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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A field experiment to evaluate the response of sugarcane varieties to waterlogging
(ASSCT, 2018) Salter, B; Park, G; Kok, E
RECENT PRODUCTIVITY REVIEWS in the Herbert and Central regions identified strong negative correlations between excessive rainfall and productivity. Waterlogging has a significant effect on sugarcane productivity. It was estimated that yield is reduced by 0.5 t/ha for every day the water-table is within 50 cm of the soil surface. Waterlogging tolerance of sugarcane varieties is not assessed in the current variety selection program. Identification of varieties that perform better under waterlogged conditions is based on anecdotal observations from the field, after a variety is released. If a variety’s tolerance to waterlogging was known closer to the time of release, growers could make informed decisions on whether particular varieties are best suited to their farm or blocks within their farm. A field experiment was conducted near Ingham where the waterlogging tolerance of eight sugarcane varieties was assessed.
A sugarcane tissue culture system for mass propagation and transformation : SRDC final report BSS242
(2004) Lakshmanan, P; Grof, C; Geijskes, R
The core research strategy we conceived was to develop the initial observation of direct shoot regeneration in sugarcane leaf tissues to a generic and efficient plant production technology for sugarcane and probably for other major monocot crops, and then use that system to develop a novel method for sugarcane transformation. The main objectives of this project were: 1. Protect identified IP by patent; 2. Develop an efficient direct plant regeneration system for sugarcane and determine clonal stability of plants produced by this method (now referred to as the SmartSett® system); 3. Develop microprojectile and/or Agrobacterium-mediated transformation systems based on SmartSett®; 4. Establish the utility of SmartSett® to other monocot crops; 5. Technology transfer to other groups. These objectives were met.
Advancing yield, disease resistance and ratooning by exploiting new sources of genetic variability from wild relatives of sugarcane : phase 1
(2017) Piperidis, G
This project was originally planned and designed for six years to allow collection of data over 2 or 3 ratoon crops. In this first phase of the project, all propagations and trials were well established and good quality data collected from the plant crop trial harvests. Analysis and interpretation of results will be an on-going task. Some introgression clones were identified as close to commercial potential. The average performance of introgression clone trials according to their generation was as expected for CCS, Fibre and the selection index rEGV. Continued backcrossing to elite material, after the initial cross to produce the F1, increases CCS and rEGV and decreases Fibre with each backcross generation. The variation observed for each of these traits also decreases with each backcross. Introgression clones producing high value progeny have been identified and further crossing cycles will focus on using these clones. In general, seedling families derived from S. spontaneum appear to ratoon faster than E. arundinaceus progeny, regardless of the generation (BC3 or BC4). There was a very high correlation between stalk numbers per plot and stalk numbers of the best 2 stools per plot based on visual assessment, which suggests the latter to be a more efficient and cost effective method of measuring this trait in seedling trials. High and low nematode treatments were successfully achieved at 2 sites using cover crops and nematicide. No association between nematode numbers and cane yield could be identified at this stage. It is expected that cane yield differences between treatments will be more pronounced in the ratoon crops.
AGR2008150 : Provision of research and development services for the Ord Sugarcane project
(2010) Croft, BJ; Webb, B; Piperidis, G
The requirements for year 2 of the contract for the delivery of research and development services to the Ord sugar project have been fully achieved. The harvest results from two second ratoon, two first ratoon and two plant crop yield trials were analysed using BSES statistical procedures and the analysed results were provided to the WA Dept of Agriculture and Food. These data were used to identify promising new varieties for further propagation. Barry Croft, BSES Program leader biosecurity (Plant pathologist), and George Piperidis, BSES Program Leader Variety Adoption (Plant Breeder), visited the Ord from the 24-27 May 2010. They inspected selected varieties in yield trials and propagation plots for sugarcane smut, top rot and other diseases and made notes on growth of the varieties. Recommendations were made on the maintenance and further propagation of varieties that have performed well in yield trials and have acceptable reaction to sugarcane smut and top rot. A heavy infestation of scale insects was noted on a few varieties in the 2008 propagation plot in block 6B. These insects have been seen before but this was a particularly severe infestation and the variety Q208 which has performed well in the Ord and is the major variety in Queensland was one of the varieties affected. A borer that was attacking rice was collected. BSES is currently involved in an Australian Centre for Agricultural Research (ACIAR) funded project investigating biological control of borer species attacking sugarcane in Indonesia. Part of this study is to collaborate with other research groups that are DNA barcoding endemic and exotic moth borers and these samples will be submitted for DNA barcoding.
AGR2008150 : Provision of research and development services for the Ord Sugarcane project
(2009) Croft, BJ; Webb, B; Piperidis, G
BSES has provided the research and extension services to the Ord River Irrigation Area (ORIA) sugar industry under a cooperative agreement with the WA Dept of Agriculture and Food since 2003. This contract was terminated in April 2008 after the Ord sugar mill ceased operations in 2007. A new contract was signed to provide continued Plant breeding and plant pathology services to WA Dept of Agriculture and Food to continue plant-breeding trials, inspect sugarcane plots for diseases and pests and to advise WA Dept of Agriculture and Food on maintenance of sugarcane varieties so they could be available for potential new sugar industries in the ORIA.
Alternative selection strategies for the Burdekin sugarcane improvement program : SRDC final report BS4S
(1994) McRae, TA; Hogarth, DM
An assessment of the application of DNA markers to studies of genetic diversity and marker assisted selection in sugarcane : SRDC Final report SD99001
(1999) Carroll, B; McIntyre, L; Berding, N
The project objectives were as follows:
An automated cane billet sampler for research trials : SRDC final report BS118S
(1998) McRae, TA
The Australian sugar industry invests millions of dollars annually on sugarcane breeding programs and associated research. Improved selection efficiency as a result of more accurate estimates of commercial cane sugar (ccs) will greatly enhance returns on this investment. Sugarcane breeding and research programs use hand cut sound whole-stalk samples for determination of ccs and other quality components. Whole-stalk provide a biased sample of the material harvested for milling from experimental plots as they are free from extraneous matter and inferior quality cane. The small mill has low efficiency of juice extraction from whole-stalks, extracting only 26-50% of the absolute juice, and this also leads to bias. The bias in processing billet and whole-stalk samples through a small laboratory roller mill and a hydraulic press with higher levels of juice extraction was quantified in experiments at Tully, Burdekin, Bundaberg and Broadwater. The use of sound whole-stalk samples processed through a small laboratory roller mill with low levels of juice extraction seriously biases the accuracy of estimation of sugar content of sugarcane. Bias for whole-stalk samples was quantified and compared with samples of commercially harvested cane in selection experiments at Broadwater and Tully. A bias of more than seven units of ccs was measured in badly lodged, heavily suckered and deteriorated cane harvested green at Tully. A bias of three units of ccs was less serious in burnt cane at Broadwater. Despite these biases and the inaccurate over-estimation of sugar content of harvested cane from experimental plots, sound whole-stalk samples are usually adequate for ranking of clones for selection purposes. However, billet samples provide a far more accurate estimate of commercial ccs and are preferable for predicting the true responses of commercial varieties to various agronomic treatments. There is a need for an automated method of sampling harvested cane from experimental plots for the unbiased collection of samples. The use of unbiased samples should greatly improve the accuracy of ccs assessment and provide a direct measure of the commercial value of the harvested material. Automated sampling of billets should be more efficient than the manual collection of whole-stalk samples and, with appropriate strategies, will result in greater genetic gain for sugar content. The acquisition of an automated billet sampler will greatly improve labour use efficiency and workplace safety. Information collected in project BS118S has resulted in SRDC funding project BS156S and the construction of an automated sampler.
Analysis of sugarcane productivity trends in the wet tropics at a district level : SRDC final report
(2001) McDonald, L
This project provided an in-depth re-analysis of district level data for cane yield, sugar content, and sugar content per hectare for the mill districts of Mulgrave, Babinda, and Tully and an evaluation of the estimates of changes in productivity for the period from 1958 to 1995, as derived by Leslie and Wilson (1996). Restricted Maximum Likelihood (REML) methodology (Patterson and Thompson, 1971) was shown to be applicable to the analysis of productivity data at the district level. Importantly, this methodology can now be implemented with readily available computer software (Gilmour et al., 1996). Its capacity to deal with unbalanced data sets (varieties change over time and across districts) is particularly useful. REML enables a more rigorous and complete estimation of productivity trends over time when adjusting for variety and variety  environment interactions than previously used methods. For the period under investigation, some of the increased cane yield (tonnes of sugarcane per hectare) was due to improved varieties while the decrease in sugar content was due to other factors. As a result, sugar content per hectare remained relatively stable during this time.
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.
Assessment of bulk segregant analysis and marker- assisted selection for economically important traits in sugarcane : SRDC final report BS138
(1998) Carroll, B; Berding, N; McIntyre, L
The main aim of this project was to assess the feasibility of bulk segregant analysis (BSA) and marker-assisted selection for important traits in sugarcane. The target trait for this feasibility study was rust resistance. Initially, crosses were successfully made between susceptible and resistant parents to produce two mapping populations. Unfortunately and surprisingly, we were not able to identify fully susceptible clones in four separate rust trials on the two populations. Poor rust development occurred in the first bench trial in 1996 at Meringa (including clones known to be susceptible), and the second trial in January 1997 was a total failure due to lack of rust development. The third rust resistance trial was conducted in Meringa in July 1997, but all of the clones in the mapping populations were resistant. The fourth rust trial on these two populations was completed at the start of 1998, and the results confirmed that all of the clones in these two initial mapping populations were resistant to common rust. Lack of segregation for rust resistance within progeny of sugarcane crosses had not been observed previously by sugarcane breeders in Meringa. This unexpected problem delayed the project as BSA could only proceed after a mapping population segregating for rust resistance had been identified.
Assessment of new soft cane varieties : final report 2015/081
(Sugar Research Australia Limited, 2016) Kent, G; Parfitt, R
The project objectives were to: experimentally determine whether extraneous matter affects the fibre quality parameters measured by SRA; experimentally determine whether the commercial cane preparation process affects the fibre quality parameters measured by SRA; experimentally compare the handle-ability properties of SRA1 andQC04-1411 to the major variety in the central and southern regions - Q208. In 2016, three new cane varieties, SRA1, SRA4 and QC04-1411, were either released or were proposed for release into the Bundaberg and Mackay districts. According to the pre-release fibre quality measurements undertaken by Sugar Research Australia, all three varieties were classified as a soft cane. This report documents a series of experiments undertaken to better define soft canes and to measure the effect that these three varieties had on factory operation and performance.
Australian component Genetic diversity within Sugarcane yellow leaf virus : ICSB final report 99-15
(2001) Borg, Z; Braithwaite, KS; Smith, GR
Sugarcane yellow leaf virus (SCYLV) is widespread in many sugarcane growing countries of the world. The aim of this study was to determine the extent of genomic variation in SCYLV isolates from various countries. Isolates were obtained from Mauritius, Reunion, South Africa, Australia, Papua New Guinea, Hawaii, U.S.A. and Brazil. Four regions of the SCYLV genome (ORF 1, Replicase, Coat Protein and Readthrough) were analysed for variation using both RFLP analysis and sequence comparisons. Of the fifty isolates used, several did not produce RT-PCR amplicons in one or more of the regions covered, suggesting variation in regions where the primers bind. Of the amplicons produced across the four regions studied, RFLP analysis and sequencing results revealed the Coat Protein (CP) region to be the most conserved, followed by the Replicase (REP) region. These areas should be targeted for diagnosis of SCYLV and for use in viral mediated transgenic resistance in sugarcane varieties. Phylogenetic studies of the nucleotide and protein sequences of the four regions covered were performed using eighteen isolates. Representative isolates from each country were used where possible. In a second round of phylogenetic studies, covering the REP and CP regions, nine isolates from North, South and Central America, sequenced by our American collaborators on this project, were included. Variation in nucleotide and protein sequences revealed that many haplotypes of SCYLV exist across the countries tested. Most isolates from the various countries are very closely related across all four regions. Phylograms produced from REP and CP sequences in Phylogeny study #2 revealed that isolates from Hawaii and Australia tend to group together as do isolates from Mauritius and Reunion. Phylogenetic analyses on the sequences used in this study have not identified any significant variants of SCYLV. In conclusion, we recommend that the YLS111 and 462 RT-PCR primers originally developed by Mike Irey and colleagues continue to be used for routine SCYLV diagnosis. Also, the viral coat protein and replicase regions being the most conserved, should be targeted in research to genetically engineer resistance to SCYLV.
Best linear unbiased prediction as a method for predicting cross potential : SRDC final report BS119S
(1999) Stringer, JK
Until recently, BSES breeders used an empirical formula to assess the breeding potential of a parent (Hogarth and Skinner, 1986). Although this method uses data from many sources, it needs to draw on data accumulated for up to ten years to provide reliable estimates. An alternative is the statistical technique called Best Linear Unbiased Prediction (BLUP) which was developed to predict breeding values from dairy cattle data sets which are typically highly unbalanced and from diverse sources.The main objective of this study was to compare the relative efficiencies of BLUP and the existing empirical method for identifying superior sugarcane cross combinations. There was little difference in the agronomic performance of crosses selected using either BLUP or the empirical method but BLUP proved to be the quicker method and should allow more rapid progress from breeding and selection.
Better frost tolerant varieties for NSW : SRDC Grower Group Innovation Project
(2010) Munro, A; Beattie, R
Frost damage to sugarcane crops affects about one third of the NSW cane
Better targeting new cultivars : SRDC Grower Group Innovation Project
(2012) Rudd, A
Aim: Better targeting of new cultivars for soiltypes/environments not covered by BSES. Conduct: Trials with advanced clones and other best bet’s were planted in 2009, 2010 & 2011 were planted in both the Mossman and Tableland mill areas. The 2009 trials were assessed in 2010 and 2011 and the 2010 trials assessed in 2011. Ten overseas clones with a degree of smut resistance were included in the Mossman trial at the request of the local industry. Key Results: Provided key personnel and district growers with yield data supporting recently released and prospective varieties on local soil types and in local environments. No overseas clones warranted further testing. Key Learnings: Data obtained was a factor in the providing local growers with the confidence to rapidly adopt new varieties.
Biomass accumulation in sugarcane : final report 79/9028
(1984) Kingston, G; Ham, GJ; Ridge, DR; Leverington, KC
Growth analysis experiments were conducted at Ayr and Bundaberg from 1979 to 1982 to study biomass accumulation in plant and ratoon crops of sugarcane. Crops were planted and ratooned in March, June, September and December, and harvested at 6, 9, 12 and 15 months of age. Data were acquired for yields of total fresh and dry matter, in addition to yields of the following vegetative components: dry leaf, green leaf, tops and stalks. Fibre analyses were determined on all components, while glucose, fructose and sucrose % were also determined in the latter three components. It was shown that yield of total dry matter increased with age at harvest for all months of crop initiation. Potential for dry matter accumulation was closely associated with intercepted solar radiation. Growth for three months was ranked December-March > March-June > September-December > June-September. These rankings represented the interaction of crop growth stage with solar radition. The proportion of total dry matter allocated to soluble and structural carbohydrate was shown to be dependent on variety as well as an interaction between age at harvest and month of harvest. Canes older than nine months of age, harvested between June and December, had established a plateau type equilibrium between the proportion of total dry matter in soluble and structural carbohydrate. Good prospects existed for forward extension of the crushing season to March for ethanol production based on 15 month old cane. Models were developed to describe the growth of yield components of the biomass in relation to intercepted solar radition, month of crop initiation, age at harvest and crop class.
Breeding clones with high early sugar content : SRDC final report BSS93
(2002) Cox, MC
The project BSS25 ?Breeding of clones with high early sugar content? concluded that the potential for increasing CCS through breeding and selection was greatest early in the season. BSS25 commenced a recurrent selection program with short generation interval aimed mainly at population improvement. The aim of BSS93 was to continue a recurrent selection program for early CCS and to assess the realised genetic gain made in the previous project.At the start of BSS93, BSES had changed its selection program from family assessment in clonal 4-sett plots to family assessment as original seedlings. The recurrent selection program for high early CCS reflected this change. Twenty families with high early CCS parents were selected for planting in New South Wales, southern, central, Burdekin, Herbert and northern regions from 1993 to 1996. At each location, the best 600 out of 1 200 seedlings (based on visual appearance) were sampled in May and June in the following year for CCS. The best 10 clones, based on mean CCS, were selected as parents and sent to Meringa for further crossing. Two hundred clones in total were selected as parents. The 10 parent clones and up to 10 additional clones were selected for testing in Clonal Assessment Trials. A total of 377 clones were selected over the duration of this project. Of these 377 clones, 107 clones were derived from families with at least one recurrent parent from the previous project. Good performing clones from this stage were promoted to advanced selection stages. A number of clones from both the current and previous projects have performed well in advanced trials. To date, two varieties have been released, Q185A (central region) and Q205A (southern region).Replicated trials were planted in the southern, central and northern regions to assess the genetic gain realised in the selected clones from the previous project (BSS25). Parents and elite (selected) clones from the families tested were included along with a base population (a group of 29 randomly selected clones from the breeding population) and a core population (a group of 30 clones from core selection programs with known high early CCS). Trials were sampled for CCS in May and June in plant and first-ratoon crops. Mean CCS was calculated and the various populations were compared.At all locations, the parent population had significantly higher CCS than the base population, and the core and elite populations had significantly higher CCS than the parent population. At Bundaberg, the elite population had significantly higher CCS than the core population, but there were no differences in mean CCS between these two populations at Mackay or Meringa.In terms of realised genetic gain, at Bundaberg both southern parent and elite populations showed steady gains from 1987 to 1991, averaging about 0.26 unit of CCS per year. There were no indications of a decrease in variability in these populations and it was concluded that it was likely further genetic gains would be sustained in the future.At Mackay, the central parent populations showed a modest but somewhat inconsistent improvement over the period and this was repeated for these populations tested at Bundaberg and Meringa. The central elite populations showed good improvement for the first 3 years, but this was not sustained over the subsequent 2 years. Extremely difficult selection environments (flooding and extreme moisture stress) impacted on the clonesselected in the final two elite populations and may explain this decline. It was difficult to come to a firm conclusion on continued genetic gain for the central region.At Meringa, the northern parent populations showed a small, but significant improvement over the 4 years of about 0.13 units of CCS per year. However, the northern elite populations showed no improvement over this period. This was not expected, as the parent populations showed a fairly steady improvement. Interestingly, good improvement was shown by the northern elite populations (first 3 years only) when grown at Bundaberg (0.39 unit CCS per year) and Mackay (0.21 unit of CCS per year). It is difficult to explain these results, but it may indicate that the wet tropics pose some unique difficulties in breeding and selection for high early CCS.
Building strategic research capacity for the sugar industry aimed at overcoming physiological, biochemical and environmental constraints to cane growth, breeding and sucrose yield
(1999) Grof, C; Campbell, J
Using the CSIRO Controlled Environment Facility, the discrete effects on the rate and extent of sucrose accumulation in sugarcane of four significant environmental parameters (daily light integral, radiation levels, temperature and humidity) have been investigated. These experiments have attempted to address some existing industry problems and have provided some basic understanding of sugarcane physiology, a platform from which to launch a more detailed investigation of the metabolic processes that control the rate and final level of sucrose accumUlation.
Characterisation of proteinase inhibitors from canegrubs for possible application to genetically engineer pest-derived resistance into sugarcane : SRDC final report STU032
(2005) Nutt, KA
The primary objective of this research was to identify, isolate and clone a proteinase inhibitor from the haemolymph of a canegrub species with activity against the major midgut proteases of the source insect. The potential for using this canegrub-derived proteinase inhibitor as a novel source of insect resistance in transgenic sugarcane was also to be determined. The project has formed the basis of a PhD thesis submitted to the Queensland University of Technology.