Linkage disequilibrium patterns and persistence of phase in purebred and crossbred pig (Sus scrofa) populations

BMC Genetics

Paulo S Lopes¹  Marcos S Lopes³  Barbara Harlizius³  Fabyano F Silva¹  Simone EF Guimarães¹  Egbert F Knol³  John WM Bastiaansen²  Renata Veroneze² 

[1] Departamento de Zootecnia, Universidade Federal de Viçosa, Av. PH Holfs, Viçosa 36570-000, MG, Brazil;Animal Breeding and Genomics Centre, Wageningen University, Droevendaalsesteeg 1, Wageningen 6708 PB, The Netherlands;Topigs Norsvin, Beuningen 6640 AA, The Netherlands

关键词: Genomic selection;    SNP;    Single nucleotide polymorphism;    Nonlinear model;   

Others  :  1085241
DOI  :  10.1186/s12863-014-0126-3

 received in 2014-04-10, accepted in 2014-11-05,  发布年份 2014

【 摘 要 】

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.

【 授权许可】

   
2014 Veroneze et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 3.

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