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Advancing genetic improvements in barley heat tolerance during flowering and grain fill

Advancing genetic improvements in barley heat tolerance during flowering and grain fill

Reference number: PROC-9177047

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Release date:: Monday 06 May 2024
Closing time:: Thursday 03 October 2024, at 05:00 PM ACT local time
Enquiry deadline:: Thursday 26 September 2024, at 05:00 PM ACT local time

Summary

This five-year project will leverage foundational knowledge and outputs at varying levels of development from previous pre-breeding research, integrating, and transitioning them from the discovery phase to the delivery phase.

There is scope also to explore alternative and cost-effective high-throughput phenotyping (HTP) methods for heat stress screening and novel sources.

Document contact and enquiries

Attention: Sarah Marchioro
Grains Research and Development Corporation
Email: tenders@grdc.com.au

All requests for further information or clarification in relation to this investment should be made in writing (email) prior to Thursday 26th of September 2024, 05:00 PM ACT local time

All requests and responses to requests will be published on the GRDC website under Questions and Answers at the bottom of this webpage.

Consortia response

GRDC will accept Tenders from Consortia.

Lodgement

Tenderers must submit their responses electronically through the Grains Investment Portal. Please read this entire page before lodging an application in the Grains Investment Portal.

AusTender

https://www.tenders.gov.au/Advert/Show/c501be09-d927-4f6c-a217-c899ba3472ca

Description

GRDC is looking to invest to deliver a suite of breeder-deployable outputs that will support commercial barley breeding companies develop genetically improved late-stage heat-stress tolerant barley varieties. This five-year project will leverage foundational knowledge and outputs at varying levels of development from previous pre-breeding research, integrating, and transitioning them from the discovery phase to the delivery phase. There is scope also to explore alternative and cost-effective high-throughput phenotyping (HTP) methods for heat stress screening and novel sources.

Barley (Hordeum vulgare) is the second largest cereal crop in Australia after wheat, with recent five-year production levels averaging 12.4M tonnes annually and gross value of $3.7B per annum (ABARES, 2023). Australian barley represents 30% of the world’s malting barley trade and 20% of the feed barley exports. Heat stress is a key constraint to Australia’s barley production reducing both grain yield and grain quality (i.e., market value). Exposure of barley crops to acute and chronic heat stresses (> 30°C) during flowering and grain filling causes reduced grain plumpness, grain screenings (< 2.2mm), and grain loss. It is estimated that heat stress leads to average reductions of 13-15% in cereal yields. In barley, this is expected to increase by a further 6-7% reductions with every 1oC rise in ambient temperature. For Australia to remain a dominant global barley producer and exporter, developing new varieties that cope better with rising temperatures, protecting Australian barley production against future climate change, will be critical.

The discovery phase of previous pre-breeding research in late-season barley heat tolerance have generated substantial genetic resources and foundational knowledge. In the next phase, these advances will be leveraged, expanded, validated, integrated, and delivered to commercial barley breeders.

Please note key points as outlined below:

Early and ongoing breeding company engagement and consultation
Co-design process that involves key commercial breeding entities must be adopted from project conception stage and throughout project life cycle for effective output development and delivery.
Background IP
Substantial background IP that could be leveraged for this project is co-owned by GRDC and previous co-investors. GRDC can confirm approval for use of co-owned IP under terms specified on our Material Transfer Agreement (MTA). Noting, however, that access to existing IP will be subject to full approval from other relevant parties. Applicants are therefore advised to approach relevant IP co-owners well in advance (preferably prior to application submission). Details of previous GRDC co-investments in barley heat tolerance can be searched for on the GRDC Website.
Collaboration with the Australian Plant Phenomics Facility (APPF)
Output 4, although a relatively smaller component of the overall project, will require applicants to partner with APPF to access and leverage capabilities/capacity which GRDC has funded to establish. GRDC expects applicants to establish this collaboration.
Project size
GRDC is looking to invest in a medium sized five-year project. For example, this could include 1-2 postdoctoral fellows and PhD students, plus operating and travel expenses.
Co-Investment
GRDC is seeking co-investment that at least matches GRDC investment for this project.
AGGI support
Analytics for the Australian Grains Industry (AAGI) is a GRDC strategic partnership with University of Queensland, Curtin University and University of Adelaide. AAGI has capacity in experimental design and analysis of field trials. Applicants are encouraged to discuss potential support and collaborations with AAGI. To access AAGI support in the first instance, applicants must make enquiries to the AAGI Director, Dr Nathan O’Callaghan.

Outcome

By 2030, Australian barley breeders have access to elite germplasm and breeding tools that will enable development of new barley varieties with at least 5% superior yield under heat stress at either flowering or grain filling stages [or both] and no yield penalty under non-stressed conditions compared to the current highest yielding barley cultivars.
By 2035, Australian barley growers and industry achieve higher productivity, sustainability, and resilience to climate changes.

Outputs

Output 1: By 2030, elite germplasm available to Australian breeders with combinations of existing genes for heat-stress resilience at flowering and grain filling.

Description:

- Highest performing, large effect QTLs are identified that confer improved heat tolerance (eg. maintenance of grain plumpness, minimisation of grain screening, and higher spikelet fertility) and their stability validated across multiple environments.

- Single and multiple thermo-resilient gene combinations in adapted backgrounds that provide at least a 5% yield improvement under heat-stress events occurring at either flowering or grain filling stages [or both], and no yield penalty under non-stressed conditions compared to the current highest yielding cultivars.

- Elite germplasm, all associated data, and breeder-deployable molecular markers to be delivered to Australian barley breeders via the GRDC Approved Breeders MTA.

Output 2: From 2028 new sources of heat-stress resilience are identified and relevant molecular markers are delivered to Australian breeding companies.

Description: At least 10-15 new sources of heat tolerance/resistance are identified, introgressed into Australian adapted genetic backgrounds, and evaluated under multi-environmental trials then delivered to breeders along with specific markers under the GRDC Approved Breeders MTA.

Output 3: By 2030, genes and mechanisms for heat-stress resilience at different barley developmental stages identified.

Description: Dissect the molecular mechanisms (and casual genes) driving thermo-resilience in the ‘best-bet’ sources for grain plumpness and spikelet fertility to better inform pyramiding strategies and targets for gene editing.

Output 4: By 2030, the Australian pre-breeding and breeding community are provided with genomic and performance information on barley heat resilience genetics, novel high throughput cost effective tools to phenotype heat resilience, and methods/information for best combining and tracking heat resilience sources.

Description:

- Refine the precision and affordability of phenotyping heat stress. This would involve improved protocols for implementing time specific heat stress events (e.g. using heat chambers/polyhouses, and in-field heat chambers); development of high-throughput low-cost proxy measures (tolerance indicators) for normally difficult to measure physiological traits (e.g. metabolite marker, hyperspec, NIR, etc.); and methods to more easily phenotype otherwise laborious traits, for example, X-ray CT scans to study undissected barley heads and measure unfertilised ovule numbers, aborted grain numbers, and extent of grain fill.

- Use these ‘easier/faster' protocols to better interrogate ‘best-bet’ thermo-resilience sources, for example, determining heat load ranges of best bet sources, pushing them to their extremes to exactly define the extent of their thermo-resilience.

- In the latter years of the project, take the top candidate thermo-resilient sources and characterise them further for grain quality attributes (e.g. malting, brewing, and feed attributes) using established high-throughput proxy techniques (i.e. NIR).

- Provide genomic breeding tools (thermo-resilient genetic catalogue, quality and yield performance database, breeder-deployable markers, prediction model, whole genome selection, AI-informed gene pyramiding designs) to support breeders in the development of varieties with broadly applicable heat stress resilience via the GRDC Approved Breeders MTA.

Proposed Budget

Proposed Contract & Term

GRDC will contract under the terms of the GRDC Standard Two-Party Research Contract.

The schedule(s) attached to the contract will detail the project details: the outcomes, outputs, milestones, budget, participating personnel and required intellectual property.

The template contract containing the proposed terms and conditions is available from the Application resources page on the GRDC website.

It is anticipated that any resultant contract in relation to this procurement will commence with a proposed term of 5 years (2025 – 2030).

Conditions for Participation

The following are mandatory conditions with which a Tenderer must comply to participate in this procurement process:

The Tenderer and any subcontractor must not be named on the Consolidated List, being the list of persons and entities who are subject to targeted financial sanctions or travel bans under Australian sanction laws, as maintained by the Department of Foreign Affairs and Trade.
The Tenderer and any subcontractor must not have a judicial decision against it (not including decisions under appeal) relating to employee entitlements and who have not paid the claim.
The Tenderer must be a single legal entity or recognised firm of partners except where the Tender is submitted by a consortium and the Tender specifies that each member of the proposed consortium will be party to the contract.
The Tenderer and any proposed subcontractor must be compliant with the Workplace Gender Equality Act 2012, the Modern Slavery Act 2018 and any other applicable labour laws and standards in the jurisdiction in which they operate.
In accordance with the Black Economy Procurement Connected Policy, a Tenderer must include a satisfactory and valid Statement of Tax Records (STR). If the total value of all work under any proposed subcontract is expected to be equal to or above $4 million (inclusive of GST), also include a separate satisfactory and valid STR of that proposed subcontractor.

Minimum Form and Content Requirements

The following are the mandatory content and format requirements that the Tenderer must complete and provide to participate in this procurement process:

Submit Tenders using the Grains Investment Portal.
Write Tenders in English and express any measurements in Australian legal units of measurement.
Budget details must be submitted on the ‘GRDC Budget Template’ provided in the Grains Investment Portal.
DRAFT Intellectual Property and Project Output (IPPO) Register
DRAFT Milestone Schedule
DRAFT Data Management Plan
Detailed stakeholder co-design plan

Evaluation Criteria

In the table below are the Evaluation Criteria that the Tender Evaluation Team will use to assess the value for money of all Tenders.

No	Type	Weighting
	Technical – Qualitative evaluation criteria related to non-price factors such as methodology, project plan, track record, experience.
1	Project Plan A detailed plan to deliver outcomes and outputs directly relevant to key stakeholders. This will include: a) Context of the research (eg. background, hypothesis, and scope) b) Detailed plan for stakeholder co-design process that also demonstrates early implementation (e.g. specific outputs and insights from the early co-design process, key stakeholders engaged, established common grounds particularly with regards to technical approach and output formats at project conception stage etc.). Provide as an attachment (max 5 pages). c) Specific information, products and/or services to be delivered for each output that is considerate of stakeholder consultation and advice d) Key tasks, responsible parties, and indicative timeframes (e) Project team structure and management arrangements, including collaborations with organisations (including international organisations), commercial companies and/or other projects with relevant data	20%
2	Personnel and Organisational Capability a) A list of all key personnel, including proposed sub-contractors, detailing relevant knowledge; experience, including collaborating with industry personnel and stakeholders; achievements of the project lead in providing effective leadership, management, and timely delivery of high-quality outputs to industry etc. b) A summary of the organisations capability to effectively deliver the tendered work, including infrastructure, equipment, timely business support etc. *Please also complete full details of 'Specified Personnel' and 'Subcontractors' in the sections of the Application form.	20%
3	Methodology Detailed description of method/s to achieve the investment outputs, including: a) Detailed rationale, approach, and specifics (e.g. number of years and seasons of field testing, lab work, germplasm or populations to be studied, proposed locations of activities, management and design of experiments, statistical design and analysis capacity etc.) b) Include infographics and tools (Gantt Chart) to help clarify the methodology/work plan, identify IP/resources, proposed activities against timelines for each Output delivery. c) A draft Milestones Schedule that is considerate of stakeholder engagement requirements	15%
4	Path to Market A detailed plan to deliver relevant project outputs to target audience/s, specifying: a) The target audiences for each output - e.g. plant breeders, GRDC, international research community b) Information, products and/or services for each output c) Communication of project updates and findings to Australian industry (e.g. growers, advisors) d) Plans for continued engagement throughout project life cycle i.e. the methods and structures that will engage and foster participation of Australian barley breeding entities enabling the updating, reviewing, refinement, delivering, and adoption of the outputs, which may include co-investment, commercialisation, communication, milestones, and/or additional R&D	20%
5	Intellectual Property (IP) A summary of the IP including: a) Existing IP that you intend to use during the project and whether this would cause any restrictions on the use, publication or commercialisation of the intended project outputs b) New IP that may be created in the course of the project c) Expectations for any commercialisation of project outputs d) How IP will be managed Provide a draft Intellectual Property and Project Output (IPPO) Register using the GRDC template.	15%
6	Data Management An overview of your approach to data management in accordance with the GRDC RD&E Data Management Guidelines (https://grdc.com.au/research/partnering-in-rde-investment/contract-templates), including: a) Existing data that you intend to use during the project and any potential restrictions on its use, publication or the subsequent commercialisation of the intended project outputs b) New data that may be created in the course of the project; and c) How all data will be managed and stored during, and post investment Provide a draft Data Management Plan using the GRDC template.	10%
	Price – The tendered budget.	N/A
	Risk – Risks inherent in the application including the degree of compliance with the draft contract and any actual or perceived conflict of interest.	N/A
	Australian economy – The economic benefit of the procurement to the Australian economy.	N/A

Lodging a Tender

Questions and Answers

Q1. Request for clarity on Output 4 ‘applicants are required to partner with APPF to access and leverage capabilities/capacity which GRDC has funded’. Specifically, what capabilities is this referring to and at what level are applicants required to engage the APPF?

A1. GRDC has co-funded the recent establishment of an X-ray CT scanner at the University of Adelaide APPF site. The custom-built system enables non-destructive scanning of grain spikes that increases the accuracy, cost effectiveness, and higher throughput measurement of key traits (e.g. grain number, grain weight, density, volume and physical size and shape).

The APPF manages access to X-ray CT Scanner through service and collaborative arrangements. It is anticipated that applicants would reach out to the APPF to explore opportunities to access the X-ray CT Scanner technology for potential use in their projects and discuss appropriate arrangements to utilise the technology in their proposed projects.

Q2. Request for final report for “UMU1606-002RMX: UMU00049 - 2016.02.01F - Maintenance of grain plumpness and transfer of heat tolerance into Australian barley germplasm”? This seems to be particularly relevant to the “Advancing genetic improvements in barley heat tolerance during flowering and grain fill”. I have searched the GRDC data catalogue and final reports website but can’t locate it.

A2. GRDC has stopped publishing Final Technical Reports (FTRs) for public release since 2018. Generally, FTRs are used for internal purposes only. For this procurement, however, please consider these alternative options a) accessing publicly available key research publications and/or data generated by previous projects (see example reference list below); b) contacting lead researcher of relevant projects to provide any specific, non-confidential information, for research and education purposes.

Li, C et al. (2022) Grain-Filling Rate Improves Physical Grain Quality in Barley Under Heat Stress Conditions During the Grain-Filling Period.

Li, C et al . (2023) Maintenance of grain plumpness and transfer of heat tolerance into Australian barley germplasm (phenotype datasets).

Hill, C et al. (2019) Minimising the impact of high temperature at flowering on spikelet fertility (phenotype datasets).

Q3. I am reaching out to enquire if I could have access to the data and also the final report submitted to GRDC from the previous GRDC Barley Heat Stress project code number: GRDC Code: UMU1606-002RMX https://grdc.com.au/grdc-investments/investments/investment?code=UMU1606-002RMX.

A3. Kindly be advised that this inquiry has been previously submitted and addressed under Questions and Answers section on the tender site. However, for the sake of clarity, we reiterate that while we are unable to share Final Technical Reports (FTRs) to the public, the research publication Grain-Filling Rate Improves Physical Grain Quality in Barley Under Heat Stress Conditions During the Grain-Filling Period (Li, C et al. 2022) has effectively documented the majority of the knowledge and data produced by UMU1606-002RMX (UMU00049). Details in this paper can therefore serve as the foundation for developing a new proposal. For further, non-confidential details, please don't hesitate to check the links provided earlier in the Q&A section and/or contact the principal investigator.

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