GMACE Pilot #4: Adjusting the National Reliability Input Data
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1 INTERBULL BULLETIN NO. 48. Berlin, Germany, May 20 21, 2014 GMACE Pilot #4: Adjuting the National Reliability Input Data P. G. Sullivan 1 and J. H. Jakoben 2 1 Canadian Dairy Network, Guelph, ON, Canada 2 Interbull Centre, Box 7023, SE70 07 Uppala, Sweden Abtract International tandard do not exit for the approximation of national genomic reliabilitie, which are ued a input data for the GMACE international genomic evaluation ytem. The focue of the preent tudy were to develop a method of reducing difference among the national reliabilitie approximated by different countrie, to apply GMACE uing modified national reliabilitie, and to ue crovalidation tet to determine if GMACE reult could be meaurably improved. A nonlinear international regreion model wa applied to the average national reliabilitie provided by countrie for ue in GMACE. Reidual of prediction for the average national reliabilitie were maller, indicating greater conitency among the approximation of different countrie, for protein and tature relative to trait more difficult to evaluate, uch a matiti, tillbirth and cow conception rate. GMACE input reliabilitie were modified by ubtracting either ome or all of the average prediction error for each combination of trait by country. The impact of modifying the national reliabilitie on GMACE reult were relatively mall. Predictability of national genomic evaluation by GMACE with only foreign genomic data a input, wa eentially the ame uing either modified or unmodified national reliabilitie. However, the international reliabilitie produced by GMACE were more conitent if national reliabilitie were modified a input and then the modification were revered for the GMACE reliability output. The approach wa to eentially apply an international tandardization of reliability on the way into GMACE and then a detandardization back to each of the original national cale of expreion on the way out. Key word: genomic, international evaluation, GMACE, reliability, crovalidation Introduction Genomic variance etimate are a function of Mendelian ampling prediction and the correponding reliabilitie (Sullivan & Jakoben, 2012). A bia in the etimation of national genomic reliabilitie can directly impact genomic variance etimate and ubequent bull ranking from GMACE. A working group ha been formed to review approximation method for national genomic reliabilitie. Currently there i no tandard methodology to enure conitency among the countrie. In a recent tudy (preented in Nante, 2013) we quantified the potential impact of biaed input reliabilitie on genomic variance and GMACE prediction, by imulating reliability biae. Uing an international regreion of the average reliabilitie provided by countrie, we derived expected value for the average reliability of each trait and country, then aumed deviation from expectation 40 were biae. Thi i not trictly true, but allowed for a enitivity analyi of the effect of changing input reliabilitie on GMACE reult. The preent tudy focued on which reliabilitie hould be ued for GMACE in practice. The firt objective wa to refine the reliability prediction and regreion of national reliabilitie toward a globally tandardized et of expectation. The econd objective wa to tudy the merit of uing predicted (fully regreed) reliabilitie, partially regreed reliabilitie, or the provided (not regreed) reliabilitie in GMACE. Crovalidation tet were ued to compare the different approache. Material and Method Eleven countrie participated with young bull GEBV data for a many a 37 different trait for the GMACE implementation run in
2 INTERBULL BULLETIN NO. 48. Berlin, Germany, May 20 21, 2014 December Thee countrie were Autralia (AUS), Canada (CAN), Switzerland Red Holtein (CHR), Germany (DEU), DenmarkFinlandSweden (DFS), France (FRA), Great Britain (GBR), Italy (ITA), the Netherland (NLD), Poland (POL), and the United State (USA). Data were edited for variance etimation to minimize election bia, by including only young GEBV bull born between December 2008 and November 2011, without a claical MACE proof, and with ire and MGS having a MACE proof. Thi time interval wa choen to balance the goal of a ufficiently large variance etimation data et, minimal withinyear election bia, and the current population of young genomically teted bull with no progeny. Reliabilitie are bounded between 0 and 100%, and increae at a decreaing rate. Thu, a nonlinear model of prediction wa ued: exp(grel n ) = trait + b rel_loc + c rel_for + e The predicted reliability wa equal to: Grel =log(trait p + b rel_loc + c rel_for), and the average difference between provided and predicted national genomic reliability wa computed a: re = Grel n Grel p. For individual: Grel p = Grel n re. The Greln wa an average of the national genomic reliabilitie for bull born between Augut 2008 to July Trait in the prediction model included 37 of the uual MACE trait, but for the preent report we how reult for only ix of the trait: protein (pro), tature (ta), omatic cell core (c), matiti (ma), direct tillbirth (db) and cow conception 1 (cc1). The rel_loc wa the um of reliabilitie for the local reference population, which were bull with a national EBV ubmitted to MACE for the given trait, and coded a a reference bull for protein in the country' GenoLit file provided to Interbull. The rel_for wa the um of MACE reliabilitie for the foreign reference population, which were bull with a MACE proof baed on only foreign EBV for the given trait, and coded a a reference bull for protein in the country' GenoLit file. The model being compared are ummarized in Table 1. Model G, which wa denoted a model rgm_m(v) in Sullivan & Jakoben (2012), wa the operational model ued by Interbull prior to the preent tudy. Model GP ued predicted (i.e. fullyregreed) reliabilitie a input rather than the individual reliabilitie provided by the countrie. Uing a different et of national reliabilitie a input affect both the GMACE variance etimate ued for caling, and the relative weighting of national genomic evaluation when a bull ha been evaluated in more than one country. Table 1. GMACE model of evaluation. Model Decription Current model in ue for GMACE G uing provided reliability a input Model G uing predicted reliability GP a input Input i a.regreed reliability GP. (predicted +.provided) Model GP. combine the idea and merit of international tandardization veru utilizing national expertie and cutomized information. Specific knowledge about the genomic evaluation cutomized by each country, including aumption about polygenic variance, ditributional propertie of SNP, denitie of SNP panel ued for genotyping, number of SNP included for genomic evaluation, method to blend SNP evaluation with EBV, etc. are conidered in the Grel n provided by the countrie, while difference in thee factor are ignored in the predicted Grel p. Thu an averaging of thee two reliabilitie i a fair compromie. 41
3 INTERBULL BULLETIN NO. 48. Berlin, Germany, May 20 21, 2014 Table 2. Average genomic reliability (Grel) and reidual (re) by trait for Autralia (AUS), Canada (CAN), Switzerland Red (CHR), Germany (DEU), DenmarkFinlandSweden (DFS), France (FRA), Great Britain (GBR), Italy (ITA), The Netherland (NLD), Poland (POL), and The United State (USA). Protein Stature Somatic Cell Direct Stillbirth Fertility CC1 Matiti Grel re Grel re Grel re Grel re Grel re Grel Re AUS CAN CHR DEU DFS FRA GBR ITA NLD POL USA Crovalidation tet were conducted by country. Implied aumption were that GMACE evaluation baed on input data from only foreign cale were unbiaed predictor of the excluded (i.e. crovalidated) national GEBV for the given country, and that the national GEBV were alo unbiaed. Correlation and regreion of national GEBV on GMACE prediction were ued a tet tatitic, but are not reported here. The main difference among model were in the relative caling of evaluation between the different countrie. To demontrate thee difference, we how etimate of Top Bull bia; the relative difference between a GMACE prediction of +3 tandard deviation (z = X + 3σ) and the expected value for z baed on crovalidation regreion of national GEBV on GMACE: w = a + b x, at the value x = z. We define, a in Sullivan and Jakoben (2012): TopBia = 100% (z w) / w Regreion equation etimated with different level of truncation election on the xvariable (GMACE prediction) were imilar, a expected, ince regreion etimate are not biaed by election on x. Therefore, to focu on key bull of interet we ued the regreion equation for bull with a GMACE prediction above +1σ to etimate TopBia (of a +3σ bull). Reult and Dicuion The average genomic reliability provided by countrie and the difference from predicted reliability (re) are in Table 2. There wa greater variation in re for the functional trait relative to protein and tature. Modifying the reliability input had the expected impact on genomic variance etimate (e.g. a decreae in reliability increaed the variance etimate). Decreae in genomic variance etimate (lower gsd in 42
4 INTERBULL BULLETIN NO. 48. Berlin, Germany, May 20 21, 2014 Table 3) caued decreae in value of TopBia (i.e. le poitive or more negative), alo a expected. There wa, however, very little practical impact. The 9% confidence range acro all countrie were imilar for the three model, and while there were individual cae of notable impact, there wa no one model with conitently bet reult. Routine GMACE ue GEBV input from all countrie, and lead to reliabilitie that are conitently equal or higher than the input reliabilitie. With crovalidation, however, the local GEBV are not included a input, making it le likely for GMACE reliabilitie to be higher than the national. In the preent tudy, thi wa epecially true when GMACE reult were baed on input data from only one foreign country, or from two countrie from the ame national conortium. When data were available from everal foreign countrie, however, the average reliability from GMACE wa generally higher than the national reliability (Table 4). A approximate reliabilitie thee do not guarantee higher true reliabilitie. However, it can be concluded that GMACE reult hould be more accurate for bull genotyped in more countrie and in multiple genomic conortia. Uing predicted equation to modify the national reliability input data (GP. v G) generally improved the conitency of output reliabilitie, relative to national, for bull from different conortia. For example, reliability difference for db and cc1 were much more imilar between "A 0 1" and "B 0 1" with model GP.. GMACE ranking from either G or GP. can be ued to identify foreign bull that are bet candidate for local regenotyping, or to target an expanded haring of elected genotype among more countrie. Reference Sullivan, P.G. & Jakoben, J.H Robut GMACE for young bull methodology. Interbull Bulletin 4, 37. Acknowledgement Dicuion and uggetion from the GMACE working group were very much appreciated. 43
5 INTERBULL BULLETIN NO. 48. Berlin, Germany, May 20 21, 2014 Table 3. Bia (a a % of local GEBV) in the GMACE prediction of a top (+3 tandard deviation) bull, for elected countrie and 9% confidence range (L9 to U9) acro all countrie y. Country (n Protein) CAN (3708) USA (3876) NLD (97) FRA (1379) DEU (14430) DFS (84) Somatic Direct Fertility Protein Stature Mode Cell Stillbirth CC1 y Matiti l gsd Bia Bia Bia Bia Bia Bia z gsd gsd gsd gsd gsd G GP GP G GP GP G GP GP G GP GP G GP GP G GP GP All U9 U9 U9 U9 U9 U9 L9 L9 L9 L9 L9 L9 Countrie Confidenc G e GP Range of TopBia GP z gsd i the genomic etimate of SD a a percentage of the genetic SD ued for MACE. y one country wa excluded for cc1 due to an extreme bia > 20% for all model. gsd truncated in thee cae to the edge of the range [80120]. 44
6 INTERBULL BULLETIN NO. 48. Berlin, Germany, May 20 21, 2014 Table 4. Average genomic reliability difference: GMACE with only foreign data, minu national. Data z Protein Stature Somatic Cell Direct Fertility Stillbirth CC1 Matiti G GP. G GP. G GP. G GP. G GP. G GP. A B A B A B A B A B A B A A z A (CAN, GBR, ITA, USA) and B (DEU, DFS, FRA, NLD) are the 2 main conortia that hare data for national genomic evaluation. The number for "Data" that follow A B are the number of foreign countrie, with a GEBV included in GMACE for the bull, from the ame and different conortia, repectively. For example, A 3 1 i the group of bull with a GEBV from all 4 countrie in conortia A and 1 country in conortia B. 4
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