Biodiversità animale e sistemi zootecnici Alessio Valentini 13/04/2010 Accademia Nazionale delle Scienze detta dei XL

Accademia Nazionale delle Scienze detta dei XL Comparisons of domesticated wild species (left of each pair) and their never-domesticated close relatives (right) reveal the subtle factors that can derail domestication. J. Diamond, Nature 2002 13/04/2010 Accademia Nazionale delle Scienze detta dei XL

Rules for animal domestication a diet not easily supplied by humans (hence no domestic anteaters), slow growth rate and long birth spacing (for example, elephants and gorillas), nasty disposition (grizzly bears and rhinoceroses), reluctance to breed in captivity (pandas and cheetahs), lack of follow-the-leader dominance hierarchies (bighorn sheep and antelope), and tendency to panic in enclosures or when faced with predators (gazelles and deer, except reindeer) 13/04/2010 Accademia Nazionale delle Scienze detta dei XL

Accademia Nazionale delle Scienze detta dei XL 13/04/2010 Accademia Nazionale delle Scienze detta dei XL

The mystery of Etruscan origins: novel clues from Bos taurus mitochondrial DNA Marco Pellecchia,1 Riccardo Negrini,1 Licia Colli,1 Massimiliano Patrini,1 Elisabetta Milanesi,1† Alessandro Achilli,2 Giorgio Bertorelle,3 Luigi L Cavalli-Sforza,4 Alberto Piazza,5 Antonio Torroni,2 and Paolo Ajmone-Marsan1* Proc Biol Sci. 2007 May 7; 274(1614): 1175–1179.

B. Chessa et al., Science 324, 532 -536 (2009) Fig. 2 Combination of enJSRV proviruses (retrotypes) in the domestic sheep B. Chessa et al., Science 324, 532 -536 (2009) Published by AAAS

B. Chessa et al., Science 324, 532 -536 (2009) Fig. 3 Genetic distances between sheep populations on the basis of enJSRVs insertion frequencies B. Chessa et al., Science 324, 532 -536 (2009) Published by AAAS

Accademia Nazionale delle Scienze detta dei XL Lactose intolerance by region (African countries are only a rough guess). Red indicates a high percentage of intolerance, green a low percentage. Wikipedia.org 13/04/2010 Accademia Nazionale delle Scienze detta dei XL

Accademia Nazionale delle Scienze detta dei XL Approximate posterior density of region of origin for LP/dairying co-evolution. Itan Y, Powell A, Beaumont MA, Burger J, Thomas MG, 2009 The Origins of Lactase Persistence in Europe. PLoS Comput Biol 5(8) 13/04/2010 Accademia Nazionale delle Scienze detta dei XL

Central Dogma of Genetics

Breeds of cattle Why so many colors?

Molecular causes of Mc1r loss-of-function DG104 red cow (Klungland, 1995) DC183 yellow mouse (Robbins, 1993) R306ter Irish Setter (Newton, 2000) C33T red chicken (Takeuchi, 1996) S83F chestnut horse (Marklunk, 1996) A240T red pig (Kijas, 1998) R151C red hair (Rees, 1997)

And the dominant black phenotype in several species is due to activating mutations in the melanocortin 1 receptor.Activation of the Mc1r results in an increase in cAMP and eumelanin production and this allele is dominant to all other Mc1r alleles. Each of these mutations seems to localize to the second and third transmembrane domains. This region must be crucial for generating a constitutively active receptor Given the number of animals that are black due to activating mutations at Mc1r, we analyzed mc1r for variants associated with coat color phenotypes

Important genes affecting production traits Leptin - fat deposition DGAT1 – milk production and fat BHGR – milk components Thyroglobulin - marbling Calpastatin - tenderness Calpain - tenderness Somatostatin -- marbling

Myostatin (double muscling) Belgian blue

Double Muscling in cattle Marchigiana Piemontese

Effect of abolishing GDF8 expression General increase in muscle mass Muscular Hyperplasia up to 86% increase in muscle fibers and Hypertrophy up to 20% increase in fiber diameter

The way from DNA to functional proteins is much longer than envisaged by the “central dogma”!

Control of Gene Expression Repression of Transcription - Mechanisms: Binding to promoter elements Blocking assembly of the preinitiation complex Topic 8-2

Control of Gene Expression Repression of Transcription - Mechanisms: Inhibiting binding or functioning of transcriptional activators Topic 8-2

Control of Gene Expression Repression of Transcription DNA Methylation Methyl groups may be attached to cytosine (C5 position) Methyltransferases Methyl groups provide a tag In mammals always part of a symmetrical sequence Concentrated in CG-rich domains Often in promoter regions Methylation of promoter DNA highly correlated with gene repression Topic 8-2

Callipyge “Beautiful buttocks” A mutation which arose in a Dorset Ram “Polar Overdominance”

Polar overdominance Heterozygote expresses the phenotype but neither homozygote does Heterozygote only expresses the phenotype if the mutant gene is inherited from the father

Positional identification of genes influencing muscle mass … « Double-muscled » Belgian Blues: MSTN KO Hypermuscled Piétrains: IGF2 upregulation Callipyge sheep: Ectopic DLK1 expression polar overdominance Hypermuscled Texel: Patrocles mutation miRNA biology

A QTL affecting muscle mass maps to OAR2 … Chromosome 2

Texel sheep produce normal levels of normal MSTN mRNA Sequencing the MSTN ORF from gDNA & cDNA: no polymorphism. Northern blot and qRT-PCR: no obvious qualitative or quantitative difference.

Resequencing the MSTN gene identifies 20 non-coding SNPs … 3 Texels – 7 controls

G+6723G-A reveals one of « Kellis’s octamer motifs » …

-central role of Dicer in RNAi pathway -cleaves 2nt-3´-overhang-dsRNA; endogenous (pre-miRNA) and exogenous dsRNA into miRNA and siRNA -products interact with RISC for sequence-specific gene-silencing

Expected Finish: Spring 2007 Genomic Sequencing Launch: Dec. 2003 Expected Finish: Spring 2007

International Collaboration NIH / NHGRI -- $25M State of Texas – $10M USDA -- $11M Australia -- $1M Genome Canada -- $5M New Zealand -- $1M Beef Councils (US, TX, SD) – $0.82M Project Total = $53M

SNP Discovery in the Genome Age Dominette ...AGCTTTAAGCCATACCTTAGGACATTACCTAGG GCCATACCTTAGGACATTACCTAGGAGCTTTAAGCCATAC... ...AGCTTTAAGCCATACCTTAGGACATTACCTAGGAGCTTTAAGCCATAC... Consensus ...AGCTTTAAGCCATACCTTAGGACATTACCTAGGAGCTTTAAGCCATAC... ...AGCTTTAAGCCATACCTTAGGATATTACCTAGGAGCTTTAAGCCATAC... Martha SNP

Genomic selection Predicted EBV Training EBV

From whole to focus devices DATA COST Whole genome Screening Statistical path Patient stratification High density Optimization Metabolic SNP Reduction amount scrap data Medium- low density Focused array New focusing target DIAGNOSTIC Low COST Limited DATA EASY-to-USE Reliability NUMBER OF SAMPLE EASY OF USE – REPORT GENERATION From A. Fischetti, Bioteltech, modified

Gain from genomic selection 13/04/2010 Accademia Nazionale delle Scienze detta dei XL

Cattle breed Country Period Census population sizea Effective population size (Ne) Reference Holstein Denmark 1983-1992 - 68 Sørensen et al. 2005 Germany 1999 ≈ 2,200,000 52 Koenig & Simianer 2006 1993-2003 ≈ 3,700,000 49 France 1988-1991 (?) ≈ 2,500,000 46 Boichard et al. 1996 USA ≈ 8,500,000 39 Weigel 2001 Jersey 1977-1991 87 ≈ 640,000 53 ≈ 550,000 30 Danish red 1977-1998 157 2001-2003 ≈ 560,000 47 Japanese black Japan 1986-1990 Nomura et al. 2001 1993-1997 ≈ 530,000 17 Montbéliarde ≈ 700,000 125 Abondance ≈ 65,000 106 Normande ≈ 800,000 Tarentaise ≈ 14,000 27 Taberlet P, Valentini A., Rezaei Hr, Naderi S, Pompanon F, Negrini R, Ajmone-Marsan P. (2008). Are cattle, sheep, and goats endangered species?. Molecular Ecology. vol. 17(1), pp. 275-284 13/04/2010 Accademia Nazionale delle Scienze detta dei XL