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Ongoing project

National pineapple breeding and evaluation program (PI17000)

Key research provider: The Queensland Department of Agriculture and Fisheries

What’s it all about?

Contracted in August 2018, this investment is working towards the release of new pineapple varieties suited to Australia’s key pineapple growing regions. There is a focus on developing and evaluating high-yielding varieties with improved disease resistance and flowering control, as well improved fruit consistency and quality, to meet the needs of both growers and consumers.

The program is looking at the industry’s main commercial varieties and advanced varieties developed through previous breeding work, while implementing a novel approach to pineapple breeding – utilising a low level of in-breeding – to develop new elite lines.

Performance data for the new varieties, and varieties produced under previous industry investments, will also be produced and delivered to industry.

Two phases of the program have now been completed:

  1. Selecting varieties with improved eating quality and resistance to translucency
  2. Improving yield without compromising on eating quality

The intent was to develop pineapple varieties suited to the main summer production season in tropical and subtropical production regions of Australia with superior yield, disease resistance, plant vigor, crop control and eating quality as compared to current commercial varieties.

For the first time in the breeding program, the traits of resistance to Phytophthora cinnamomi (Pc) and Natural flower initiation (NI) were incorporated, and molecular markers were used to assist selection.

Over the five years of the project so far, 35,000 seedlings were fruited across Queensland pineapple growing districts including SE Qld, Wide Bay, Coastal Central and Far Nth Qld. A total of 335 selections were made from a broad range of parent combinations. Planting material was retained from all selections and a low level of multiplication achieved in most cases. Selection was biased towards strong, vigorous plants with good fruit size and good eating quality. It is expected there will be several selections with good potential suited to each of the regions.

Work on molecular markers was completed to fast track the final selection process of the preliminary selections. A replicated field trial examining resistance to natural flowering over the winter of 2022 was completed. Genetic analysis identified an associated position on chromosome 4 and a causal gene was proposed. Re-analysis of previously collected data on resistance to natural flowering from drought identified an associated position on chromosome 6 and a causal gene was proposed. This work now allows the use of molecular markers to assist the final selection process.

31 varieties held in the DAF pineapple germplasm collection were re-sequenced using the Illumina platform to produce a high quality, high density set of single nucleotide polymorphism (SNP) markers to assist with improved genetic analysis. DArTseq markers sets held for approximately 1,000 accessions, were also re-referenced against several new pineapple genomes to allow more accurate positioning of genes of interest. This work will improve the accuracy and usefulness of our pineapple genetic analysis tool kit.

Plant and fruit data was collected on a diverse population of genotyped seedlings and varieties to identify molecular markers associated with many traits of importance other than just resistance to root disease and natural flowering, including fruit size, sugar and acid content, flesh color, core diameter and slip number. This data now allows marker-assisted selection and genomic selection for many traits of interest to be included as breeding tools in pineapple.

DAF now holds a very good germplasm collection complete with high quality genomic data to allow further gene identification and improved breeding outcomes. In addition, a large population of new selections are now held ready for further multiplication, selection and testing in growing regions.

This project has successfully harvested over 10,000 seedlings across three regions, with 91 selections made, many of which show strong growth attributes. The seedling fields were also subjected to a genomic selection trial.

From this genomic selection trial, a preliminary genetic analysis was conducted on trait data and a large part of the Queensland Department of Agriculture and Fisheries pineapple germplasm collection was sequenced with good coverage.

Seedling production is almost complete, and the focus has not shifted into the multiplication and testing of selections.

Another outcome that has been achieved is the selection of 347 seedlings from the targeted 35, 000 at Maroochy Research Facility.

The team report progress in the following areas:

  • The seedling trial planted at Wide Bay was harvested ahead of schedule, with a total of 43 selections from 3,706 seedlings obtained
  • Harvest commenced for a genomic selection trial of 840 plants comprised of seedlings of 17 diverse families and 53 parents / grandparents at the Maroochy Research Facility (MRF) in December 2021. A second genomic selection trial was also established at MRF in October 2021, comprised of a bi-parental population of 1,164 plants.
  • Harvest commenced for a ratoon crop of seedlings at Townsville in December 2021
  • An additional 1,750 seedlings were planted at Wide Bay in August 2021
  • Testing of 17 varieties for resistance to the virulent strain of Dickeya was completed in Katherine in the Northern Territory in October 2021
  • A planting comprised of 5,064 seedlings in Yeppoon was induced to flower and is scheduled for harvest in April 2022.

Over the past year, the project team has progressed its work, with all pollinations now complete and more than 35,000 seedlings developed.

Approximately 32,700 seedlings were planted across four of the five main growing regions and have now been harvested at Glasshouse Mountains, Beerwah, Elimbah and Far North Queensland locations. Fields are currently being harvested at Maryborough and a second Elimbah site. A new field of 1,000 plants was recently established at Bundaberg.

Improvements are being made in fruit size, total soluble solids (TSS), and slip and fruit stem reduction. Arrangements are underway to commence tests on a range of varieties for resistance to Dickeya sp in the Northern Territory.

Evaluation of seedling trials and multiplication of selections are the team’s priorities going forward. Results will continue to be shared with industry as the program progresses.

The seedling population has now been established, with over 15,000 planted across four farms to bring total numbers to more than 25,000 seedlings. Planting sites include approximately 8,000 seedlings across two sites at Beerwah and Glasshouse Mountains in south east Queensland, 4,000 in the Wide Bay region (Maryborough) and 4,400 in Tar North Queensland (Townsville) district.

Pathogen testing has been conducted on thirty varieties representing a broad range of genetics from wild to modern, domesticated. Trials were established at the Department of Agriculture and Fisheries Mareeba site to investigate the recently discovered bacterial pathogen, Dickeya sp. Further testing is required using the Northern Territory strain of Dickeya which is more genetically similar to virulent overseas isolates.

Molecular markers associated with root disease are being identified. Comprehensive analysis on previously generated data has identified candidate genes associated with resistance to the root pathogen Phytophthora cinnamomi. Several other potential genes have been identified for further validation tests.

Discussions were held with growers about the project’s progress with industry groups in Townsville and Maryborough. A field presentation was also given to all growers at the Annual Pineapple Field Day in August 2018.

Further updates will be provided to industry as research continues.

Related levy funds

This project is a strategic levy investment in the Hort Innovation Pineapple Fund.