Dissecting complex traits in pigs: metabotypes illuminate genomics for practical applications

Transcription

1 Dissecting complex traits in pigs: metabotypes illuminate genomics for practical applications Luca Fontanesi Department of Agricultural and Food Sciences Division of Animal Sciences University of Bologna Bologna, Italy

2 Metabolomics

3 Metabolomics measures all endogenous metabolites of a tissue or body fluid under given conditions From Junot et al. 2014

4 Metabolomics measures all endogenous metabolites of a tissue or body fluid under given conditions From Junot et al. 2014

5 Metabolomics measures all endogenous metabolites of a tissue or body fluid under given conditions From Junot et al. 2014

6 Animal resources ~15,000 performance tested Italian Large White ~8,000 performance tested Italian Duroc ~6,000 performance tested Italian Landrace

7 Animal resources ~15,000 performance tested Italian Large White ~8,000 performance tested Italian Duroc ~6,000 performance tested Italian Landrace Pilot study ~200 metabolites 24 pigs Metabolomic differences between two pig breeds

8 METABOTYPES Metabolyte classes No. Biological relevance (selected examples) Acylcarnitines 40 Energy metabolism, fatty acid transport and mitochondrial fatty acid oxidation, ketosis, oxidative stress, mitochondrial membrane damage (apoptosis) Amino acids 21 Biogenic amines 19 Hexoses 1 Carbohydrate metabolism Glycerophospholipids 90 Amino acid metabolism, urea cycle, activity of gluconeogenesis and glycolysis, insulin sensitivity/resistance, neurotransmitter metabolism, oxidative stress Neurological disorders, cell proliferation, cell cycle progression, DNA stability, oxidative stress - lysophosphatidylcholine acyl lysopc a Cx:x 14 Degradation of phospholipids (phospholipase activity), membrane damage, signalling cascades, fatty acid profile - Phosphatidylcholine diacyl PC aa Cx:x 38 Dyslipidemia, membrane composition and damage, fatty acid - Phosphatidylcholine acyl-alkyl PC ae Cx:x 38 profile, activity of desaturases Sphingolipids 15 Signalling cascades, membrane damage (e.g. neurodegeneration)

9 METABOTYPES Metabolomic differences between breeds: Partial Least Square Discriminant Analysis (PLS- DA) on plasma and serum collected on pigs just after jugulation (slaughtering weight of about 160 kg)

10 METABOTYPES spls results Biofluid Metabolic class Metabolite ID ILW Stability Significance Direction Mean SD Mean SD t P t P Sphingomyelins SM (OH) C14:1 1.69E E E E ID Plasma Serum Biogenic Amines Sphingomyelins Ac.Orn 6.93E E E E ILW Kynurenine 4.75E E E E ILW SM (OH) C14:1 1.74E E E E ID SM (OH) C16:1 2.43E E E E ID SM C 16: E E E ID Biogenic Amines Ac.Orn 6.23E E E E ILW

11 METABOTYPES spls results Biofluid Metabolic class Metabolite ID ILW Stability Significance Direction Mean SD Mean SD t P t P Sphingomyelins SM (OH) C14:1 1.69E E E E ID Plasma Serum Biogenic Amines Sphingomyelins Ac.Orn 6.93E E E E ILW Kynurenine 4.75E E E E ILW SM (OH) C14:1 1.74E E E E ID SM (OH) C16:1 2.43E E E E ID SM C 16: E E E ID Biogenic Amines Ac.Orn 6.23E E E E ILW

12 Animal resources ~1,000 pigs ~300 phenotypes ~15,000 performance tested Italian Large White ~8,000 performance tested Italian Duroc ~6,000 performance tested Italian Landrace ~400 pigs ~300 phenotypes

13 METABOTYPES

14 Genomics + Metabolomics

15 PorcineSNP60 BeadChip Genotype space Metabotypes External phenotypes

16 Kynurenine Italian Large White Italian Duroc

17 Kynurenine level Box plot with the three genotypes 1/1 1/2 2/2 SNP1 Genotypes

18 METABOTYPES spls results Biofluid Metabolic class Metabolite ID ILW Stability Significance Direction Mean SD Mean SD t P t P Sphingomyelins SM (OH) C14:1 1.69E E E E ID Plasma Serum Biogenic Amines Sphingomyelins Ac.Orn 6.93E E E E ILW Kynurenine 4.75E E E E ILW SM (OH) C14:1 1.74E E E E ID SM (OH) C16:1 2.43E E E E ID SM C 16: E E E ID Biogenic Amines Ac.Orn 6.23E E E E ILW

19 Italian Large White Wild boar Belgian Landrace Italian Landrace Italian Duroc Kynurenine level Box plot with the three genotypes Allele frequencies of SNP1 in different breeds Allele 2 Allele 1 1/1 1/2 2/2 SNP1 Genotypes

20 SNP7 SNP6 SNP5 SNP4 SNP1 SNP2 SNP3 Kynurenine Kynurenine 3-monooxygenase (KMO)

21 SNP7 SNP6 SNP5 SNP4 SNP1 SNP2 SNP3 Kynurenine Tryptophan catabolism KMO Kynurenine 3-monooxygenase (KMO)

22 Behavio ur SNP7 SNP6 SNP5 SNP4 SNP1 SNP2 SNP3 Immunity/ inflammat ion Kynurenine Tryptophan catabolism IDO, TDO KMO Kynurenine 3-monooxygenase (KMO)

23 Can these results on KMO be useful for practical applications?

24 Can these results on KMO be useful for practical applications? 1/2 1/2 x 1/1 1/2 2/2 - baseline conditions - TRP dietary load - TRP dietary load and challenge with enterotoxigenic E. coli K88 Partition of the different metabolites

25 KYN, µmol/l Kynurenine in blood plasma "AA" "AG" "GG" 2/2 2/2 2/2 1/1 2/2 1/2 1/1 Baseline Trp Load Trp load + challenge

26 Can these results on KMO be useful for practical applications? 1/2 1/2 x We are developing the first 1/1 nutrigenomics 1/2 2/2 approaches in pigs Partition of the different metabolites - baseline conditions - TRP dietary load - TRP dietary load and challenge with enterotoxigenic E. coli K88 Definition of amino acid requirement based on animal genotype and environmental

27 Conclusions a) Metabotypes + genomics = fine biological mechanisms b) Applications that merge metabolomics and genomics information are possibile c) Many other questions and opportunities can be opened by integrating genomics and metabolomics using nonconventional approaches (not presented here)

28 We are just at the beginning of a very interesting story.. Metabolites we have analysed Molecular phenotypes

29 University of Bologna Department of Agricultural and Food Sciences Samuele Bovo Gian Luca Mazzoni Giuseppina Schiavo Anisa Ribani Valerio Joe Utzeri Antonia Bianca Samoré Emilio Scotti Francesca Bertolini Diana Luise Stefania Dall Olio Paolo Trevisi Paolo Bosi Department of Surgical and Medical Sciences Endocrinology Unit Flaminia Fanelli Marco Mezzullo Uberto Pagotto Department of Statistical Sciences Giuliano Galimberti Associazione Nazionale Allevatori Suini Funded by: Innovagen project (MiPAAF) AGER project (Fondazioni Bancarie) FARB project (University of Bologna)

30 Dissecting complex traits in pigs: metabotypes illuminate genomics for practical applications Luca Fontanesi Department of Agricultural and Food Sciences Division of Animal Sciences University of Bologna Bologna, Italy