Genomics (Dairy)

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Genomics (Dairy)

Landscape DesignTaking design cues from the landscapeAmenia Hills, Running Wall


National breeding goal (PLI)Relative importance of traitsin in the Profitable Lifetime IndexUdder 5.6%Locomotion41%4.1%SCC 5.5%£PIN 45.2%a) milk 24.1%b) fat 27.5%,Fertility 18.5% 185%c) prot. 48.5%Lifespan 21.1%


Genetic Evaluations - Present• Performance = Genetics + Environment• Genetic evaluations based on:– Pedigree information– Performance recording (eg. Milk, SCC)• Correcting for environmental effects– Progeny performanceTime• Proven methodology and Accurate– But takes time to build up data on individuals


Progeny test• Bull dam mated0 (year)• Bull calf born 1• Semen collected 2• Progeny born 3• Progeny bred 4• Progeny milking 5• Bull ‘proven’ 6Rlb35%35%35%35%35%75%90%


Why progeny test ?• Example of two full brothers:• Trait Addison Slogan• Milk 848 -4• Lifespan -0.3 +0.1• Foot Angle +1.66 -1.58• Could Genomic data have informed us earlier ?– Thereby reducing Generation Interval


Genome• Cows have (around):– 30 Chromosome pairs– 3 billion base pairs– 25,000 genes– 99.5% DNA consistent– >45 million SNP’s• Single Nucleotide Polymorphism• Basis of genetic variation


Genomic Evaluations• Use SNPs as marker post along DNAsequence• SNPs not picked for effect !– Chooses to get best ‘coverage’


Genomic Selection• Idea was first formulated in 2001– (Meuwissen et al)– Extension on Marker Assisted Selection (MAS)– Allows for use of Markers across families• Cost of genotyping g was prohibiting ($1/SNP)• Rapid DNA screening developments made itreality in Dec 2007 ($0.005/SNP) 005/SNP)– (Cost today come down 10 fold again)


Most used technology• So called 50K ‘SNP Chip’• SNP Chip developed in USA– 54,000 evenly spread SNP’s– Same chip used around the world– Therefore same genotypes used by all– Allowing for international co-operation


Genotype Data for ElevationChromosome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


Application in Humans


Genomic Evaluations• Estimating ggenetic merit from animal’s DNA• Using ggenetic ‘marker posts’– 54,000 SNPs• Linking ‘markers’ to bull PTA– Training data to get ‘Key’• Unfortunately t associations often not very clear• However – there is power in numbers !– Large resource population with accurate data needed,


Marker Effects for Milk 2008Real or Random ??Lots of bulls needed to gain confidence


Need for many Bull genotypes


Net Merit by Chromosome for O-Man


Using Genomic information• Direct Genomic evaluation (DG)– Total sum of SNP effects• Traditional Genetic information (PTA)– Parents– Performance– Progeny• Genomic PTA = PTA + DG– Same scale, so can be used as normal


Genomics• Able to make predictions of genetic merit early– without Progeny or Performance info• Improve accuracy for difficult to measure traits– e.g. Lifespan, Fertility, (TB, Feed efficiency, i GHG ?)• However, reliability still lower than progeny test– 35% Pedigree index– 60% Genomic enhanced evaluation– 75% First crop progeny test– 95+ High reliability progeny proven


Progeny test with GenomicsRlbRlb• Bull dam mated0 (year) 35% 35%• Bull calf born 1 35% 60%• Semen collected 235%60%• Progeny born 3 35% 60%• Progeny bred 4 35% 60%• Progeny milking 575%80%• Bull ‘proven’ 6 90% 90%


Genetic progress - Theory• Genetic progress (dG)– Selection intensity (i)– Accuracy of selection (r)– Variation available for selection (V)– Generation Interval (L)dG =i * r * VL


Reliability in context• Using teams of bulls spreads the risk• However, Teams do not increase Reliability !14 young bulls at 35% reliability, arestill only 35% reliable, not 95%


Genetic gain• Best estimates at 100% take-up– >100% improvement on genetic gain– UK estimate conservative 15% (still >£20M in 10 years)• Due to more use of (younger) high £PLI bulls• However, long term gain needs to be protected– Fixation of SNPs (and QTLs)– Need to carefully manage inbreeding– Keep improving understanding and methodology


Genomic Selection - Cows• Current method too expensive for widespread use– Still ~£100 (54K) or ~£250 (HD 770K) per animal• Used to improve accuracy of bull dams– Better able to cope with preferential treatment bias• However, Smaller, cheaper chip could providesolution for widespread use– 3K evenly spaced SNPs (


Imputation• Imput_tion tion is a met_od by which you tryand pred_ct, as ac_urately as po_sible,the genot_pe of an ani_al at a hig_erdensi_y than the genoty_es you actuallyhave. This can subs_quently be used toobtain geno_ic PT_s


Imputation• Imputation is a method by which you tryand predict, as accurately as possible,the genotype of an animal at a higherdensity than the genotypes you actuallyhave. This can subsequently be used toobtain genomic PTAs


Imputation results• International research results:– Correlation of >0.95– Loss in reliability ~5%• Practical applications for cows– Performance prediction• Select which calves to rear– Disease susceptibility ?– Response to vaccinations ?– Parentage verification– Other…


Take home messagesGenomics is additional tool for improved selection– Better than traditional Parent Average alone– But not as good as progeny test yet– So use with necessary care• PTAs published will look/feel the same– Should be used the same on farm– Buy semen on Quality of bull (not hype)• Stronger need for data recording !


Genomic Evaluation• Exciting opportunities– Increased genetic gain expected• Especially for difficult to asses ‘Fitness’ traits– Still lots to do to fully understand the genome• UK Industry collaboration (Dairy)– Expected official genomic evaluations Autumn 2011• Fundamentals of breeding still apply– Get your breeding goals right first !!– Using PLI as a guide

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