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Livestock genetic improvement tools

Work Package Livestock production, health, welfare and disease control

Research Deliverable 
Livestock genetic improvement tools

Introduction

The application of genetics is a cost effective way to improve productivity and sustainability of livestock, as progress is permanent, sustainable and cumulative. Genetic improvement is estimated to have resulted in between 50-90% of the overall animal improvements seen over the last 60 years and will be a major driver for the improvements in efficiency, productivity and sustainability of Scotland’s livestock sector. However, despite widespread uptake of genetic improvement in some sectors, such improvements have not necessarily been disseminated across the entire Scottish livestock population, particularly in the beef cattle and sheep sectors – a key driver for this RD.

Aim of Research

The aim of this RD is to improve livestock production, efficiency and welfare, whilst decreasing the use of resources and impact on the environment. This will be achieved using current and next generation tools, focussing on genomics and targeted gene approaches for production (growth, efficiency), maternal and health characteristics (including economically important endemic diseases). Advances in genetics include the use of genome wide selection (GWS), the application of which in some plant and livestock species shows that improvements can be substantially enhanced over and above the use of conventional genetic improvement tools, particularly for traits that are difficult to record. The new research will build on existing research and national data platforms, to collect novel genotypes and phenotypes. This will include merging public and industry data and will show how our genetic improvement tools can be enhanced by sharing data across the Scottish food supply chain. Building on international collaborations we will examine the optimal way to include information from sequence in genomic breeding programmes (and manage genetic diversity, linked with RD2.3.2).

Progress

2019
2019

Using the data collected at part of the Beef Efficiency Scheme during the reporting year we have explored genetics of calving performance traits in Beef Efficiency Scheme. We also continue to identify the best animals to genotype to support the aims of the scheme. Analysis of the BES recorded traits have yielded some significant results to demonstrate that they can be altered through genetic selection. For farmer recorded calving ease, 87% of cows were recorded as self calved. Calving interval, direct calving ease and dam longevity were shown to demonstrate some genetic control demonstrating that data collected as part of BES could be selected for using these farmer recorded data on pure and cross bred animals. The scheme aims to genotype 20% of the calf crop and sires on holdings each year. Implementing the selection systems previously developed, we have selected calves for the reporting year for the first time without preferential selection of female calves. Analyses of the population have identified 78 different breed and cross types to which calves were allocated. 11.1% of calves were identified as being “purebred” (not crossbred) of one of 32 different breeds.

During the reporting year we have focussed on testing the computer and data systems for storing and analysing genetic, genomic and genome-wide sequence data on “real” cattle and sheep data from the UK and further afield such that is could be usefully and routinely deployed where benefit can be demonstrated.  Potential benefit for genomic based tools includes hard-to-measure traits related to growth, health, carcass and meat quality traits in sheep. Genomic analysis has continued to enable delivery of the first genomic breeding values (gEBVs) to industry for two important ovine diseases (footrot and mastitis) and mechanisms are being put in place to expand the number of gEBVs available for crossbred and purebred sheep.

During this reporting year a number of new computer tomography derives traits will become available to breeders including traits related to welfare (body dimensions affecting lambing difficulty) and product quality (fat and muscle distribution).

Data collected from a SEFARI research flock of sheep have been analysed linking lamb performance, disease and immunological traits at phenotypic and genetic levels. Favourable genetic and phenotypic associations among disease indicators and lamb growth indicate that selection for reduced faecal egg counts will not impact on lamb growth potential. The new immunological data linked to faecal egg counts, animal growth and parasite egg counts were collated and data set now includes 10,351 records from 4,898 sheep with known pedigree. Estimated breeding values were computed for the resource flock of which 1/3 has been selected for resistance to parasites. Analysis shows that genetic selection of sheep for resistance to internal parasites is feasible and will not compromise productivity (lamb growth).

Variation in immunity to disease or response to vaccination is likely to be linked to sequence variation within immune response genes. We continue to study innate immune receptor genes of sheep to detect genetic variation that may be related to disease phenotypes highlighted over 40 genetic variant positions with allele frequencies of 20-50%.  Identification of genetic variants linked to disease could allow the development of novel tools to help guide breeding efforts for improved health and welfare.

Highlights:

  • Evidence from this and linked RDs on the potential role of genetic and genomics in driving efficiency improvements to help meeting Scotlands carbon targets from agriculture was discussed with the Environment, Climate Change and Land Reform Committee (Nov, 2018).
  • Genetic analysis of beef data have been communicated with farmers at the British Cattle Breeders Club (Jan 2019) to demonstrate the economic value of improving feed efficiency in growing beef cattle, which can be used to inform management decisions.
  • Working with industry partners, the potential for selecting animals based on genomic breeding values for mastitis was summarised and presented in a range of industry meetings and informed potential implementation routes.
  • Potential challenges of implementing genomics in sheep populations was discussed with academic and industry partners as European Association of Animal Production meeting, Belfast, August 2016
2018
2018

Using the data collected at part of the Beef Efficiency Scheme during the reporting year we have explored genetics of maternal and lifetime efficiency traits in Beef Efficiency Scheme. We also continue to identify the best animals to genotype to support the aims of the scheme. Analysis of the BES recorded traits have yielded some significant results to demonstrate that they can be altered through genetic selection. By the end of the second year of the scheme of over 328,000 calves across approx. 2,000 herds had been entered in the BES database. Over 10,000 bulls sired the calves in the scheme. Over 40 different breeds (and crosses of that breed) are represented by the scheme. The largest breeds in the scheme are Charolais, Limousin, Aberdeen Angus, Simmental and Salers (between 75,000 – 12,000 calves per breed, including crosses). Analysis of maternal performance showed that both age at first calving and calving interval were under genetic control in Scottish Beef populations. In BES herds the overall the mean age at first calving was about 32 months of age has been quite stable at about 32 months from 2006 to 2016.  Overall the mean calving interval between first and second calving was ~ 405 days. The difference between the top and bottom 10% of animals for genetic merit for age at first calving was 64.5 days – meaning that the top 10% of animals were had the genetic potential to calve for the first time on average over 2 months earlier than the bottom 10%. The difference between the top and bottom 10% of animals for genetic merit for first calving interval was 1.5 days– meaning that the top 10% of animals had the genetic potential to reduce calving interval by 1.5 days compared to the bottom 10% of animals.

We have developed a bioinformatics pipeline to integrate and jointly analyse genetic information on livestock from a range of sources, including basic pedigree information through to whole genome sequence data. This platform was designed with compute efficiency in mind such that the platform can be used to support larger population analyses rather than a smaller research context. To date the systems have been tested with UK dairy and beef cattle genotype and sequence data and international sequence databases. This will help to unify genetic and genomic data for further analyses.

Genomic analysis of commercial sheep data has identified genomic regions associated with litter size, carcass, growth, health and welfare traits. A paper showed ‘New mastitis phenotypes suitable for genomic selection in meat sheep and their genetic relationships with udder conformation and lamb live weights’.

To allow incorporation of new Computer Tomography traits into national breeding programmes, genetic parameters have been estimated in three main UK terminal sire breeds and across breeds for all new CT traits including - spine traits, eye muscle dimensions and area, intramuscular fat (meat quality proxy).

These results will feed into the development of new estimated breeding values for sheep breeders.

Work is progressing well in this Objective and much of the year has focussed on continued collection of production and health phenotypes and the establishment of immune traits measurement systems to support the side aims of this objective. 

Data collection on a SEFARI research flock continued in this year including data on birth and live weights, faecal egg scores and systems for measuring immune associated traits. These data will be used to explore the relationships between disease and production traits in hill sheep. Disease data (feacal egg counts for strongyles, nematodirus, coccidia, dagg score) from 2016 and 2017-born lambs were combined with those from 2011-2016 (n=3951) together with lamb live weight data at birth, mid and late lactation (weaning) and analysed. At the genetic level, these were significant and positive for live weight and strongyles indicating that similar genes are responsible for the same trait at different time points. The significant positive genetic correlations between strongyles and nematodirus as well as coccidia indicate that selection of sheep for resistance to any of these confers increased resistance against the others at the first sampling occasion.

Variation in immunity to disease or response to vaccination is likely to be linked to sequence variation within immune response genes. Protocols were developed for amplification of 22 sheep immune receptor genes to study genetic variation in the context of disease resistance. Initial tests on sheep from 4 breeds showed that 20 of 22 genes contained polymorphic sites. Identification of genetic variants linked to disease could allow the development of novel tools to help guide breeding efforts for improved health and welfare. Results from this work demonstrated that immune gene sequence differences are present even within a single flock and that analysing larger numbers of animals should tell us whether this approach has merit in tracking resistance to nematode infestation

Highlights:

  • Material prepared and presented to various (inter-)national industry related meetings including the use of national data sources to improved female fertility in beef cattle at the 2017 International Committee for Animal Recording via genetic and genomic improvement
  • Farmer/industry information generated and presented at the launch of national carcass trait genetic evaluations in collaboration with AHDB (May 2017).
2017
2017

During the first year of the programme we have focussed in developing the underpinning tools to support the delivery and implementation of the Beef Efficiency Scheme (BES). This has included developing recording protocols, advice and support in developing genotyping contract, tools to select best animals for genotyping and attending routine meetings with Scottish Government and other BES service providers During the first reporting we examined the genetics of traits related with lifetime efficiency using industry data. Building on previous Strategic Research Programme and work with AHDB we examined the genetics of age at slaughter for animals in the BES and demonstrated a moderate heritability for the trait meaning that it is amenable to genetic improvement.

Industry data from the Texel breed were used to relate animal growth and carcass attributes to new genomic data using the latest technology ‘SNP chip’. This has allowed us to determine which part of DNA (which chromosome, which part of the chromosome) contributes to animals’ genetic propensity to be more efficient in  the way they perform on-farm and how that might be associated with carcass merit, once they have been served up on consumers’ plates.

New information from screening 3500 sheep from a commercial terminal sire breed has been collected two key endemic diseases related to udder and hoof health, (that is linked to lameness). Using the same method as for O3.1, we have linked the new disease information with the DNA data to produce profiles of resistant and susceptible animals. This information can be used to screen animals of the same breed, for their propensity to be more or less susceptible to disease and which will help in the development of more resistant sheep to endemic disease. A new data platform for estimating genetic merit for 12 breeds at the same time, has been delivered to industry and is currently being tested alongside the conventional system.

New image analysis methods to speed data extraction from CT images have been tested and software refinements are underway. In collaboration with the national genetic evaluations providers, 11 new production/product quality phenotypes have been measured from all historic commercial CT images and loaded into the national database (~90,000 measurements). Genetic analyses are underway on these new CT traits, which will enable their incorporation into national breeding programmes, if results suggest that this is appropriate.

Data collection began in 2016 and 809 birth records were registered on a SEFARI experimental flock. Birthweight data was collected on 793 lambs born dead and alive. Lambs (n=724) were weighed at #8 weeks of age and again at 17 weeks (n=706). We collected 1330 individual animal rectal faecal samples from 708 lambs and 6 parasite species were recorded from these samples. Blood samples were collected for lab analyses of immunological traits which have nearly been completed.

The whole blood collected from each sheep in 2016 described above have been analysed using whole blood stimulation assays have been optimised to characterise immunological responses (‘T cell’) using different methods to get the best methodology to generate useful data.  These will subsequently be combined with the disease information (faecal egg counts), lamb performance and genotype data to quantify these and their role in the development of more resistant animals to internal parasites.

Protocols were developed to study genetic variation in relation to animal disease resistance by focussing on 22 sheep immune receptor. Initial tests on sheep from 4 breeds showed that one sample amplified poorly and clear sequence was recovered from over 80% of samples. Of the 22 genes, only two did not contain any polymorphic sites in the samples tested and the average number of polymorphic sites per gene was 3. This approach will be extended in future years in selected sheep samples to examine potential relationships between disease status and immune gene variation.

Highlights:

  • Key messages and presentations were developed and presented at a range of (inter-) national events including at Livestock Gentec Conference (Canada, October 2016) and Sheep Breeders Round Table on analysing national carcass traits and economics of age at slaughter.
  • An academic and industry workshop was held in April 2018 bringing together 60 industry and academic (including multiple MRPs) stakeholders, from UK and overseas to present key developments in genomics from plant and animals.
  • Farming for a Better Climate Events: presentation on the potential role of genetics and genomics for reducing the environmental footprint of beef production

Future Activities

Going forward we will focus on analyzing the genomic data generated as part of the Beef Efficiency Scheme and if whole genome sequence data can enhance the prediction of genomic breeding values in crossbred beef. We will also explore how new prediction methods (i.e., artificial intelligence and machine learning) for generating new phenotypes can enhance trait development and genetic improvement programmes, with a particular focus on generating traits for simple and complex images such as those generated from computer tomography and hyperspectral imaging. Building on the SEFARI research flock data already collected we will analyse the genetic relationships between production, health and immune traits in sheep and explore best route for their implementation in breeding programmes. Linked to this we will continue to mine the immune genes of sheep to see how the influence disease resistance in practice.

Research Deliverable Lead

Professor Eileen Wall

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