Studi genomici negli animali

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1 Studi genomici negli animali John Williams Parco Tecnologico Padano

2 Agricultural needs

3 Need for increased meat produc:on! World consump;on of meat products! M Tonnes! M Tonnes! Consump;on set to grow by 50% to 2020!.and a another 50% by 2050

4 Tradi:onal phenotype based selec:on

5 Phenotypic selec:on works!

6 Using genomic informa;on X X X X A B C D

7 Double muscling

8 Myosta;n: South Devon

9 Feno:pi semplice e complesso

10 Phenotype selec:on has had great success and failures! In the USA there are 19,000,000 registered Holstein ca8le! Ne of the Holstein = 50!! < 2

11 Trypanosomosis: A fatal disease of livestock. The livestock equivalent of sleeping sickness in humans T. congolense, T. vivax T brucei rhodesiense T gambiense

12 CaCle, trypanosomosis, trypanotolerance NʼDama tolerant! Boran susceptible! Bovins Cattle Glossines Tsetse Bovins Cattle et and Glossines tsetse Trypanosomosis is the largest disease constraint on cattle production in sub- Saharan Africa, costing $1.3 to $10 billion per annum; 60 million cattle at constant risk

13 Mapping genes for trypanotolerance X! Boran x N Dama pedigree! 177 F2, 1989 start, MOET! T. congolense challenge! Genome- wide coverage with molecular markers (n = 477) Hanotte et al., 2003 PNAS 100, 7443

14 Trypanotolerance loci Chromosome! PCV N Dama Boran ` * Parasitima N Dama Boran Hanotte et al (2003) PNAS From N Dama From Boran Not significant * Body Weight only

15 Using genomic informa;on! Meishan superior reproduc;ve performance! Large White superior growth and carcass traits Shoulder Back Loin Threshold S0025 SW2155 TNFB S0066 SW632 S0101 SW764

16 Meat quality QTL

17 Genome Sequence

18 Copy number variation (CNV) Genome Varia:ons

19 Genotyping High throughput low cost! Illumina! 54K SNP panel! 800K SNP panel! 3K SNP panel! Afimetrix! Axiom Genome- Wide BOS 1 Array! 648,000 SNPs

20 Johnes Disease! Mycobacterium avium subsp. paratubercolosis (MAP)! in cadle sheep, goats, deer, llamas, camels, goats, bison, antelope..! Long incuba;on period! High rates of infec;on Clinical Disease Diseased, thinner and showing early signs Shedding bacteria and serologically positive Shedding bacteria but serologically negative Exposed, but serologically negative and no bacteria detected

21 Johnes: Genome Wide Associa:on (GWAS) Field samples, 120 Farms High Johnes incidence Lodi, Lombardia Is;tuto Zooprofilagco Sperimentale della Lombardia e dell' Emilia Romagna (ISZLER) Holstein Elisa test ParaTB Over 5000 samples samples (495 +ve / 496 ve) markers Illumina 54K panel

22 Associa;on between markers and disease GenABEL (Aulchenko Y.S., Ripke S., Isaacs A., van Duijn C.M. Bioinformatics. 2007, 23(10): )

23 From QTL to GWAS! Milk Traits! 200 samples! 150 microsatellite markers! 2 years Johnes Disease 991 samples (495 +ve / 496 ve) markers Illumina 54K panel 2 months

24 Gene:cs of height! Heritability 80%! 500,000 SNP! 63,000 individuals! 54 Loci! Effect % of varia;on Weedon, M.N. et al. Nat. Genet. 40, (2008). Lettre, G. et al. Nat. Genet. 40, (2008). Gudbjartsson, D.F. et al. Nat. Genet. 40, (2008).

25 Genome- wide selec;on! Informa;on is lost by just considering major peaks! To achieve reliable predic;ons of phenotypes it is essen;al to use all the genomic informa;on

26 Progeny tes:ng

27 Genome- wide selec:on! Molecular selec;on has been focussed on individual loci! Now high density markers allow us to consider whole chromosomes, or the whole genome Chromosome 1 Chromosome 2 Genome-wide = = = = = = 100

28 The reality! Genotyping In the USA! April ,000! June ,000! Currently 6,000 per month! Mining the data! Missing homozygotes! Recessive lethal muta;ons

29 Lost diversity

30 Advanced Biotechnology! Improved breeding strategies! Technological advances! Use of molecular markers! Earlier selec;on! Addi;onal traits! Protec;on of diversity

31 Conclusions! Genome sequence data provides addi;onal opportuni;es for selec;on, but! We need data on phenotypes: the correct phenotypes! and sufficient numbers of records to es;mate the effects of the large number of loci with small effect! Then know how to use the informa;on!

32

33 Genomics of Methane Progedo Ruminonics

34 What is required from livestock produc;on?! Wealthy countries! Disadvantaged areas! Increased produc;on! Improved quality! Environmentally friendly systems! Survival! Disease resistance! Drought resistance! Efficient food conversion

35 Improving produc:on! Tackling animal health is a route out of poverty for some of the world s poorest people! Na;onal prosperity and individual livelihood dependent on efficient and appropriate livestock produc;on

36 Use of improved gene:cs?

37 Haplotypes Affec;ng Fer;lity Name Chrom- osome Carrier Freq BTA Mbase % Earliest Known Ancestors HH Pawnee Farm Arlinda Chief HH Willowholme Mark Anthony HH Glendell Arlinda Chief, Gray View Skyliner JH Observer Chocolate Soldier BH West Lawn Stretch Improver

38 Applica:on of Technology! Selec;on and use of natural gene;c varia;on! can improve produc;vity! change the characteris;cs of produc;on! have unexpected or unwanted effects! The new technologies! will op;mise and increase the rate the selec;on is implemented! could avoid the pivalls revealed using tradi;onal approaches! But all situa;ons should be thoroughly reviewed before ac;on is taken

39 Illumina HiSeq! Runs from 1Gb to 1 Tb since 2008! More than 80Gb sequence a day! 30X mammalian genome! 20 Transcritomes! 50 Million 100bp reads! ¼ the capacity! Illumina! Forbes fastest growing Technology company 2007 and 2009

40 Low cost instruments

41 Ion Torrent! Iden;fies incorpora;on by release of H+! The instrument is cheap! Up grades in the chip, not the instrument! This year 318 chip will deliver! 1GB! 400bp

42 Almost here?! The promise of single molecule sequencing! Long reads on Kbp! Genome assemble! Epigene;cs

43 The impact of sequencing

44 Gene:c sub- structure in samples Principal Components analysis of genomic kinship

45 Comparison with HapMap data Limousin Holstein Unknowns Eliminated

46 What will be Next?! Sequening of individuals! Australia plans to sequence XXX bulls! Epigene;cs! The Cohort of 58! Genome and Epi- genome driven selec;on! Metabiome and interactomes! Sequencing and genotyping is not an issue, we now need (we always needed) the biological iinforma;on

47

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