13TSB_AgriFood: Optimising the delivery of superior genetics through advanced genomic selection of embryos

Lead Research Organisation: University of Kent
Department Name: Sch of Biosciences

Abstract

This proposal is a natural but significant extension of two existing TSB funded projects involving the two collaborating
academic institutions (i.e. TS/101069 ['Applying advanced breeding technologies to amplify and distribute bovine genetics
to Increase production efficiency and sustainability', involving the University of Nottingham], and TS/J003182/1 [Pig IVF and
genetics: a route to global sustainability, involving the University of Kent]) to develop advanced breeding technologies in
cattle with commercial partners (i.e. Paragon/XLVets, Cogent Breeding Ltd and Illumina Inc) that will allow the marketing of
embryos that have undergone a complete genomic evaluation (including sexing) in order to estimate the breeding value of
progeny for traits of commercial importance at the earliest possible stage of development.
This project will apply advanced breeding technologies to produce (both in-vivo and in-vitro) pre-implantation bovine
embryos from which biopsies will be taken to interrogate their genomic makeup using single nucleotide polymorphism
arrays (SNP chips). It is currently possible to screen dairy and beef cattle genomically, but responses to selection are
impeded by waiting for the gestation of the calf on which genomic selection is performed. The screening of bovine
embryos, however, would optimise the delivery and amplification of superior genetics by advancing the time of selection
and reducing "wastage" of unwanted calves of inappropriate sex. This project will, therefore, combine advanced embryo
breeding technologies with state-of-the-art genomic screening (so called pre-implantation genetic diagnosis), and
karyomapping (combining parental DNA information with the offspring's genomic information to provide more genetic
detail). It will develop strategies for: (i) optimal bovine embryo culture using sexed semen, (ii) embryo biopsy in order to
extract a small number of blastomeres for genomic analysis, (iii) karyomapping SNP genotype data from Multiple
Displacement Amplification products and (iv) ehnancing pregnancy establishment of frozen-thawed embryos. Proof of
principle that the new technologies can be used to deliver superior genetics more efficiently to the breeding herd will be
confirmed by conducting genomic analyses of calves.
Importantly, this project is geared towards the development and use of a unique and highly marketable product (i.e.
genetically evaluated sexed embryos) that will deliver superior genetics to the global market at low cost, and in a highwelfare and bio-secure manner. This will have huge economic benefits for the UK based commercial companies concerned, and for both the dairy and beef sectors of the UK cattle industry; and ensure that the UK remains at the cutting edge of technical innovation retaining its competitive advantage over larger breeding companies currently situated in
Europe, North and South America.

Technical Summary

We will apply advanced breeding technologies to produce (both in-vivo and in-vitro) pre-implantation bovine embryos from which biopsies will be taken to interrogate their genomic makeup using single nucleotide polymorphism arrays (SNP chips). It is currently possible to screen dairy and beef cattle genomically, but responses to selection are impeded by waiting for the gestation of the calf on which genomic selection is performed. The screening of bovine embryos, however, would optimise the delivery and amplification of superior genetics by advancing the time of selection and reducing "wastage" of unwanted calves of inappropriate sex. This project will, therefore, combine advanced embryo breeding technologies with state-of-the-art genomic screening (so called pre-implantation genetic diagnosis), and karyomapping (combining parental DNA information with the offspring's genomic information to provide more genetic detail). It will develop strategies for: (i) optimal bovine embryo culture using sexed semen, (ii) embryo biopsy in order to extract a small number of blastomeres for genomic analysis, (iii) karyomapping SNP genotype data from Multiple Displacement Amplification products and (iv) ehnancing pregnancy establishment of frozen-thawed embryos. Proof of principle that the new technologies can be used to deliver superior genetics more efficiently to the breeding herd will be confirmed by conducting genomic analyses of calves.

Importantly, this project is geared towards the development and use of a unique and highly marketable product (i.e. genetically evaluated sexed embryos) that will deliver superior genetics to the global market at low cost, and in a high-welfare and bio-secure manner. This will have huge economic benefits for the UK based commercial companies concerned, and for both the dairy and beef sectors of the UK cattle industry; and ensure that the UK remains at the cutting edge of technical innovation retaining its international competitive advantage.

Planned Impact

This project is geared towards the use of a unique and highly desirable saleable product; that is the marketing of embryos
that have undergone a complete genomic evaluation (including sexing) in order to estimate the breeding value of progeny
for traits of commercial importance at the earliest possible stage of development. This new 'product' (approach) has the
benefit of significantly reducing the generation interval (by at least 9 months). The additional introduction of sexed
semen/embryos has the advantage of increasing the number of embryos/progeny of the desirable sex for genomic
analysis, and this facilitates greater selection intensity. Collectively these approaches will increase response to selection for
desirable traits associated with yield, fertility and animal health.
Such an approach will have huge economic benefits for both the dairy and beef sectors of the UK cattle industry, and
ensure that the UK remains at the cutting edge of technical innovation retaining its competitive advantage over larger
breeding companies currently situated in Europe, North and South America. It also offers important environmental, ethical,
biosecurity and animal welfare benefits. The judicious selection of calf sex avoids the production of 'unwanted' greenhouse gas emitting ruminant offspring (which may otherwise need to be destroyed), and facilitates increased selection intensity for
desirable traits that may include increased disease resistance (e.g. bovine tuberculosis). Developmentally competent and
genetically evaluated sexed embryos are also a highly marketable commodity that can deliver superior genetics to the
global market at low cost, and in a high-welfare and bio-secure manner.
The primary route to market will exploit an embryo transfer service offered by Activf-ET (established as part of TSB Project
101069, 'Applying Advanced Breeding Technologies to Amplify and Distribute Bovine Genetics to Increase Production
Efficiency and Sustainability' of which the University of Nottingham is a partner), in collaboration with Cogent Breeding Ltd,
who are also partners in this TSB project, and in the current application. A new partner to our consortium is Professor
Darren Griffin (University of Kent), who has experience with a separate TSB project (TS/J003182/1: Pig IVF and genetics: a
route to global sustainability). In the current proposal sexed and genetically evaluated embryos would not only be created
for the domestic UK market, but would also become available for export to new and rapidly expanding markets in China
and India, as well as to more established markets across Europe and North America. This is readily achievable in parallel
with Cogent's established frozen semen worldwide distribution (spanning 35 countries).
A significant element of training exists in the current proposal, not simply among the various partners most closely
associated with this bid, but also to the extensive network of XLVets (based in 51 geographically distributed practices
throughout the UK). Many of these practices will be trained in techniques of oocyte retrieval from donor cows (OPU) and
embryo transfer (ET) into recipient cows. There are also aspects of oocyte donor and embryo recipient management that
need to be extended to participating farmers. This will be achieved through the publication of technical literature and via a
series of stake-holder meetings during the 3 years of this project, during which advice and guidance would be offered on
general cow management and health, but more specifically on aspects such as oestrus synchronisation and heat detection,
and strategies to enhance early embryo survival following transfer. The Kent group will take the lead with a significant
training element. Recently they launched an MSc course in Reproductive Medicine that contains a 'hands on' one week
practical course. This module is being developed for individuals wishing to enter both clinical and animal IVF.

Publications

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publication icon
Griffin DK (2015) 20th International Chromosome Conference (ICCXX) : 50th Anniversary, University of Kent, Canterbury, 1st-4th September 2014. in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

 
Description The objectives of the grant have mostly been met. We have established screening of bovine embryos using SNP chips. See summary below

Introduction
Karyomapping was originally developed as a universal means of detecting monogenic and chromosome disorders simultaneously in human IVF embryo using SNP chips. The major non-human applications of SNP chips however lie in animal breeding. Traditional practice in the UK beef and dairy breeding industry involves the selection of dam (female) and sire (male) lines based on phenotypic progeny testing of live born animals. Genomic estimated breeding values (EBVs) are increasingly identified through SNP chip interrogation strategies, especially for sires.
With continued advancements in multiple ovulation and embryo transfer (MOET), ovum pickup (OPU) and in vitro production (IVP) of embryos (analogous to superovulation, egg collection and IVF in humans), the ability to produce a greater number of genetically superior animals has enabled significant improvements to beef and dairy production. However, the combination of inherited parental genotypes is random and therefore the inheritance of specific traits is not guaranteed. Furthermore, live birth rates of IVP embryos remain relatively low, indicating poor ability to select the 'healthiest' embryos using commonly applied morphology grading systems.

Materials and Methods
Combining SNP chip genotyping with IVP technology (generating EBVs from embryos rather than liveborn animals) is a much-needed advance as it significantly increases selection intensity whilst shortening the generation interval, thereby expediting the introduction of new genetics into the supply chain. To this end, we have adapted PGD technology involving IVP of cattle embryos, blastocyst biopsy, whole genome amplification then interrogation of SNP ships for the screening of cattle embryos. Simultaneous genotyping for EBVs is possible, as is aneuploidy screening using karyomapping. This approach complements traditional morphology screening to enable the selection of embryos with the best chance of survival to term, and ensures that resulting calves are proven carriers of desirable traits (e.g. those associated with health, welfare and productivity). Moreover, Karyomapping effectively acts as a genetic fingerprint to confirm the diagnosis of the embryo by matching it with that of the live born calf.

Results
At time of writing, 77 embryos have been genotyped in this way and we have made the first preliminary estimates of aneuploidy rates and high-resolution recombination patterns in cattle. A total of 50 embryo transfers have been made, of which 18 led to pregnancies: 9 of these are ongoing, 4 aborted, 5 were born but 1 died soon after birth of a post-natal infection. More transfers and pregnancies are imminent and we continue to improve protocols. In the most recent run, following transfer of 2 chromosomally normal blastocysts, 2 live births of phenotypically normal Holstein calves ensued.

Conclusions
The results herein presented represent the first examples of the use of karyomapping for non-human purposes and will allow the study of aneuploidy and recombination in a physiologically relevant animal model.
Exploitation Route We intend that the genetic screening of bovine embryos will become commonplace as a result of this grant.
Sectors Agriculture, Food and Drink

 
Description Calves have been born as a result of this procedure, which is now in use in farms.
First Year Of Impact 2016
Sector Agriculture, Food and Drink
Impact Types Cultural,Societal,Economic

 
Description JSR 
Organisation JSR Genetics
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution Setting up research lab, establishing embryo culture
Collaborator Contribution Contacts, materials
Impact Multi-dicipliary. Agriculture, genomics
Start Year 2007