Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds

Burren, A; Neuditschko, Markus; Signer-Hasler, H; Frischknecht, Mirjam; Reber, Irene; Menzi, Fiona; Drögemüller, Cord; Flury, C (2016). Genetic diversity analyses reveal first insights into breed-specific selection signatures within Swiss goat breeds. Animal genetics, 47(6), pp. 727-739. Blackwell 10.1111/age.12476

[img] Text
Burren_et_al-2016-Animal_Genetics.pdf - Published Version
Restricted to registered users only
Available under License Publisher holds Copyright.

Download (1MB) | Request a copy

We used genotype data from the caprine 50k Illumina BeadChip for the assessment of genetic diversity within and between 10 local Swiss goat breeds. Three different cluster methods allowed the goat samples to be assigned to the respective breed groups, whilst the samples of Nera Verzasca and Tessin Grey goats could not be differentiated from each other. The results of the different genetic diversity measures show that Appenzell, Toggenburg, Valais and Booted goats should be prioritized in future conservation activities. Furthermore, we examined runs of homozygosity (ROH) and compared genomic inbreeding coefficients based on ROH (FROH ) with pedigree-based inbreeding coefficients (FPED ). The linear relationship between FROH and FPED was confirmed for goats by including samples from the three main breeds (Saanen, Chamois and Toggenburg goats). FROH appears to be a suitable measure for describing levels of inbreeding in goat breeds with missing pedigree information. Finally, we derived selection signatures between the breeds. We report a total of 384 putative selection signals. The 25 most significant windows contained genes known for traits such as: coat color variation (MITF, KIT, ASIP), growth (IGF2, IGF2R, HRAS, FGFR3) and milk composition (PITX2). Several other putative genes involved in the formation of populations, which might have been selected for adaptation to the alpine environment, are highlighted. The results provide a contemporary background for the management of genetic diversity in local Swiss goat breeds.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

UniBE Contributor:

Neuditschko, Markus; Frischknecht, Mirjam; Reber, Irene; Menzi, Fiona and Drögemüller, Cord

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 590 Animals (Zoology)
600 Technology > 630 Agriculture

ISSN:

0268-9146

Publisher:

Blackwell

Language:

English

Submitter:

Cord Drögemüller

Date Deposited:

29 Aug 2016 09:21

Last Modified:

12 Jan 2017 01:30

Publisher DOI:

10.1111/age.12476

PubMed ID:

27436146

Uncontrolled Keywords:

SNP ; inbreeding coefficient; pedigree; runs of homozygosity; selection signals

BORIS DOI:

10.7892/boris.86018

URI:

https://boris.unibe.ch/id/eprint/86018

Actions (login required)

Edit item Edit item
Provide Feedback