (62,163 markers).ResultsThe overall LD (r 2) between adjacent SNPs was 0.49, 0.38, 0.40 and 0.31 for Duroc, Landrace, Yorkshire and Crossbred (Landrace x Yorkshire) populations, respectively. The highest correlation of phase (r) across breeds was observed between Crossbred animals and either Landrace or Yorkshire breeds, in which r was approximately 0.80 at 1 Mbp of distance. Landrace and Yorkshire breeds presented r ≥ 0.80 in distances up to 0.1 Mbp, while Duroc breed showed r ≥ 0.80 for distances up to 0.03 Mbp with all other populations. The persistence of phase across herds were strong for all breeds, with r ≥ 0.80 up to 1.81 Mbp for Yorkshire, 1.20 Mbp for Duroc, and 0.70 Mbp for Landrace. The first two principal components clearly discriminate all the breeds. Similar levels of genetic diversity were observed among all breed groups. The current effective population size was equal to 75 for Duroc and 92 for both Landrace and Yorkshire.ConclusionsAn overview of population structure, LD decay, demographic history and inbreeding of important pig breeds in Canada was presented. The rate of LD decay for the three Canadian pig breeds indicates that genomic selection can be successfully implemented within breeds with the current 60 K SNP panel. The use of a multi-breed training population involving Landrace and Yorkshire to estimate the genomic breeding values of crossbred animals (Landrace × Yorkshire) should be further evaluated. The lower correlation of phase at short distances between Duroc and the other breeds indicates that a denser panel may be required for the use of a multi-breed training population including Duroc.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-017-0473-y) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 63%

Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

et al. 2017

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“…However, in some studies (e.g. Herrero-Viedma et al, 2013) N e (LD) have large standard errors and are also sensitive to assumptions of constant N e (Corbin et al, 2012). Suggesting that the assumptions of the Wright equation are sometimes met in actual populations, Harmegnies et al (2006) found that in two commercial pig populations (each maintained at about ten boars and 250 to 300 sows) N e (LD) agreed 'reasonably well' with N e (Wright).…”

Section: Discussionmentioning

confidence: 75%

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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“…The white phenotype of the Rongchang pig is a recessive trait (Lai et al, 2007) and there is high conservation-related interest in investigating the origin of the PW breed. Knowledge of the genetic structure, based on genomic data, has been important in revealing the demographic and evolutionary history of pig breeds worldwide (Ai et al, 2013;Herrero-Medrano et al, 2013;Pham et al, 2014;Traspov et al, 2016). However, to date, the genetic structure of PW has scarcely been investigated, despite the specific, desirable qualities of this breed, including high prolificacy, high meat quality and good adaptability.…”

Section: Discussionmentioning

confidence: 99%

“…Genetic markers, particularly SNPs, are widely used to explore important questions in population genetics and domestication. High-density SNP analysis plays an essential role in revealing the past and current population demographics (Herrero-Medrano et al, 2013). In our study, highquality reads (removing primer/adaptor contaminated reads) with average base quality scores ⩾20 (indicating an error rate of base calling of 1 in 100) were used to call SNPs, and the average sequencing depth for SNP calling was 16.3×, providing high confidence in the identified variants.…”

Section: Discussionmentioning

confidence: 99%

Pudong White pig: a unique genetic resource disclosed by sequencing data

Xiao

Zhang

Sun

et al. 2017

Animal

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Pudong White (PW) pigs are distributed in the Taihu region of China and are characterized by their completely white coats. A heated debate concerning this genetic resource and its relationship to Taihu and western pig breeds has arisen, due to the white coat of the animals. To determine whether PW is a unique genetic resource, we performed a detailed assessment of the genetic relationships among PW, six breeds from the Taihu population and three western pig breeds, based on whole-genome single nucleotide polymorphism (SNP) data. A total of 68 102 SNPs were identified in the genomes of the tested populations by nextgeneration sequencing technology, of which, 64 were determined as the potentially specific to PW breed. The genetic distance between PW pigs and the Taihu population was shorter than that between PW and western breeds. The genetic distance within the PW population was small and neighbour-joining tree analysis revealed that all PW individuals clustered into a separated group, indicating a close genetic relationship among PW individuals which may result from a small effective population size ( N e ) and inbreeding. The results of both principal component analysis and evaluation using fastSTRUCTURE demonstrated that PW was clearly differentiated from other breeds. Together, these results indicate that PW is a distinctive genetic resource with a unique genetic structure separate from other Taihu and western pig breeds. Furthermore, this genome-wide comprehensive survey of the relationships among PW, Taihu and western pig breeds, demonstrates the rationality of the current breed classification of PW. The results also provide evidence about the unique genetic resource of PW, based on genome-wide genetic markers. These data will improve our understanding of the genetic structure and current state of PW breed, and facilitate the development of a national project for the conservation and utilization of these pigs.

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Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula

Cited by 99 publications

References 61 publications

Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

Genetic diversity, extent of linkage disequilibrium and persistence of gametic phase in Canadian pigs

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

Pudong White pig: a unique genetic resource disclosed by sequencing data

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