2007 Paul VanRaden Animal Improvement Programs Laboratory, USDA Agricultural Research Service, Beltsville, MD, USA 2007 Genetic evaluation.

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Presentation transcript:

2007 Paul VanRaden Animal Improvement Programs Laboratory, USDA Agricultural Research Service, Beltsville, MD, USA 2007 Genetic evaluation using combined data from all breeds and crossbred cows

Petersen Symposium 2007 (2) P.M. VanRaden 2007 USDA Yearbook of Agriculture 1947 Jersey  Holstein Cow # Pounds of Milk % Butterfat Pounds of Butterfat X-1 9, X-313, X-1713, From USDA research herd at Beltsville, MD

Petersen Symposium 2007 (3) P.M. VanRaden 2007 Crossbreds averaged 12,904 pounds of milk and 588 pounds of butterfat, outperforming dams by more than sire proof predictions (Fohrman,1947). Advanced register Holsteins averaged 13,833 pounds of milk and 493 pounds of fat in USDA Yearbook of Agriculture 1947 Red Dane  Jersey

Petersen Symposium 2007 (4) P.M. VanRaden 2007 Goals  Evaluate crossbred animals without biasing purebred evaluations  Accurately estimate breed differences  Compare crossbreeding strategies  Compute national evaluations and examine changes  Display results without confusion

Petersen Symposium 2007 (5) P.M. VanRaden 2007 All-Breed Analyses  Crossbred animals Will have PTAs, only 3% did before if in breed association grading-up programs Reliable PTAs from both parents  Purebred animals Information from crossbred relatives More herdmates (other breeds, crossbreds)  Routinely used in other populations New Zealand (1994), Netherlands (1997) USA goats (1989), calving ease (2005)

Petersen Symposium 2007 (6) P.M. VanRaden 2007 Methods  All-breed animal model Purebreds and crossbreds together Relationship matrix among all Unknown parents grouped by breed Variance adjustments by breed Age adjust to 36 months, not mature  Within-breed-of-sire model examined but not used

Petersen Symposium 2007 (7) P.M. VanRaden 2007 Data  Numbers of cows of all breeds 22.6 million for milk and fat 16.1 million for protein 22.5 million for productive life 19.9 million for daughter pregnancy rate 10.5 million for somatic cell score  Type traits are still collected and evaluated in separate breed files

Petersen Symposium 2007 (8) P.M. VanRaden 2007 Purebred and Crossbred Data USA milk yield records Breed% of totalCows born 2003 Holstein ,354 Jersey6.445,151 Brown Swiss.85,960 Guernsey.42,563 Ayrshire.31,926 F1 Crossbred1.28,647

Petersen Symposium 2007 (9) P.M. VanRaden 2007 Crossbred Cows with 1 st parity records Fresh year F1 (%) F1 cows Back- cross Het > 0 XX cows

Petersen Symposium 2007 (10) P.M. VanRaden 2007 Number of Cows with Records Number of Cows with Records (with > 50% heterosis; March 2007) DamSire Breed BreedAYBSGUJEMSXXHO AY — BS 20— GU 4696— JE — MS —5965 XX —8859 HO —

Petersen Symposium 2007 (11) P.M. VanRaden 2007 Number of Cows with Records Number of Cows with Records (with > 50% heterosis; March 2007) Sire Breed Dam Breed# Sire Breed Dam Breed# BS SM25 HO DL47 DL HO109 HO LD195 MO HO73 HO MI60 NO HO38 HO NR21 NR HO23 HO RE22 SR HO118 HO SM16

Petersen Symposium 2007 (12) P.M. VanRaden 2007 Crossbred Daughters Added for sires in top 10 NM$ within breed Sire breed Daughters Sire NameFeb ‘07Added LegacyAY15733 AgendaBS3521 ExciteBS14457 Q ImpulsJE24120 StetsonMS3631

Petersen Symposium 2007 (13) P.M. VanRaden 2007 Heterosis for Yield Traits Heterosis for Yield Traits Percent of Parent Breed Average MilkFatProtein Breed HO Sire HO Dam HO Sire HO Dam HO Sire HO Dam Ayrshire Brown Swiss Guernsey Jersey M. Shorthrn Heterosis

Petersen Symposium 2007 (14) P.M. VanRaden 2007 Breed Effects and Heterosis  Three estimates of breed differences: From phenotypic breed differences From herds containing crossbred cows From all-breed model using all data All three estimates were similar  Estimates of general heterosis from 2001 and 2003 studies were used in the current research and not re-estimated

Petersen Symposium 2007 (15) P.M. VanRaden 2007 Unknown Parent Groups  Look up PTAs of known parents  Estimate averages for unknowns  Group unknown parents by Birth year Breed Path (dams of cows, sires of cows, parents of bulls) Origin (domestic vs other countries)

Petersen Symposium 2007 (16) P.M. VanRaden 2007 All- vs Within-Breed Evaluations Correlations of PTA Milk Breed 99% REL bulls Recent bulls Recent cows Holstein > Jersey Brown Swiss Guernsey Ayrshire Milking Shorthorn

Petersen Symposium 2007 (17) P.M. VanRaden 2007 Display of PTAs  Genetic base Convert all-breed base to within-breed bases (or vice versa) PTA brd = (PTA all – mean brd ) SD brd /SD HO PTA all = PTA brd (SD HO /SD brd ) + mean brd  Heterosis and inbreeding Both effects removed in the animal model Heterosis added to crossbred animal PTA Expected Future Inbreeding (EFI) and merit differ with mate breed

Petersen Symposium 2007 (18) P.M. VanRaden 2007 Milk (kg) Genetic trend on all-breed base

Petersen Symposium 2007 (19) P.M. VanRaden 2007 Fat (kg) Genetic trend on all-breed base

Petersen Symposium 2007 (20) P.M. VanRaden 2007 Protein (kg) Genetic trend on all-breed base

Petersen Symposium 2007 (21) P.M. VanRaden 2007 Somatic Cell Score Genetic trend on all-breed base

Petersen Symposium 2007 (22) P.M. VanRaden 2007 Productive Life Genetic trend on all-breed base

Petersen Symposium 2007 (23) P.M. VanRaden 2007 Daughter Pregnancy Rate Genetic trend on all-breed base

Petersen Symposium 2007 (24) P.M. VanRaden 2007 EBV differences from Holstein estimated from an all-breed model Difference from Holstein (pounds) MilkFatProtein AY BS GU JE MS

Petersen Symposium 2007 (25) P.M. VanRaden 2007 Phenotypic breed differences from Holstein from an all-breed model Difference from Holstein (pounds) MilkFatProtein AY BS GU JE MS HO

Petersen Symposium 2007 (26) P.M. VanRaden 2007 EBV differences from Holstein estimated from an all-breed model Difference from Holstein SCSPL (mo)DPR (%) AY BS GU JE MS

Petersen Symposium 2007 (27) P.M. VanRaden 2007 Phenotypic breed differences from Holstein from an all-breed model Difference from Holstein SCSPL (mo) DPR AY BS GU JE MS HO

Petersen Symposium 2007 (28) P.M. VanRaden 2007 Net Merit Relative Emphasis In cooperation with Dr. Tony Seykora et al. Trait Trait Protein3323Udder76 Fat2223F&L43 Milk00Size34 PL1117DPR79 SCS99CA$46 DPR = daughter pregnancy rate (fertility), CA$ is index of calving ease and stillbirth

Petersen Symposium 2007 (29) P.M. VanRaden 2007 NM$, FM$, CM$ Economic Values NM$FM$CM$ Milk −0.07 Fat2.70 Protein Other values are same in each index: PL 29, SCS -150, Size -14, Udder 28, F&L 13, DPR 21, CA$ 1

Petersen Symposium 2007 (30) P.M. VanRaden 2007 Other Trait Estimates  Calving ease and stillbirth estimated from breed means 7.3 million HO, JE, BS, 2000 GU, 2000 AY, 300 MS  Body size composite estimated from mature weight  Udder composite, Feet / Leg composite extrapolated from regressions on other traits within Holsteins Size, PL, milk, DPR, SCS

Petersen Symposium 2007 (31) P.M. VanRaden 2007 Correlations used in Predictions Corr withSizePLSCSDPRMilk Udder.26.30−.33.03−.20 F&L.22.19−.02−.04−.02 Canada now scores linear conformation traits of all breeds on the same scale

Petersen Symposium 2007 (32) P.M. VanRaden 2007 Assumed Effects – Other Traits Transmitting ability differences from Holstein SizeUdderF&L Calving Difficulty Still- birth Jersey −10.4−1.4−2.1−7.1−1.5 B. Swiss −3.2−0.7 Guernsey −7.3−0.5−1.3− Ayrshire −5.8−1.6−0.9−3.5−1.2 M. Short. −4.20.1−0.6−0.1−2.4 Heterosis

Petersen Symposium 2007 (33) P.M. VanRaden 2007 Merit of F 1 Holstein Crossbreds Second Breed NM$CM$FM$ Ayrshire −304 −261−364 Brown Swiss −78 Guernsey −408−405−503 Jersey 31153−158 M. Shorthorn −498−461−547 Compared to 2005 genetic base for Holstein

Petersen Symposium 2007 (34) P.M. VanRaden 2007 Later Generation Crosses Holstein backcross or multi-breed NM$CM$ FM$ HO x (BS x HO) −39 HO x (JE x HO) −79 BS x (JE x HO) −32+109−251 JE x (BS x HO) −44+116−292 HO x (BS x JE) −118 Compared to 2005 genetic base for Holstein

Petersen Symposium 2007 (35) P.M. VanRaden 2007 Butterfat yield of three breed crosses was greater than from their F 1 crossbred dams. Three breed crosses averaged 14,927 pounds of milk and 641 pounds of butterfat as 2-year-olds in USDA Yearbook of Agriculture 1947 Three-Breed Crosses

Petersen Symposium 2007 (36) P.M. VanRaden 2007 Scandinavian and French Breeds  AIPL has pedigree records for other breeds (NR, SR, MO); but few production records yet  For further information: Interbull conversions to Ayrshire base U. Minnesota scientists (Heins et al.)

Petersen Symposium 2007 (37) P.M. VanRaden 2007 Conclusions

Petersen Symposium 2007 (38) P.M. VanRaden 2007 Conclusions (1)  All-breed model accounts for: Breed effects and general heterosis Unequal variances within breed  May 2007 implementation expected PTA converted back to within-breed bases, crossbreds to breed of sire PTA changes larger in breeds with fewer animals

Petersen Symposium 2007 (39) P.M. VanRaden 2007 Conclusions (2)  Breed effects were estimated Yield, PL, SCS, DPR by all-breed model Calving ease and stillbirth breed means Udder, F&L composites from other traits  Lifetime Net Merit formula for August 2006 applied  Holsteins still superior for FM$

Petersen Symposium 2007 (40) P.M. VanRaden 2007 Conclusions (3)  BS x HO and JE x HO crosses had higher NM$ and CM$ than HO  BS x JE had higher CM$ than HO  Three-breed crosses (HO, BS, JE) are higher than HO backcrosses for CM$, similar for NM$  Use best bulls within each breed

Petersen Symposium 2007 (41) P.M. VanRaden 2007 Acknowledgments  Several others at AIPL contributed greatly to this project, including Mel Tooker, George Wiggans, John Cole, Jay Megonigal, and Ashley Sanders