| 1. |
- Anderung, C, et al.
(författare)
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Investigation of X- and Y-specific single nucleotide polymorphisms in taurine (Bos taurus) and indicine (Bos indicus) cattle
- 2007
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Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 38:6, s. 595-600
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Tidskriftsartikel (refereegranskat)abstract
- Initially, domesticated African cattle were of taurine type. Today, we find both African Bos taurus and Bos indicus cattle, as well as their crossbreeds, on the continent of Africa and they all share the same set of African taurine mitochondrial DNA haplogroups. In this study, we report genetic variation as substitutions and insertions/deletions (indels) on both the X and Y chromosomes, and use the variation to assess hybridization between taurine and indicine cattle. Six African cattle breeds (four Sanga breeds, including Raya Azebu, Danakil, Caprivi, Nguni; and two Zebu breeds, including Kilimanjaro Zebu and South Kavirondo Zebu) were screened for six new X-chromosomal markers, specifically three single nucleotide polymorphisms and three indels in the DDX3X (previously DBX) and ZFX genes, and five previously identified Y-chromosomal markers in the DDX3Y (previously DBY) and ZFY genes. In total, 90 (57 bulls and 33 cows) samples from the African breeds were analysed. We identify five diagnostic haplotypes of indicine and taurine origins on both the X and Y chromosomes. For each breed, the level of indicine introgression varies; in addition to pure taurine, indicine and hybrid X-chromosome individuals, recombinant X-chromosome variants were also detected. These markers are useful molecular tools for assessing the level of indicine admixture in African cattle breeds.
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| 2. |
- Andersson-Eklund, Lena
(författare)
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Fine mapping of quantitative trait loci for mastitis resistance on bovine chromosome 11
- 2009
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Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 40, s. 509-515
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Tidskriftsartikel (refereegranskat)abstract
- P>Quantitative trait loci (QTL) affecting clinical mastitis (CM) and somatic cell score (SCS) were mapped on bovine chromosome 11. The mapping population consisted of 14 grandsire families belonging to three Nordic red cattle breeds: Finnish Ayrshire (FA), Swedish Red and White (SRB) and Danish Red. The families had previously been shown to segregate for udder health QTL. A total of 524 progeny tested bulls were included in the analysis. A linkage map including 33 microsatellite and five SNP markers was constructed. We performed combined linkage disequilibrium and linkage analysis (LDLA) using the whole data set. Further analyses were performed for FA and SRB separately to study the origin of the identified QTL/haplotype and to examine if it was common in both populations. Finally, different two-trait models were fitted. These postulated either a pleiotropic QTL affecting both traits; two linked QTL, each affecting one trait; or one QTL affecting a single trait. A QTL affecting CM was fine-mapped. In FA, a haplotype having a strong association with a high negative effect on mastitis resistance was identified. The mapping precision of an earlier detected SCS-QTL was not improved by the LDLA analysis because of lack of linkage disequilibrium between the markers used and the QTL in the region.
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| 3. |
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| 4. |
- De Koning, Dirk-Jan
(författare)
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Genome-wide associations for investigating time-dependent genetic effects for milk production traits in dairy cattle
- 2012
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Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 43, s. 375-382
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Tidskriftsartikel (refereegranskat)abstract
- Phenotypic variation in milk production traits has been described over the course of a lactation as well as between different parities. The objective of this study was to investigate whether variation in production is affected by different loci across lactations. A genome-wide association study (GWAS) using a 50-k SNP chip was conducted in 152 divergent German Holstein Friesian cows to test for association with milk production traits over different lactations. The first four lactations were analysed regarding milk yield, fat, protein, lactose, milk urea nitrogen yield and content as well as somatic cell score. Two approaches were used: (i) Wilmink curve parameters were used to assess the genetic effects over the course of a lactation and (ii) test-day yield deviations (YD) were used as a normative approach for a GWAS. The significant effects were largest for markers affecting curve parameters for which there was a statistical power <0.8 of detection even in this small design. While significant markers for YDs were detected in this study, the power to detect effects of a similar magnitude was only 0.11, suggesting that many loci may have been missed with this approach in the present design. Furthermore, all significant effects were specific for a single lactation, leading to the conclusion that the variance explained by a certain locus changes from lactation to lactation. We confirm the common evidence that most production traits vary in the degree of persistency after the peak as a result of genetic influence.
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| 5. |
- Fang, M., et al.
(författare)
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Mitochondrial haplotypes of European wild boars with 2n=36 are closely related to those of European domestic pigs with 2n=38
- 2006
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Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 37:5, s. 459-464
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Tidskriftsartikel (refereegranskat)abstract
- Wild boars from Western Europe have a 2n = 36 karyotype, in contrast to a karyotype of 2n = 38 in wild boars from Central Europe and Asia and in all domestic pigs. The phylogenetic status of this wild boar population is unclear, and it is not known if it has contributed to pig domestication. We have now sequenced the mtDNA control region from 30 European wild boars (22 with a confirmed 2n = 36 karyotype) and six Asian wild boars (two Hainan and four Dongbei wild boars) to address this question. The results revealed a close genetic relationship between mtDNA haplotypes from wild boars with 2n = 36 to those from domestic pigs with 2n = 38. Thus, we cannot exclude the possibility that wild boars with 2n = 36 may have contributed to pig domestication despite the karyotype difference. One of the European wild boars carried an Asian mtDNA haplotype, and this most likely reflects gene flow from domestic pigs to European wild boars. However, this gene flow does not appear to be extensive because the frequency of Asian haplotypes detected among European wild boars (c. 3%) were 10-fold lower than among European domestic pigs (c. 30%). Previous studies of mtDNA haplotypes have indicated that pig populations in Europe and Asia have experienced a population expansion, but it is not clear if the expansion occurred before or after domestication. The results of the present study are consistent with an expansion that primarily occurred prior to domestication because the mtDNA haplotypes found in European and Asian wild boars did not form their own clusters but were intermingled with haplotypes found in domestic pigs, indicating that they originated from the same population expansion.
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| 6. |
- Fitzsimmons, C. J., et al.
(författare)
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Detection of sequence polymorphisms in red junglefowl and White Leghorn ESTs
- 2004
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Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 35:5, s. 391-396
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Tidskriftsartikel (refereegranskat)abstract
- Over 16 000 high quality expressed sequence tags (ESTs) from red junglefowl (RJ) and White Leghorn (WL) brain and testis cDNA libraries were generated. Here, we have used this resource for detection of single nucleotide polymorphisms (SNPs), and also completed full-length sequencing of 46 pairs of clones, representing the same gene from both the RJ and WL libraries. From the main set of ESTs, which were assembled using Phrap, 746 putative SNPs were identified, of which 76% were transitions and 24% were transversions. A subset of SNPs was evaluated by sequence analysis of five RJ and five WL birds. Nine of 12 SNPs were verified in this limited sample, suggesting that a majority of the putative polymorphisms documented in this study represent real SNPs. During full-length sequencing of the 46 RJ/WL clones 100 SNPs were identified, which translated to a frequency of 1.90 SNPs/1000 bp. The number of transitions and transversions were 77% and 23%, respectively, and the proportion of non-synonymous vs. synonymous SNPs was 20% and 80%, respectively. Four large insertions/deletions were identified between the RJ and WL full-length sequences, and they appear to represent different splice variants.
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| 7. |
- Jacobsen, M, et al.
(författare)
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Refined candidate region specified by haplotype sharing for Escherichia coli F4ab/F4ac susceptibility alleles in pigs
- 2010
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Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 41:1, s. 21-25
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Tidskriftsartikel (refereegranskat)abstract
- Infection of the small intestine by enterotoxigenic Escherichia coli F4ab/ac is a major welfare problem and financial burden for the pig industry. Natural resistance to this infection is inherited as a Mendelian recessive trait, and a polymorphism in the MUC4 gene segregating for susceptibility/resistance is presently used in a selection programme by the Danish pig breeding industry. To elucidate the genetic background involved in E. coli F4ab/ac susceptibility in pigs, a detailed haplotype map of the porcine candidate region was established. This region covers approximately 3.7 Mb. The material used for the study is a three generation family, where the founders are two Wild boars and eight Large White sows. All pigs have been phenotyped for susceptibility to F4ab/ac using an adhesion assay. Their haplotypes are known from segregation analysis using flanking markers. By a targeted approach, the candidate region was subjected to screening for polymorphisms, mainly focusing on intronic sequences. A total of 18 genes were partially sequenced, and polymorphisms were identified in GP5, CENTB2, APOD, PCYT1A, OSTalpha, ZDHHC19, TFRC, ACK1, MUC4, MUC20, KIAA0226, LRCH3 and MUC13. Overall, 227 polymorphisms were discovered in the founder generation. The analysis revealed a large haplotype block, spanning at least 1.5 Mb around MUC4, to be associated with F4ab/ac susceptibility.
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| 8. |
- Johansson, A, et al.
(författare)
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Polymorphism at the porcine Dominant white/KIT locus influence coat colour and peripheral blood cell measures
- 2005
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Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 36:4, s. 288-296
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Tidskriftsartikel (refereegranskat)abstract
- We have examined the phenotype of different KIT genotypes with regard to coat colour and several blood parameters (erythrocyte numbers and measures, total and differential leucocyte numbers, haematocrit and haemoglobin levels and serum components). The effect of two different iron supplement regimes (one or two iron injections) on the blood parameters was also examined. For a total of 184 cross-bred piglets (different combinations of Hampshire, Landrace and Yorkshire) blood parameters were measured four times during their first month of life, and the KIT genotypes of these and 70 additional cross-bred piglets were determined. Eight different KIT genotypes were identified, which confirms the large allelic diversity at the KIT locus in commercial pig populations. The results showed that pigs with different KIT genotypes differ both in coat colour and in haematological parameters. In general, homozygous Dominant white (I/I) piglets had larger erythrocytes with lower haemoglobin concentration, indicating a mild macrocytic anaemia. The effect of two compared with one iron injection was also most pronounced for the I/I piglets.
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| 9. |
- Joller, D, et al.
(författare)
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Refined localization of the Escherichia coli F4ab/F4ac receptor locus on pig chromosome 13
- 2009
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Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 40:5, s. 749-752
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Tidskriftsartikel (refereegranskat)abstract
- Diarrhoea in newborn and weaned pigs caused by enterotoxigenic Escherichia coli (ETEC) expressing F4 fimbriae leads to considerable losses in pig production. In this study, we refined the mapping of the receptor locus for ETEC F4ab/F4ac adhesion (F4bcR) by joint analysis of Nordic and Swiss data. A total of 236 pigs from a Nordic experimental herd, 331 pigs from a Swiss experimental herd and 143 pigs from the Swiss performing station were used for linkage analysis. Genotyping data of six known microsatellite markers, two newly developed markers (MUC4gt and HSA125gt) and an intronic SNP in MUC4 (MUC4-8227) were used to create the linkage map. The region for F4bcR was refined to the interval SW207-S0075 on pig chromosome 13. The most probable position of F4bcR was in the SW207-MUC4 region. The order of six markers was supported by physical mapping on the BAC fingerprint contig from the Wellcome Trust Sanger Institute. Thus, the region for F4bcR could be reduced from 26 to 14 Mb.
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| 10. |
- Karlskov-Mortensen, Peter, et al.
(författare)
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Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace I : carcass traits
- 2006
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Ingår i: Animal Genetics. - : Wiley. - 0268-9146 .- 1365-2052. ; 37:2, s. 156-162
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Tidskriftsartikel (refereegranskat)abstract
- We report the identification of quantitative trait loci (QTL) affecting carcass composition, carcass length, fat deposition and lean meat content using a genome scan across 462 animals from a combined intercross and backcross between Hampshire and Landrace pigs. Data were analysed using multiple linear regression fitting additive and dominance effects. This model was compared with a model including a parent-of-origin effect to spot evidence of imprinting. Several precisely defined muscle phenotypes were measured in order to dissect body composition in more detail. Three significant QTL were detected in the study at the 1% genome-wide level, and twelve significant QTL were detected at the 5% genome-wide level. These QTL comprise loci affecting fat deposition and lean meat content on SSC1, 4, 9, 10, 13 and 16, a locus on SSC2 affecting the ratio between weight of meat and bone in back and weight of meat and bone in ham and two loci affecting carcass length on SSC12 and 17. The well-defined phenotypes in this study enabled us to detect QTL for sizes of individual muscles and to obtain information of relevance for the description of the complexity underlying other carcass traits.
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