Select stallions - Virtual mate selection - Explanations

Select stallions - Virtual mate selection - Explanations Select stallions Progress in breeding is obtained by effective use of the genetically best individuals in the population for the production of the next generation of horses. The BLUP index is the best evaluation of the genetic quality of the breeding horses for many of the traits that are included in the official breeding goal for Icelandic horses (see www.feif.org). Therefore it is very important to stimulate the use of stallions with the highest genetic evaluation (BLUP) for the valuable traits included in the general breeding goal. Many breeders need guidance in selection of stallions for their broodmares to benefit the future of the population and for better fulfilment of their private horse production goals. The new application select stallions is meant to be a tool for the breeders to accomplish genetic improvement in the traits included in the breeding goal. It is meant to stimulate the use of the best stallions, help breeders to avoid close inbreeding and help to maintain the great coat colour variation in the population of Icelandic horses. The preservation of the coat colour variation is stated as a part of the general breeding goal. But as some of the colours may be considered as genetic defects in a homozygote state mating of two carriers should be avoided. The lists of stallions that are candidates for selection are obtained from Worldfengur and include all registered living stallions which have completed a FEIF breeding field test (breeding show). The location of the stallion at the time of listing is used to indicate where the stallion is in service. The lists will be updated several times per year. Criteria for selection of stallion to a broodmare can be chosen from a scroll list including BLUP total score, conformation, riding ability and each of the 17 individual traits. Restrictions on the inbreeding (F%) in the potential offspring can be varied from no restriction (100) to very low inbreeding allowed (2%). The recommended values are 5-7%. The country where the stallion is in service is chosen from a list of all countries with registered Icelandic horses. The accuracy of the stallion s BLUP index depends on the amount of pedigree and offspring information which contributes to the genetic evaluation. A reasonable value is 60% accuracy of R TI. Higher degree of accuracy based on much offspring information can be chosen by scrolling to a value of 85 95%. Several different maximum list length values can be selected. By pressing Forward a list of stallions ranked on the selected criterion and fulfilling the restrictions chosen will be displayed showing the BLUP index for conformation, riding ability and total score, in addition to the selected criterion, for the selected stallions and for the potential foals. The accuracy (R TI ) of the stallion s BLUP and the inbreeding coefficient (F%) of the potential foal is also displayed. A mouse click on the stallion s FEIF-id number links to the Virtual mate selection screen. Virtual Mate Selection The virtual mate selection java application (servlet) computes BLUP indices on the potential offspring of the selected parents. BLUP indices are computed as the mean of the BLUP indices of the parents for the 17 following traits: 1) Height at withers 2) Mane and tail 3) Slow toelt

4) Walk 5) Head 6) Neck, withers and shoulders 7) Back and hindquarters 8) Proportions 9) Leg quality 10) Leg stance (Correctness of legs) 11) Hooves 12) Toelt 13) Trot 14) Pace 15) Gallop 16) General impression (Form under rider) 17) Spirit Weighted aggregate indices are computed for: 18) Conformation, 19) Riding ability and 20) Total score. The methods used for computation of the BLUP indices are described in Árnason, et al. (2006). The data is from WorldFengur the global database on Icelandic horses. Inbreeding coefficient The relationship (R) between the selected parents is computed by a recursive method of ter Heijden et al. (1977). The diagonal elements of the numerator relationship matrix (A) had been calculated in advance by the algorithm of Sigurdsson (Sigurdsson & Árnason, 1995). The inbreeding coefficient (F) of the offspring is half the coefficient of relationship (R). Both the coefficients are multiplied by 100 and expressed as %. The average inbreeding coefficient in the population is about 2,8%. Close inbreeding should be avoided as risk for genetic defects in the offspring increases with increased inbreeding (inbreeding depression). Matings resulting in inbreeding coefficients above 5% should be avoided. Inbreeding coefficients between 5% and 7% will be shown in purple colour and inbreeding coefficients above 7% are shown in red colour to indicate that this mating is not to be recommended. Colour and pace-gene genotype probabilities The basic colour variation of the Icelandic horse can be explained by segregation of alleles (genes) in 8 known loci (Adalsteinsson, 2001). One more loci for splashed white is known in Icelandic horses, but the registration of that colour is yet incomplete in the data and is therefore ignored. Five other colour loci are known in horses, but have not been found or confirmed in Icelandic horses. Thorvaldsson (2004) has shown that the black smoky colour (glóbrúnn) is caused by the C cr acting on a black basic colour. The same gene causes palomino when acting on chestnut basic colour and buckskin when acting on bay basic colour. In many cases carrier of the C cr gene are registered as black. Thorvaldsson (2004) concludes that the dilutional effects of the C cr gene on black basic colour depends on an interaction with other genes, probably the same genes that control the strength of the black colour which may vary from pale black (2200) to dark black (2700). In similar way the yellowness of the palomino and buckskin colour probably depends on the strength of the chestnut and bay colour, respectively. The champagne gene which was claimed to exist in Tennessee Walking Horses by Sponenberg & Bowling (1996) is therefore almost certainly not to be found in the Icelandic horse population according to the results of Thorvaldsson (2004). Combination of A (agouti) gene, C cr gene, D (dun) gene and E (extension) gene results in dark

yellow colour (often followed by light mane and tail). These horses should actually be registered as bucskin (5???) but are often registered as palomino (4???) instead. For more thorough description of coat colour genetics in horses, see Adalsteinsson (2001) or Bowling (1996, 2000). Overview on the colour genes and their effects are given in the linked explanatory table. [insert link] The estimated gene frequency and the corresponding genotype frequency in the eight colour loci in the Icelandic horse population is shown in a special linked table here. [insert link] The estimates are based on the assumptions that the gene and genotype frequencies are in Hardy Weinberg equilibrium, i. e. not seriously affected by selection, mutation or migration (Falconer, 1989). Coat colour of the horses registered in WorldFengur is given by a 4 digit code which was developed by Stefánsdóttir (1991). Detailed description of the colour code is to be found on www.worldfengur.com. The recent discovery of the fundamental effect of mutations in the DMRT3 gene on neural functions in the spinal cord affecting locomotion in horses has revolutionized the possibilities to predict the basic gaiting ability in Icelandic horses, making it possible to estimate whether the horse is predisposed to be 4-gaited or 5-gaited (Andersson et al., 2012). The DMRT3 gene mutation termed A is also called the pace gene. Almost all horses with flying pace are homozygous for the mutation (AA) while most 4-gaited horses (with toelt) are heterozygous (AC). Horses in non-gaited horse breeds are exclusively homozygous for the wild type CC. Within the breed of Icelandic horses the CC genotype is likely to affect the gaiting ability very negatively, even if some horses with CC genotype have received good toelt scores at breeding field test. Generally it can be assumed that all horses receiving scores 7,5 for pace at breeding field test are of the AA genotype. Most horses receiving pace scores 6,0-7,0 are AA but AC genotypes can t be excluded. In data from breeding field tests about 30% of the horses obtaining pace scores 5,0-5,5 are AA, while the remaining 70% are either AC or CC. There may be various reasons why so many AA horses are shown without pace at breeding field tests. In many cases young horses (four- and five-year-olds) are not yet trained in pace and therefore shown as 4-gaited. Sometimes exceptionally good toelters of AA genotype are not trained in pace in order to preserve the quality in toelt and sometimes even action in the basic gaits. Other reasons related to training and other genetic factors will hopefully be clarified in future studies. Information about pace and trot scores from breeding field tests was used to obtain rough estimates of genotype probabilities for the pace gene in parents and their potential progenies. Prior genotype estimate for any individual horse was based on its highest score for pace at a breeding field test (breeding show). Pace score 7,5 strongly suggest an AA genotype. A pace score = 5,0 and a score for trot 7,0 was taken as a preliminary indication of C- genotype. All other horses were assigned unknown prior genotype --. The Genotype Elimination Algorithm (GEA) of Lange (1997) was used to make the data more consistent, i.e. eliminate impossible genotypes (e.g. by making offspring of two AA parents also AA). About 200 horses had been tested for the pace-gene genotype. The values for these horses were fixed in the analysis. The number of genotyped horses is expected to increase rapidly in the future, which will increase the accuracy of the calculated genotype probabilities for the pace-gene. The application for coat colour and pace-gene show possible genotypes of the parents and of the offspring. The possible genotypes of the parent have been computed in advance by the Genotype Elimination Algorithm (GEA) of Lange (1997). The algorithm works iteratively and eliminates all genotypes of the individuals which are incompatible with the phenotype of the individual or some

of the related animals. By convention a capital letter stands for the dominant allele in each locus while the small letter denotes the recessive allele. The sign - means that the allele type can not be determined. When both alleles in a pair are the same (e.g. EE or ee) the animal is said to be homozygous in that locus and when the pair has different alleles (e.g. Ee) the animal is heterozygos. For further details see e.g. Bowling (1996). The resulting possible genotypes of the parents from the run of the GEA program were used to assign phenotypic code to the animals in the following manner: (e.g. for E-locus) 1 = ee, 2 = Ee (or ee), 3 = EE, 4 = E-, 5 = e-,and 9 = -- (genotype completely unknown). The computer program for calculation of genotype probabilities was obtained from Kerr and Kinghorn (1996) and used to compute the genotype probabilities shown in three rows in the tables for Sire and Dam. The method calculates the conditional probability that the individual animal has a certain genotype given all the data. The genotype probabilities are given with maximum of 3 significant decimals. Genotype probabilities are given on the scale 0.0 to 1.0 (100%). All loci are assumed unlinked in the calculations, even though some of the loci are known to be linked (located on the same chromosome). Homozygous C cr C cr (cc) causes strong dilution of the coat colour towards almost an albino like state (pseudo-albino, cremello, perlino; Icel.: hvítingi). Since many breeders like to avoid mating of two carriers of this gene, a positive probability of this genotype cc is warned for by a red colour in the table showing the genotype probabilities of the offspring. Homozygous RnRn (RR) are claimed to be lethal (at least in some breeds) and mating of two carriers of this gene is recommended to be avoided. A positive probability for the genotype state RR is coloured red in the table. Horses which are homozygote in the silver colour gene (ZZ) tend to have poor vision and have even been found to be nearly blind in some cases. Therefore mating of two carriers of the Z gene should definitely be avoided and a positive probability for the genotype state ZZ is also coloured red in the table. Possible coat colours of the progeny and probabilities of each colour type Finally the the possible phenotypes associated with the offspring's genotypes are illustrated by pictures. The conditional probabilities of each phenotype given the three possible genotypes in each locus are calculated for the offspring. These conditional probabilities are shown in Árnason and Sigurdsson (1998). The conditional probabilities of the additional colours Gray, Tobiano and Roan, which may act independently on any basic colour are given separately. The pictures are used in this servlet by the permission of WorldFengur. The photographer is late Mr Fridthjófur Thorkelsson, who's contribution is greatly acknowledged. References Adalsteinsson, Stefán, 2001. Íslenski hesturinn litir og erfdir. Ormstunga, Reykjavík, Iceland. Andersson, L.S., Larhammar, M., Memic; F., Wootz, H., Schwochow, D., Rubin, C-J., Patra, K., Árnason, T., Wellbring, L., Hjälm, G., Imsland, F., Petersen, J.L., McCue, M.E., Mickelson, J.R., Cothran, G., Ahituv, N., Roepstorff, L., Mikko, S., Vallstedt, A., Lindgren, G., Andersson L., Kullander, K., 2012. Mutations in DMRT3 affect locomotion in horses and spinal circuit function in mice. Nature 488:642-646. Árnason, Thorvaldur & Sigurdsson, Ágúst, 1998. A computing procedure for estimating genotype probabilities at eight individual colour loci in the Icelandic toelter horse. 49 th Annual Meeting of the European Association for Animal Production, Poland, 24-27 August 1998. Bowling, A.T., 1996. Horse Genetics. CAB International. Wallingford, Oxon, UK.

Bowling, A.T., 2000. The Genetics of the Horse. Chapter 3. CAB International. Wallingford, Oxon, UK. Falconer. D.S., 1989. Introduction to Quantitative Genetics. Longman Scientific & Technical, Harlow, Essex, UK. & John Wiley & Sons, Inc., New York, USA. Kerr, R.J. & Kinghorn, B.P., 1996. An efficient algorithm for segregation analysis in large populations. J. Anim. Breed. Genet. 113:457-469. Lange, K., 1997. Mathematical and Statistical Methods for Genetic Analysis. Springer-Verlag, New York, USA. Sigurdsson, Ágúst & Árnason, Thorvaldur, 1995. Predicting genetic trend by uni- and multitrait models. Acta Agric. Scand. Sect. A, Animal Sci. 45:1-10. Stefánsdóttir, Gudrún, Jóhanna, 1991. Litaerfdir hrossa og könnun á tídni lita íslenskra hrossa. B.Sci. Thesis, Agricultural University of Iceland. Hvanneyri, Iceland. Ter Heijden, E., Chesnais, J.P., Hickman, C.G., 1977. An efficient method of computing the numerator relationship matrix and its inverse matrix with inbreeding for large sets of animals. Theor. Appl. Genet. 49:237-241. Thorvaldsson, Gudni, 2004. Eru til kampavínslitir í íslenska hrossastofninum? Report RALA 027/BU-004. Agricultural University of Iceland, Hvanneyri, Iceland.