Varieties, plant breeding and release

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Research outcomes: Comprehensive and efficient variety breeding, selection and release programs responding to yield expectations, environmental constraints, resource scarcity and regional preferences. Faster varietal adoption using advanced methods for bulking, distribution and planting.

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Selecting clones for better ratooning under wet harvesting conditions : SRDC final report CSR10S
(1997) Jackson, P; Braunack, M; Foreman, J; Peatey, T; Wood, A
There were three broad aims of this project: (i) To develop and evaluate a method for screening genetic material under conditions where there is (a) stool damage from harvesting machinery under wet conditions, and (b) waterlogging shortly after harvest. (ii) To evaluate a range of genetic material for ratooning under these conditions, including material generated from previous introgression breeding programs by CSR. (iii) To determine if a breeding program aimed at improving ratooning under wet conditions would be worthwhile, and if so, what sort of methods should be used.
The transfer of high CCS traits from wild relatives to sugarcane using biochemical markers
(2003) Grof, C; Manners, J
Over the last 40 years of sugarcane breeding in Australia there have been significant improvements in cane yield but little to no improvement in commercial cane sugar (CCS). It has been hypothesised that this lack of gain is due to the narrow genetic base of current breeding programs and has provided the impetus to examine new sources of germplasm that may provide desirable traits. Broadening the genetic base through the introgression of new Saccharum germplasm could allow the incorporation of 'new' genes for CCS into commercial sugarcane and result in increased CCS. However carefully targeted approaches are required to identify favourable genetic components of value from available new germplasm for introgression.
Evaluation and re-structuring of regional selection programs to maximise efficiency and speed of cultivar release
(2002) Chapman, SC; Rattey, A; Jackson, PA
Continual delivery of new cultivars is required to maintain resistance to existing and new pests and diseases, and to provide constant improvement in crop productivity, quality and profitability for an internationally competitive sugar industry. Sugarcane breeding comprises two major activities: genetic variation is created by crossing parents (selected on historical performance of their progeny in the case of proven parents, or performance for heritable traits in trials in the case of new parents), and the best clones for release are selected through a multi-stage selection process that involves progressively more intensive testing of fewer clones over several years in multiple sites. In Australia, the geographic variation in climate and other conditions in the different regions, the difficulties of moving sugar cane planting material, and differences between regions for some diseases (e.g. the Fiji disease line between the Central and Burdekin regions) had resulted in six cultivar crossing and selection programs, each targeting different regions: North (inc. Atherton Tableland), Herbert, Burdekin, Central, South and northern NSW. The small Ord irrigation area is serviced via testing and selection of elite clones from all of these regional trials. Currently crosses are made in each of four specific regions based on performance of parents (in trials or via progeny performance) in that region. Clones from crosses are initially chosen from small plots in one site per region. In further selection, breeders conduct multi-row plot trials across sites and seasons, with intensive testing within regions, and later exchange of the most promising clones between regions. At the start of this project, there was no basic information on whether clones generated directly from crosses generally perform consistently relative to each other between regions, or whether many clones exhibit specific adaptation to regional environments. This information, and quantifying the relative sizes of genotype, genotype x region interaction, and genotype x within-region interaction variances, in genetic populations generated in breeding programs, is basic information needed for designing an optimal selection system that collectively targets all regions.
Functional genomics for enhanced sugar accumulation in sugarcane : final report CPI002
(2003) Manners, J; Casu, R
Improvement in CCS of sugarcane would provide considerable benefits to the whole sugar industry by improving profitability via enhanced efficiencies in both sugarcane and raw sugar production. Improvements in CCS bring benefits by increasing sugar input to mills with no new costs in cane growing, harvesting and transport and enhanced sugar output with only moderate changes in the sugar milling process. Despite the economic attractions of the CCS plant trait for plant improvement there has been little progress made in improving CCS in released varieties in the past forty years and new approaches are needed. One new approach to breeding high CCS sugarcane varieties is to use DNA markers to select for diverse attributes that contribute to CCS and combine these attributes to produce improved varieties. The CCS trait is complex and involves many genes and a range of plant functions. A key contributor to high CCS is sucrose accumulation and the aim of this project was to identify sugarcane genes that are associated with high levels of sucrose accumulation. These genes provide an input to further research where the CCS trait is being mapped on the sugarcane genome and genes identified in CPI002 are tested as markers. Ultimately, benefits to growers will accrue through the use of these markers in the breeding program to select improved varieties.
Environmental stimuli for sugarcane suckering in the wet tropics : SRDC final report BSS221
(2003) Berding, N; Hurney, AP; Bonnett, GD; Joseph, F
The northern section of the industry has been in crisis for most of the years in the decade up to 2002 because of declining CCS. This decline has been due to increased extraneous matter levels due largely to increased sucker culm content of the crop. These have developed because of marked wet episodes during the harvest period in the majority of years in this period. This resulted in open canopy situations, because of sprawling and lodging, increased light penetration, and initiation and development of sucker culm populations.A hypothesis was proposed that excessive mature-crop moisture, combined with continued excessive nitrogen use, particularly early in the decade were initiating variables for the problem. Observations suggested that light, via an open canopy situation, also was a driver.The project tackled the problem with a preliminary series of experiments that allowed optimisation of management and data collection techniques for use in a main experiment proposed. The main experiment sought to establish the importance of levels of three environmental variables, light, nitrogen and moisture, on sucker initiation, and their interaction with each other and with two cultivars of known suckering propensity under commercial conditions.The preliminary experiments allowed us to make the following recommendations for the design and methods for the main experiment:1. The late nitrogen application of 70 kg N will be in late April early May if the weather is suitable and as soon as possible thereafter if the weather is too wet to allow the application at the desired time.2. That spectroradiometry measurements will be made in the core plots at a height of 10 cm and 1 m to determine the effect of plant spacing on the spectral composition received. Photosynthetically active radiation measurements will also be made.3. A similar soil sampling and nitrate measurement regime will be made in the main experiment as that in the preliminary experiment with the exception that more frequent smaller diameter cores will be taken to speed up sampling.4. Sucker counting and other trial management will continue as originally proposed.5. Applications of late N will be made in separate experiments on different cultivars and if possible to soils with low basal nitrate levels.
Improving the Plant breeding selection system for Fiji Disease Resistance : SRDC final report BSS255
(2005) Croft, BJ; Ridley, AW; Dhileepan, K; James, AP
Fiji leaf gall (FLG) has caused major epidemics in the Australian sugar industry in the past. All new cultivars of sugarcane released in areas affected by FLG should be resistant to the disease. New cultivars have been tested for resistance in field trials in the past but the field trials are unreliable with only a third of trials in the last 28 years giving reliable ratings. The aim of this project was to develop a method of rating clones for resistance to FLG that would be accurate, reliable and practical to implement in the BSES-CSIRO variety improvement program.
Whole-farm planning for management of varieties to maximise productivity and reduce losses from diseases : SRDC final report BSS294
(2009) Croft, BJ; Cox, MC; Millard, D; Burrows, A
The appropriate selection of sugarcane varieties is critical for maximising profitability and sustainability for both growers and millers in the Australian sugarcane industry. Growers are faced with many complex decisions when selecting varieties such as yield potential, suitability to soil type, optimum mix of varieties to maximize sugar content throughout the season, resistance to diseases and pests, ratooning ability and tolerance to stresses such as drought, frost and flooding. This project has developed a web-based variety decision support tool and information resource for the Australian sugarcane industry named QCANESelect to help growers make the best variety choices.
Maximising whole-of-industry benefits from the Australian sugarcane improvement program through an optimal genetic evaluation system
(2007) Wei, X; Stringer, J; Jackson, P; Cox, MC
An optimal genetic evaluation system (GES) is the backbone of any breeding program because maximising genetic gains is primarily a matter of efficient selection. A GES provides information to breeders about which individuals should be selected as parents for crossing and which ones should be selected for commercial production.At the commencement of this project, selection of both parents and clones for commercial production was principally based on the index knows as net merit grade (NMG). NMG is based on the performance of a test clone (or a cross) relative to the average of a number of commercial varieties (or corsses) for the traits of commercial cane sugar (CCS), tonnes of cane per hectare (TCH), appearance grade and fibre content. NMG was used to generate a breeding code for selecting parental clones for crossing. Cross ratio, a measure of each cross's performance relative to the whole population at each selection stage, was used to determine priority of crosses. For selecting elite clones to be retained for further testing, NMG was used in all three selection stages to determine which clones would be advanced to next stage.
Application of molecular markers to sugarcane breeding
(2006) Jackson, P; Aitken, K; Baker, P; Foreman, J; Hewitt, M; Luckell, J; Piperidis, G; Li, J; Morgan, T; Wei, X
The CRC SIIB marker application research aims to develop and evaluate ways to apply DNA markers to Australian sugarcane breeding programs to improve breeding, selection and fast release of high performing cultivars. This research was designed as a 7-year plan, taking account of the length of time to develop relevant sugarcane genetic populations, to evaluate these in field trials for QTL mapping, and to test marker assisted selection through realised genetic gains measured in further field trials. Project 1cii (2003-2006) comprised the first phase. Research done in 1cii is being advanced further in the CRC SIIB, under project 1c7. Key results and interim progress to date toward the end objectives are reported here. Project 1cii incorporated activity already underway at the commencement of the CRC in the area of introgression breeding, and added new activities in the areas of association mapping, and improvement of elite populations. Results are presented under these three areas separately. However, data from all three components will also ultimately be combined to develop consensus linkage and QTL maps of ancestral chromosomes, and interpreted collectively for developing future practical applications. In the association mapping component of the project a “pilot study” was first conducted on a set of (154) clones representing cultivars, parents and advanced stage selections in Australian breeding programs. Marker data (approx. 1700 markers) was collected and disease resistance ratings obtained from the BSES breeding program database. Marker-trait associations were readily found, which did not appear to be due simply to variable contributions from key ancestors (ie. population structure effects). The results for smut disease were the most encouraging, and further association mapping research was planned. In a second study, 480 clones were chosen, about half of which already had data on smut resistance, and the other half selected as a family design, ultimately allowing more powerful data analysis. This population was established in three field trials in 2006 (Burdekin and Herbert regions) and will be measured for cane yield and CCS in 2007. Approximately 2600 AFLP markers were screened across all clones by July 2006, together with 22 markers identified as being significantly associated with smut resistance in the pilot study. Of the 22 markers, seven were found to be significantly associated with smut resistance (P<0.10) in a multiple regression model in the independent data, and these collectively accounted for 19.9% of the phenotypic variation in smut resistance. This result is interpreted as encouraging considering the relatively small scale of effort in the pilot study, and suggests association mapping approaches may be successful in sugarcane. However, the results also highlight (as expected) that a high proportion of marker-trait associations are not repeatable, most likely due to type 1 statistical errors and variation in linkage disequilibrium between marker and QTL. Although data in the second study are still being analysed, analyses done to date show evidence for marker-smut resistance associations: a larger number of markers are showing significance at different threshold values (P<0.05, 0.01, 0.001) than expected by the type 1 error rate. Overall we interpret the results as indicating that it should be possible to find repeatable markers for smut resistance which could be cost-effectively implemented in practice in breeding programs. However this will be a challenging activity without 4 guarantee of success. Approaches suggested for doing this, and rationale are described in section 10. Given the urgency in the Australian sugar industry to move clonal populations at all stages of selection within breeding programs toward resistance in the next few years, it is recommended that consideration be given to accelerating this component of work, with a view toward possible implementation in core breeding programs (if the activity is successful), by mid 2007.
Knowledge of sugarcane physiology and climate-crop-soil interactions : SRDC final report
(2003) Inman-Bamber, NG
Compared to other crops, knowledge of growth mechanisms in sugarcane is inadequate. The question arises as to how much longer can we continue to prosper from sugarcane if knowledge of the growth processes on which our industry depends, remains outdated? Sucrose accumulation and efficient use of resources are primary concerns for this industry. To date we have only limited understanding of climate and management links to sucrose content or CCS and this undermines our ability to manage water, nutrients, varieties and the harvest schedule for maximum CCS and optimum cane yield. Cane and sucrose yields are often below potential for reasons about which we can only speculate (Leslie and Byth, 2000). In the past, research funds have been directed at opportunities for raising limitations to yield and efficiency of resource use at the gene and enzyme level as well as at the crop and paddock level. There has been no attempt to integrate research or information across these disciplines or to assess where progress toward sustainable production is most likely to be achieved. SRDC recognized that it was now time for each discipline interested in the same processes to get together to find out how their different approaches could be complementary. SRDC also recognised the need to review past data relating to crop growth in the later stages of crop development to see if something could be done about under performing crops during this stage.

Varieties, plant breeding and release

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