Proceeding of Veterinary and Animal Science Days 2015, 15th- 17t  July, Milan, Italy 

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CORRESPONDING AUTHOR 

Andrea Talenti,  

andrea.talenti@unimi.it 

 

 

ABSTRACT  

The recent availability of a medium density SNPs chip in goat offers the possibility to develop a useful and less 
expensive tool for parentage assessment. However, standard approaches of SNP selection for parentage 
assignment are still ineffective due to a lack of information about markers position. In this study, we describe 
the identification of a 200 SNPs panel for parentage testing in goat. Data on 350 goats of 14 different Italian 
breeds genotyped with the Illumina 50K SNP array were provided by the Italian Goat Consortium (IGC). 
The 200 SNPs panel was identified by a three-step procedure, as follows: 1) parentage assessment by mendelian 
errors and genomic parentage to identify true parent-offspring pairs; 2) identification of informative SNPs by 
canonical discriminant analysis and 3) reduction by mendelian errors and stepwise regression. 
The 200 SNPs panel was tested on pairwise comparison of all animals at each locus. Sensitivity, specificity and 
accuracy of the panel were assessed. The probability of exclusion (Pe) and the probability of a random 
coincidental match inclusion (Pi) for each breed were estimated. 
The panel showed good assessment power, with high sensitivity (0.9429), specificity (1.0) and accuracy 
(0.99997). Pe values ranged from a minimum of 0.99999981 for Maltese from Sardinia to a maximum of 
0.999999999996 for Nicastrese. We further reduced panel size by stepwise regression to 174 SNPs showing the 
same performance of the 200 SNP panel. The development of tools for parentage assessment could improv e 
breeding management also in species with low genetic information, as goat. 

 
ACKNOWLEDGEMENTS 
Dataset was provided by the Italian Goat Consortium. The research was supported by the project "INNOVAGEN" 
(Italian MIPAAF Ministry). 

 
REFERENCES  
Heaton, M. P., G. P. Harhay, G. L. Bennett, R. T. Stone, W. M. Grosse, E. Casas, J. W. Keele, T. P. L. Smith, C. G. Chitko -
McKown, and W. W. Laegreid. 2002. Selection and use of SNP markers for animal identification and paternity 
analysis in U.S. beef cattle. Mammalian Genome 13(5):272-281; Tosser-Klopp, G., P. Bardou, O. Bouchez, C. Cabau, R. 
Crooijmans, Y. Dong, C. Donnadieu-Tonon, A. Eggen, H. C. M. Heuven, J. Saadiah, J. Abdullah Johari, C. Klopp, C. T. 
Lawley, J. McEwan, P. Martin, C. R. Moreno, P. Mulsant, I. Nabihoudine, E. Pailhoux, I. Palhiere, R. Rupp, J. Sarry, B. L. 
Sayre, A.  
 

Development of a 200 single nucleotide 

polymorphism panel for parentage 

assessment for 14 Italian goat breeds 

A.Talenti
1
, E. L. Nicolazzi

2
, L. Nicoloso

1
, S. Frattini

1
, B. Coizet

1
, S. 

Chessa
3
, G. Pagnacco

1
, F. Pilla

4
, P. Ajmone-Marsan

5
 and P. Crepaldi

1
 

1
 Department of veterinary science and public health, University of Milan, Milan, 

Italy. 
 

2
 Parco Tecnologico Padano Foundation, Lodi, Italy

. 

 

3 
CNR – IBBA, Milan, Italy. 

 

4 
Department of Agriculture, Environment and Food, University of Molise, 

Campobasso, Italy. 
 

5 
University Cattolica del Sacro Cuore, Piacenza, Italy.