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FFL-JA-Forskningsmidlene for jordbruk og matindustri

Genotyping goats to cost effectively increase genetic progress

Alternative title: Genotyping for å øke netto nåverdi av avlsframgangen på geit

Awarded: NOK 2.3 mill.

Genomic Selection (GS) is expected to result in an increase in accuracy of selection of young animals and an increase in rate of genetic improvement for the population. GS has been successfully introduced in many dairy cattle populations around the world but is less widespread in small ruminants. The cost for SNP chip genotyping compared to the revenue in small ruminants has been a limitation to broad introduction of GS. GBS is a cheaper alternative to SNP chip genotyping and will be used in this project. AgResearch, New Zealand, is world known for use of GBS as genotyping procedure for goats and many other species and is partner of the current project. Norway has a well-structured dairy goat breeding program, consisting of 45 breeding herds (7000 does) and 200 commercial herds (20000 does). Artificial insemination (AI) plays an important role in the program. The breeding goal has 11 traits, combined into a total merit index (TMI) used for selection. The main aim of this project was to implement Single Step GBLUP (ssGBLUP) into the monthly routine genetic evaluations of Norwegian dairy goats. Building an informative and representative reference population is a pre-requisite for implementation of GS. So far, we have genotyped more than 7000 does with milk recordings and bucks with daughters with production. All goats are from breeding herds with good genetic connectedness. The usage of genotypes is threefold. Firstly, for genomic selection, secondly to screen animals for undesirable known mutations, and thirdly for parentage test. AgResearch has developed a parentage test based on GBS genotypes. Genotyping of both bucks and does open the opportunity of testing for correctness of recorded sire and dam if genotyped. In case of identification of wrong recorded parentage, a search for a better match has been done and corrected in the goat recording system. Such improvements result in a more correct pedigree which in turn improves the genetic evaluations and further gives more correct computations of inbreeding estimates of the individual. Breeding bucks have over several years been tested for the casein variants in everyday speech known as «Norwegian null allele» in the alfa s1 casein gene. AgResearch developed a test for the «Norwegian null» as a part of their genotyping procedure. The result is reported to the Norwegian goat breeders and used in their breeding decisions. As a part of the project, we searched for undiscovered gene variants that affects the 11 traits in the breeding goal. In addition, we also searched for single genes for the new trait «supernumerary teats». The searches did not show any new single genes variants that is not yet known internationally. It is costly to build a sufficiently large reference population. As a part of the project, we investigated if the Norwegian goat population could benefit from collaboration with other populations using same genotyping platform in establishing a sufficiently large reference population. GBS genotypes from New Zealand, Australia and Norway was therefore compared in a PCA-analysis. Results showed that goats from New Zealand and Australia are too genetically distant from the Norwegian goat population. The Norwegian dairy goat population will therefore not benefit from joint reference population with New Zealand and Australia. In April 2021 ssGBLUP was introduced into the routine genetic evaluation for goat for all 11 traits currently included in the breeding goal. Including a genotypic information into the genetic evaluation results in a raise in accuracy of EBV (Estimated Breeding Value) especially for bucks that has not yet had their own daughters in production. When bucks were selected for AI in 2022, we included the 1.5-year-old bucks among the AI candidates, and more than half of the selected bucks were from the youngest year class. The reasoning for doing so is the increased accuracy of breeding values in young animals. In addition, more bucks are alive at 1.5 years of age, which makes the pool for selection larger, raises the selection intensity and results in a larger genetic progress. Further, with a reduced age of bucks in AI the generation interval of AI ram and progeny will decrease. Implementation of genomic selection in the breeding program of Norwegian Dairy Goats will, due to the increase in accuracy of selection and the reduced generation interval, result in an increase in genetic progress per year.

OUTCOME 1. Genotyping pipeline A cost-effective genotyping pipeline has been built, including the complete process from tissue sampling, DNA extraction, genotyping and publishing of results. 2. Parentage test AgResearch has developed a parentage test based on GBS genotypes. Genotyping of both bucks and does open the opportunity of testing for correctness of recorded sire and dam if genotyped. In case of identification of wrong recorded parentage, a search for a better match has been done and corrected in the goat recording system. 3. Casein gene variant test Breeding bucks have over several years been tested for the casein variants in everyday speech known as «Norwegian null allele» in the alfa s1 casein gene. AgResearch developed a test for the «Norwegian null» as a part of their genotyping procedure. 4. Gene variants with major impact As a part of the project, we searched for undiscovered gene variants that affects the 11 traits in the breeding goal. In addition, we also searched for single genes for the new trait «supernumerary teats». The searches did not show any new single genes variants that is not yet known internationally. 5. Joint reference population We investigated if the Norwegian goat population could benefit from collaboration with other populations using same genotyping platform in establishing a sufficiently large reference population. GBS genotypes from New Zealand, Australia and Norway was compared in a PCA-analysis. Results showed that goats from New Zealand and Australia are too genetically distant from the Norwegian goat population. 6. Reference population of Norwegian goats An informative reference population of more than 7000 does with lactation and bucks with daughters in production has been build. 7. Genomic breeding values in the routine evaluation In April 2021 ssGBLUP was introduced into the routine genetic evaluation for goat for all 11 traits currently included in the breeding goal. 8. Change in the breeding program Including genotypic information into the genetic evaluation results in a raise in accuracy of EBV (Estimated Breeding Value) especially for bucks that has not yet had their own daughters in production. When bucks were selected for AI in 2022, we included the 1.5-year-old bucks among the AI candidates, and more than half of the selected bucks were from the youngest year class. The reasoning for doing so is the increased accuracy of breeding values in young animals. In addition, more bucks are alive at 1.5 years of age, which makes the pool for selection larger, raises the selection intensity and results in a larger genetic progress. Further, with a reduced age of bucks in AI the generation interval of AI ram and progeny will decrease. IMPACT Implementation of genomic selection in the breeding program of Norwegian Dairy Goats will, due to the increase in accuracy of selection and the reduced generation interval, result in an increase in genetic progress per year.

Genomic Selection (GS) is expected to result in an increase in accuracy of selection of young animals and an increase in rate of genetic improvement for the population. GS has been successfully introduced in many dairy cattle populations around the world, but is less widespread in small ruminants. The lower use of genomic selection in small ruminant populations are related to issues like low linkage disequilibrium, small reference population size, and lack of structured breeding programs. Also the cost for SNP chip genotyping compared to the revenue in small ruminants has been a limitation to broad introduction of GS. Recently, genotyping by sequencing (GBS) has been developed. GBS is a cheaper alternative to SNP chip genotyping. The aim of the current project is to cost-effectively implement GS for traits in the breeding goal in the Norwegian Dairy Goat population by use of GBS as genotyping procedure. At least 7,000 animals will be genotyped and phenotyped and be included in the reference population. These animals will be A.I. bucks, natural service bucks and does from well-connected breeding herds. A search for major genes for existing traits in the breeding goal will be done. If major genes are found, they will be weighted in the single-step GBLUP procedure used for genomic evaluation. The implementation will be optimized in terms of weight parameters for genomic and polygenic information using model validation. Norway has a well structured dairy goat breeding program, consisting of 48 breeding herds (7000 does) and 230 commercial herds (23000 does). Artificial insemination (AI) plays an important role in the program. The breeding goal has 11 traits, combined into a total merit index (TMI) to be used for selection. Implementation of GS in the breeding program for Norwegian Dairy Goats is expected to increase the yearly genetic gain in the TMI by in excess of 20% mainly caused by an increase in accuracy of TMI for young animals.

Funding scheme:

FFL-JA-Forskningsmidlene for jordbruk og matindustri