Decoding genomic selection and the benefit for unconventional traits Pete Hansen Dept. of Animal Sciences University of Florida Change in Breeding Value for Milk Yield in Holsteins 1957-2013 Breeding Value for Milk (lb) 2000 0-2000 -4000-6000 -8000 Cows Bulls -10000 1950 1960 1970 1980 1990 2000 2010 Year www.cdcb.us/eval/summary/trend.cfm 23
Traditional Genetic Selection Progeny Testing Don t know the genes responsible for the trait (milk yield) We know that bulls with daughters that produce more milk are more likely to have the genes that confer higher milk production reliability Estimated genetic value - - - - - - - - True genetic value ILLUMINA Bovine SNP50 Bead Chip Development of Genomics in 2009 Changed Genetic Selection For the first time, can identify the genes responsible for the trait or genetic markers close to the genes 24
Gene a blueprint that tells the cell how to make a protein (~22,000 in cow) Protein the main work horses in a cell or animal Mammary Gland Secreted to feed the neonate (milk protein) Synthesize milk fat, sugars Cause contraction of alveoli to allow milk ejection Prevent bacterial growth Mutation a change in the blueprint so the protein is made differently Protein functions better, functions worse, or doesn t function at all 25
DOUBLE-MUSCLED PIEDMONTESE BULL Caused by a single nucleotide mutation in a gene called myostatin (abbreviated MSTN) limits muscle growth in fetal life Normal muscling Excessive muscling Myostatin inhibits muscle growth MSTN gene 26
Single Nucleotide Polymorphism (SNP) Occurs when one of the base pairs making up the DNA is changed 3 billion base pairs in cattle) Most common mutation - estimated to account for 84% of the variation in gene expression in animals Most SNPs do not occur in genes but in regions of the DNA between genes SNP far from gene SNP near gene SNP in gene ILLUMINA Bovine SNP50 Bead Chip Basis of SNP Chip Relates inheritance at each SNP on chip to trait of interest SNPs in a gene or close to a gene will explain some of the genetic variability in a trait 27
Most SNP are not on the chip Bovine HD chip -777,000 SNP 777,000 SNP 3,000,000,000 bases Not related to trait related to trait strongly related to trait SNP Effects on Genetic Variation in Milk Fat % USDA, AIPL 28
Genetic Selection After Genomics reliability OPU-IVF When to Genotype When the Opportunity for Heifer Selection is High Sexed semen, high fertility, good heifer program When Embryo Transfer Programs are Used To identify genetically superior females 29
How Far Can We Take Genetic Selection? Decoding genomic selection and the benefit for unconventional traits Pete Hansen Dept. of Animal Sciences University of Florida 30
Daughter Pregnancy Rate PR = Number of cows that became pregnant during a given 21-day period Number of cows that were eligible for breeding National average for PR ~16% DPR = PR of a bull s daughters PR (DPR) = 21/(days open voluntary waiting period + 11) A 1% increase in DPR = ~ -4 days open Heritability is 0.04 Welcome Super Petrone-ET (Dec 2014) +3.7 (-15 days open) 31
BovineSNP50 does not Provide Much Improvement in Genetic Estimates for DPR Trait REL (%) REL gain (%) Milk (kg) 67.5 29.4 Fat (kg) 73.1 35.0 Protein (kg) 63.7 25.6 Fat (%) 85.7 47.6 Protein (%) 77.9 39.8 PL (months) 64.2 33.2 SCS 60.4 26.5 DPR (%) 46.8 17.0 Sire CE 40.9 13.8 Daughter CE 44.3 18.1 Sire SB 29.8 7.2 Daughter SB 29.3 2.7 Wiggans et al., 2011 SNP Effects on Genetic Variation in Milk Fat % USDA, AIPL 32
SNP Effects on Genetic Variation in DPR USDA, AIPL Many Factors determine Whether or Not a Cow Gets Pregnant Soon After Calving Walsh et al., Animal Reproduction Science, Volume 123, Issues 3 4, 2011, 127-138 33
Differences in fertility between high & low DPR groups from 11 FL and CA dairies LSMEANS (SEM) Trait N P value High DPR Low DPR Services /conception (Lact 1) 2192 1.9 (0.07) 3.5 (0.13) <0.001 Services /conception (Lact 2) 1969 2.2 (0.08) 3.3 (0.13) <0.001 Services /conception (Lact 3) 1321 2.3 (0.10) 3.4 (0.16) <0.001 Days open (Lact 1) 2282 105.6 (3.12) 184.7 (5.50) <0.001 Days open (Lact 2) 2057 112.5 (3.24) 165.6 (5.40) <0.001 Days open (Lact 3) 1370 112.7 (3.83) 162.3 (6.23) <0.001 Problems with Unconventional Traits Not always measured or not always measured the same way Increases the value of genomic tests since they are not dependent on a phenotype for every animal Unconventional traits also often have low heritability Increase in reliability using genomics less than for more heritable traits 34
Alternatives to Health Traits (Productive Life and Somatic Cell Score) Trait Displaced abomasum Heritability 0.17 0.11 Ketosis 0.08 0.13 Lameness 0.03 0.15 Mastitis 0.05 0.12 Metritis 0.06 0.13 Retained placenta 0.07 0.09 Improvement in reliability using genomics Parker Gaddis et al., J Dairy Sci. 97:3190 (2014) Single Nucleotide Polymorphism (SNP) Occurs when one of the base pairs making up the DNA is changed 3 billion base pairs in cattle) Most common mutation - estimated to account for 84% of the variation in gene expression in animals Most SNPs do not occur in genes but in regions of the DNA between genes One approach find SNP in gene (more predictive) SNP far from gene SNP near gene SNP in gene 35
Haplotypes found to cause pregnancy failure in dairy cattle AH-Ayrshire, BH-Brown Swiss, HH-Holstein, JH-Jersey http://genex.crinet.com/page6018/fertilityhaplotypes 36
Carrier Frequency of the JH1 haplotype Observer Chocolate Soldier (b 1962) COQ9 genotype effect on phenotypic measurements Trait N Genotype GG AG AA P value LSMEANS (SEM) Serv/conc (Lact1) 2213 2.80 (0.10) 2.50 (0.10) 2.40 (0.10) 0.0001 Serv/conc (Lact2) 1969 2.74 (0.09) 2.64 (0.07) 2.53 (0.08) 0.0487 Days open (Lact 1) 2213 139.40 (3.5) 134.30 (2.8) 123.60 (3.5) <0.0001 Days open (Lact 2) 1969 143.14 (3.59) 137.85 (2.81) 128.80 (3.58) 0.0052 Milk yield, kg (Lact 1) 2213 9776 (57) 9727 (44.4) 9610 (57) 0.015 Milk yield, kg (Lact 2) 1969 11504 (69) 11375 (54) 11433 (69) 0.440 37
Estradiol Secretion Antibody Response Milk yield Progesterone Secretion FERTILITY INDEX Mastitis Resistance DISEASE RESISTANCE INDEX hansen@animal.ufl.edu 38