April 2020: Genetic Base Change

April 2020: Genetic Base Change

By H. Duane Norman, Paul VanRaden and George Wiggans
The base for U.S. genetic evaluations will be updated, effective with the April 7, 2020, triannual evaluations.
The genetic bases to which (most) dairy traits are expressed in the United States have been updated every five
years since 1980. With the base change, users of genetic evaluations may become aware that the standards they
set for choosing service bulls or valuing females in the past may no longer meet the genetic quality to remain
competitive, due to genetic progress.

Since 1980, some have suggested that the base should be updated more often. A few have lobbied for a fixed
base, or one that’s never updated. The reasoning for the latter is that if the best bulls are chosen, the magnitude
of the numbers are not particularly important and all evaluations are comparable regardless of when published.
For the last base change in 2015, the average predicted transmitting abilities (PTA) of cows born in 2010 were set
to zero. Progress continued to be made for most traits, as shown by Table 1 with the PTAs of cows born in 2015.
These milking cows born in 2015 define the new base. With the April evaluations, their PTAs will be set back to
zero. Stated differently, the averages in Table 1 will be subtracted from the current PTAs of all animals. These are
the changes in PTAs expected in April.

Because gains were made across five years for most traits, most of these PTAs will be lowered by the amount
shown. However, if the trends were unfavorable, the PTAs will generally increase. The exceptions can be for
somatic cell score (SCS) and the four calving traits which may do the opposite because lower values are
preferable for these traits. The average PTAs in the table are the differences in transmitting ability for animals
over the five-year period. A note of caution, these will not be the exact changes coming because all will be
recalculated before the April 2020 run using more complete and current data. Any updates in the traits’
variation will also cause these approximations to vary from the estimates presented.

Key progress points demonstrated in Table 1 include:

  • Favorable gains are shown for 81 of the 102 traits (excluding conformation), while 18 were unfavorable.
  • The most important traits (all lifetime merit indexes) showed genetic improvement for all the breeds; the
    largest gains were for Holsteins, Jerseys and Ayrshires. Thus, the merit indexes for all breeds will be
    lowered in April.
  • Genetic gains were made in all three yield traits (milk, fat, protein) for all breeds. Gains were particularly
    impressive for Holsteins and Jerseys; so the base change will reduce PTA milk for these breeds by about
    492 and 524 pounds, respectively.
  • PTAs for fat and protein will be adjusted down by about 18 to 25 pounds.
  • Changes in PTAs for somatic cell score (SCS) will be small (-.01 to +.02) for all breeds except Holsteins
    which will increase by 0.08 due to their progress in lowering SCSs.
  • PTAs for productive life will be reduced by about 0.6 to 1.9 months for Guernseys, Holsteins, Jerseys and
    Milking Shorthorn due to increasing their genetic capacity for longer life.
  • Unfortunately, 13 of the 18 fertility estimates showed unfavorable changes over the five years; only
    Holsteins improved for all three traits.
  • PTAs for cow livability, launched in August 2016, improved for three of the six breeds (0.74 for Holsteins).
  • Resistance against diseases in Holsteins improved for five of the six traits.

PTAs increased for 80 of the 90 breed conformation traits, which indicates that selection has been for the
higher scores. In most cases this probably was desirable, but in others, perhaps not. The 10 traits with
PTAs that did not increase were ones that had an intermediate optimum.

Table 1. Difference in predicted transmitting abilities (PTAs) of cows born in 2015 compared to those born in 2010. PTAs will decrease by these amounts to implement the 2020 genetic base change1.

Revisions made 2.21.2020 affect the genetic base numbers for Holstein conformation traits, reflecting revised
Holstein Association USA requirements to determine which cows born in 2015 met criteria for inclusion.

Caution: These will not be the precise changes applied in April, because all will be recalculated before the April 2020 run using more complete and current data.

Performance Differences Attributed to Genetic and Environmental Changes
The PTAs in Table 1 represent only half the genetic change achieved, as each animal only transmits half of their
genes to their offspring. Table 2 shows the total changes in performance between cows born in 2015 and 2010
and an indication of how much of the changes were attributed to genetics and environment.

Key points:

  • For the milk traits, all breeds but Guernsey revealed a positive contribution from both components.
  • Genetic gain for somatic cell score (SCS) was made for three breeds, and Holsteins improved by 0.17.
    Two breeds were unchanged, and Milking Shorthorn increased by 0.05.
  • Environmental trends for SCS and productive life (PL) generally were unfavorable.
  • Environmental trends for daughter pregnancy rate (DPR) and cow conception rate (CCR) were favorable.
  • For heifer conception rate (HCR), environmental trends were negative for Holsteins, Jerseys and Milking
    Shorthorn.
  • All six breeds showed reduced age at first calving (AFC), particularly via the environment (10 to 26 days).
    Genetics reduced age at first calving up to three days.
  • Phenotypic reductions in gestation length for Holsteins and Jerseys seemed surprising, especially since
    the genetic component for Holsteins decreased while Jerseys increased.
  • Phenotypic changes for resistance to the six health disorders introduced in April 2018 were all positive.

Table 2. Differences in actual (phenotypic) performance between cows born in 2015 and those born in
2010 attributed to genetic (BV=breeding value1) and environmental changes.

Impact of Genomics
The genomic revolution initiated in 2008 brought an increase in the rate of genetic improvement, primarily due to
a reduction in the generation interval. A small portion of genomic benefits would have been revealed in the
previous base change for cows born in 2010, but the current update will reflect all benefits from genomics
achieved from 2010 to 2015.

Key points:

  • For illustration, 150% would indicate 50% more gain was made than in the previous five-year period.
  • Use of genomics is responsible for the accelerated gains for milk traits shown in Table 3 for Brown Swiss,
    Holsteins and Jerseys, but genomics were not available for Guernseys until 2016. Ayrshires and Milking
    Shorthorn – having limited use of genomics – show smaller gains in milk traits than during the previous
    five-year period.
  • The benefits of genomics for productive life (PL) were impressive for Holsteins and Jerseys.
  • The Guernsey, Holstein and Jersey breeds showed larger gains (43 to 100% more) in the lifetime merit
    indexes for this base update, than they did during the previous period.

Table 3. Relative size in percentage of the 2020 genetic base changes1 compared to the base changes five
years earlier (2015).

Percentage of Change Attributed to Genetics
To answer the question of what is contributing to the phenotypic improvement being made in dairy production
traits, Table 4 was derived from the information in Table 2 for traits that have had evaluations initiated since 2008.

The genetic contribution averaged 45% but was greater (averaged 69%) for the three traits with the greatest
emphasis in net merit index (NM$) and for Holsteins (71%), the breed with the largest population.

Table 4. Percentage of the change in phenotype attributed to genetics for cows born in 2015 compared to
those born in 2010 for traits with published evaluations initiated before 20101

When the base is changed every five years, most PTAs are lowered – and the standard deviations (SD) are also
updated. In most cases, the variation increases. Yield and SCS records are adjusted for variance within herd and
year to keep the same SD as the base year using SD ratios shown in Table 5.

Table 5. Ratio of trait SD for base cows born in 2015 vs. those in 2010. The PTAs will be expanded (or contracted) by these ratios.

Table 6. Ratio of trait SD for base cows born in 2015 compared to Holsteins. The PTAs will be expanded
(or contracted) by these ratios.

The Bottom Line
Advocates for improving sustainability and eliminating world hunger should be amazed to see the changes in
productivity in U.S. dairy.

Greenhouse gases are being reduced per unit of product because of greater production per animal. We are
seeing significant changes in the animals’ appearance and health as well.

Since we’re approaching another base change, this may be a good time to remind dairy producers to adopt
genetic selection strategies that could virtually eliminate any complacency of decisions between base changes.
For example, if selection is based on standards like percentiles (recalculated every run) or by simply selecting the
top-ranked bulls on an economic index of their choice, forward progress would occur, devoid of any delays.
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