Detection of quantitative trait loci for maternal traits using high-density genotypes of Blonde d'Aquitaine beef cattle.

Alexis Michenet,Florence Phocas,Romain Saintilan,Marine Barbat,Eric Venot

doi:10.1186/s12863-016-0397-y

Alexis Michenet, Florence Phocas + Show 3 more

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https://doi.org/10.1186/s12863-016-0397-y

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Abstract

BackgroundThe genetic determinism of the calving and suckling performance of beef cows is little known whereas these maternal traits are of major economic importance in beef cattle production systems. This paper aims to identify QTL regions and candidate genes that affect maternal performance traits in the Blonde d’Aquitaine breed. Three calving performance traits were studied: the maternal effect on calving score from field data, the calving score and pelvic opening recorded in station for primiparous cows. Three other traits related to suckling performance were also analysed: the maternal effect on weaning weight from field data, milk yield and the udder swelling score recorded in station for primiparous cows. A total of 2,505 animals were genotyped from various chip densities and imputed in high density chips for 706,791 SNP. The number of genotyped animals with phenotypes ranged from 1,151 to 2,284, depending on the trait considered.ResultsQTL detections were performed using a Bayes C approach. Evidence for a QTL was based on Bayes Factor values. Putative candidate genes were proposed for the QTL with major evidence for one of the six traits and for the QTL shared by at least two of the three traits underlying either calving or suckling performance. Nine candidate genes were proposed for calving performance among the nine highlighted QTL regions. The neuroregulin gene on chromosome 27 was notably identified as a very likely candidate gene for maternal calving performance. As for suckling abilities, seven candidate genes were identified among the 15 highlighted QTL. In particular, the Group-Specific Component gene on chromosome 6, which encodes vitamin D binding protein, is likely to have a major effect on maternal weaning weight in the Blonde d’Aquitaine breed. This gene had already been linked to milk production and clinical mastitis in dairy cattle.ConclusionIn the near future, these QTL findings and the preliminary proposals of candidate genes which act on the maternal performance of beef cows should help to identify putative causal mutations based on sequence data from different cattle breeds.Electronic supplementary materialThe online version of this article (doi:10.1186/s12863-016-0397-y) contains supplementary material, which is available to authorized users.

Highlights

The genetic determinism of the calving and suckling performance of beef cows is little known whereas these maternal traits are of major economic importance in beef cattle production systems
Kass and Raftery [20] considered that a logBF value within this interval corresponded to strong evidence for an association, we considered that such evidence was somewhat speculative because we observed that the proportion of post-burn-in iterations that included the corresponding putative quantitative trait locus (QTL) regions was always lower than 50 %
Three of the nine QTL regions detected had previously been reported in the literature

Summary

Introduction

The genetic determinism of the calving and suckling performance of beef cows is little known whereas these maternal traits are of major economic importance in beef cattle production systems. Three other traits related to suckling performance were analysed: the maternal effect on weaning weight from field data, milk yield and the udder swelling score recorded in station for primiparous cows. Maternal performance traits are of major economic and ethical importance to the sustainable breeding of beef cattle worldwide. Because of the cost and difficulty in recording such phenotypes at a large scale, the literature contains very few studies dedicated to quantitative trait locus (QTL) detection for maternal traits in beef cattle, and these studies are based on field data [5,6,7]. The second aim was to identify as accurately as possible the principal genomic regions affecting the calving and suckling performance of Blonde d’Aquitaine cows

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