Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles) such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping  ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity

A. Talenti

F. Bertolini

G. Pagnacco

M.F. Rothschild

P. Crepaldi

S. Frattini

English

AIR Universita degli studi di Milano

Proceeding of Veterinary and Animal Science Days 2017, 6th- 8th June, Milan, Italy 
HAF © 2013 
Vol. IV, No. 1s   ISSN: 2283-3927 
   
 
l 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
Keywords 
Goat, SNP, Selection 
signatures 
 
CORRESPONDING AUTHOR 
Andrea Talenti  
andrea.talenti@unimi.it 
 
JOURNAL HOME PAGE 
riviste.unimi.it/index.php/haf 
Detection of selection signatures for ear 
 carriage in Maltese goat breed 
Andrea Talenti1*, Francesca Bertolini2, Stefano Frattini1,  
Giulio Pagnacco1, Max F. Rothschild2, Paola Crepaldi1 and  
the Italian Goat Consortium 
 
 
 
1University of Milan, Department of Veterinary Medicine, Italy  
2Iowa State University, Department of Animal Science, USA  
 
Abstract 
Selection and breeding practices in goats have led to the fixation of several traits. This is probably due 
to the standardization of several peculiar morphological characteristics that have always been one of 
the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most 
ancient and considered a signature of domestication in several species, such as the dog, pig, sheep 
and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may 
provide useful information on genes involved in this trait. By studying, for example, the homozygosity 
decay of haplotypes (contiguous length of alleles) such information can be detected. In the current 
study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian 
breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 
369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within 
population excluding markers without known position on the current genome assembly (ARS1, 
Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the 
good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was 
performed for each population, comparing the regions detected on the Maltese breed with the others 
considered to detect genes that may be involved into shaping  ear morphology. These results may 
provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping 
the goat phenotypic diversity. 
 
Acknowledgement 
The research was funded by INNOVAGEN project. 
Proceeding of Veterinary and Animal Science Days 2017, 6th- 8th June, Milan, Italy 
HAF © 2013 
Vol. IV, No. 1s   ISSN: 2283-3927 
 
 
 
 
 
 
 
 
 
 
 
References 
Bickhart, D.M.; Rosen, B.D.; Koren, S.; Sayre, B.L.; Hastie, A.R.; Chan, S.; Lee, J.; Lam, E.T.; Liachko, I.; Sullivan, S.T.; 
Burton, J.N.; Huson, H.J.; Nystrom, J.C.; Kelley, C.M.; Hutchison, J.L.; Zhou, Y.; Sun, J.; Crisà, A.; Abel Ponce de León, 
F.; Schwartz, J.C.; Hammond, J.A.; Waldbieser, G.C.; Schroeder, S.G.; Liu, G.E.; Dunham, M.J.; Shendure, J.; 
Sonstegard, T.S.; Phillippy, A.M.; Van Tassell, C.P.; L Smith, T.P., 2017. Single-molecule sequencing and chromatin 
conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics, 49, 4–3. 
Boyko, A.R.; Quignon, P.; Li, L.; Schoenebeck, J.J.; Degenhardt, J.D.; Lohmueller, K.E.; Zhao, K.; Brisbin, A.; Parker, 
H.G.; vonHoldt, B.M.; Cargill, M.; Auton, A.; Reynolds, A.; Elkahloun, A.G.; Castelhano, M.; Mosher, D.S.; Sutter, N.B.; 
Johnson, G.S.; Novembre, J.; Hubisz, M.J.; Siepel, A.; Wayne, R.K.; Bustamante, C.D.; Ostrander, E.A., 2010. A Simple 
Genetic Architecture Underlies Morphological Variation in Dogs. PLoS Biology, 8, e1000451 
Nicoloso, L.; Bomba, L.; Colli, L.; Negrini, R.; Milanesi, M.; Mazza, R.; Sechi, T.; Frattini, S.; Talenti, A.; Coizet, B.; Chessa, 
S.; Marletta, D.; D’Andrea, M.; Bordonaro, S.; Ptak, G.; Carta, A.; Pagnacco, G.; Valentini, A.; Pilla, F.; Ajmone-Marsan, 
P.; Crepaldi, P., 2015. Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip. Genetics 
Selection Evolution, 47, 1–10. 
Sabeti, P.C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E.H., Mccarroll, S.A., 
Schaffner, S.F., Lander, E.S., The International Hapmap, 2007. Genome-wide detection and characterization of 
positive selection in human populations. Nature 449(7164), 913-918 
 


Detection of selection signatures for ear carriage in Maltese goat breed

Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles) such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping  ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity.Acknowledgement The research was funded by INNOVAGEN project

Talenti, Andrea

Bertolini, Francesca

Frattini, Stefano

Pagnacco, Giulio

Rothschild, Max F

Crepaldi, Paola

Riviste UNIMI

Proceeding of Veterinary and Animal Science Days 2017, 6th- 8th June, Milan, Italy HAF © 2013 Vol. IV, No. 1s   ISSN: 2283-3927     l                                       Keywords Goat, SNP, Selection signatures  CORRESPONDING AUTHOR Andrea Talenti  andrea.talenti@unimi.it  JOURNAL HOME PAGE riviste.unimi.it/index.php/haf Detection of selection signatures for ear  carriage in Maltese goat breed Andrea Talenti1*, Francesca Bertolini2, Stefano Frattini1,  Giulio Pagnacco1, Max F. Rothschild2, Paola Crepaldi1 and  the Italian Goat Consortium    1University of Milan, Department of Veterinary Medicine, Italy  2Iowa State University, Department of Animal Science, USA   Abstract Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles) such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping  ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity.  Acknowledgement The research was funded by INNOVAGEN project. Proceeding of Veterinary and Animal Science Days 2017, 6th- 8th June, Milan, Italy HAF © 2013 Vol. IV, No. 1s   ISSN: 2283-3927            References Bickhart, D.M.; Rosen, B.D.; Koren, S.; Sayre, B.L.; Hastie, A.R.; Chan, S.; Lee, J.; Lam, E.T.; Liachko, I.; Sullivan, S.T.; Burton, J.N.; Huson, H.J.; Nystrom, J.C.; Kelley, C.M.; Hutchison, J.L.; Zhou, Y.; Sun, J.; Crisà, A.; Abel Ponce de León, F.; Schwartz, J.C.; Hammond, J.A.; Waldbieser, G.C.; Schroeder, S.G.; Liu, G.E.; Dunham, M.J.; Shendure, J.; Sonstegard, T.S.; Phillippy, A.M.; Van Tassell, C.P.; L Smith, T.P., 2017. Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome. Nature Genetics, 49, 4–3. Boyko, A.R.; Quignon, P.; Li, L.; Schoenebeck, J.J.; Degenhardt, J.D.; Lohmueller, K.E.; Zhao, K.; Brisbin, A.; Parker, H.G.; vonHoldt, B.M.; Cargill, M.; Auton, A.; Reynolds, A.; Elkahloun, A.G.; Castelhano, M.; Mosher, D.S.; Sutter, N.B.; Johnson, G.S.; Novembre, J.; Hubisz, M.J.; Siepel, A.; Wayne, R.K.; Bustamante, C.D.; Ostrander, E.A., 2010. A Simple Genetic Architecture Underlies Morphological Variation in Dogs. PLoS Biology, 8, e1000451 Nicoloso, L.; Bomba, L.; Colli, L.; Negrini, R.; Milanesi, M.; Mazza, R.; Sechi, T.; Frattini, S.; Talenti, A.; Coizet, B.; Chessa, S.; Marletta, D.; D’Andrea, M.; Bordonaro, S.; Ptak, G.; Carta, A.; Pagnacco, G.; Valentini, A.; Pilla, F.; Ajmone-Marsan, P.; Crepaldi, P., 2015. Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip. Genetics Selection Evolution, 47, 1–10. Sabeti, P.C., Varilly, P., Fry, B., Lohmueller, J., Hostetter, E., Cotsapas, C., Xie, X., Byrne, E.H., Mccarroll, S.A., Schaffner, S.F., Lander, E.S., The International Hapmap, 2007. Genome-wide detection and characterization of positive selection in human populations. Nature 449(7164), 913-918  

Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles) such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping  ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity.

Acknowledgement 

The research was funded by INNOVAGEN project

Detection of selection signatures for ear carriage in Maltese goat breed

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