PoultryTechnical NEWS. GenomChicks Advanced layer genetics using genomic breeding values. For further information, please contact us:

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1 PoultryTechnical LOHMANN TIERZUCHT LOHMANN TIERZUCHT GmbH will continue to conduct comprehensive performance testing and is continuously investing in extending the testing capacities as well as looking for potential new traits which provide an advantage for egg producers and hatcheries. Many of these new potential traits involve bird behaviour and traits related with animal welfare and livability. The maximum number of saleable eggs per hen housed highly determines the commercial success of laying hens. This is achieved by combining outstanding laying performance with excellent eggshell quality and of course, commendable vitality. These are our major selection goals. No other competitor has managed to achieve anything close to the good shell stability of the laying hens at LOHMANN TIERZUCHT, which is definitely a prerequisite for an extended laying cycle. The comprehensive phenotypic measurements at LOHMANN TIERZUCHT will now be supplemented with genomic information which will promote further genetic improvements and enhance the leading posi- tion of layers from LOHMANN TIERZUCHT GmbH. GenomChicks is a practical application within the framework of the Synbreed project. Synbreed is a network of excellence for interdisciplinary, genome based research in plant and animal breeding and is funded by the German Federal Ministry of Education and Research (FKZ C). NEWS With this selection and product campaign, GenomChicks, LOHMANN TIERZUCHT GmbH will once again set a milestone in terms of applied research and fast implementation in breeding practice. The first parent stocks of white as well as brown layers of GenomChicks will be available soon. Synbreed project partners For further information, please contact us: info@ltz.de GenomChicks Advanced layer genetics using genomic breeding values Affymetrix array LOHMANN TIERZUCHT GmbH Am Seedeich Cuxhaven Germany P.O. Box Cuxhaven Germany Phone +9 (0) Telefax +9 (0) info@ltz.de

2 Blood sample preparation conditions, respectively. Due to sex limited data recording, the selection of males for egg quality and production traits are based mainly on female sibling tests. progress ( G/t), by increasing the accuracy of the estimated breeding values (rai) and by shortening the generation interval ( T). the possibility of genotyping many individuals for these markers, make it feasible to predict total genetic merit on the basis of SNPs. In dairy cattle for instance, genomic selection has been proven to work and has become the standard breeding procedure in the last years. The introduction of genomic selection leads to an increase in genetic progress. The first step in genomic selection is to genotype an extended reference population which must have high accurate phenotypes or breeding values, also known as training data set. Based on this information, the effect of individual SNP alleles for each interesting trait will be estimated in this reference population. Selection candidate birds without phenotypes can be genotyped and their breeding values will be predicted just by summing up all the individual effects of their SNP alleles. Molecular genetics and especially the science of genomics, have advanced exponentially in recent years and there are ongoing discussions on the various models of applications for the different species of farm animals. Dramatic advances in the identification of DNA variants and consi- G / t = i x rai x σa T Formula for breeding progress Single Nucleotide Polymorphisms (SNPs) are single nucleotide variants within the DNA sequence. With a large number of SNPs, the genetic breeding values of the birds can be estimated for all performance traits with a higher accuracy at an early age even if they do not have phenotypes. The availability of many thousands of SNP markers spread across the whole genome and has been developed for comprehensive genotyping of all commercial lines. The highest potential in layer breeding lies undoubtedly in the male side, since they are selected based on the female sibling test, as mentioned above. Selection of the Preparation of DNA New selection candidate most promising male within full sib families already in the rearing period will improve the rate of genetic progress and can substantially reduce the generation interval. The pre-requisite for the application is, however, up-stream performance testing for all traits of commercial interest. Since the estimation of the SNPs effects for predicting genomic breeding values is based on phenotypes of the training data set, it is evident that extensive testing in different housing systems and challenge situations, as well as the recording of new traits, set the fundamentals to maximise the use of this new tool. A continuous retraining should take place. New birds with both their phenotypes and genotypes should therefore be regularly included in Genotypes Pedigree Phenotypes PCA Pedigree relationship Conventional BV the reference population in order to maintain the highest accuracy. First Results... Graphic 2 shows the effect of each individual SNP for a given trait in which different colours refer to different chromosomes. As shown in the plot, there are many SNPs that contribute to explain the variation within one trait, thus justifying the use of a whole genome approach instead of the use of a small number of markers only. Since the true breeding value is unknown, the only posibility to assess the goodness of the genomic breeding values (GBV) is to compare them with the conventional breeding values (EBV) which are estimated based on phenotypes and pedigree relationships. Graphic 3 shows the relationship between EBV and GBV for a subset of 5 birds. As expected, both values show a good agreement, although a relative high deviation was assessed for some birds. If the best 20 % of the birds were selected based on GBV or EBV, 63.6 % of the selected birds would be in both groups. Graphic 3 Example of overlapping between genomic and conventional breeding values 6 Filter 5 Conventional performance test Illustration of a SNP DNA molecule 1 differs from DNA molecule 2 at a single base-pair location (source: wikipedia/david Hall) Within the framework of the research project Synbreed, dense genotyping has been implemented in order to find more SNPs which can be used as markers for selection. After sequencing all major Lohmann lines, a customised 600 K chip Imputation g derable decreases in genotyping costs, enable the use of this technology in animal breeding. Genomic selection can contribute significantly to the enhancement of breeding SNPeffect/σ x 10 For decades now, selection has been done within closed populations based on comprehensive phenotypic data recording in both, pure and cross-line birds under standardised and commercial housing Genomic relationship Genomic Prediction Cross Validation Graphic 1 Pipeline establishment Commercial application 0e e e e + 05 SNPnr Graphic 2 Example of the SNPs effects on a Mahattan Plot e e + 05

3 Blood sample preparation conditions, respectively. Due to sex limited data recording, the selection of males for egg quality and production traits are based mainly on female sibling tests. progress ( G/t), by increasing the accuracy of the estimated breeding values (rai) and by shortening the generation interval ( T). the possibility of genotyping many individuals for these markers, make it feasible to predict total genetic merit on the basis of SNPs. In dairy cattle for instance, genomic selection has been proven to work and has become the standard breeding procedure in the last years. The introduction of genomic selection leads to an increase in genetic progress. The first step in genomic selection is to genotype an extended reference population which must have high accurate phenotypes or breeding values, also known as training data set. Based on this information, the effect of individual SNP alleles for each interesting trait will be estimated in this reference population. Selection candidate birds without phenotypes can be genotyped and their breeding values will be predicted just by summing up all the individual effects of their SNP alleles. Molecular genetics and especially the science of genomics, have advanced exponentially in recent years and there are ongoing discussions on the various models of applications for the different species of farm animals. Dramatic advances in the identification of DNA variants and consi- G / t = i x rai x σa T Formula for breeding progress Single Nucleotide Polymorphisms (SNPs) are single nucleotide variants within the DNA sequence. With a large number of SNPs, the genetic breeding values of the birds can be estimated for all performance traits with a higher accuracy at an early age even if they do not have phenotypes. The availability of many thousands of SNP markers spread across the whole genome and has been developed for comprehensive genotyping of all commercial lines. The highest potential in layer breeding lies undoubtedly in the male side, since they are selected based on the female sibling test, as mentioned above. Selection of the Preparation of DNA New selection candidate most promising male within full sib families already in the rearing period will improve the rate of genetic progress and can substantially reduce the generation interval. The pre-requisite for the application is, however, up-stream performance testing for all traits of commercial interest. Since the estimation of the SNPs effects for predicting genomic breeding values is based on phenotypes of the training data set, it is evident that extensive testing in different housing systems and challenge situations, as well as the recording of new traits, set the fundamentals to maximise the use of this new tool. A continuous retraining should take place. New birds with both their phenotypes and genotypes should therefore be regularly included in Genotypes Pedigree Phenotypes PCA Pedigree relationship Conventional BV the reference population in order to maintain the highest accuracy. First Results... Graphic 2 shows the effect of each individual SNP for a given trait in which different colours refer to different chromosomes. As shown in the plot, there are many SNPs that contribute to explain the variation within one trait, thus justifying the use of a whole genome approach instead of the use of a small number of markers only. Since the true breeding value is unknown, the only posibility to assess the goodness of the genomic breeding values (GBV) is to compare them with the conventional breeding values (EBV) which are estimated based on phenotypes and pedigree relationships. Graphic 3 shows the relationship between EBV and GBV for a subset of 5 birds. As expected, both values show a good agreement, although a relative high deviation was assessed for some birds. If the best 20 % of the birds were selected based on GBV or EBV, 63.6 % of the selected birds would be in both groups. Graphic 3 Example of overlapping between genomic and conventional breeding values 6 Filter 5 Conventional performance test Illustration of a SNP DNA molecule 1 differs from DNA molecule 2 at a single base-pair location (source: wikipedia/david Hall) Within the framework of the research project Synbreed, dense genotyping has been implemented in order to find more SNPs which can be used as markers for selection. After sequencing all major Lohmann lines, a customised 600 K chip Imputation g derable decreases in genotyping costs, enable the use of this technology in animal breeding. Genomic selection can contribute significantly to the enhancement of breeding SNPeffect/σ x 10 For decades now, selection has been done within closed populations based on comprehensive phenotypic data recording in both, pure and cross-line birds under standardised and commercial housing Genomic relationship Genomic Prediction Cross Validation Graphic 1 Pipeline establishment Commercial application 0e e e e + 05 SNPnr Graphic 2 Example of the SNPs effects on a Mahattan Plot e e + 05

4 Blood sample preparation conditions, respectively. Due to sex limited data recording, the selection of males for egg quality and production traits are based mainly on female sibling tests. progress ( G/t), by increasing the accuracy of the estimated breeding values (rai) and by shortening the generation interval ( T). the possibility of genotyping many individuals for these markers, make it feasible to predict total genetic merit on the basis of SNPs. In dairy cattle for instance, genomic selection has been proven to work and has become the standard breeding procedure in the last years. The introduction of genomic selection leads to an increase in genetic progress. The first step in genomic selection is to genotype an extended reference population which must have high accurate phenotypes or breeding values, also known as training data set. Based on this information, the effect of individual SNP alleles for each interesting trait will be estimated in this reference population. Selection candidate birds without phenotypes can be genotyped and their breeding values will be predicted just by summing up all the individual effects of their SNP alleles. Molecular genetics and especially the science of genomics, have advanced exponentially in recent years and there are ongoing discussions on the various models of applications for the different species of farm animals. Dramatic advances in the identification of DNA variants and consi- G / t = i x rai x σa T Formula for breeding progress Single Nucleotide Polymorphisms (SNPs) are single nucleotide variants within the DNA sequence. With a large number of SNPs, the genetic breeding values of the birds can be estimated for all performance traits with a higher accuracy at an early age even if they do not have phenotypes. The availability of many thousands of SNP markers spread across the whole genome and has been developed for comprehensive genotyping of all commercial lines. The highest potential in layer breeding lies undoubtedly in the male side, since they are selected based on the female sibling test, as mentioned above. Selection of the Preparation of DNA New selection candidate most promising male within full sib families already in the rearing period will improve the rate of genetic progress and can substantially reduce the generation interval. The pre-requisite for the application is, however, up-stream performance testing for all traits of commercial interest. Since the estimation of the SNPs effects for predicting genomic breeding values is based on phenotypes of the training data set, it is evident that extensive testing in different housing systems and challenge situations, as well as the recording of new traits, set the fundamentals to maximise the use of this new tool. A continuous retraining should take place. New birds with both their phenotypes and genotypes should therefore be regularly included in Genotypes Pedigree Phenotypes PCA Pedigree relationship Conventional BV the reference population in order to maintain the highest accuracy. First Results... Graphic 2 shows the effect of each individual SNP for a given trait in which different colours refer to different chromosomes. As shown in the plot, there are many SNPs that contribute to explain the variation within one trait, thus justifying the use of a whole genome approach instead of the use of a small number of markers only. Since the true breeding value is unknown, the only posibility to assess the goodness of the genomic breeding values (GBV) is to compare them with the conventional breeding values (EBV) which are estimated based on phenotypes and pedigree relationships. Graphic 3 shows the relationship between EBV and GBV for a subset of 5 birds. As expected, both values show a good agreement, although a relative high deviation was assessed for some birds. If the best 20 % of the birds were selected based on GBV or EBV, 63.6 % of the selected birds would be in both groups. Graphic 3 Example of overlapping between genomic and conventional breeding values 6 Filter 5 Conventional performance test Illustration of a SNP DNA molecule 1 differs from DNA molecule 2 at a single base-pair location (source: wikipedia/david Hall) Within the framework of the research project Synbreed, dense genotyping has been implemented in order to find more SNPs which can be used as markers for selection. After sequencing all major Lohmann lines, a customised 600 K chip Imputation g derable decreases in genotyping costs, enable the use of this technology in animal breeding. Genomic selection can contribute significantly to the enhancement of breeding SNPeffect/σ x 10 For decades now, selection has been done within closed populations based on comprehensive phenotypic data recording in both, pure and cross-line birds under standardised and commercial housing Genomic relationship Genomic Prediction Cross Validation Graphic 1 Pipeline establishment Commercial application 0e e e e + 05 SNPnr Graphic 2 Example of the SNPs effects on a Mahattan Plot e e + 05

5 LOHMANN TIERZUCHT GmbH will continue to conduct comprehensive performance testing and is continuously investing in extending the testing capacities as well as looking for potential new traits which provide an advantage for egg producers and hatcheries. Many of these new potential traits involve bird behaviour and traits related with animal welfare and livability. The maximum number of saleable eggs per hen housed highly determines the commercial success of laying hens. This is achieved by combining outstanding laying performance with excellent eggshell qua - lity and of course, commendable vita lity. These are our major selection goals. No other competitor has managed to achieve anything close to the good shell stability of the laying hens at LOHMANN TIERZUCHT, which is definitely a prerequisite for an extended laying cycle. The comprehensive phenotypic measurements at LOHMANN TIERZUCHT will now be supplemented with genomic information which will promote further genetic improvements and enhance the leading posi- tion of layers from LOHMANN TIERZUCHT GmbH. GenomChicks is a practical application within the framework of the Synbreed project. Synbreed is a network of excellence for interdisciplinary, genome based research in plant and animal breeding and is funded by the German Federal Ministry of Education and Research (FKZ C). Synbreed project partners With this selection and product campaign, GenomChicks, LOHMANN TIERZUCHT GmbH will once again set a milestone in terms of applied research and fast implementation in breeding practice. The first parent stocks of white as well as brown layers of GenomChicks will be available soon. Affymetrix array

6 PoultryTechnical LOHMANN TIERZUCHT LOHMANN TIERZUCHT GmbH will continue to conduct comprehensive performance testing and is continuously investing in extending the testing capacities as well as looking for potential new traits which provide an advantage for egg producers and hatcheries. Many of these new potential traits involve bird behaviour and traits related with animal welfare and livability. The maximum number of saleable eggs per hen housed highly determines the commercial success of laying hens. This is achieved by combining outstanding laying performance with excellent eggshell quality and of course, commendable vitality. These are our major selection goals. No other competitor has managed to achieve anything close to the good shell stability of the laying hens at LOHMANN TIERZUCHT, which is definitely a prerequisite for an extended laying cycle. The comprehensive phenotypic measurements at LOHMANN TIERZUCHT will now be supplemented with genomic information which will promote further genetic improvements and enhance the leading posi- tion of layers from LOHMANN TIERZUCHT GmbH. GenomChicks is a practical application within the framework of the Synbreed project. Synbreed is a network of excellence for interdisciplinary, genome based research in plant and animal breeding and is funded by the German Federal Ministry of Education and Research (FKZ C). NEWS With this selection and product campaign, GenomChicks, LOHMANN TIERZUCHT GmbH will once again set a milestone in terms of applied research and fast implementation in breeding practice. The first parent stocks of white as well as brown layers of GenomChicks will be available soon. Synbreed project partners For further information, please contact us: info@ltz.de GenomChicks Advanced layer genetics using genomic breeding values Affymetrix array LOHMANN TIERZUCHT GmbH Am Seedeich Cuxhaven Germany P.O. Box Cuxhaven Germany Phone +9 (0) Telefax +9 (0) info@ltz.de