Analysis of Estimated Breeding Values for Marble Score, Carcase Weight and the Terminal Carcase Index Authors: 1. Matthew McDonagh CEO 2. Carel Teseling Technical Service Manager Australian Wagyu association PURPOSE 1) To describe for members, the relationships between Estimated Breeding Values (EBVs) for Marble Score (MS) and Carcase Weight (CW) and the carcase data that underpins them; 2) To describe the relationship between these EBVs with the Terminal Carcase Index (TCI); and 3) To explain how differences in growth and marbling are taken into account in calculating these EBVs, along with an explanation of how the TCI would rank animals based on hypothetical carcase data. BACKGROUND How EBVs are calculated: In livestock production, a trait is a characteristic of an animal that is measurable or has value. An animals phenotype is the sum of all of its traits. An individual animals phenotype is therefore dependent on how much its genes (genotype) influence these traits and to what extent the environment allows or restricts the expression of the animals genetic potential. Most cattle production traits are heritable, that is, genes (that are inherited from the parents) have a level of influence on the trait which is expressed in their progeny. The higher the influence genes have on the phenotype of a trait the more heritable that trait is (heritability). Heritability is how much of the phenotypic difference of a trait is determined by the genetics of an animal. In Wagyu, marbling and carcase weight are approximately 50% heritable. Hence, 50% of the phenotypic difference between individual animals for the trait is due to genetics and 50% of the phenotypic difference between animals is a result of the management system, or environment, that an animal is raised in. This needs to be taken into consideration when comparing raw data with EBVs. Environmental and management influences on traits can be large. For example, rate of gain in live weight and carcase weight in a starvation situation (eg. drought) vs. a feedlot environment. The environmental conditions should at least allow the animal to express its genetic potential. Therefore, it is necessary to take into account variation in environment between animals when estimating the relative genetic merit of an individual. This helps to ensure the environmental influences are accounted for accurately. The purpose of an EBV is to provide an estimate of the genetic potential of an animal at a common point, to allow comparison of apples with apples. Wagyu BREEDPLAN is the software system
developed by the Animal Genetics and Breeding Unit (AGBU) which enables the genetic merit of an individual animal (the EBV) to be determined. To effectively compare individuals, eg., 2 sires with EBVs, it is obviously important for Wagyu BREEDPLAN to account for differences in the management systems that the progeny of these sires were produced in. Wagyu BREEDPLAN takes the influence of environment into account by comparing the performance of progeny of sires relative to each other within contemporary groups. A contemporary group is a group of progeny from different sires and dams which has been grown and slaughtered together, i.e., the animals are contemporaries to each other. Contemporary groups allow us to compare the performance of progeny from individual sires and dams to each other within a management group. We can then also compare how the relative ranking of sires changes across contemporary groups. For example, a sire like Michifuku or Itoshigenami will be represented in most contemporary groups in BREEDPLAN, so other sires are effectively benchmarked to Michifuku and Itoshigenami within BREEDPLAN and the EBVs are influenced by this ranking. Adjustments are also made within Wagyu BREEDPLAN for carcase traits so that the genetic merit of sires and dams can be compared at a common carcase weight and age point to enable comparison of apples with apples. An individuals EBVs are therefore determined by estimating the genetic and environmental components for each trait comparing the performance of an animals progeny across several different production groups taking into account: 1) The heritability of each trait; 2) The performance of relatives within the animals pedigree for that trait; 3) The known relationship a single trait has with other traits (eg. 200 day weight is highly related to 400 day weight); 4) The stage of development or growth that an animal is measured at; 5) The comparative difference between progeny of other sires or dams within a production group 6) The comparative difference between progeny of other sires or dams across multiple production groups. Three papers have been prepared to assist explaining the marble score (MS) and carcase weight (CW) EBVs and Terminal Carcase Index calculation. These are: SECTION 1: Audit of MS and CW EBV contribution to TCI for foundation sires Michifuku and Itoshigenami SECTION 2: Whole of Wagyu BREEDPLAN data audit of MS and CW EBV contribution to TCI SECTION 3. Hypothetical calculation of MS, CW and the TCI using Australian production extremes
EBV AND TERMINAL CARCASE INDEX PAPER SERIES SECTION 1: Audit of MS and CW EBV contribution to TCI for foundation sires Michifuku and Itoshigenami An analysis of two widely used and high performing Australian Wagyu foundation bulls (IMUFQTF148 - Itoshigenami and WKSFM0164 - World K S Michifuku) was conducted to ascertain the consistency in data between these sires. An analysis of the Wagyu carcase database was undertaken to determine the CW and MS average values for Michifuku and Itoshigenami. The average MS and CW from 230 carcases within the Wagyu Database that were sired by Itoshigenami is MS 8.0 and 421kg respectively. The average MS and CW from 365 carcases within the Wagyu Database that were sired by Michifuku is MS 7.4 and 405kg respectively. The July 2017 figures for Itoshigenami and Michifuku are shown in Table 1, along with the average figures for their sons. Table 1. Comparison of Wagyu BREEDPLAN EBVs and TCI for the Australian Wagyu herd sires Takeda Farm s Itoshigenami and World K s Michifuku and their male progeny Database ID Name CW EBV CW acc MS EBV MS acc TCI IMUFQTF148 ITOSHIGENAMI (IMP USA) -2 98% +1.9 97% 390 Average of ITOSHIGENAMI sons (n=77) 9.5 64% 0.93 63% 237 WKSFM0164 WORLD K'S MICHIFUKU -3 98% 1.4 97% 282 Average of Michifuku sons (n=60) 8.4 63% 0.77 63% 198 Table 1 shows that the TCI for Itoshigenami is $108 higher than Michifuku. This is primarily driven by the 0.5 unit difference in MS EBV between the sires based on the July 2017 Wagyu BREEDPLAN analysis. The MS EBV difference is consistent with that noted through analysis of the 595 carcases sired by these bulls within the Wagyu carcase database at that time. The average difference in MS EBV between the progeny of the sires is 0.16 units. As a result, the average TCI for the male progeny of Itoshigenami is $39 higher than that of Michifuku, with CW EBV again being approximately the same. The average TCI of sons of Itoshigenami are 40%, or $153 less than Itoshigenami himself, with approximately 49% of the sire MS EBV displayed in his progeny. The average TCI of sons of Michifuku are 30%, or $84 less than Michifuku himself, with approximately 55% of the sire MS EBV displayed in his progeny. This indicates that on average, the sons of Michifuku perform more consistent to their sire than do the sons of Itoshigenami. However, it should be noted that the Dam side of the matings reported here will also influence the outcome and that Wagyu BREEDPLAN
figures can change as additional carcase data is added to the database and this will influence the analysis provided here. An overall comparison between these two Australian Wagyu herd sires and their progeny is shown in Figure 1 and Figure 2 below which compare the MS EBV against TCI for each sire and their progeny. These figures show the relatively high TCI and MS EBV of Itoshigenami and Michifuku compared to their sons. These figures also demonstrate that the relationship between TCI and MS for each of the sire progeny groups is highly consistent (the slope of the regression line through each data set is within 5% of the other). Relationship between MS EBV and TCI for Itoshigenami sons vs Michifuku sons.
Summary of Section 1: This analysis of Itoshigenami, Michifuku and their sons compares the relationship between these bulls and their carcase data within the Wagyu BREEDPLAN database. This comparative analysis demonstrates the consistency between EBVs for Itoshigenami and Michifuku and their progeny against their actual carcase records and demonstrates that the relationship between MS EBV and the TCI is consistent across these groups of bulls. SECTION 2: Whole of Wagyu BREEDPLAN data audit of MS and CW EBV contribution to TCI To examine the consistency in relationships between the MS and CW EBVs and the TCI across the whole of the Wagyu BREEDPLAN database, all sire records were downloaded for 2016 and 2017 (n > 2,500 for both). Figures 3 and 4 show the relationship between MS and TCI for sires with neutral CW EBVs in the -1 to +1 kg range for sires in Wagyu BREEDPLAN from 2016 and 2017 respectively. Although the Wagyu BREEDPLAN analyses for the 2016 and 2017 years have roughly the same number of sires within the -1 to +1kg CW EBV range (average of 175 individuals), only 83 sires, or
48% are common to both years as EBVs do change to reflect carcase data submitted by members. Hence, although more than 50% of the individuals are unique to each year (due to changes in EBVs with data addition), the relationships are very similar (ie, the same) across years. The slope of the lines of best fit through these data sets is very similar (within 0.1% error). The intercepts of both lines are within 0.5 of a TCI $ index value, indicating that when CW EBV of an animal is approximately 0, there is no residual value in the TCI index that is not explained by MS EBV. The slope of the line of best fit through each graph is 210, indicating that at a fixed carcase weight (eg. 0), an increase in MS EBV of 1 unit increases the TCI by $210. To examine the nature of the relationship between MS EBV and the TCI at high CW EBVs, this approach was repeated for 2017 sires within the +26 to +30 kg CW EBV range (Figure 5). This relationship shows a very similar slope (215 vs 210; within 2% error), indicating that each increase in MS EBV of 1 unit for high CW EBV sires adds equivalent value to the TCI compared to average CW EBV sires. Another way of stating this is that the influence of MS EBV on the TCI is effectively the same for neutral and high CW EBV sires.
Of note in Figure 5 is that the intercept of the line of best fit through the data is 117.75. That is, for sires with a MS EBV of 0 and an average CW EBV of + 28 (the average of the data used in Figure 5), the contribution of +28 CW EBV to the TCI is estimated at $117.75. To cross-check this estimated value, an analysis of the relationship between CW and TCI for 2017 Wagyu BREEDPLAN sires with MS EBVs of 0 units was conducted (Figure 6). The slope of this line of best fit is 4.245, which means that for every 1kg of increase in CW EBV, it adds $4.245 in value to the TCI of an animal. Hence, at an average CW EBV of +28 as used for generating Fig 3 (above), the contribution of carcase weight to the TCI based on the equation in Fig 5 should be 28 X $4.245 = $118. This is highly consistent with the intercept value (at MS 0) of 117.75. Summary Section 2: The above analysis simply shows that the way Wagyu BREEDPLAN EBV s perform across a range of high to low MS and CW EBV sires is consistent with regard to their effects on the TCI. SECTION 3: Hypothetical calculation of MS, CW and the TCI using Australian production extremes The following example table (Table 2) is provided to assist in demonstrating the relationship between Days of Age at slaughter (DOA), AusMeat Marble Score and Price (AusMeat MS*$) and Hot Standard Carcase Weight (HSCW) and EBVs for MS, CW and the TCI. Table 2 is a hypothetical example of the local market 'actual carcass value' and uses just two 'unadjusted' traits to indicate a 'real market' value ranking. In this table, DOA are not relevant to market value, as indicated. Table 2: Market Based Valuation of hypothetical carcases for a TCI comparison DOA AusMeat MS*$ HSCW Estimated Market Value Sire 1 950 9@$9 500*$9 $4500 Sire 2 730 9 414*$9 $3726 Sire 3 950 7@$7 500*$7 $3500 Sire 4 730 7 414*$7 $2898 Sire 5 950 5@$5 500*$5 $2500 Sire 6 730 5 414*$5 $2070 Table 3 (below) was produced by using the hypothetical carcases provided in Table 2 and using the Wagyu BREEDPLAN adjustments for days of age and carcase weight. It was noted that completing it should show the simple value impact of the environmental/management adjustments of DOA and actual carcase weight on the CW and MS EBVs respectively, and the $$ impact to the TCI value.
To complete this example table, the author has used the following assumptions. Over more than 5,000 carcases in the Wagyu BREEDPLAN database, the average 417kg carcase is approximately 6.8 MS following 480 days on feed at an average age of approximately 900 days. At a common age point of 750 days of age, as per Wagyu BREEDPLAN parameters, adjusted mean CW is 398kg. At a common CW point of 400kg, as per the Wagyu BREEDPLAN parameters, adjusted mean MS is 6.5. The adjustments used in the Wagyu BREEDPLAN paraments are as follows for CW and MS. CWT = 0.0727*x + 343.2 (where x is days of age and 343.2 is the intercept of the line of best fit) MS = 0.0173x - 0.4107 (where x is kg CWT and -.04107 is the intercept of the line of best fit) Using these same adjustments, the estimated EBV s and TCI for the sires provided in table 2 were calculated and are presented in Table 3 below. Table 3. Terminal Carcase Index calculation for example sires based on provided parameters and Wagyu BREEDPLAN adjustment equations to derive predicted values for MS, CW and the TCI DOA AusMeat MS*$ HSCW Avg. HSCW Avg. MS MS EBV CW EBV Calculated TCI $$ Est. Market Value Sire 1 950 9@$9 500 412.265 8.24 0.76 87.7 551 $4,500 Sire 2 730 9 414 396.21 6.75 2.25 17.8 526 $3,726 Sire 3 950 7@$7 500 412.265 8.24-1.24 87.7 51 $3,500 Sire 4 730 7 414 396.21 6.75 0.25 17.8 112 $2,898 Sire 5 950 5@$5 500 412.265 8.24-3.24 87.7-449 $2,500 Sire 6 730 5 414 396.21 6.75-1.75 17.8-302 $2,070 The value that the market places on carcase weight, marble score and hence, carcase value, changes continually depending on supply and demand. Hence, the TCI is an index only to allow comparative ranking of sires and is not a direct indication of difference in the real market value of progeny between sires. Comparing the top sires (1 and 2) in Table 3, we can see that the Sire 1 is the highest ranking sire by TCI value and has the highest estimated value for carcases of his progeny. Sire 2 is the second highest ranking sire by TCI value with the second highest value for carcases of his progeny. Comparing the bottom sires (5 and 6) in Table 3, carcases from sire 5 progeny have a higher estimated value than those of sire 6, however, the TCI for sire 6 is higher than sire 5. This is driven by the fact that the MS EBV is significantly poorer for sire 5 compared and sire six, with progeny of sire 5 taking 950 days to reach AusMeat MS 5 whereas progeny of sire 6 take 730 days to reach MS 5. The MS EBV reflects this as does the calculated TCI. To compare the relationship between the Estimated Market Value with the calculated TCI for the 6 sires listed within Table 3, these figures were plotted against each other for comparison in Figure 7 below. Figure 7 shows that the calculated TCI, based on current Wagyu BREEDPLAN equations explains 80% of estimated carcase value in this example.
Another way to consider this hypothetical comparison of TCI to estimated market value is to consider the efficiency of marbling gain across the life of an animal. In livestock production Average Daily Gain (ADG), is the metric used to define growth rate, being the number of kg gained per day of life to a fixed point. We can do the same thing with Marble Score to a fixed point for carcase weight, calculating the relative proportion of marbling per kg carcase weight gain. That is, MS/kg provides a metric to allow comparison of carcase value that adjusts for CW variation at a constant marble score. The table below shows the relative MS/kg for the sires in this example and the ADG in the table for reference. Table 4. Marbling gain per kg carcase weight (MS/kg) compared to hypothetical carcase figures and calculated EBVs for MS and CW DOA AusMeat MS*$ HSCW MS EBV CW EBV MS/kg ADG kg/d Sire 1 950 9@$9 500 0.76 87.7 0.018 0.526316 Sire 2 730 9 414 2.25 17.8 0.021739 0.567123 Sire 3 950 7@$7 500-1.24 87.7 0.014 0.526316 Sire 4 730 7 414 0.25 17.8 0.016908 0.567123 Sire 5 950 5@$5 500-3.24 87.7 0.005556 0.526316 Sire 6 730 5 414-1.75 17.8 0.012077 0.567123 Table 4 allows us to compare the amount of marbling gained per kg of liveweight for each sire. This should be a pretty fair predictor of relative carcase value at any given liveweight. In this example, Sire 2 is the best performing sire for MS/kg, with 0.02 MS gained per kg liveweight gain. Sire 5 is the worst performing sire, with 0.005 MS gained per kg liveweight. Specifically, to compare Sire 1 with Sire 2, at 414kg lw, progeny of sire 1 would have a MS of 7.5 compared to progeny of Sire 2 with MS of 9.0.
We can then compare the MS/kg against Marble score EBV to see if they predict the same thing, ie, they are correlated (explain the same thing). This is shown in the Figure 8 below. Based on this relationship, it is apparent that the MS EBV as calculated in this example set is explaining MS/kg very accurately. In other words, the MS EBV is doing the right job of explaining marbling gained per kg of liveweight in this example. Again, Sire 2 is the highest for MS EBV and MS/kg. with Sire 5 being the lowest. The line of best fit shows that 97% of MS/kg is explained by the MS EBV calculated (the R 2 on the graph). Summary Section 3: The purpose of an EBV is to provide an estimate of the genetic potential of an animal at a common point, to allow comparison of apples with apples. To effectively compare sires within Tables 2, 3 and 4 above, it is obviously important to account for differences in the management systems that the progeny of these sires were produced in. Adjustments are made within BREEDPLAN for carcase traits so that the expression of genetic potential of sires can be compared at a common carcase weight and age point. The analysis in Section 3 of this paper does not take pedigree or contemporary group into account and is presented only for the purpose of explaining the influence of DOA and CW on the EBVs discussed and the TCI. Hence, it is not appropriate to determine from the analysis presented here, that the influence of the adjustments for DOA and CW on EBVs is consistent with what occurs within Wagyu BREEDPLAN for any given sire. The EBVs generated by Wagyu BREEDPLAN are also strongly influenced by pedigree and contemporary group rankings in addition to carcase data and the adjustments made. The analysis provided within Section 3 demonstrates that the TCI, which is an index for comparing the relative genetic merit of sires for carcase value, is highly correlated with estimated market value in an example carcase set which was designed to demonstrate relative extremes of Australian Fullblood Wagyu production. The way that Wagyu BREEDPLAN accounts for variation in age at slaughter and in carcase weight was explained.
OVERALL SUMMARY The influence of genetic potential on a phenotype is dependent on heritability of the trait, that is, how much of the phenotype is on-average determined by the genetics of an animal. In Wagyu, marbling and carcase weight are approximately 50% heritable. Hence, 50% of the phenotypic difference between animals is not a result of genetics, but is a result of the management system, or environment, that an animal is raised in. This needs to be taken into consideration when comparing raw data with EBVs, especially where EBVs have few records associated with them. Wagyu BREEDPLAN also takes the influences of environment and management into account by comparing the performance of sires such as Itoshigenami and Michifuku relative to each other within contemporary groups and it compares how the relative ranking of sires changes across contemporary groups. This paper describes aspects of MS and CW EBV and more than 5,000 carcase records that sit within Wagyu BREEDPLAN. A comparative analysis of Itoshigenami, Michifuku and their sons in Section 1, compared the relationship between these bulls and their carcase data within the Wagyu BREEDPLAN database. This comparative analysis demonstrated the consistency between EBVs for Itoshigenami and Michifuku and their progeny against their actual carcase records at that time and demonstrates that the relationship between MS EBV and the TCI is consistent across these groups of bulls. A whole-of-wagyu BREEDPLAN analysis in Section 2, showed that the way Wagyu BREEDPLAN EBV s perform across a range of high to low MS and CW EBV sires and that this performance was consistent with regard to their effects on the TCI. An example analysis was provided within Section 3 of this paper which demonstrated that the TCI, which is an index for comparing the relative genetic merit of sires for carcase value, is highly correlated with estimated market value in an example carcase set which was designed to demonstrate relative extremes of Australian Fullblood Wagyu production. The way that Wagyu BREEDPLAN accounts for variation in age at slaughter and in carcase weight was explained. Matt McDonagh CEO