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Veroneze R.,Wageningen University | Bastiaansen J.W.,Wageningen University | Knol E.F.,Topigs Norsvin | Guimaraes S.E.,Federal University of Viçosa | And 4 more authors.
BMC genetics | Year: 2014

BACKGROUND: Genomic selection and genomic wide association studies are widely used methods that aim to exploit the linkage disequilibrium (LD) between markers and quantitative trait loci (QTL). Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor that may be overcome by combining data from multiple breeds or using crossbred information. However, the estimated effect of a marker in one breed or a crossbred can only be useful for the selection of animals in another breed if there is a correspondence of the phase between the marker and the QTL across breeds. Using data of five pure pig (Sus scrofa) lines (SL1, SL2, SL3, DL1, DL2), one F1 cross (DLF1) and two commercial finishing crosses (TER1 and TER2), the objectives of this study were: (i) to compare the equality of LD decay curves of different pig populations; and (ii) to evaluate the persistence of the LD phase across lines or final crosses.RESULTS: Almost all of the lines presented different extents of LD, except for the SL2 and DL3, both of which exhibited the same extent of LD. Similar levels of LD over large distances were found in crossbred and pure lines. The crossbred animals (DLF1, TER1 and TER2) presented a high persistence of phase with their parental lines, suggesting that the available porcine single nucleotide polymorphism (SNP) chip should be dense enough to include markers that have the same LD phase with QTL across crossbred and parental pure lines. The persistence of phase across pure lines varied considerably between the different line comparisons; however, correlations were above 0.8 for all line comparisons when marker distances were smaller than 50 kb.CONCLUSIONS: This study showed that crossbred populations could be very useful as a reference for the selection of pure lines by means of the available SNP chip panel. Here, we also pinpoint pure lines that could be combined in a multiline training population. However, if multiline reference populations are used for genomic selection, the required density of SNP panels should be higher compared with a single breed reference population.


PubMed | Wageningen University, Federal University of Viçosa and Topigs Norsvin
Type: | Journal: BMC genetics | Year: 2015

Genomic selection and genomic wide association studies are widely used methods that aim to exploit the linkage disequilibrium (LD) between markers and quantitative trait loci (QTL). Securing a sufficiently large set of genotypes and phenotypes can be a limiting factor that may be overcome by combining data from multiple breeds or using crossbred information. However, the estimated effect of a marker in one breed or a crossbred can only be useful for the selection of animals in another breed if there is a correspondence of the phase between the marker and the QTL across breeds. Using data of five pure pig (Sus scrofa) lines (SL1, SL2, SL3, DL1, DL2), one F1 cross (DLF1) and two commercial finishing crosses (TER1 and TER2), the objectives of this study were: (i) to compare the equality of LD decay curves of different pig populations; and (ii) to evaluate the persistence of the LD phase across lines or final crosses.Almost all of the lines presented different extents of LD, except for the SL2 and DL3, both of which exhibited the same extent of LD. Similar levels of LD over large distances were found in crossbred and pure lines. The crossbred animals (DLF1, TER1 and TER2) presented a high persistence of phase with their parental lines, suggesting that the available porcine single nucleotide polymorphism (SNP) chip should be dense enough to include markers that have the same LD phase with QTL across crossbred and parental pure lines. The persistence of phase across pure lines varied considerably between the different line comparisons; however, correlations were above 0.8 for all line comparisons when marker distances were smaller than 50 kb.This study showed that crossbred populations could be very useful as a reference for the selection of pure lines by means of the available SNP chip panel. Here, we also pinpoint pure lines that could be combined in a multiline training population. However, if multiline reference populations are used for genomic selection, the required density of SNP panels should be higher compared with a single breed reference population.


Roca J.,University of Murcia | Parrilla I.,University of Murcia | Bolarin A.,Topigs Norsvin | Martinez E.A.,University of Murcia | Rodriguez-Martinez H.,Linköping University
Theriogenology | Year: 2016

AI is commercially applied worldwide to breed pigs, yielding fertility outcomes similar to those of natural mating. However, it is not fully efficient, as only liquid-stored semen is used, with a single boar inseminating about 2000 sows yearly. The use of liquid semen, moreover, constrains international trade and slows genetic improvement. Research efforts, reviewed hereby, are underway to reverse this inefficient scenario. Special attention is paid to studies intended to decrease the number of sperm used per pregnant sow, facilitating the practical use of sexed frozen-thawed semen in swine commercial insemination programs. © 2015 Elsevier Inc.


PubMed | University of Murcia, Topigs Norsvin and Linköping University
Type: Journal Article | Journal: Theriogenology | Year: 2016

AI is commercially applied worldwide to breed pigs, yielding fertility outcomes similar to those of natural mating. However, it is not fully efficient, as only liquid-stored semen is used, with a single boar inseminating about 2000 sows yearly. The use of liquid semen, moreover, constrains international trade and slows genetic improvement. Research efforts, reviewed hereby, are underway to reverse this inefficient scenario. Special attention is paid to studies intended to decrease the number of sperm used per pregnant sow, facilitating the practical use of sexed frozen-thawed semen in swine commercial insemination programs.


de Hollander C.A.,Wageningen University | Knol E.F.,Topigs Norsvin | Heuven H.C.M.,Wageningen University | van Grevenhof E.M.,Wageningen University
Livestock Science | Year: 2015

This study studied the relation between longevity, the interval from last insemination to culling in days (IL2C) with 7 different cull classes; 1. Reproduction cull class, 2. Production cull class, 3. Locomotion cull class, 4. Accident cull class, 5. General disorder cull class, 6. Peri-partum cull class and 7. Unknown cull class. Overall, the most important cull classes were reproduction (19%) and production (50%). The IL2C for production (146.3±1.2) and reproduction (87.4±1.9) were significantly different from each other but also from locomotion (127.0±3.6), accident (120.1±7.3), general disorder (105.4±5.5), peri-partum (109.6±5.7) cull classes. Sows that were culled for production reasons had significantly the highest average parity number at culling (4.6±0.2) compared to all other culling reasons such as reproduction (3.1±0.2), locomotion (2.3±0.3), accident (2.9±0.5), general disorder (3.3±0.4) and peri-partum (3.3±0.4) cull classes. Furthermore, it was found that age in days, parity number at culling and IL2C showed to be heritable traits (0.13±0.05, 0.16±0.05 and 0.10±0.04 respectively). The genetic correlation between parity number at culling and IL2C was not significantly different from 0 (-0.04±0.28). Because IL2C is a heritable trait and sows that are culled within the production cull class obtain on average a higher parity and show the longest IL2C, this study showed the potential to select on longer IL2C and thereby select against sows to be culled within the reproduction, locomotion, accident, general disorder and peri-partum cull class and to be culled at the end of a parity. © 2015 Elsevier B.V..


Sevillano C.A.,Wageningen University | Lopes M.S.,Wageningen University | Harlizius B.,Topigs Norsvin | Hanenberg E.H.,Topigs Norsvin | And 2 more authors.
Genetics, selection, evolution : GSE | Year: 2015

BACKGROUND: Cryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, both from an animal welfare point of view as well as for economic reasons. The aim of this genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) that are strongly associated with these congenital defects. Genotypes were available for 2570 Large White (LW) and 2272 Landrace (LR) pigs. Breeding values were estimated based on 1 359 765 purebred and crossbred male offspring, using a binary trait animal model. Estimated breeding values were deregressed (DEBV) and taken as the response variable in the GWAS.RESULTS: Heritability estimates were equal to 0.26 ± 0.02 for cryptorchidism and to 0.31 ± 0.01 for scrotal/inguinal hernia. Seven and 31 distinct QTL regions were associated with cryptorchidism in the LW and LR datasets, respectively. The top SNP per region explained between 0.96% and 1.10% and between 0.48% and 2.77% of the total variance of cryptorchidism incidence in the LW and LR populations, respectively. Five distinct QTL regions associated with scrotal/inguinal hernia were detected in both LW and LR datasets. The top SNP per region explained between 1.22% and 1.60% and between 1.15% and 1.46% of the total variance of scrotal/inguinal hernia incidence in the LW and LR populations, respectively. For each trait, we identified one overlapping region between the LW and LR datasets, i.e. a region on SSC8 (Sus scrofa chromosome) between 65 and 73 Mb for cryptorchidism and a region on SSC13 between 34 and 37 Mb for scrotal/inguinal hernia.CONCLUSIONS: The use of DEBV in combination with a binary trait model was a powerful approach to detect regions associated with difficult traits such as cryptorchidism and scrotal/inguinal hernia that have a low incidence and for which affected animals are generally not available for genotyping. Several novel QTL regions were detected for cryptorchidism and scrotal/inguinal hernia, and for several previously known QTL regions, the confidence interval was narrowed down.


Da Silva C.L.A.,Wageningen University | van den Brand H.,Wageningen University | Laurenssen B.F.A.,Wageningen University | Broekhuijse M.L.W.J.,Topigs Norsvin | And 3 more authors.
Animal | Year: 2016

The objective of this study was to investigate relationships between ovulation rate (OR) and embryonic and placental development in sows. Topigs Norsvin® sows (n=91, parity 2 to 17) from three different genetic backgrounds were slaughtered at 35 days of pregnancy and the reproductive tract was collected. The corpora lutea (CL) were counted and the number of vital and non-vital embryos, embryonic spacing (distance between two embryos), implantation length, placental length, placental weight and embryonic weight were assessed. The difference between number of CL and total number of embryos was considered as early embryonic mortality. The number of non-vital embryos was considered as late mortality. Relationships between OR and all other variables were investigated using two models: the first considered parity as class effect (n=91) and the second used a subset of sows with parities 4 to 10 (n=47) to analyse the genetic background as class effect. OR was significantly affected by parity (P<0.0001), but was not affected by the genetic background of the sows. Parity and genetic background did not affect embryonic and placental characteristics at 35 days of pregnancy. OR (varying from 17 to 38 CL) was positively related with early embryonic mortality (β=0.49±0.1 n/ovulations, P<0.0001), with late embryonic mortality or number of non-vital embryos (β=0.24±0.1 n/ovulations, P=0.001) and with the number of vital embryos (β=0.26±0.1 n/ovulations, P=0.01). However, dividing OR in four classes, showed that the number of vital embryos was lowest in OR class 1 (17 to 21 CL), but not different for the other OR classes, suggesting a plateau for number of vital embryos for OR above 22. There was a negative linear relationship between OR and vital embryonic spacing (β=−0.45±0.1 cm/ovulation, P=0.001), implantation length (β=−0.35±0.1 cm/ovulation, P=0.003), placental length (β=−0.38±0.2 cm/ovulation, P=0.05) and empty space around embryonic-placental unit (β=−0.4±0.2 cm/ovulation, P=0.02), indicating uterine crowding. Further analyses showed that effects of OR on embryonic and uterine parameters were related with the increase in late mortality and not early embryonic mortality. Therefore, we conclude that a high OR results in an moderate increase in the number of vital embryos at day 35 of pregnancy, but compromises development in the surviving embryonic/placental units, suggesting that the future growth and survival of the embryos might be further compromised. © The Animal Consortium 2016


Broekhuijse M.L.,Topigs Norsvin Research Center | Gaustad A.H.,Topigs Norsvin | Gaustad A.H.,Hedmark University College | Bolarin Guillen A.,Topigs Norsvin AIM Iberica | Knol E.F.,Topigs Norsvin Research Center
Reproduction in domestic animals = Zuchthygiene | Year: 2015

Diluting semen from high fertile breeding boars, and by that inseminating many sows, is the core business for artificial insemination (AI) companies worldwide. Knowledge about fertility results is the reason by which an AI company can lower the concentration of a dose. Efficient use of AI boars with high genetic merit by decreasing the number of sperm cells per insemination dose is important to maximize dissemination of the genetic progress made in the breeding nucleus. However, a potential decrease in fertility performance in the field should be weighed against the added value of improved genetics and, in general, is not tolerated in commercial production. This overview provides some important aspects that influence the impact of low-dose AI on fertility: (i) the importance of monitoring field fertility, (ii) the need for accurate and precise semen assessment, (iii) the parameters that are taken into account, (iv) the application of information from genetic and genomic selection and (v) the optimization when using different AI techniques. Efficient semen production, processing and insemination in combination with increasing use of genetic and genomic applications result in maximum impact of genetic trend. © 2015 Blackwell Verlag GmbH.


Sell-Kubiak E.,Wageningen University | Wang S.,Wageningen University | Knol E.F.,Topigs Norsvin | Mulder H.A.,Wageningen University
Journal of Animal Science | Year: 2015

The objective of this study was to estimate the genetic variance for within-litter variation of birth weight (BW0) using genomic (GRM) or pedigree relationship matrices (PRM) and to compare the accuracy of estimated breeding values (EBV) for within-litter variation of BW0 using GRM and PRM. The BW0 and residual variance of BW0 were modeled by the double hierarchical generalized linear model using GRM or PRM. Data came from 2 dam lines: Landrace and Large White. After editing, the data set in Landrace consisted of 748 sows with 1,938 litters and 29,430 piglets and in Large White of 989 sows with 3,320 litters and 51,818 piglets. To construct GRM, 46,466 (Landrace) and 44,826 (Large White) single nucleotide polymorphisms were used, whereas to construct PRM, 5 generations of pedigree were used. The accuracy of EBV with GRM was estimated with 8-fold cross-validation and compared to PRM. Estimated variance components were highly similar for GRM and PRM. The maternal genetic variance in residual variance of BW0 in Landrace was 0.05 with GRM and 0.06 with PRM. In Large White these were 0.04 with GRM and 0.05 with PRM. The genetic coefficient of variation (GCVSDe) was about 0.10 in both dam lines. This indicates a change of 10% in residual SD of BW0 when achieving a genetic response of 1 genetic standard deviation. The genetic correlation between birth weight and its residual variance was about 0.6 in both dam lines. The accuracies of selection for within-litter variation of birth weight were 0.35 with GRM and 0.23 with PRM in Landrace and 0.29 with GRM and 0.34 with PRM in Large White. In this case, using GRM did not significantly increase accuracies of selection. Results, however, show good opportunities to select for reduced within-litter variation of BW0. Genomic selection can increase accuracy of selection when reference populations contain at least 2,000 sows. © 2015 American Society of Animal Science. All rights reserved.


PubMed | Wageningen University and Topigs Norsvin
Type: | Journal: Genetics, selection, evolution : GSE | Year: 2015

Cryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, both from an animal welfare point of view as well as for economic reasons. The aim of this genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) that are strongly associated with these congenital defects. Genotypes were available for 2570 Large White (LW) and 2272 Landrace (LR) pigs. Breeding values were estimated based on 1 359 765 purebred and crossbred male offspring, using a binary trait animal model. Estimated breeding values were deregressed (DEBV) and taken as the response variable in the GWAS.Heritability estimates were equal to 0.26 0.02 for cryptorchidism and to 0.31 0.01 for scrotal/inguinal hernia. Seven and 31 distinct QTL regions were associated with cryptorchidism in the LW and LR datasets, respectively. The top SNP per region explained between 0.96% and 1.10% and between 0.48% and 2.77% of the total variance of cryptorchidism incidence in the LW and LR populations, respectively. Five distinct QTL regions associated with scrotal/inguinal hernia were detected in both LW and LR datasets. The top SNP per region explained between 1.22% and 1.60% and between 1.15% and 1.46% of the total variance of scrotal/inguinal hernia incidence in the LW and LR populations, respectively. For each trait, we identified one overlapping region between the LW and LR datasets, i.e. a region on SSC8 (Sus scrofa chromosome) between 65 and 73 Mb for cryptorchidism and a region on SSC13 between 34 and 37 Mb for scrotal/inguinal hernia.The use of DEBV in combination with a binary trait model was a powerful approach to detect regions associated with difficult traits such as cryptorchidism and scrotal/inguinal hernia that have a low incidence and for which affected animals are generally not available for genotyping. Several novel QTL regions were detected for cryptorchidism and scrotal/inguinal hernia, and for several previously known QTL regions, the confidence interval was narrowed down.

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