Sheep Enviro-Indexes Creating an index to breed sheep in Terminal Sire Breeds with a low carbon footprint

Sheep Enviro-Indexes

Creating an index to breed sheep in Terminal Sire Breeds with a low carbon footprint

Introduction

The Agriculture and Horticulture Development Board (AHDB) is a non-departmental government body, funded by levy income from farmers, growers and others in the supply chain, and managed as an independent organisation (independent of both commercial industry and of Government). The role of the AHDB is to help improve the efficiency and competitiveness of various agriculture sectors within the UK. Our purpose is to inspire our farmers, growers and industry to succeed in a rapidly changing world.

As AHDB is funded in this manner, value for money is paramount, we welcome suppliers who can offer innovative and cost-efficient solutions to meet our needs, whilst also offering superlative service that will enable us to create a world-class food and farming industry. Solutions should look to help us not only reduce costs but increase business flexibility, lift productivity, bring people together to collaborate, innovate and drive change throughout.

Further information about AHDB can be found here: https://ahdb.org.uk/

Background

AHDB assesses over 50 different genetic attributes for sheep farmers as part of the genetic evaluation service delivered by Signet Breeding Services. Each attribute is expressed as an estimated breeding value (EBV) to show the relative superiority of an animal for that trait. However, to aid breeding decisions, EBVs can also be combined into Breeding Indexes to simplify selection decisions and achieve an overarching breeding objective.

Most breeding indexes are based on economic principles to identify the most profitable animal; however, breeding indexes can be designed for other purposes. One such approach would be the creation of a breeding index that identified those animals in the population with the lowest carbon footprint.

AHDB currently produce three distinct breeding evaluations for the different breed types in the UK.

Maternal Evaluation – through which an environmental breeding index or indexes will be developed as part of Breed for CH4nge
Hill Evaluation – through which an environmental breeding index may be developed, based on the work above.
Terminal Sire Evaluation – for which an environmental index doesn’t exist at present.

AHDB wishes to obtain information that would enable the ranking of sheep within our terminal sire evaluation on the basis of their breeding potential for both environmental and economic credentials.

Scope

It is important that the economic and environmental indexes that are produced for Terminal Sires work in tandem and optimise the decisions made by farmers.

The current quasi-economic indexes (developed on a desired-gains basis) have not been updated recently and were developed in the absence of breeding values for abattoir traits (or the sub-index, Lamb Value, which was developed from abattoir traits).

With historic approaches and current service provision in mind, this Invitation to Tender aims to enhance all the breeding indexes that are currently published for terminal sire breeders and their customers. Information derived from this research will be published for wider use by the UK sheep industry.

We are looking for one or more providers to deliver the following research. The work is split into four sections (work packages 1 -4). Providers may bid for one or more of these work packages.

AHDB may fund all or some of the work packages. AHDB reserves the right to award different work packages to different organisations. Funding may not be awarded if the proposed solutions don’t provide a deliverable solution based on the original objective.

Each work package must deliver all the information that is required; so that each can be delivered separately or in combination.

This tender is for

Work package A. Update the Terminal Sire Index (in economic terms)
Work package B. Update the Maternal Index (in economic terms)
Work package C. Create an Enviro-Index for Terminal Sires - when all progeny are slaughtered
Work package D. Create an Enviro-Index for Terminal Sires - when females are retained for breeding

To complete this work AHDB will provide a full set of breeding values to enable models to be tested. AHDB will answer any queries relating to the construction of existing EBVs and indexes that may prove relevant to this work.

A budget has not been provided as part of this tender. If further clarity is sought regarding any individual work package, please contact AHDB directly. Information provided to a specific supplier may be shared with other potential suppliers.

Work package A. Update the Terminal Sire Index (in economic terms)

Review the suitability of the current terminal sire index and lamb value (sub-index) as tools for selective breeding and commercial ram selection.

The project team should use their expertise (taking into account feedback from focus groups that have been run by the supplier as part of the project) to create a new economic index that brings information together on growth and carcase traits to create a single index that is expressed in economic terms to represent the relative value of a finished lamb produced by a recorded ram.

It is expected that this index will take into account:-

breeding values for abattoir traits; days to slaughter, carcase weight, conformation and fat classification)
proxy traits for abattoir traits measured on the farm (scan weight/muscle depth) and via CT (CT lean weight, muscularity)

With results modelled to show the impact of changing the balance of selection between direct and proxy traits.

Research findings should determine how these weightings would change through the inclusion of lamb survival and highlight the economic impact and robustness of including lamb survival in the new economic index.

Index values should be expressed in financial terms, as £ per lamb born.

Work package B. Update the Maternal Index (in economic terms)

AHDB publish a very simple maternal/self-replacing index. AHDB are aware that the maternal characteristics of terminal sires tend to be a secondary consideration – though important for breeds like the Poll Dorset.

The project team will review the maternal index that is produced for terminal sire breeds and show how we can express the output in economic terms.

Bearing in mind those factors listed here that have tailored the current maternal breeding index, the supplier is asked to develop an updated maternal index. This index can be created using a desired gains approach, but it should be expressed in economic terms, as £ per lamb born.

Work package C. Create an Enviro-Index for Terminal Sires - when all progeny are slaughtered

Develop a new breeding index to identify those terminal sires with a lower carbon footprint (when used by commercial farmers as terminal sires and all their progeny are slaughtered) using existing traits.

Explain how the information derived from this index will be expressed relative to the output of the animal in terms of either output or intensity. It is assumed that a recommendation will be made that carbon footprint is adjusted to a fixed level of output.

This index should then be developed further to enable two novel traits to be incorporated in the future.

Methane production (as determined using a methane chamber)
Rumen volume (a proxy trait for methane production determined using CT).

A table should be provided to show how a change in one unit of any of the given EBVs that are included in the index influence the overall carbon footprint.

Work package D. Create an Enviro-Index for Terminal Sires - when females are retained for breeding

Repeat the work above, but in a scenario where 50% of the females (25% of the lambs) that are produced are retained for breeding purposes.

Develop a new breeding index to identify those terminal sires with a lower carbon footprint (when used by commercial farmers as terminal sires, but with 75% of their progeny being slaughtered and 25% retained as breeding females) using existing traits.

This index should then be developed further to enable two novel traits to be incorporated in the future.

Methane production (as determined using a methane chamber)
Rumen volume (a proxy trait for methane production determined using CT).

A table should be provided to show how a change in one unit of any of the given EBVs that are included in the index influence the overall carbon footprint.

Stakeholder Engagement

In delivering any of the work packages it is a requirement of contract award that the project team will initiate and deliver the following steps (as a minimum level of engagement)

Host a briefing with AHDB's Sheep Genetic Advisory Group to explain the approach.
Meet with AHDB and genetic service providers at SRUC to understand the current service, the current aspirations of Signet clients and obtain any genetic information required for this work (data and genetic parameters).
Engage in a meeting with stakeholders, including Signet clients, to understand their current breeding goals and concerns regarding changes to the index.
Engage in a meeting with the Breed for CH4nge project with an openness to sharing findings and support any potential useful collaboration with this project.
Deliver a feedback session with stakeholders prior to final report publication.
Generate a report summarising project findings that explains the proposed index weightings and a technical note written for knowledge exchange purposes explaining both the construction and interpretation of the indexes.

Meetings don’t need to be held in person, although it is recognised that this is often the best way to obtain informative feedback. Please state in the tender if meetings will be held in person or remotely.

Expected project output

The output from the project will be a report that documents the creation of (at least) four breeding indexes and a set of index weightings that are ready for implementation.

Terminal Sire Index – Expressed in Economic Terms (focussed on optimising economic performance)
- With a version that includes lamb survival (from WP 1)
Maternal Index – Expressed in Economic Terms (focussed on optimising economic performance)
- With a version that includes lamb survival (from WP2)
Eco-Index for Terminal Sires slaughtering all progeny – (focussing on reducing carbon footprint)
- With options that include methane production and/or rumen volume (from WP 3)
Eco-Index for Terminal Sire retaining female replacements – (focussing on reducing carbon footprint)
- With options that include methane production and/or rumen volume (from WP 4)

A sensitivity analysis should be provided to indicate how changes in the balance of index weightings influence the desired outcome, be it economic or environmental.

Tables should be provided that show how a change in one unit of any of the given EBVs influences value (profitability) and carbon footprint.

Full methodology should be included within the report.

Exiting Arrangements

For each work package, at the end of the project:-

A report should be submitted for implementation containing the detail as outlined in the scope.
Any animal data or breeding values used for modelling must be deleted.

Reporting

As part of the services and for each work package, the Supplier shall provide the following reports to AHDB:

Report Type	Content	Frequency
Short written report and verbal update	Progress against milestones	Monthly
Final report on work package	Detailed above	End of project

Contract Term

The work will commence no later than 1^st October 2024 and be completed within 6 months.

Contract Management

AHDB and the successful supplier/s shall each appoint a contract manager, specific roles will be agreed between both parties at award of contract/s.

AHDB will appoint the Head of Animal Breeding & Product Quality to lead the project, with support from the Senior Animal Breeding Manager (Signet) and the Lead Animal Genetics Expert. Monthly meetings will be scheduled to review progress.

Milestones

At the start of the contract/s, AHDB shall host a project commencement meeting with the Supplier/s. During this meeting, the programme of work and payment schedule submitted as part of the tender shall be refined and key milestones agreed.

The programme of work shall be regularly reviewed and updated by the Supplier/s, in agreement with AHDB. The programme of work shall be used to monitor project delivery. Payment shall only be made monthly in arrears upon completion of the relevant key milestones and reporting by the Supplier/s in agreement with AHDB.

Each key milestone shall comprise a number of the deliverables described within this specification document.

Upon achievement of each deliverable, the Supplier shall notify AHDB who shall ratify that it has been achieved and update the programme.

Pricing

Service providers must quote separately for each of the four work packages, A-D listed in the scope (section 3), in addition to providing a price to complete the whole project.

Prices are to be fixed for the duration of the contract, with invoices submitted at the end of each milestone and no later than 3 months after the completion of the project.

All prices should be quoted exclusive of VAT.

Please note AHDB’s Terms and Conditions apply.

On submitting a proposal please ensure you have read and accepted our terms and conditions, these are available on our website here under the “Applying for funding” heading. Any organisation receiving funding from AHDB shall comply with the terms and conditions specified in the Goods and Services Contract. AHDB will not be held responsible for any expenses or losses incurred by applicants in the preparation of an application(s).

Update: 29th of July 2024

Application Process

To apply applicants are asked to make a written submission outlining their chosen methodology and approach to delivering Work Packages A-D.

Their submission must:

Detail the methodology, including any named software that will be used to complete the task.

Provide a clear statement of the aim of the work
State the core objectives, numbering each objective separately

Outline the planned stakeholder engagement and the teams approach to engagement (for example in person or online)
Provide an outline of what will be reviewed as part of the sensitivity analysis
Give an indication of how the environmental benefits will be expressed as part of the new environmental index.
List any requirements for data that will need to be supplied by AHDB to complete the work.
Outline a timeline with appropriate milestones.
Reference the team’s track record in delivering similar work, with examples of work completed in this area. Please report which staff (with any of their relevant qualifications) will be actively engaged in delivering the project and highlight who will lead each work package. Please highlight any planned collaboration and any potential conflicts of interest.
Provide a price which is broken down by work package, with a total amount if the project was delivered in full.

The price quoted should include any travel and subsistence envisaged.
The price should be quoted exclusive of VAT.

Please contact AHDB if you have any further queries relating to the submission.

Questions

If you have a specific question related to this call please email research@ahdb.org.uk. As part of the open tender process AHDB cannot discuss specific project details prior to submission of a proposal. All responses to questions will be anonymised and published.

Question 1: What proposal form should be completed for this tender?

Answer 1:

Application Process

To apply applicants are asked to make a written submission outlining their chosen methodology and approach to delivering Work Packages A-D.

Their submission must:

Detail the methodology, including any named software that will be used to complete the task.

Provide a clear statement of the aim of the work
State the core objectives, numbering each objective separately

Outline the planned stakeholder engagement and the teams approach to engagement (for example in person or online)
Provide an outline of what will be reviewed as part of the sensitivity analysis
Give an indication of how the environmental benefits will be expressed as part of the new environmental index.
List any requirements for data that will need to be supplied by AHDB to complete the work.
Outline a timeline with appropriate milestones.
Reference the team’s track record in delivering similar work, with examples of work completed in this area. Please report which staff (with any of their relevant qualifications) will be actively engaged in delivering the project and highlight who will lead each work package. Please highlight any planned collaboration and any potential conflicts of interest.
Provide a price which is broken down by work package, with a total amount if the project was delivered in full.

The price quoted should include any travel and subsistence envisaged.
The price should be quoted exclusive of VAT.

Question 2: Do we submit on one of the standard templates or make our own? Is there a limit in length of the application?

Answer 2: AHDB are happy for applicants to submit tenders using their own template providing that is clearly covers the issues raised. There is no limit to the length of application that can be submitted.

Question 3: Can you please provide a full list of the EBVs in the terminal sire evaluation (or better still, a list of the EBVs that you see potentially having economic weights in the indexes).

Answer 3:

We currently produce and publish the following traits for Terminal Sires.

Breeding Values derived from on-farm measurements

Birth Weight

Lambing Ease

Lambing Ease Maternal

Lamb Survival

Eight Week Weight

Shearling Weight (Note we don't have an EBV for Mature Ewe Weight or Body Condition Score for Terminal Sires)

Litter Size

Litter Size Reared

Maternal Ability

Scan Weight

Muscle Depth

Fat Depth

Breeding Values derived from CT scanning

CT Lean Weight

CT Fat Weight

CT Muscularity

CT Eye Muscle Area

Total Spine Length

Total Spine Number

Predicted IMF %

Breeding Values derived from Abattoir Traits

Days To Slaughter

Carcase Weight

Carcase Conformation

Fat Class

The current index weights are shown in the table below, which is taken from the following link.

https://signetdata.com/technical/genetic-notes/terminal-sire-index/

These have been developed over time using a desired gains basis taking into account economic principles. We currently have one terminal sire index for breeds that CT scan and one for those that don’t.

Raw Index Weightings

	Terminal Sire (CT index)	Terminal Sire (Non-CT index)	Maternal Index
Eight Week Weight EBV	0.1	0.9	2.8
Scan Weight EBV	0.85	0.8	0.1
Muscle Depth EBV	0.8	2.5	2
Fat Depth EBV	0.5	0.5	0.5
Litter Size Born EBV	0	0	14
Litter Size Reared EBV	0	0	37
Maternal Ability EBV	0	0	5
CT Lean Weight EBV	4.5	0	0
Ct Fat Weight EBV	1	0	0
CT Gigot EBV	0.1	0	0

AHDB will be guided by those delivering the tender on which traits they believe will require focus in the new indexes, bearing in mind that the abattoir traits are relatively new and only based on 40,000 animal records (crossbred progeny from just 500 rams); unlike CT data which has been collected over two decades and the on-farm records, which will number in the hundreds of thousands of phenotypic records. Previous approaches have split our index weighting emphasis between on-farm traits and CT traits to reward sheep that excel in both areas, but these indexes were developed on a desired gains basis and prior to having a set of abattoir traits available.

Question 4: Confirm whether you expect to have an EBV for methane production to use in testing the new indexes (or do you just want to have the trait GHG weighting available)?

Answer 4: We don’t and won’t (in the medium term) have an EBV for methane production generated as part of our terminal sire breeding evaluation.

Question 5: The text says “a sensitivity analysis should be provided to indicate how changes in the balance of index weightings influence the desired outcome, be it economic or environmental.” This read as though it involves testing based on desired gains. Do you want sensitivity analysis based on changes to model inputs like lamb price, ewe mature weight, and litter size (for example)?

Answer 5: This suggestion sounds a sensible approach to assessing robustness, we will be guided by those delivering the project as to the best manner to express and test the sensitivity analysis.

Question 6: Please confirm if you want to test environmental indexes with and without a survival EBV included?

Answer 6: We can confirm that AHDB would like to see (and compare) environmental indexes with and without lamb survival including.

Question 7: Will the indexes need to be breed specific or is the evaluation comparable across breeds?

Answer 7: The indexes will not be breed specific. We have a multi-breed evaluation with a degree of comparison between breeds.

Question 8: Apart from the “technical note written for knowledge exchange purposes explaining both the construction and interpretation of the indexes” and the listed five engagements. Is there any desire by AHDB to have project team members available for post-project industry KE meetings?

Answer 8: The technical note should be written in a manner that will allow AHDB to deliver the required knowledge exchange to industry, but half a day should be set aside to present results to industry on a webinar (to be organised by AHDB) in addition to time allocated to feed results back to the AHDB Genetics Guidance Group.

Question 9: Will you have genetic parameters for Rumen volume?

Answer 9: No, this information is not known to AHDB at present.

Question 10: Do you have the correlations between all traits that need to be included in the indexes?

Answer 10: AHDB have genetic correlations that can be shared post award between our current maternal traits, growth and carcase traits measured on farm, CT traits and abattoir traits. For some traits, like lamb survival few genetic correlations are currently fitted at present.