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John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350 Biological Insights.

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Presentation on theme: "John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350 Biological Insights."— Presentation transcript:

1 John B. Cole Animal Improvement Programs Laboratory Agricultural Research Service, USDA Beltsville, MD 20705-2350 john.cole@ars.usda.gov Biological Insights Gained from Genomic Prediction

2 University of Bern, November 23, 2009 (2) Cole What is whole-genome selection? Many markers used to track inheritance of chromosomal segments Impact of each segment estimated for each trait Estimates combined with traditional predicted transmitting ability (PTA) to produce genomic evaluation (GPTA) Animals can be selected shortly after birth

3 University of Bern, November 23, 2009 (3) Cole What is a SNP? Location on a chromosome at which nucleotides differ among animals Usually not a quantitative trait locus (QTL) With enough SNP, association between SNP and QTL alleles allows useful genetic evaluation SNP chosen to be distributed evenly and have both alleles well represented in the population

4 University of Bern, November 23, 2009 (4) Cole Source of genomic evaluations DNA is extracted from blood, hair, or semen 43,385 SNP are evaluated SNP effect is difference in PTA from having 1 more A (BB v AB or AB v AA) Genomic evaluation combines SNP effect estimates with existing parent average (PA) or PTA

5 University of Bern, November 23, 2009 (5) Cole Preparation for genotyping Nominate animal for genotyping Collect hair, blood, or semen from animal Blood may not be suitable for twins Send to laboratory for DNA extraction Laboratory transfers DNA to BeadChip (12 samples/chip) for 3-day genotyping process

6 University of Bern, November 23, 2009 (6) Cole Genotyping Read red/green intensities from chip Call genotypes from intensity file Check genotypes: Duplicates Parent-progeny conflicts Wrong breed Wrong sex

7 University of Bern, November 23, 2009 (7) Cole Clustering

8 University of Bern, November 23, 2009 (8) Cole 1000111220020012111011112111101111001121100020122 0022201111202101200211122110021112001111001011011 0102200110022011011200201101020222121122102010011 1000112202212221120211201202010020220200002110001 1202011221112111022011110000212202000221012020002 2112201110121001112111021121100201021000220002201 0002011000022022110221121011211101222200121121222 0020002002020201222110022222220022121111210021111 2001101110112002022200011120110102111212111020221 0021120121100111110211121102111220001011011102022 0022111010201112111101120210210212110110221220012 1101121101202201100222002100211000111002110211011 1000222002022121211000222010200222212122112111200 2011020200122222211221202121121011001211011020022 0002001002000111101100121102121211120101012120221 0101011111021102112211111121211121011012001111102 1111011111220121012121101022202021211222120222002 121210121210201100111222121101 Genotype for Elevation Chromosome 1

9 University of Bern, November 23, 2009 (9) Cole 102122210102102101110211011211221121100220200022202 000202022000002200202222022020000200202222220000202 222000002202000020022002000000222200022220000000000 020222022002000222020222220002202222222220000200220 202220200020002200000000220222000000220020200022220 020200200202022202222222202220200020220220222202022 202020202200022002220220022200000220200002002002000 200222220002222020200222002220200002020000002222202 020000200200222200020220222200220002222022002222020 200022022022220022200220002002202000002200220222000 022000022000222202002222000220020020202202000222000 222002220220220000022022002002002022000200022220220 022200202202002222022200000202200020200202020002200 220000022022200202220200022002000200022002002000200 220222220022022000200002000200002022002022020020000 222000022200200020022200002202200200220022022020202 020202000222020002202002022022202200002020200002020 200022222200222200020022022220000020220020200202022 022020200002000200220220002200 Genotype for inbred bull (Megastar) Chromosome 24 Double grandson of Aerostar

10 University of Bern, November 23, 2009 (10) Cole What can go wrong? Inadequate DNA quality or quantity Genotype has many SNP that can’t be determined (90% call rate required) Conflicts between parents and progeny Pedigree error Sample ID error Laboratory error An unrelated animal qualifies as parent or progeny

11 University of Bern, November 23, 2009 (11) Cole Parent-progeny conflict Parent 10212002101201211001020120100 Progeny 10202010100200221001120120220 The two genotypes are inconsistent because parents and offspring can’t be homozygous for different alleles at the same locus

12 University of Bern, November 23, 2009 (12) Cole Data & evaluation flow Animal Improvement Programs Laboratory, USDA AI organizations, breed associations Dairy producers DNA laboratories samples genotypes nominations evaluations

13 University of Bern, November 23, 2009 (13) Cole Genotyped animals (n=6,005) In North America as of April 2008

14 University of Bern, November 23, 2009 (14) Cole Genotyped animals (n=19,464) In North America as of December 2008

15 University of Bern, November 23, 2009 (15) Cole Genotyped animals (n=29,313) In North America as of June 2009

16 University of Bern, November 23, 2009 (16) Cole Reliability test Holstein, Jersey, and Brown Swiss breeds HOLJERBSW Predictor: Bulls born <20004,4221,149472 Cows with data94721240 Total5,3691,361512 Predicted: Bulls born >20002,035388150 Data from 2004 used to predict independent data from 2009

17 University of Bern, November 23, 2009 (17) Cole Reliability gain 1 for young bulls (Yield) TraitHOJEBS Net merit2489 Milk26617 Fat321110 Protein24214 Fat %50368 Protein %382910 1 Gain above parent average reliability of ~35%

18 University of Bern, November 23, 2009 (18) Cole Reliability gain for young bulls (Non-yield) TraitHOJEBS Productive life32712 Somatic cell score23317 Dtr pregnancy rate28718 Final score2025 Udder depth37208 Foot angle2511 All-traits average29128

19 University of Bern, November 23, 2009 (19) Cole Reliability frequency

20 University of Bern, November 23, 2009 (20) Cole Protein PTA

21 University of Bern, November 23, 2009 (21) Cole Protein reliability

22 University of Bern, November 23, 2009 (22) Cole Adoption of genomic testing US young bulls with NAAB codes, Apr 2009 Birth Year Bulls Sampled Bulls Tested Genomic Tested % 2008*64961595 2007*1548117276 20061726111865 20051677121773 2004165599160 * 2007-2008 counts are incomplete

23 University of Bern, November 23, 2009 (23) Cole Actual results from 50K chip High correlation between genomic merit in November 2004 and August 2009 merit that includes performance data Bull with highest genomic net merit in November 2004 (Man O Man) now ranks 4th of 1,925 bulls Bull with highest genomic net merit in January 2009 (Freddie) now ranks 2nd

24 University of Bern, November 23, 2009 (24) Cole Use of genomic evaluations Determine which young bulls to bring into AI Aid in selection of mating sires Increasing impact on bull dam selection Market semen from 2-year-old bulls

25 University of Bern, November 23, 2009 (25) Cole Updates between official evaluations Genomic evaluations calculated every 2 months Not released for animals that already have an official evaluation Evaluations of new animals distributed to owners Females by breed associations Males by NAAB Usually 2,000 new genotypes included

26 University of Bern, November 23, 2009 (26) Cole Impact on producers Young-bull evaluations with accuracy of early 1st-crop evaluations AI organizations marketing genomically evaluated 2-year-olds Bull dams likely to be required to be genotyped Rate of genetic improvement likely to increase by up to 50% Progeny-test programs changing

27 University of Bern, November 23, 2009 (27) Cole International implications All major dairy countries investigating genomic selection Interbull researching how to integrate genomic evaluations European collaboration to share genotypes Prediction accuracy continues to increase with increasing numbers of predictor animals Importing countries must change rules to allow for genomically evaluated young bulls

28 University of Bern, November 23, 2009 (28) Cole Possible selection of embryos In vitro fertilization of embryos from immature animals Further reduces generation interval Not yet feasible Frozen, genotyped embryo market Cost of genotyping < cost of ET Could replace AI if accuracy high and vitality not affected

29 University of Bern, November 23, 2009 (29) Cole Net merit by chromosome Freddie (1HO08784) - high Net Merit bull

30 University of Bern, November 23, 2009 (30) Cole Best chromosome 1 Co-Op Boliver Lisha- ET

31 University of Bern, November 23, 2009 (31) Cole Best chromosome 2 Kellercrest Earnit Hank

32 University of Bern, November 23, 2009 (32) Cole Best 30 chromosomes Genomics Extraordinare Overall net merit = $3,148

33 University of Bern, November 23, 2009 (33) Cole Finding QTL quickly and easily

34 University of Bern, November 23, 2009 (34) Cole Locating autosomal recessives

35 University of Bern, November 23, 2009 (35) Cole Relationships among genotyped Holsteins

36 University of Bern, November 23, 2009 (36) Cole Interbreed relationships

37 University of Bern, November 23, 2009 (37) Cole Closing thoughts Extraordinarily rapid implementation of genomic evaluations Young-bull acquisition and marketing now based on genomic evaluations Genomic evaluations may allow more cows from commercial herds to be used as bull dams SNP data are valuable tools for basic research

38 University of Bern, November 23, 2009 (38) Cole Acknowledgments Genotyping and DNA extraction: BFGL, U. Missouri, U. Alberta, GeneSeek, Genetics & IVF Institute, Genetic Visions, and Illumina Computing: AIPL staff (Leigh Walton, Jay Megonigal) Funding: NRI grants 2006-35205-16888 and 2006- 35205-16701 Agriculture Research Service Holstein, Jersey and Brown Swiss breed associations Cooperative Dairy DNA Repository (CDDR)

39 University of Bern, November 23, 2009 (39) Cole CDDR contributors National Association of Animal Breeders (Columbia, MO) ABS Global (DeForest, WI) Accelerated Genetics (Baraboo, WI) Alta (Balzac, AB, Canada) Genex (Shawano, WI) New Generation Genetics (Fort Atkinson, WI) Select Sires (Plain City, OH) Semex Alliance (Guelph, ON, Canada) Taurus-Service (Mehoopany, PA)

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