1 00:00:02,760 --> 00:00:11,050 Today's topic will focus on the area of estimating the genetic value of various characteristics and features of the quantitative character of livestock. 2 00:00:11,510 --> 00:00:17,810 The lecture is part of module number 3 – Animal breeding, which is part of the ISAGREED project. 3 00:00:18,510 --> 00:00:24,536 This presentation was supported by the Erasmus plus KA2 Partnership grant for cooperation entitled: 4 00:00:24,536 --> 00:00:33,241 Innovation of the structure and content of study programs in the field of management of animal genetic and food resources using digitalization. 5 00:00:33,241 --> 00:00:43,910 The genetic value of an animal represents the genetic potential of a particular trait that the animal can pass on to its offspring, usually associated with quantitative traits. 6 00:00:44,410 --> 00:00:52,510 We don't really know the genetic value of an individual. We only estimate it in the form of the breeding value of a particular trait. 7 00:00:52,970 --> 00:00:58,870 Estimating the genetic value (breeding value) is a key element in livestock breeding. 8 00:00:59,250 --> 00:01:06,910 It allows breeders to identify and select individuals that have the greatest potential to improve certain traits within the entire population. 9 00:01:07,610 --> 00:01:15,190 In the breeding process itself, the estimation of the breeding values of livestock occupies a central and irreplaceable place. 10 00:01:16,170 --> 00:01:24,390 Estimation of breeding values (knowledge of the genetic quality of animals) is now carried out on the basis of two basic approaches. 11 00:01:24,860 --> 00:01:34,304 The first (classical) approach is an estimate based on several phenotypic manifestations of individual animal characteristics over a longer period of time, 12 00:01:34,304 --> 00:01:40,640 usually related to the length of the generation interval of a particular species and breed of livestock. 13 00:01:41,180 --> 00:01:46,920 Knowledge of the pedigree information of individual animals also plays an important role in this approach. 14 00:01:47,820 --> 00:01:55,840 The second approach is to estimate the breeding value based on molecular-genetic information obtained during the so-called genotyping of animals. 15 00:01:56,440 --> 00:02:02,500 Currently, genomic information is most widely used at the level of its different abundance and density. 16 00:02:03,000 --> 00:02:10,020 Both of these approaches can be used separately or combined into a single system for estimating the genetic quality of animals. 17 00:02:10,920 --> 00:02:21,054 The importance of knowing the breeding value of an individual is in the subsequent improvement of several productive but also non-productive characteristics of animals in the next generation, 18 00:02:21,232 --> 00:02:26,150 production of milk, meat, eggs, wool, sports performance. 19 00:02:26,930 --> 00:02:37,830 An important element is also the current genetic improvement of health, reproductive characteristics, fertility, disease resistance, longevity, viability. 20 00:02:38,530 --> 00:02:49,630 The final goal is in fact the economic efficiency of individual livestock farms: reduction of costs, increase of economic revenues from the production or sale of breeding animals. 21 00:02:50,160 --> 00:03:01,920 For this reason, individual breed values enter into different types of selection indices (global-aggregate selection indices, or selection indices specific to a given group of traits, 22 00:03:02,080 --> 00:03:12,871 exterior, fertility, quality of animal products). In the past, important methods were based mainly on the knowledge of pedigree information and information 23 00:03:12,871 --> 00:03:18,440 about the performance (phenotype) of individual animals in a wider time horizon. 24 00:03:18,900 --> 00:03:26,080 In the past, mother-daughter methods and especially the peer method (CC test) played an important role. 25 00:03:26,580 --> 00:03:36,640 Gradually, with the advent of computer technology, the BLUP (Best Linear Unbiased Prediction) method began to be used very intensively. 26 00:03:37,060 --> 00:03:47,040 It was an advanced statistical method that combines in various forms and depths the pedigree information and information on the performance of animals needed to estimate their breeding value. 27 00:03:47,960 --> 00:03:59,322 Recently, new (modern) genomic approaches have emerged in the estimation of breed values, which are carried out either in the form of so-called 28 00:03:59,322 --> 00:04:10,048 direct (pure) genomic breed values, or as part (extension) of existing (traditional) approaches based on the BLUP method in the form of 29 00:04:10,184 --> 00:04:27,310 several forms of the GBLUP method (Genomic BLUP). Best Linear Prediction. Linear model with mixed effects. Simultaneous use of fixed and random effects. 30 00:04:27,770 --> 00:04:31,750 BLUP is the basis of the methods known as the Animal model. 31 00:04:32,130 --> 00:04:35,114 In 1999, STN (Slovak Technical Norm) 32 00:04:35,282 --> 00:04:44,790 466114-1 Estimation of breeding values of cattle milk yield indicators, 33 00:04:44,970 --> 00:04:49,930 Part 1: BLUP method, was published in the Slovak Republic. 34 00:04:50,790 --> 00:04:57,574 Linear mixed models in the form of BLUP are the basis of traditional estimation of livestock breeding values (BLUP models). 35 00:04:57,702 --> 00:05:09,490 BLUP - sire model (paternal model) - estimation of the breeding values of only some individuals in the population (usually males). 36 00:05:10,000 --> 00:05:20,449 BLUP - animal model (individual model) - estimation of the breeding values of all individuals in the population. If we estimate breed values for one trait, 37 00:05:20,449 --> 00:05:31,100 these are so-called single-trait models, if for several traits at the same time, these are multi-traits models using correlation relationships between traits. 38 00:05:31,920 --> 00:05:41,420 An important condition for the use of the BLUP method is the initial knowledge of the basic genetic parameters necessary for the estimation of the breeding values themselves. 39 00:05:42,070 --> 00:05:45,410 The BLUP method is used in many modifications. 40 00:05:46,230 --> 00:05:50,550 Probably the most well-known use of this method is the BLUP-Animal model (additive genetic model of breeding value estimation). 41 00:05:50,670 --> 00:05:59,520 The basic principle of using the BLUP Animal model is the knowledge of four basic groups of information about animals: 42 00:05:59,520 --> 00:06:08,370 pedigree information, own performance, offspring performance and performance of other relatives in the collateral row. 43 00:06:08,720 --> 00:06:15,860 Knowing all groups of information is time-consuming, but it brings an extremely reliable estimate of breeding values. 44 00:06:16,280 --> 00:06:26,580 The advantage of this method is that the absence of a certain group of information does not have a limiting effect on the estimate itself (but the reliability of the estimate usually decreases). 45 00:06:27,560 --> 00:06:35,508 The BLUP method (Best Linear Unbiased Prediction) is a solution to a large system of equations where the individual breeding 46 00:06:35,508 --> 00:06:41,790 values of animals are unknown, as well as the levels of all effects affecting the evaluated trait. 47 00:06:42,130 --> 00:06:46,714 The best prediction means the best of all possible linear unbiased estimates 48 00:06:46,842 --> 00:06:51,090 The correlation between true and estimated breed values is maximized, 49 00:06:51,250 --> 00:06:55,230 with this method the smallest residual variance of the trait is achieved. 50 00:06:55,770 --> 00:07:02,910 Linear means that the measured phenotypic expression of the trait is distributed in a linear combination of all monitored effects. 51 00:07:03,300 --> 00:07:15,280 An unbiased (unbiased) prediction is the fact that the average value of the calculated estimated breeding values is equal to the mean value of the actual (true) genetic values. 52 00:07:15,700 --> 00:07:19,228 The prediction is because it is an estimate of random effects 53 00:07:19,364 --> 00:07:24,280 An estimate of breed value is a typical estimate of a random, genetic effect. 54 00:07:24,820 --> 00:07:31,640 The BLUP method is very closely related to the method of estimating the main components of variance in these models. 55 00:07:32,350 --> 00:07:41,174 The above model (without taking into account kinship) estimates the individual levels of unknown fixed effects b and unknown random effects (breed values) a. 56 00:07:41,302 --> 00:07:55,450 For solving large problems (large numbers of animals, large numbers of equations), it is usually not possible to use the previous procedure using the inversion of the coefficient matrix. 57 00:07:56,110 --> 00:08:04,514 Several iterative procedures and methods have been created that solve the problem in practice quite accurately. When using a kinship model, 58 00:08:04,642 --> 00:08:12,470 kinship relationships are expressed using a kinship matrix (A), which is actually a matrix of additive genetic similarity. 59 00:08:12,970 --> 00:08:19,950 The correctness and truthfulness of pedigree information plays a very important role in this case of using the Animal model. 60 00:08:20,570 --> 00:08:26,270 There are several methods of taking genomic information into account when estimating breed values. 61 00:08:26,770 --> 00:08:32,070 Most of these methods are created on the basis of or modification of the BLUP method. 62 00:08:32,520 --> 00:08:36,600 In general, all these methods can be divided into two groups: 63 00:08:36,720 --> 00:08:44,060 the first uses multi-step approaches when considering genomic information, and the second group uses one-step approaches. 64 00:08:44,600 --> 00:08:51,700 Methods based on a one-step approach, which are intensively verified and applied, are proving to be very promising. 65 00:08:52,600 --> 00:09:01,620 The essence of the one-step approach: the basic principle is the modification of the additive genetic similarity matrix by the genomic similarity matrix 66 00:09:01,760 --> 00:09:08,440 the modification consists of inversion of the additive genetic similarity matrix using the genomic affinity matrix). 67 00:09:08,940 --> 00:09:16,560 Apart from taking into account the genomic matrix of similarity, nothing changes in the method of estimating breed values. 68 00:09:16,980 --> 00:09:23,520 The advantage is that genomically modified breed values are estimated even for animals that are not genotyped. 69 00:09:23,860 --> 00:09:30,192 The one-step procedure is quite computationally demanding in the case of a large number of genotyped animals. 70 00:09:30,356 --> 00:09:35,700 However, the current performance of computer technology partially eliminates this problem. 71 00:09:36,560 --> 00:09:42,340 There are features and characteristics of livestock that are significantly affected by the maternal effect. 72 00:09:43,000 --> 00:09:46,100 Such models are called models with a maternal effect. 73 00:09:46,720 --> 00:09:57,820 This is mainly an estimate of the breed values of traits, where the mother has a relatively significant influence on her offspring during pregnancy, which is typical only for female mammals. 74 00:09:58,390 --> 00:10:05,410 Models with maternal effects are typical in estimating breed values, fertility indicators and calving ease traits. 75 00:10:06,390 --> 00:10:15,570 Estimating breed values based on nonlinear models is not so typical, but there are indicators where it is more advantageous to use nonlinear approaches. 76 00:10:16,030 --> 00:10:21,090 Most often, nonlinear models evaluate some indirect utility properties. 77 00:10:21,630 --> 00:10:28,170 Nonlinear systems for evaluating the growth and development of livestock are known with direct performance properties. 78 00:10:28,660 --> 00:10:36,120 The growth of animals generally behaves in a non-linear manner, especially if we observe growth over a longer period of time. 79 00:10:36,580 --> 00:10:46,572 In a short period of time, the growth of animals, as a rule, behaves linearly. Within the indirect performance characteristics of livestock, 80 00:10:46,716 --> 00:10:53,760 the evaluation of longevity and survivability of animals has recently become increasingly important in modern breeding. 81 00:10:54,230 --> 00:11:02,570 In fact, longevity appears to be a summary indicator that, in its essence, expresses all the characteristics of animals. 82 00:11:03,110 --> 00:11:11,274 As an example, we can mention the longevity of cows in reproduction and their lifelong performance, which is currently coming to the forefront 83 00:11:11,274 --> 00:11:17,770 of selection criteria and has a very close relationship with the economic efficiency of milk and meat production. 84 00:11:18,430 --> 00:11:19,510 Thank you for your attention.