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

BMC Genomics

Research Article

Maria G. Strillacci¹  Dorian Garrick²  Beat Bapst³  Franz R. Seefried³  Birgit Gredler-Grandl³  Mirjam Frischknecht⁴  Anna Bieber⁵  Christine Flury⁶  Heidi Signer-Hasler⁶  Ruedi Fries⁷  Ingolf Russ⁸  Johann Sölkner⁹  Christian Stricker^1,10 

[1] Department of Veterinary Medicine, University of Milan, Via Celoria 10, 20133, Milan, Italy;Institute of Veterinary, Animal & Biomedical Sciences, Massey University, Hamilton, New Zealand;Qualitas AG, Chamerstrasse 56a, 6300, Zug, Switzerland;Qualitas AG, Chamerstrasse 56a, 6300, Zug, Switzerland;School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland;Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, 5070, Frick, Switzerland;School of Agricultural, Forest and Food Sciences HAFL, Bern University of Applied Sciences, Länggasse 85, 3052, Zollikofen, Switzerland;Technische Universität München, Liesel-Beckmann-Straße 1, 85354, Freising-Weihenstephan, Germany;Tierzuchtforschung e.V, Senator-Gerauer-Str. 23, 85586, Poing, Germany;University of Natural Resources and Life Sciences, Gregor-Mendel-Str 33, 1180, Wien, Austria;agn Genetics GmbH, 8b Börtjistrasse, 7260, Davos, Switzerland;

关键词: Whole genome sequencing;    Genome-wide association study;    QTL discovery;    Functional traits;    Brown Swiss;    Dairy cattle;    Calving ease;    Fertility;   

DOI  :  10.1186/s12864-017-4308-z

 received in 2017-08-14, accepted in 2017-11-15,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsWe 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.ConclusionThe 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.

【 授权许可】

CC BY   
© The Author(s). 2017