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. 2017 May;58(2):249-259.
doi: 10.1007/s13353-016-0382-1. Epub 2017 Jan 4.

Identification of novel candidate genes for the inverted teat defect in sows using a genome-wide marker panel

Helena Chalkias  1 , Elisabeth Jonas  2 , Lisa S Andersson  1 , Magdalena Jacobson  3 , Dirk Jan de Koning  1 , Nils Lundeheim  1 , Gabriella Lindgren  1   4
Affiliations

Identification of novel candidate genes for the inverted teat defect in sows using a genome-wide marker panel

Helena Chalkias et al. J Appl Genet. 2017 May.

Abstract

The number of functional teats is an important selection criterion in pig breeding. Inherited defects of the udder, such as the inverted teat, do have a considerable negative impact on the nursing ability of the sow. To investigate the genetic background of this defect and the number of functional teats in Swedish maternal lines, samples from 230 Yorkshire pigs were selected for genotyping using the PorcineSNP60K BeadChip (Illumina Inc.), each pig with at least one inverted teat was matched with one non-affected pig (fullsib or pairs with matching herd and gender). A genome-wide association study on these 230 pigs was performed using the two-step approach implemented in GenABEL using 46,652 single nucleotide polymorphisms across all autosomes and the X chromosome. A number of significant regions were identified for the inverted teat defect on chromosomes 2, 10, and 18. Many of the regions associated with the number of functional teats were located in the same or close regions, except two associated markers on the X chromosome and one on chromosome 3. We identified some of the regions on chromosomes previously reported in one linkage and one gene expression study. We conclude, despite being able to suggest new candidate genes, that further studies are needed to better understand the biologic background of the teat development. Despite the in-depth comparison of identified regions for the inverted teat defect done here, more studies are required to allow a clear identification of genetic regions relevant for this defect across many pig populations.

Keywords: Functional teats; Genetic markers; Genome-wide association study; SNP; Teat number; Yorkshire breed.

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Conflict of interest statement

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

All applicable international, national and institutional guidelines for the care and use of animals were followed. The study was approved by the Ethics Committee for Animal Experimentation, Uppsala, Sweden (C149/8 and C215/11).

Figures

Fig. 1
Fig. 1
The association with the number of inverted teats and QQ-plot for the number of inverted teats. a Manhattan plot showing the negative logarithm of the p-value from the genome-wide association analysis for the number of inverted teats. Different colours represent chromosomes from 1 to X; results from unmapped markers not yet mapped to the pig reference genome are shown on the left side. b QQ plot from the GRAMMAR–Gamma analysis, inflation factor =0.65)
Fig. 2
Fig. 2
The association with the number of functional teats and QQ-plot for the number of functional teats. a Manhattan plot showing the negative logarithm of the p-value from the genome-wide association analysis for the number of functional teats. Different colours represent chromosomes from 1 to X; results from unmapped markers not yet mapped to the pig reference genome are shown on the left side. b QQ plot from the GRAMMAR–Gamma analysis, inflation factor =0.74
Fig. 3
Fig. 3
The association with total number of teats and QQ-plots for total number of teats. a Manhattan plot showing the negative logarithm of the p-value from the genome-wide association analysis for total number of teats. Different colours represent chromosomes from 1 to X; results from unmapped markers not yet mapped to the pig reference genome are shown on the left side. b QQ plot from the GRAMMAR–Gamma analysis, inflation factor =1.05
See this image and copyright information in PMC

References

    1. Akers RM. Major advances associated with hormone and growth factor regulation of mammary growth and lactation in dairy cows. J Dairy Sci. 2006;89:1222–1234. doi: 10.3168/jds.S0022-0302(06)72191-9. - DOI - PubMed
    1. Amin N, van Duijn CM, Aulchenko YS. A genomic background based method for association analysis in related individuals. PLoS ONE. 2007;2(12):e1274. doi: 10.1371/journal.pone.0001274. - DOI - PMC - PubMed
    1. Arakawa A, et al. Genome-wide association QTL mapping for teat number in a purebred population of Duroc pigs. Anim Genet. 2015;46:571–575. doi: 10.1111/age.12331. - DOI - PubMed
    1. Aulchenko YS, de Koning D-J, Haley C. Genomewide rapid association using mixed model and regression: a fast and simple method for genomewide pedigree-based quantitative trait loci association analysis. Genetics. 2007;177:577–585. doi: 10.1534/genetics.107.075614. - DOI - PMC - PubMed
    1. Aulchenko YS, Ripke S, Isaacs A, Van Duijn CM. GenABEL: an R library for genorne-wide association analysis. Bioinformatics. 2007;23:1294–1296. doi: 10.1093/bioinformatics/btm108. - DOI - PubMed

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