Base Change 2014
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AIP RESEARCH REPORT
BASE3 (10-14)

Genetic base changes for December 2014

P.M. VanRaden,1 M.E. Tooker,1 J.R. Wright,1 J.B. Cole,1 D.J. Null,1 and T.J. Lawlor2
1Animal Improvement Program, Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705-2350
301-504-8334 (voice) ~ 301-504-8092 (fax) ~  paul.vanraden@ars.usda.gov ~ http://aipl.arsusda.gov
2Holstein Association USA Inc., Brattleboro, VT 05301
802-254-4551, ext. 4228 (voice) ~ 802-254-8251 ~ tlawlor@holstein.com
 
Genetic (PTA) progress  |  Standard deviations  |  Phenotypic progress  |  References
 

Genetic bases were updated previously in the United States in 1965, 1974, 1984, 1989, 1995, 2000, 2005, and 2010, and the next base change is scheduled for December 2014. Base changes for yield, health, fertility, and type traits in December 2014 are reported below. Stepwise genetic bases allow predicted transmitting abilities (PTAs) from new evaluations to be easily compared with previous evaluations except at base changes, when accumulated genetic gain is subtracted so that all animals are compared with a more recent cow population. A particular animal's PTA is supposed to decrease when the base is changed and remain fairly constant between base changes.

Genetic (PTA) progress (base change) 

For most traits, genetic trend comparing PTA of cows born in 2010 with those of cows born in 2005 is equal to or slightly less than the trend for the preceding 5 years reported at the previous base change in January 2010 (VanRaden et al., 2009). However, cows born in 2010 were before genomic selection had much impact, and trends are faster for calves born during the last 4 years (Norman et al., 2014).

For the December 2014 base change, the differences in PTAs are provided for Holstein, Jersey, Brown Swiss, Guernsey, Ayrshire, and Milking Shorthorn cows, and those changes are also applied to bulls:

Trait Unit PTA progress (2010 − 2005 birth year)
Holstein Jersey Brown
Swiss
Guernsey Ayrshire Milking
Shorthorn
Net merit Lifetime $ 184 124 58 55 75 54
Protein Pounds 12 12 6 3 7 6
Fat Pounds 17 19 6 6 9 7
Milk Pounds 382 327 157 66 222 214
Productive life Months 1.0 0.8 0.3 0.5 0.5 0.5
Somatic cell score Log (base 2) −0.07 0.04 −0.02 0.01 −0.01 0.02
Daughter pregnancy rate % 0.2 0.0 0.0 −0.2 −0.1 −0.3
Cow conception rate % 0.1 0.1 −0.1 −0.6 −0.2 −0.5
Heifer conception rate % 0.3 0.3 0.1 −0.5 0.0 −0.2
Service sire calving difficulty % −0.4 0.1
Daughter calving difficulty % −1.6 −0.3
Service sire stillbirth rate % −0.3
Daughter stillbirth rate % −0.5
Udder composite   0.92 0.33 0.30 0.41 0.29 0.34
Feet and legs composite   0.78 0.15 0.13 0.42 0.23 0.09
Body size composite   0.61 0.24 0.28 0.09 0.18 0.21
Stature   0.81 0.40 0.43 0.30 0.46 0.45
Strength   0.36 0.13 0.08 0.03 0.06 0.13
Dairy form   0.71 0.36 0.31 0.21 0.21 0.31
Foot angle   0.82 0.17 0.13 0.20 0.23 0.06
Rear legs (side view)   −0.04 0.05 0.03 −0.11 −0.00 −0.02
Rear legs (rear view)   0.79 0.08 0.23 0.06
Body depth   0.47 0.12 −0.07 0.12 0.17
Rump angle   0.11 0.04 −0.07 −0.01 −0.17 −0.08
Thurl width   0.61 0.19 0.13 0.06 0.12 0.10
Fore udder attachment   1.09 0.50 0.40 0.82 0.30 0.40
Rear udder height   1.45 0.48 0.37 0.68 0.26 0.37
Rear udder width   1.17 0.27 0.25 0.28 0.14 0.27
Udder depth   0.83 0.48 0.29 0.73 0.35 0.34
Udder cleft   0.81 0.13 0.22 0.07 0.13 0.11
Front teat placement   0.60 0.39 0.31 0.40 0.20 0.25
Rear teat placement   0.60
Teat length   −0.02 0.10 −0.17 −0.09 −0.08 −0.13
Final score   0.99 0.53 0.28 0.56 0.24 0.25

Progress for Holstein PTA service sire calving difficulty and stillbirth is the change between bulls born in 2010 and those born in 2005; progress for Holstein PTA daughter calving difficulty and stillbirth rate is the change between bulls born in 2005 and those born in 2000. For Brown Swiss, PTA progress for service sire calving difficulty is calculated as the change between bulls born from 2006 through 2010 and those born from 2001 through 2005; PTA progress for Brown Swiss daughter calving ease is the change between bulls born from 2001 through 2005 and those born from 1996 through 2000. Brown Swiss bulls had to be grouped because of their limited numbers.

Standard deviations (SDs) 

As a result of updating the base year, the SD of PTA for each breed is adjusted along with the mean. Yield and SCS records are adjusted for variance within herd and year to have the same SD as the base year using an SD ratio based on calving year:

Herd variance adjustment SD ratio (2012/2007 calving year)
Holstein Jersey Brown Swiss Guernsey Ayrshire Milking
Shorthorn
Yield (milk, fat, and protein) 0.96 1.02 .99 0.96 1.14 0.96
SCS 0.91 0.93 0.96 0.97 0.99 1.06

The SD for daughter pregnancy rate was also updated, but that update was because of a change in trait definition explained separately.

A PTA from before the base change (PTAold) can be converted to a PTA after the base change (PTAnew) by using the formula

PTAnew = SD ratio × (PTAold − base change),

where the base change is the appropriate breed PTA progress in the table above. For example, a Holstein bull with a PTA protein of +50 pounds before the base change is expected to have a PTA protein of 0.96(50 − 12) = +36 pounds after the base change.

Phenotypic progress 

Phenotypic trends comparing cows born in 2010 with cows born in 2005 are equal to or slightly less than the trends for the preceding 5 years reported at the previous base change in January 2010 (VanRaden et al., 2009). For the December 2014 base change, the phenotypic differences for standardized first-lactation traits are provided for Holstein, Jersey, Brown Swiss, Guernsey, Ayrshire, and Milking Shorthorn cows.

Trait Unit Progress Progress (2010 − 2005 birth year)
Holstein Jersey Brown
Swiss
Guernsey Ayrshire Milking
Shorthorn
Protein Pounds Phenotypic (total) 29 44 11 6 5 27
Genetic (BV)1 25 25 12 6 14 11
Environmental 4 19 −9 −1 −9 15
Fat Pounds Phenotypic (total) 39 78 21 13 11 30
Genetic (BV) 34 39 13 13 19 13
Environmental 5 39 8 0 −8 17
Milk Pounds Phenotypic (total) 579 1,016 292 116 158 860
Genetic (BV) 764 655 315 133 444 429
Environmental −185 362 −23 −17 −286 432
Productive life Months Phenotypic (total) 1.2 −2.0 −2.0 1.4 −2.5 −2.7
Genetic (BV) 1.9 1.6 0.7 1.1 1.0 0.9
Environmental −0.7 −3.6 −2.7 0.4 −3.5 −3.6
Somatic cell score Log (base 2) Phenotypic (total) −0.37 −0.28 −0.17 −0.30 −0.24 −0.27
Genetic (BV) −0.13 0.07 −0.04 0.02 −0.02 0.04
Environmental −0.24 −0.35 −0.13 −0.33 −0.22 −0.31
Daughter pregnancy rate % Phenotypic (total) 2.1 2.3 2.4 1.7 0.3 1.2
Genetic (BV) 0.4 −0.1 0.0 −0.4 −0.2 −0.6
Environmental 1.7 2.4 2.4 2.1 0.5 1.8
Service sire calving difficulty % Phenotypic (total) −0.3 −0.4
Genetic (BV) −0.8 0.1
Environmental 0.5 −0.5
Daughter calving difficulty % Phenotypic (total) −0.3 −0.4
Genetic (BV) −3.2 −0.5
Environmental 2.9 0.1
Service sire stillbirth rate % Phenotypic (total) −1.2
Genetic (BV) −0.5
Environmental −0.7
Daughter stillbirth rate % Phenotypic (total) 0.7
Genetic (BV) −0.9
Environmental 1.6
1Genetic progress based on breeding value (BV) is twice PTA progress.

Phenotypic progress due to environmental factors such as management is the difference between genotypic and total phenotypic progress. For Holsteins, genetic improvement is responsible for 86% of the increase in protein yield, 87% of the increase in fat yield, and 132% of the increase in milk yield during the past 5 years; the negative effect of environmental factors on milk yield caused the phenotypic change to be less than the genetic change. Phenotypic progress in yield traits for other breeds also was predominantly the result of genetic improvement. In general, positive progress has been made for most traits through management practices and genetics since the 2005 base change.

References 

Norman, H.D., J.R. Wright, J.L. Hutchison, and J.M. Mattison. 2014. Selection changes in the United States due to genomics. Interbull Bull. 48:37–39.

VanRaden, P.M., J.B. Cole, M.E. Tooker, and T.A. Cooper. 2009. Genetic base changes for January 2010. AIPL. Res. Rep. BASE2 (8-09).