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Genetic parameters and genome-wide associations of twinning rate in a local breed, the Maremmana cattle

Published online by Cambridge University Press:  21 February 2017

B. Moioli*
Affiliation:
Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), via Salaria 31, 00015 Monterotondo, Italy
R. Steri
Affiliation:
Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), via Salaria 31, 00015 Monterotondo, Italy
C. Marchitelli
Affiliation:
Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), via Salaria 31, 00015 Monterotondo, Italy
G. Catillo
Affiliation:
Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), via Salaria 31, 00015 Monterotondo, Italy
L. Buttazzoni
Affiliation:
Consiglio per la ricerca in agricoltura e l’analisi dell’economia agraria (CREA), via Salaria 31, 00015 Monterotondo, Italy

Abstract

This study seeks to verify the feasibility of increasing twinning in a herd of the Italian autochtonous Maremmana breed. The data set included 1260 individuals born from 1963 to 2014, 527 males and 733 females, 402 of them calving at least once from 1983 through 2015. Breeding values for twinning were estimated by a single-trait linear animal model. However, since twinning is a dichotomous trait and the frequency of twins is far smaller than the frequency of single births, breeding values were also estimated by a single-trait animal threshold model. Heritability of twinning was 0.014±0.018 and 0.062±0.093 for the linear and the threshold models, respectively. Repeatability was 0.071±0.004 and 0.286± 0.012, respectively, for the two models. Genotyping with the Illumina BovineSNP54 BeadChip was performed for cows living on farm in 2012 (119 cows) and a genome-wide association analysis was performed on the corrected phenotype of all calving during the lifespan of each cow, using the GenABEL package in R and a three step GRAMMAR-GC approach. Genomic heritability, calculated from the genomic kinship matrix estimated through genomic marker data, was 0.29±0.021. The most significant detected single nucleotide polymorphisms (Hapmap22923-BTA-129564) was located in proximity of two genes, ARHGAP8 and TMEM200C, which might be potential functional candidates for twinning rate in cattle.

Information

Type
Research Article
Copyright
© The Animal Consortium 2017 
Figure 0

Table 1 Twinning rate from 2012 to 2015

Figure 1

Table 2 Calf mortality in single and twin births, in the Maremmana (Mar) purebred v. Piedmontese crossbred (Pied)

Figure 2

Table 3 Genetic parameters for twinning (SE in parentheses) estimated by Repeatability Linear Model (R_LM) and Repeatability Threshold Model (R_ThM)

Figure 3

Table 4 EBVs estimated by Repeatability Linear Model (R_LM) and Repeatability Threshold Model (R_ThM)

Figure 4

Figure 1 Yearly averages of EBVs for twinning rate from 1963 to 2014.

Figure 5

Figure 2 Multidimensional scale plot of the entire sample set of animals included in the association analysis.

Figure 6

Figure 3 Q-Q plot of (GRAMMAR-GC) P-values/against expected P-values.

Figure 7

Figure 4 Manhattan plot displaying the results (−log10 of P-value) of the genome-wide scan using the GRAMMAR-GC method with respect to the genomic position. The horizontal lines separate single nucleotide polymorphisms (SNPs) with P-values <0.001 and <0.01, respectively.