Systems genetics and genome-wide association approaches for analysis of feed intake, feed efficiency, and performance in beef cattle.

Feed intake, feed efficiency, and weight gain are important economic traits of beef cattle in feedlots. In the present study, we investigated the physiological processes underlying such traits from the point of view of systems genetics. Firstly, using data from 1334 Nellore (Bos indicus) cattle and 943,577 single nucleotide polymorphisms (SNPs), a genome-wide association analysis was performed for dry matter intake, average daily weight gain, feed conversion ratio, and residual feed intake with a Bayesian Lasso procedure. Genes within 50-kb SNPs, most relevant for explaining the genomic variance, were annotated and the biological processes underlying the traits were inferred from Database for Annotation, Visualization and Integrated Discovery (DAVID) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Our results indicated several putative genomic regions associated with the target phenotypes and showed that almost all genomic variances were in the SNPs located in the intergenic and intronic regions. We further identified five main metabolic pathways related to ion transport, body composition, and feed intake control, which influenced the four phenotypes simultaneously. The systems genetics approach used in this study revealed novel pathways related to feed efficiency traits in beef cattle.

Genomic selection of in vitro produced and somatic cell nuclear transfer embryos for rapid genetic improvement in cattle production

This paper provides basic concepts of genomic selection (GS) methods in beef and dairy cattle production in combination with assisted reproductive technologies (ART) such as ovum-pick up and in vitroproduction (OPU-IVP). We first introduce genomic tools and discuss main methods of GS as practiced to-date. The general benefit from GS is that it enables selecting animals accurately early in life using genomic predictions particularly those phenotypes that are very difficult or expensive to measure. While it is known that GS increases genetic gain and profit in conventional cattle breeding, GS is much more desirable when combined with OPU-IVP in cattle production. The expected benefits of GS-OPU-IVP far exceed the benefits achieved by either GS or OPU-IVP alone mainly due to tremendous reduction in generation interval. The genetic improvement will increase even further, if genetic merit of donor cows and bulls used in OPU-IVP for key economic traits are maximal. The paper also highlights some challenges particularly with regard to embryo biopsies and quantity and quality of embryo DNA for whole genome genotyping and ways to overcome difficulties. We briefly discuss the somatic cell nuclear transfer (SCNT) technique in the context of applying GS on fibroblast cell lines from fetuses obtained from OPU-IVP techniques and provide our perspectives on how it might pave way for even more rapid cattle improvement. Main conclusion is that employing genomic selection in ARTs such as OPU-IVP of embryos coupled with embryo sexing and SCNT will lead to rapid dissemination of high genetic merit animals on a scale never been seen before. Finally, the paper outlines current research activities on combined genomic selection and advanced reproductive technologies in the GIFT project consortium (www.gift.ku.dk).

In vitro production of bovine embryos: revisiting oocyte development and application of systems biology

In vitro production (IVP) of bovine embryos has become a widespread technology implemented in cattle breeding and production. The implementation of genomic selection and systems biology adds great dimensions to the impact of bovine IVP. The physical procedures included in the IVP process can still be improved, and aspects related to the oocyte donor, oocyte maturation and the recipients are addressed in the following. Also, some of the future aspects of genomic selection and systems biology are addressed with particular focus on the Brazilian-Danish collaboration in the so-called GIFT-project.

In vitro production of bovine embryos: revisiting oocyte development and application of systems biology

In vitro production (IVP) of bovine embryos has become a widespread technology implemented in cattle breeding and production. The implementation of genomic selection and systems biology adds great dimensions to the impact of bovine IVP. The physical procedures included in the IVP process can still be improved, and aspects related to the oocyte donor, oocyte maturation and the recipients are addressed in the following. Also, some of the future aspects of genomic selection and systems biology are addressed with particular focus on the Brazilian-Danish collaboration in the so-called GIFT-project.(AU)

Genomic selection of in vitro produced and somatic cell nuclear transfer embryos for rapid genetic improvement in cattle production

This paper provides basic concepts of genomic selection (GS) methods in beef and dairy cattle production in combination with assisted reproductive technologies (ART) such as ovum-pick up and in vitroproduction (OPU-IVP). We first introduce genomic tools and discuss main methods of GS as practiced to-date. The general benefit from GS is that it enables selecting animals accurately early in life using genomic predictions particularly those phenotypes that are very difficult or expensive to measure. While it is known that GS increases genetic gain and profit in conventional cattle breeding, GS is much more desirable when combined with OPU-IVP in cattle production. The expected benefits of GS-OPU-IVP far exceed the benefits achieved by either GS or OPU-IVP alone mainly due to tremendous reduction in generation interval. The genetic improvement will increase even further, if genetic merit of donor cows and bulls used in OPU-IVP for key economic traits are maximal. The paper also highlights some challenges particularly with regard to embryo biopsies and quantity and quality of embryo DNA for whole genome genotyping and ways to overcome difficulties. We briefly discuss the somatic cell nuclear transfer (SCNT) technique in the context of applying GS on fibroblast cell lines from fetuses obtained from OPU-IVP techniques and provide our perspectives on how it might pave way for even more rapid cattle improvement. Main conclusion is that employing genomic selection in ARTs such as OPU-IVP of embryos coupled with embryo sexing and SCNT will lead to rapid dissemination of high genetic merit animals on a scale never been seen before. Finally, the paper outlines current research activities on combined genomic selection and advanced reproductive technologies in the GIFT project consortium (www.gift.ku.dk). (AU)