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Genome-wide association studies of fertility and calving traits in Brown Swiss cattle using imputed whole-genome sequences

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Frischknecht, Mirjam; Bapst, Beat; Seefried, Franz R.; Signer-Hasler, Heidi; Garrick, Dorian; Stricker, Christian; Consortium, Intergenomics; Fries, Ruedi; Russ, Ingolf; Sölkner, Johann; Bieber, Anna; Strillacci, Maria G.; Gredler-Grandl, Birgit and Flury, Christine (2017) Genome-wide association studies of fertility and calving traits in Brown Swiss cattle using imputed whole-genome sequences. BMC Genomics, 18 (910), pp. 1-13.

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Online at: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4308-z

Summary

Background
The detection of quantitative trait loci has accelerated with recent developments in genomics. The introduction of genomic selection in combination with sequencing efforts has made a large amount of genotypic data available. Functional traits such as fertility and calving traits have been included in routine genomic estimation of breeding values making large quantities of phenotypic data available for these traits. This data was used to investigate the genetics underlying fertility and calving traits and to identify potentially causative genomic regions and variants.
We performed genome-wide association studies for 13 functional traits related to female fertility as well as for direct and maternal calving ease based on imputed whole-genome sequences. Deregressed breeding values from ~1000–5000 bulls per trait were used to test for associations with approximately 10 million imputed sequence SNPs.
Results
We identified a QTL on BTA17 associated with non-return rate at 56 days and with interval from first to last insemination. We found two significantly associated non-synonymous SNPs within this QTL region. Two more QTL for fertility traits were identified on BTA25 and 29. A single QTL was identified for maternal calving traits on BTA13 whereas three QTL on BTA19, 21 and 25 were identified for direct calving traits. The QTL on BTA19 co-localizes with the reported BH2 haplotype. The QTL on BTA25 is concordant for fertility and calving traits and co-localizes with a QTL previously reported to influence stature and related traits in Brown Swiss dairy cattle.
Conclusion
The detection of QTL and their causative variants remains challenging. Combining comprehensive phenotypic data with imputed whole genome sequences seems promising. We present a QTL on BTA17 for female fertility in dairy cattle with two significantly associated non-synonymous SNPs, along with five additional QTL for fertility traits and calving traits. For all of these we fine mapped the regions and suggest candidate genes and candidate variants.


EPrint Type:Journal paper
Keywords:Whole genome sequencing, Genome-wide association study, QTL discovery, Functional traits, Brown Swiss, Dairy cattle, Calving ease, Fertility
Agrovoc keywords:
LanguageValueURI
Englishdairy cattlehttp://aims.fao.org/aos/agrovoc/c_2108
Englishgenomicshttp://aims.fao.org/aos/agrovoc/c_92382
Englishbreedinghttp://aims.fao.org/aos/agrovoc/c_49902
Subjects: Animal husbandry > Production systems > Dairy cattle
Animal husbandry > Breeding and genetics
Research affiliation: Austria > Univ. BOKU Wien
Switzerland > FiBL - Research Institute of Organic Agriculture Switzerland > Animal Husbandry and Breeding
Switzerland > University of Bern
Germany > University of Munich - TUM
Italy > Univ. Milano
New Zealand > Massey University
Sweden > Other organizations
Switzerland > Other organizations
Germany > Other organizations
DOI:DOI 10.1186/s12864-017-4308-z
Deposited By: Bieber, Anna
ID Code:38545
Deposited On:30 Oct 2020 10:03
Last Modified:30 Oct 2020 10:03
Document Language:English
Status:Published
Refereed:Peer-reviewed and accepted

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