Animal Genetics 2

Research title:   

Analysis of genomic data in ruminant species

Tutor: Prof.ssa Paola Crepaldi

 

Contact details

This email address is being protected from spambots. You need JavaScript enabled to view it. Contact details: Prof. Paola Crepaldi, Department of Veterinary Science and Animal Husbandry; Via Celoria 2, 20133 Milano e.mail This email address is being protected from spambots. You need JavaScript enabled to view it. ; phone: ++390250316442

 

State of the art

Ruminants breeds undergone various intensity of  natural and artificial selection that have likely shaped the genomic divergences between them. Recent advances in molecular technology have led to a widespread availability of molecular data in several species. Goat, sheep and cattle breeds have recently been genotyped with low, medium and high-density SNPs panels within national and international projects. The progress in genomic technologies has recently improved the ability to identify genomic regions useful in shedding light on biological pathways related to quantitative and qualitative traits under selection.  Many genetic population approaches, such as haplotypes-based and population differentiation based methods, could be used to identify micro-evolutionary selective events within species.  The joint usage of these methods and new reliable traits would allow the development of a more efficient identification of animals consistently with the new challenges of selection schemes.

crepaldi1

 

Pictures from www.goatit.eu

Aims of the project 

We propose a project to explore  available genomic data to improve the knowledge on selection signature for divergent phenotypes, also associated with estimated breeding values or quantitative traits recorded by breeders’ association. The study aims to the detection of genomic regions under selection and to explore pathways and the more relevant genes identified. These association would be studied within and across breeds, and even across species by comparative genomic. The investigation of genomic differences can disentangle the genetic basis of these traits and can contribute to clarify functionally important genetic variants. The successful candidate will have access to medium and high-density genotyping data in addition to phenotypes for a large series of breeds.

Applicant should have interest in bioinformatics, molecular and statistical genetics applied to livestock species. Basic laboratory skill and previous experience working with Linux, Python, R on genomic data is highly desirable.

 

Recent publications of the tutor in the field (max 5)

Background Publications showing previous experience in the proposed research area

1) A. Talenti, F. Bertolini, G. Pagnacco, F. Pilla, P. Ajmone-Marsan, M.F. Rothschild, P. Crepaldi (2017). The Valdostana goat: a genome-wide investigation of the distinctiveness of its selective sweep regions. MAMMALIAN GENOME, ISSN: 0938-8990, doi: 10.1007/s00335-017-9678-7; Scopus: 2-s2.0-85014093370

2) D.L. Dreger, B.W. Davis, R. Cocco, S. Sechi, A. Di Cerbo, H.G. Parker, M. Polli, S.P. Marelli, P. Crepaldi, E.A. Ostrander (2016). Commonalities in development of pure breeds and population isolates revealed in the genome of the Sardinian Fonni’s dog. GENETICS, vol. 204, p. 737-755, ISSN: 0016-6731, doi: 10.1534/genetics.116.192427; Scopus: 2-s2.0-84991493924

3) A. Talenti, E.L. Nicolazzi, S. Chessa, S. Frattini, R. Moretti, B. Coizet, L. Nicoloso, L. Colli, G. Pagnacco, A. Stella, P. Ajmone-Marsan, G. Ptak, P. Crepaldi (2016). A method for single nucleotide polymorphism selection for parentage assessment in goats. JOURNAL OF DAIRY SCIENCE, vol. 99, p. 3646-3653, ISSN: 0022-0302, doi: 10.3168/jds.2015-10077; 2-s2.0-84959888341

4) 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, Consortium, IG (2015) - Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip. Genet Sel Evol 47, 62.

5) Dimauro, C, Nicoloso, L, Cellesi, M, Macciotta, NPP, Ciani, E, Moioli, B, Pilla, F, Crepaldi, P (2015)  -Selection of discriminant SNP markers for breed and geographic assignment of Italian sheep. Small Ruminant Research 128, 27-33.