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Create Value, Build Trust, Deliver Results

Does Genomics Really Work? – April 2012 Genomics – they’re here to stay. This tool to accelerate genetic improvement has reinstated an intrigue for genetics and has become a very popular topic. But why is genomics such a big deal? Because it really works! Genomics have been official since January 2009. When it emerged in 2009, many were hesitant to adopt the technology. However, as the genomic success stories continue to pour in, there’s no time like the present to jump on the genetic progress train!

Selection decisions in 2009 Those who did adopt the technology in its infancy are truly reaping benefits today. If in 2009 you chose to breed with top genomic-proven G-Stars and FutureStars as opposed to the top daughter proven sires for TPI, you would have newly milking daughters of high profile marketing bulls like AltaIOTA, AltaR2, and AltaROSS. On the other hand, most chose to ‘wait and see’, and therefore used the top daughter proven bulls (Table 1). This is a great group of bulls in its own right, and they have made happy customers around the globe, but the top genomic sires at that time (Table 2) are clearly a superior group genetically. Name AltaBAXTER AltaDORNE AltaPRINCE AltaHATLEY AltaOMAR AltaTARMAC AltaARMSTEAD AltaBAYSIDE AltaMAXLIFE AltaALLEGRO Average = 1783

TPI 1924 1810 1858 1796 1781 1774 1752 1730 1681 1728

Table 1. Top 10 Daughter Proven bulls available (based on TPI) in Jan ’09 with today’s TPI values

Name AltaIOTA AltaR2 AltaROSS AltaTRINITY AltaLOCKLYN AltaTOYOTA AltaRUSH AltaOSOFINE AltaNATO AltaENDURO Average = 1954

TPI 2175 2080 2043 1966 1965 1922 1882 1863 1844 1804

Table 2. Top 10 Genomic Proven bulls available (based on TPI) in Jan ’09 with today’s TPI values

April 20th 2012 - Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson. For more information contact Alta Genetics at info@altagenetics.com or www.altaganetics.com


Create Value, Build Trust, Deliver Results Proof stability from genomic to 1st crop What about the risk of these genomic chart toppers dropping? Be not afraid – 1235 bulls were genomic tested in August 2010 and have producing daughters now in April 2012. The average drop in TPI is only 30 points (Graph 1). Yes, some dropped more, some less, some stayed the same and some increased. What matters here though is the group average, as this is how genomic bulls should be used – in groups. Further, the adjustments made by USDA in April 2012 should reduce future average changes even more. The following graphs further illustrate expected changes from a genomic to a first-crop proof. The proof change value from August 2010 to April 2012 is indicated on the horizontal axis and the number of bulls with a certain change is indicated on the vertical axis. For example, the first graph shows that of 1235 total bulls, about 40 had exactly zero change in their TPI. Meanwhile, the largest positive change was +325 TPI points and the largest drop was -350 TPI points. You can therefore infer that the chance of a genomic bull decreasing or increasing by 350 TPI points is 0.1% (1/1235). Likewise we can see about 95% of bulls are within +/- 200 TPI points from their initial genomic prediction, after they receive their daughter proofs.

Change in TPI from 2010-08 to 2012-04 60

(Genomic - 1st crop) n = 1235 / avg = -30 / stdev = 103

# bulls

50 40 30 20 10 0 -350

-300

-250

-200

-150

-100

-50

0 50 TPI Change

100

150

200

250

300

April 20th 2012 - Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson. For more information contact Alta Genetics at info@altagenetics.com or www.altaganetics.com

350


Create Value, Build Trust, Deliver Results Change in NM from 2010-08 to 2012-04 60

Genomic - 1st crop n = 1235 / avg = -28 / stdev = 83

# bulls

50 40 30 20 10 0 -350

-300

-250

-200

-150

-100

-50

0 50 NM Change

100

150

200

250

300

350

Change in PTAM from 2010-08 to 2012-04 100

Genomic to 1st crop n = 1235 / avg = -34 / stdev = 337

# bulls

90 80 70 60 50 40 30 20 10 0 -1250

-1000

-750

-500

-250

0 PTAM Change

250

500

750

1000

April 20th 2012 - Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson. For more information contact Alta Genetics at info@altagenetics.com or www.altaganetics.com

1250


Create Value, Build Trust, Deliver Results Change in PL from 2010-08 to 2012-04 Genomic to 1st crop n = 1235 / avg = -0.6 / stdev = 0.8

# bulls

80 70 60 50 40 30 20 10 0 -3,5

-3,0

-2,5

-2,0

-1,5

-1,0

-0,5

0,0 0,5 PL Change

1,0

1,5

2,0

2,5

3,0

3,5

Change in DPR from 2010-08 to 2012-04 120

Genomic to 1st crop n = 1235 / avg = +0.1 / stdev = 0.5

# bulls

110 100 90 80 70 60 50 40 30 20 10 0 -2,0

-1,5

-1,0

-0,5

0,0 DPR Change

0,5

1,0

1,5

April 20th 2012 - Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson. For more information contact Alta Genetics at info@altagenetics.com or www.altaganetics.com

2,0


Create Value, Build Trust, Deliver Results Chg in UDC from 2010-08 to 2012-04 90

Genomic - 1st crop n = 1235 / avg = -0.12 / stdev = 0.36

# bulls

80 70 60 50 40 30 20 10 0 -2,5

-2,0

-1,5

-1,0

-0,5

0,0 UDC Change

0,5

1,0

1,5

2,0

Change in CE from young sire release to 100 and more observations n = 1694 / avg = +0.8 / stdev = 1.2

# bulls 700 600 500 400 300 200 100 0 -6

-5

-4

-3

-2

-1 0 1 Change in CE

2

3

4

5

6

April 20th 2012 - Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson. For more information contact Alta Genetics at info@altagenetics.com or www.altaganetics.com

2,5


Create Value, Build Trust, Deliver Results These graphs show that proof changes are normally distributed, and for most traits, the average change is very near zero. An exception is PL, where the average change is -0.6, meaning genomic predictions are slightly overestimating this trait. That however does not mean the predictions are invalid or the trait should not be considered on a genomic sire – only that you can expect a small drop on any genomicproven sire. For PL, 95% of bulls change between -2.1 and +1.0, so the range is still relatively tight, and high ranking bulls based on genomics can be expected to continue to be high ranking bulls after they get milking daughters. The proof stability graphs also show a large number of bulls change in the positive direction for all traits, so even though we don’t know which bulls will go up or down with daughter proofs, we can’t forget the upside! Remember, the reliability of genomic proofs is around 75% for production and type, and a bit lower for health traits, thus contributing to the variation we see in the graphs: the higher the reliability, the narrower the distribution of change. Type Daughters Genomic Change Daughters Genomic Change Daughters Genomic Change Daughters Genomic Change Daughters Genomic Change

BullCode

Name

Sire

MGS

011HO10346 SYNERGY ALTAJENKINS

MAC

SHOTTLE

32

0 2078 530 1065

56

32

3.6

0

2.79

2.37

2.52

1.73

5

5

7.6

7.4

011HO10346 SYNERGY ALTAJENKINS

MAC

SHOTTLE

0

0 2071 515 1168

60

36

3.2

0

2.93

2.4

2.27

1.99

5

5

7.4

7.4

011HO10346 SYNERGY ALTAJENKINS

MAC

SHOTTLE

32

0

-103

-4

-4

0.4

0 -0.14 -0.03

0.25 -0.26

0

0

0.2

0

011HO10334 PINE-TREE ALTABUENO-ET BILLION

SHOTTLE

84

11 2070 464 1618

42

50

2.8

1.1

2.88

2.31

1.33

2.21

8

7

8.9

7.9

011HO10334 PINE-TREE ALTABUENO-ET BILLION

SHOTTLE

0

957

18

34

3.3

0.7

2.93

2.18

1.27

2.08

7

7

8.6

7.9

011HO10334 PINE-TREE ALTABUENO-ET BILLION

SHOTTLE

84

11

171 108

661

24

16 -0.5

0.4 -0.05

0.13

0.06

0.13

1

0

0.3

0

011HO10338 BOMAZ ALTAQUASAR-ET

ZENITH

MANAGER

94

22 1973 458

606

35

36

1.9

2.5

2.8

1.69

0.99

1.43

8

6

7.8

4.8

011HO10338 BOMAZ ALTAQUASAR-ET

ZENITH

MANAGER

0

0 1925 408

228

16

19

3.1

2.5

2.8

2

1.49

011HO10338 BOMAZ ALTAQUASAR-ET

ZENITH

MANAGER

94

22

50

378

19

17 -1.2

0

011HO10316 LATUCH ALTATRINITY-ET

JET STREAM BOLIVER

71

18 1966 534

396

65

28

3.9

1

2.99

011HO10316 LATUCH ALTATRINITY-ET

JET STREAM BOLIVER

0

0 2003 577

298

65

26

4.9

1.1

3

011HO10316 LATUCH ALTATRINITY-ET

JET STREAM BOLIVER

71

18

-37 -43

98

0

2

011HO10317 BOMAZ ALTAFAIRLY-ET

AIRRAID

ALTAFINLEY

94

22 1935 419

247

54

24

2.7

1.9

2.88

1.74

011HO10317 BOMAZ ALTAFAIRLY-ET

AIRRAID

ALTAFINLEY

0

0 1806 344

-165

40

15

3.3

1.9

2.83

011HO10317 BOMAZ ALTAFAIRLY-ET

AIRRAID

ALTAFINLEY

94

412

14

9 -0.6

0

0.05

Prod Dtrs

T Dtrs

TPI NM PTAM PTAF PTAP

7

15

0 1899 356

22

48

129

75

PL DPR

SCS PTAT

UDC

FLC CE DCE SSB

DSB

1.81

8

5

7.8

5.5

-0.5 -0.38

0

1

0

-0.7

1.37

1.33

1.04

7

6

7

5.8

1.42

1.69

0.76

6

6

6.9

5.4

-1 -0.1 -0.01 -0.05 -0.36

0.28

1

0

0.1

0.4

1.23

1.79

8

8

7.5

9.8

1.13

0.97

1.71

7

9

7.7 13.1

0.61

0.26

0.08

1

0 -0.31

-1 -0.2

-3.3

st

Table 3. Proofs changes from genomic to 1 crop for five individual bulls

For frame of reference, let’s look at how some individual bulls’ proofs changed from genomic to 1st crop. The sires listed in the table above are Alta’s five highest new releases in April 2012. The ‘Change’ rows show that from genomic to 1st crop proof the values generally change very little. As mentioned previously, we can assume 95% of genomic bulls will be within +/- 200 TPI points once they receive their first official daughter proof. All five bulls in the example are within this range, and as we would expect with bulls we have chosen to continue to market after they received daughter proofs, the average TPI change of the group increases (here, by 63 points). Some will be hesitant of genomics due to the fact a bull can change by as much as 300 TPI points. However, we must remember the chance of this is 0.1%, and bulls can change even after they are HIGHLY reliable. One such example is AltaBAXTER – even though his predictions were 99% reliable in

April 20th 2012 - Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson. For more information contact Alta Genetics at info@altagenetics.com or www.altaganetics.com


Create Value, Build Trust, Deliver Results August of 2010, we continue to see increases across his proof with added daughters. In fact, his TPI has increased by 107 TPI points in going from 5500 daughters to 36,000 daughters, so the range of change we see in bulls going from genomic to daughter proven is well within reason. BullCode

Name

Sire

MGS

Aug-10 011HO8196

EMERALD-ACR-SA T-BAXTER BLITZ

MTOTO

Apr-12 011HO8196

EMERALD-ACR-SA T-BAXTER BLITZ EMERALD-ACR-SA T-BAXTER BLITZ

Change

011HO8196

Prod Dtrs 5574

T Dtrs

TPI NM PTAM PTAF PTAP

PL DPR

SCS PTAT

UDC

FLC CE DCE SSB

DSB

1615 1817 358 1675

56

25

2.5 -1.7

2.93

1.83

1.20

1.64

8

6

6.9

5.2

MTOTO

36289 20162 1924 465 1742

68

28

4.1 -2.0

2.92

1.99

1.48

1.90

8

6

6.9

4.9

MTOTO

30715 18547

12

3

1.6 -0.3 -0.01

0.16

0.28

0.26

0

0

0

0.3

107 107

67

Table 4. Change in ALTABAXTER’s proof from August 2010 (99% reliability, >5000 daughters) to April 2012 (99% reliability, >30,000 daughters)

Change in CE proofs from genomic to 1st crop A common reason for hesitance to use genomic sires is due to calving ease uncertainty. The CE graph above shows a CE proof can change between genomic and 1st crop proofs, and the average bull does in fact increase when he gets his own information (0.8% SCE). For this reason, we recommend breeding heifers to genomic sires that are 6 or below SCE, until a bull has his own observations for CE. For those extremely risk-adverse to CE, Alta’s FutureStar program is the answer to deliver premier genetics from genomic sires. FutureStars offer fertility and calving ease assurance on genomic sires, obtained through observations in our Advantage® herds. Some may believe they must use ‘daughterproven’ sires on heifers, but we must remember bulls become ‘daughter-proven’ for CE as soon as their first calves are born, or about one year after semen is first released.

Proof Stability from 1st Crop to 2nd Crop A question often asked is “Are these bulls going to drop again when they get 2nd crop information?” The graph below shows the average TPI changes from 1st to 2nd crop. This change is much more stable than experienced in the past; showing the extra 35 daughter equivalents from genomics adds significant proof stability. There is basically no expected average change for TPI when a bull moves from 1st to 2nd crop.

April 20th 2012 - Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson. For more information contact Alta Genetics at info@altagenetics.com or www.altaganetics.com


Create Value, Build Trust, Deliver Results

nd

Table 5. Proof changes for bulls that received 2 crop proofs in April 2012

Today’s Selection Decisions Since 2009, many improvements have shaped genomic proofs estimates and numerous animals have been added to the reference population. Both factors contribute to genomic accuracy, while decreasing expected changes from genomic to 1st crop proofs. Today, like in 2009, selection options are much the same. You could use the best daughter-proven sires or Alta’s best G-Stars (Tables 6 and 7). While AltaIOTA and AltaROSS get a lot of publicity and have made some great daughters, the predictions of the genomic group (Table 7) far exceed the daughter-proven group – showing the extreme genetic progress made because of genomics. Name AltaIOTA AltaR2 AltJENKINS AltaBUENO AltaROSS AltaESQUIRE AltaOTTO AltaQUASAR AltaTRINITY AltaLOCKLYN Average = 2035

TPI 2175 2080 2078 2070 2043 2015 1983 1973 1966 1965

Table 6. Top 10 Daughter Proven bulls available (based on TPI), April 2012

Name AltaCASCADE AltaBANFF AltaLEO AltaKOOL AltaAIRNET AltaMELHOR AltaSUSTAIN AltaCAMROSE AltaDOM AltaBOWIE Average = 2322

TPI 2388 2369 2357 2341 2326 2298 2297 2287 2279 2278

Table 7. Top 10 Genomic Proven bulls available (based on TPI), April 2012

April 20th 2012 - Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson. For more information contact Alta Genetics at info@altagenetics.com or www.altaganetics.com


Create Value, Build Trust, Deliver Results Recall the graph which illustrated the distribution of change in TPI from genomic to 1st crop. Based on this graph, and the expectation that 95% of bulls will be +/- 200 TPI points, each individual genomic sire in Table 7 has >95% chance of being higher TPI than AltaBUENO after receiving 1st crop proofs! To maximize genetic gain and reach your breeding goal at a faster pace, genomic proven sires are certainly the way to achieve your goals. Much like a stock portfolio, you will need to accept a bit of risk to maximize your expected return. Of course risk can be mitigated in stocks by increasing the number of different companies owned; and with genomics, risk can be reduced by increasing the number of different sires used. So for those eager to maximize genetic gain and accept some risk doing so, set your genetic plan carefully. Then, select a group of at least 5-6 sires to capitalize on the opportunities your genetic plan will deliver!

April 20th 2012 - Article by: Gerbrand van Burgsteden, Nate Zwald and Lynsay Henderson. For more information contact Alta Genetics at info@altagenetics.com or www.altaganetics.com


Does Genomics Really Work? - April 2012