Measurement of Genetic Change in Twelve California Dairy Herds1

MEASUREMENT

OF GENETIC CHANGE IN TWELVE DAIRY HERDS 1

CALIFORNIA

O. W. ARAYE,: R. C. LABEN, ANn S. W. MEAD Department of Animal Husbandry, University of California, Davis SUMMARY

Genetic change in fat-corrected milk (FCM) yield was studied in a population of 11,993 lactation records of 3,900 Jersey cows in 12 herds over a 30-year period. Differences between herds as well as total genetic progress was determined. The between lactation variance of records age-corrected with factors derived from intra-herd analyses of the lactation means was reduced an average of 91%. Repeatability of the age-corrected FCM records estimated by intraclass correlation within herds ranged from .20 ± .05 to .52 -- .05. Yearly environmental effects were estimated using a maximum likelihood method developed by Henderson (6). Annual genetic change was expressed as the linear regression of FCM yield on year of records adjusted for yearly environmental effects. The average genetic change for all herds was 74 lb FCM annually. The genetic change within individual herds ranged from --51 ± 52 to 145 ± 21 lb FCM per year. A pooled intra-sh'e regression of the progeny's MPPA on generation number within the largest herd yielded an estimate of geJ~etic change agreeing closely with the maximum likelihood estimate.

One of the most difficult problems facing animal breeders is that of evaluating the results of a breeding program. The genetic change occurring in a dairy herd has been estimated by several investigators (3-5, 7, 10, 16) using a maximum likelihood method developed by Henderson (6). With this method environmental trends are estimated by measuring variation in dairy records which characteristically consist of single records and repeated records of the .same cows as well as records of contemporary paternal half-sib groups made over several years. The genetic trend is measured after correction is made for the environmental trend. I n all except one of the studies (7) of genetic change in which the maximum likelihood method has been used, analyses were of single herds. The estimated genetic change which has occurred in these independent herds located in different area.s of this country has been extremely variable, ranging from a negative change of approximately 0.7% to an increase of ].75% of the average yield annually. The objective of the present study is to Reeclved for publicatio)t September 7, 1963. ~Data taken from a thesis presented by C. W. Arave in partial fulfi]hnent of the requirements of the Ph.D. degree, University of California, September, ] 963. 2 Present address: Department of Agriculture, Chico State College, Chieo, California.

measure the genetic change which has occurred in herds of the University of California Dai, T Cattle Breeding Project and to compare the genetic progress made in these herds managed as a single unit with respect to the breeding program, but as individual herds in all other aspects. Recently, Smith (12) has suggested genetic change may be measured as an intra-sire regression of progeny performance on time. Brinks et al. (2) studied genetic progress by measuring the difference between successive generations of animals whose generation number was known with relation to foundation animals in a closed herd of beef cattle. A similar method was used in the present study to obtain sn estimate of genetic change for comparison with the maximum likelihood estimate. E X P E R I M E N T A L PROCEDURE

Source and descriptio~ of the data. Data used in this study were obtained from the University of California Dairy Cattle Breeding Project, the historical origin of which is described elsewhere (1). They consisted of 11,993 lactation records of 3,900 Jersey cows completed in 12 cooperator herds. These records were 2 × , 305-day D H I A records. Incomplete lactation records were omitted from the analyses. The records were corrected for inbreeding by adding 50 lb FCM per unit of inbreeding of the cow. The records used were started be-

278

]VIEASUP~E~c~ENT OF CxENETIG GHANGE

279

TABLE 1 Number of records used to estinmte environmental effects within 12 co-operator herds of dairy cattle Herd Year 1930 1931 1932 1933 1934 1935 1936 1937 1938 1939 1940 1941 1942 1943 1944 1945 1946 1947 1948 1949 1950 1951 1952 1953 1954 1955 1956 1957 1958 1959 1960 TotM

Att

6 13 28 24 29 37 32 39 55 53 58 48 44 39 45 42 39 39 38 43 43 35 29 22 22 28 930

AL

15 15 15 17 20 32 38 31 38 55 42 48 52 41 32 36 49 576

CO

4 7 14 13 16 28 25 35 31 25 198

FL 11 17 20 28 24 26 30 20 31 39 25 39 40 37 28 21 17 18 22 18

511

LA

MA

6 4 7 6 13 10 6 11 11 24 13 21 21 33 26 28 23 35 25 47 29 41 25 32 29 49 25 63 23 60 18 70 27 84 25 81 20 115 31 96 29 87 27 80 33 79 35 81 41 91 45 93 35 93 42 42 41 75 18 65 753 1,692

t w e e n J a n u a r y 1, 1930, a n d D e c e m b e r 31, 1960. The 12 h e r d s served as a large f e m a l e p o p u lation f o r the p u r p o s e of p r o g e n y t e s t i n g sires f r o m the i n b r e d J e r s e y lines of the U n i v e r s i t y herd. Sires selected f o r testing w e r e placed in c o o p e r a t i n g herds. E v e r y ] 2 to 14 m o n t h s these sires were r o t a t e d to o t h e r p r o j e c t herds. I n the mid-1950's, due to the increasing size o f the p r o j e c t herds, A.I. sires were used in a d d i t i o n to p r o j e c t sires. The f e e d i n g a n d m a n a g e m e n t o f these h e r d s has been typical o f p u r e b r e d a n d commercial J e r s e y h e r d s o f the central C a l i f o r n i a area. M e t h o d s o f statistical analyses. I n t r a - h e r d y e a r l y e n v i r o n m e n t a l effects were estimated asi n g a m a x i m u m likelihood m e t h o d first suggested by H e n d e r s o n (6). The m a t h e m a t i c a l mode! and m e t h o d o f solution was the same as described in detail by H e n d e r s o n et al. (8). L a c t a t i o n records were g r o u p e d by cow, sire, y e a r o f calving, a n d herd. Cows h a d f r o m one to six records each. RecoMs completed b e y o n d the sixth lactation were n o t ~sed. I n o r d e r to be within the limits of the c o m p u t e r p r o g r a m , the n u m b e r o f sire g r o u p s was limited to fifty.

MO

9 13 41 50 52 59 66 65 42

397

ME 6 9 10 11 22 16 18 20 29 26 40 45 49 70 65 66 68 66 73 79 68 51 53 68 65 72 71 56 57 106 91 1,546

MO

N.E

9 12 5 16 8 17 14 25 20 26 32 25 31 28 38 30 46 25 49 26 40 22 44 29 41 30 45 31 44 25 53 32 44 23 53 29 52 21 64 20 55 20 50 21 36 20 49 28 34 26 39 27 39 24 33 25 30 24 35 22 23 738 1,146

NN

11 11 16 15 19 24 25 28 26 25 25 20 29 28 23 18 26 31 28 33 36 28 29 30 30 614

YA

20 13 18 20 35 28 23 28 33 32 27 29 37 28

371

Total 32 47 67 93 108 161 175 217 250 276 287 299 308 376 382 373 366 389 407 439 421 389 385 448 450 483 475 370 304 369 326 9,742

Sire g r o u p s o f f e w e r t h a n f o u r cows were discarded. The n u m b e r o f records used is shown in Table 1. Y e a r l y e n v i r o n m e n t a l g r o u p s consisted o f all records b e g i n n i n g in any one year. I n cows calving twice in a given year, the two records were a v e r a g e d a n d listed as one record f o r c o m p u t a t i o n a l p u r p o s e s . S t a n d a r d e r r o r s f o r the y e a r l y e n v i r o n m e n t a l effects were o b t a i n e d f r o m the following rela, tionships. Let the v a r i a n c e o f contrasts be denoted as o-~(dk -- dr) = (A~k + A r f -- 2 A ~ ) ~ o 2 w h e r e ~ is the e n v i r o n m e n t a l effect o f the k th year, ~/r the e n v i r o n m e n t a l effect o f the final year, A a square symmetric m a t r i x o f inverse elements, and o-~2 the within cow a n d h e r d m e a n square f o r F C M yield. To solve the n o r m a l equations f o r y e a r effects, the r e s t r i c t i o n t h a t the final y e a r effect is equal to zero was imposed. Therefore, the last row and column o f the A m a t r i x c o r r e s p o n d i n g to ~ were deleted a n d the A r t - - 2 A k ~ t e r m s become zero. The s t a n d a r d e r r o r o f an estimated y e a r l y environm e n t a l effect t h e n becomes:

280

C. W. A R A Y E , 1~,. O. L.ABEN, A N D S. W. ~ E A D

The use of age-correction factors and repeatability values not appropriate to the herd under investigation has been shown to bias the estimates of environmental changes (7). F o r this reason intra-herd analyses were conducted to determine the effects o f age on milk yield and to obtain repeatability values. Age curves were calculated from a curvilinear regression of the form Y ~- a + b~ x + b2 x: where Y is the expected F C M yield, b~ the lineal" component, b~ the curvilinear component of regression, and x the average age in months. Age-correction factors were obtained first by finding the maxinmm turning point of the curve by setting the derivative of Y with respect to x equal to zero and solving for x. By sub.stituting x back into the equation, nlaximum Y (Ym) is obtained. Mature equivalent (ME) factors were then calculated as the ratio Y m / Y x where x is in monthly intervals over the range of the data. The curves were derived using the mean F C M yield and age at calving in months for each of the first six lactations. As a result of using these age-correction factors the between lactation variance was reduced by an average of 91%. Repeatability of the age-corrected F C M recor4s estimated by intra-class correlation for individual herds ranged from .20 ± .05 to .52 ± .05. Estimates of the average annual genetic change occurring in each herd were made by finding the linear regression of F C M yield on year of records adjusted for yearly environmental effects. A pooled intra-sire regression of progeny yield on generation number was obtained for one of the largest herds, to compare the maxinmm likelihood estimate of genetic change with a second method. The yield of a sire's progeny was expressed in terms of her most probable producing ability ( M P P A ) (9). There were 17 cows in the foundation or zero generation group. Daughters of these cows were considered Generation 1 cows; doughters of Generation I cows, Generation 2, etc. In this manner generation number from 1 up to 10 was assigned to 538 cows within 38 sire groups of four or more cows each. The number of generations represented within a sire ranged from two up to six. There was an average of 14 daughters per sire with a range of from four to 60. The genetic gain was estimated as the pooled intrasire regression of the progeny M P P A on generation number. RESULTS

Estimates of the yearly environmental effects

are shown in Figures 1 to 3. I t may be seen in the figures that the most favorable environmeat for .several of these herds, especially those herds in the project for the greater number of years (Figures 1 and 2), occurred during the 1940's. This suggests economic factors may have influenced these herds in a similar manner. The deviations from the average milk-feed price ratio for the years 1933 to 1960, as derived from U S D A statistics (14), are shown in Figure 4. The most favorable ratios occur from 1938 to 1946 and from 1956 to 1960. These ratios are based on nation-wide averages and local variations may differ considerably. ttowever, there is a general correspondence between the optimum milk-feed price ratios and the better levels of herd environment. An attempt was also made to study the environmental trends with relation to recorded changes of management in certain of these herds. These observations were made as a routine part of the biannual visits to the herds by University staff members. The AL herd (Figure 3) originated from females of the A H herd. Management of the two herds was the same prior to 1949. Beginning in August of 1949, the herds were managed as separate units.

I000

I000

I000

h¢-)

0

c5 ILOOO

I000

19

io

FIG. 1. Yearly variations in FCM yield in foul" co-operator dairy herds, due to intra-herd environmental effects.

:M!E)I-SUREMENT

100(

OF

GENETIC

281

OttANGE

o

VA

,¢

g ,0

I00(

ooo i

I,

NIA

MO

(~ .J 0

iO00

m3o LA

194o

195o

,96o

YEAR FIG. 4. Deviations from the mean milk-feed price ratio.

The trends are of similar magnitude prior to 1949, after which much greater fluctuations occur in the environment of the AL herd. I000 The l~¢~Aherd (Figure 2) was under the same management from its beginning until August, (930 !940 1~0 I~v 1951, when a change in management was reYEAR corded. I n 1950 it was noted that a new crew Fro. 2. Yearly variations in FCM yield ~n four took over the milking of the herd. Poor milkco-operator dairy herds, due to intra-herd environ- ing management, a high incidence of mastitis, mental effects. and a drastic drop in production followed this change. These notations are reflected in the environmental trend portrayed in the corresponding years in Figure 2. Reference to poor milkers and other management difficulties appear in the herd notes from 1950 forward. I n 1949 a similar change occurred in the MO herd (Figure 1), when a son assumed management from his father. A drastic decline may be noted in the environment following this. The LA herd was managed by the owner throughout the course of this study. During the 1950's, due to ill health, many of his duties were delegated to hired labor. A general decline in herd environment was recorded and may also be observed in Figure 2. A son assumed management of the F L herd from his father in 1944. Frequent reference was made to poor milkers and general deterioration in 0 ~ FL management for the remaining time this herd was in the study. Some improvement in feeding practices was noted up to 1950. The analysis indicates this environmental trend evi1000 dently overshadowed the effects of what was judged to be poor milking practices. While the notes taken on regular herd visits were not zg~0 ' tg~o 19'~o id~o quantitative, the trends of the analysis are YEAR quite compatible with them. The final entry Fro. 3. Yearly variations in FOM yield in four for the F L herd contains the sentence: "Conco-operator dairy herds, due to intra-herd environditions in this herd are going from bad to mental effects.

/

282

C.W.

ARAVE, l~. C. LABEN, AND S. W. MEAD

worse." The downward trend in the last year coincides with this observation. Standard errors for the yearly environmental effects ranged in the smallest herd (CO) from 342 to 769 lb and in the largest herd (MA) from 382 to ],255 lb FCM. The average annual genetic changes occurring in these herds throughout the study are shown as the linear regression of FCM yield of records adjusted for yearly environmental effects on year (Figure 5). The regressions for the CO and MC herds were not significantly different from zero. Since only about two generations are involved in estimates derived ~or these two herds, this result is not surprising. Annual genetic increases of from 53 ± 12 lb to ]45 ± 21 lb FCM were found in other herds. The increases averaged 74 lb FCM or about 0.7% of the mean annual yield. The pooled intra-sire regression of the progeny's M P P A on generation number within the MA herd was 112 lb FCM per generation. This pooled regression was found to be highly .significant (Table 2). To compare these results with those obtained by the maximum likelihood method, some assumptions had to be made. First of all, if a generation interval of four years is assumed, the annusl regression would be 28 lb FCM. Since the sire is a constant in each of' the intra-sire regression estimates, only one-half the genetic change is being measured, assuming the M P P A is the best estimate of a cow's genotype. Doubling the regression estimate accordingly, the true estimate of the genetic gain becomes 56 lb of FCM per year. This estimate compares with the maximum likelihood estimate for the MA herd of 60 ± 25 lb of FCM per year. The estimates of progress derived by the two methods are, therefore, in close agreement. DISCUSSION

The genetic change occurring in several of the herds used in this study were of approximately equal magnitude. This may be explained in part by a higher than average genetic relationship between herds attained through the sire rotation plan of the project. Since the breeding management for all herds was es.sentially the same, the similarity of results in-

t200C

Co

,. ~~ LO00C

8000

.-3 MO

AL

I OOO(

SO0(

J93o

=

=

=

i~o

.

~95o

i

19'6o

YEAR

FIG. 5. Linear regressions of FCIV[ yield ou year of records adjusted for environmental effects within 12 co-operator dairy herds. creases one's confidence in the method used to measure the genetic change. Age-correction factors and repeatability values differed considerably from herd to herd. They also differed greatly in some herds from the standard age-correction factors and from the generally assumed value for repeatability of milk yield. This further emphasizes the need for considering these factors in application of the maximum likelihood procedure for estimating environmental effects. The maximum likehhood method although computationally complicated (15) may be used to analyze large amounts of data very quickly and relatively inexpensively where an electronic computer is available. I n herds such as those t~sed in this study it would of course not

TABLE 2 Analysis of variance--pooled regression of FC~{ Field on generation number Source of variation

DF

Mean square

Regression due to b Variation among b's Pooled resldual

1 37 462

9,316,493 1,563,569 448,333

** P ~ .01.

A~t. e ',A ,

?=,~.

F 20.780** 3.488**

283

MEASUREMENT OF GENETIC CHANGE be possible to estinmte genetic change f r o m a c o m p a r i s o n of A.I. a n d n o n - A . I , c o n t e m p o r a r i e s as suggested b y V a n V l e c k a n d H e n d e r son (15). The pooled i n t r a - s i r e regression m e t h o d of e s t i m a t i n g genetic g a i n is f a r s i m p l e r c o m p u t a t i o n a l l y t h a n the m a x i m u m likelihood method a n d m a y be useful in h e r d s where pedigrees are f a i r l y complete. The estimates derived in this m a n n e r m a y be biased d o w n w a r d slightly, due to inaccuracies in classifying cows a c c o r d i n g to g e n e r a t i o n n u m b e r . F o r example, the f e m a l e o f f s p r i n g of a zero g e n e r a t i o n sire a n d d a m would p r o p e r l y be classified as a Generation i animal. I f this cow were n o w m a t e d back to h e r sire, a f e m a l e o f f s p r i n g r e s u l t i n g f r o m this m a t i n g would more correctly be classified as a 11fi2-generation cow, r a t h e r t h a n a s e c o n d - g e n e r a t i o n cow, as is the case considering only the female sequence in t h e pedigree. The 0.7% a n n u a l genetic increase in the average yield of the h e r d s in this s t u d y is below the m a x i m u m o f 1.0% t h a t one m i g h t e x p e c t (11, 13). D u r i n g the p e r i o d of this s t u d y the a v e r a g e yield o f all h e r d s on test in C a l i f o r n i a increased a n a v e r a g e of 1.0% of the m e a n ann u a l yield p e r year. A p o r t i o n of this increase h a s a h n o s t c e r t a i n l y been the r e s u l t of i m p r o v e d m a n a g e m e n t . A f a c t o r which no d o u b t r e t a r d e d the genetic p r o g r e s s in these h e r d s was h e r d size. I n t h e b e g i n n i n g y e a r s f o r most h e r d s in the s t u d y t h e i r size was small ( T a b l e 1). T h e r e was a v e r y r a p i d increase in h e r d size w i t h few outside purchases. T h i s allowed little opp o r t u n i t y f o r the selection of females. S p e c h t a n d M e G i l l i a r d (13) have i n d i c a t e d t h a t by i n c r e a s i n g the h e r d size f r o m 25 to 200 cows the g e n e t i c g a i n expected, with p r o g e n y testing, is a p p r o x i m a t e l y doubled. This theoretically occurs when f o u r y o u n g sires are m a t e d to a m a j o r i t y of the cows a n d the best of t h e f o u r r e t a i n e d in the h e r d f o r f u t u r e use. A l t h o u g h p r o g e n y t e s t i n g was p r a c t i c e d in these herds, it was n o t possible to use a n y g i v e n sire in all herds. Sixty-seven of the 141 sires used in the s t u d y were used in m o r e t h a n one herd. W i t h the help of A.I. a t p r e s e n t a single sire is b e i n g ttsed in all p r o j e c t h e r d s each m o n t h . I n this w a y it is possible to p r o g e n y - t e s t a bull in m a n y h e r d s in a s h o r t time. I t should be possible a t a l a t e r date to d e t e r m i n e w h e t h e r genetic c h a n g e is more r a p i d u n d e r such a system of m a t i n g and, thereby, confirm the theoretical expectations. ACKNOWLEDG1V[ENT The authors express their appreciation to the ])avis Computer Center and to the National InstL

tutes of Health whose Grant No. FR-00009 made the computer facilities available. REFERENCES (1) ARAVE, C. W. A Study of Genetic Change in Twelve California ])airy Herds. Ph.D. thesis, University of California. 1963. (2) BRINKS, J. S., CLARK, R. W., AND ]~ICE, F. J. Estimation of Genetic Trends in Beef Cattle. J. Animal Sci., 20: 903. ]961. (3) ])ILLON, W. M., JR., YAPP, W. W., AND TOUCHBERRY, R. W. Estimated Changes in the :Environment and Average Real Producing Ability in a Holstein Herd from 290] through ]954. J. ])airy Sci., 38: 616. 1955. (4) GAALAAS,R. F., AND PLOWMAN, A. ]). Effectlveness of Statistical Adjustments for Yearly Fluctuations in Production. J. ])airy Sci., 44: 1188. 1961. (5) HARVEY, W. A. Genetic and Environmental Changes in F a t Production in the University of Idaho Holstein and Jersey Herds. ])roe. 34th Ann. Meet., West. ])iv., Am. ])airy Sci. Assoc., p. 34, Fort Collins, Colorado. July 27-29, 1953. (6) HENDERSON, C. R. Estimation of Changes in Herd Enviromnent. J. ])airy Sci., 32: 706. 1949. (7) HENDERSON, C. R. Estimation of Environmental Trends and Biases from Errors in Age Factors and Repeatability. J. ])airy Sci., 41: 747. 1958. (8) t~ENDERSON, C. R., KE]~'J[PTtIORNE, 0., SEAICLE, S. R., AND VON KOROSIGK, C. M. The Estimation of Enviromnenta] and Genetic Trends from Records Subject to Culling. Biometrics, 15: 192. 1959. (9) LusH, J. L. Animal Breeding Plans. Iowa State College Press, Ames. 1945. (]0) MC])ANIEL, B. T., PLOW/VIAN, R. ])., AND ])AVIS, R. F. Causes and Estimation of Environmental Changes in a Dairy Herd. J. ])airy Sci., 44: 699. 1961. (11) R ENOEL, J. M., ~¢D ROBER~SO~¢, A. Estimation of Genetic Gain in Milk Yield by Selection in a Closed Herd of ])airy Cattle. J. Genetics, 50: ]. 1950. (12) SMITH, C. Estimation of Genetic Change in F a r m Livestock Using Field Records. Animal Production, 4: 239. 1962. (13) SeECH% L. W., AND McGILLIARD, L. ]). ]~ates of Improvement by Progeny Testing in ])airy Herds of Various Sizes. J. ])airy Sei., 43: 63. 1960. (14) USDA. Agricultural Statistics. U. S. Govt. P r i n t i n g Office, Washington, ]). C. 19341961. (15) VANVLECK, L. ])., AND HENDERSON, C. R. Measurement of Genetic Trend. J. ])airy Sci., 44: 1705. 1961. (16) WALTON, R. :E. Results of Selection for Production in a Holstein Herd. Ph.D. thesis, Iowa State University. 1961.