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

Frischknecht, Mirjam; Bapst, Beat; Seefried, Franz R.; Signer-Hasler, Heidi; Garrick, Dorian; Stricker, Christian; Fries, Ruedi; Russ, Ingolf; Sölkner, Johann; Bieber, Anna; Strillacci, Maria G.; Gredler-Grandl, Birgit; 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. BioMed Central 10.1186/s12864-017-4308-z

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

School of Agricultural, Forest and Food Sciences > Abteilung Agronomie

Name:

Frischknecht, Mirjam; Bapst, Beat; Seefried, Franz R.; Signer-Hasler, Heidi; Garrick, Dorian; Stricker, Christian; Fries, Ruedi; Russ, Ingolf; Sölkner, Johann; Bieber, Anna; Strillacci, Maria G.; Gredler-Grandl, Birgit and Flury, Christine

Subjects:

S Agriculture > SF Animal culture
T Technology > T Technology (General)

ISSN:

1471-2164

Publisher:

BioMed Central

Language:

English

Submitter:

David Zimmer

Date Deposited:

01 Nov 2019 11:05

Last Modified:

01 Nov 2019 11:05

Publisher DOI:

10.1186/s12864-017-4308-z

Uncontrolled Keywords:

Whole genome sequencing, Genome-wide association study, QTL discovery, Functional traits, Brown Swiss, Dairy cattle, Calving ease, Fertility

ARBOR DOI:

10.24451/arbor.8322

URI:

https://arbor.bfh.ch/id/eprint/8322

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