Varieties, plant breeding and release

Permanent URI for this collectionhttp://elibrary2.sugarresearch.com.au/handle/11079/13841

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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End date: 2009Subject: search.filters.subject.Breeding

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Now showing 1 - 9 of 9
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    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.
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    Introgression of new genes from Saccharum officinarum
    (SRDC, 2004) Jackson, P; Piperidis, G; Aitken, K; Li, J; Morgan, T; Foreman, J; Hewitt, M; McIntyre, L; Berding, N
    Modern sugarcane cultivars are derived from two main ancestral species: Saccharum officinarum, which is the main source of high sucrose levels, and S. spontaneum. Only a small number of clones of either species have ever been incorporated into commercial cane breeding programs around the world. While incremental gains in cane yield and ratooning have been made by sugarcane breeders over the last 40 years sugarcane, there is concern that improvement in CCS has been very limited. One hypothesis for this is that because of the limited genetic base of sugarcane favourable alleles for high CCS in the breeding parent pool have already been fixed in current cultivars. If this hypothesis is correct then new genetic diversity will need to be introgressed from germplasm outside current breeding programs. Clones of S. officinarum, available in germplasm collections may provide a source of valuable high sucrose genes. However, introgression breeding using traditional breeding technologies is long term and high risk. The development of new DNA marker techniques has provided new opportunities for improving introgression breeding. These techniques provide a means to (i) characterise diversity within germplasm collections, (ii) identify genes or chromosomal regions, termed quantitative trait loci (QTL), from wild parents which cause positive or negative effects on important traits, which may then be selected for or against during breeding cycles. With this background in mind, this project had two concurrent aims: (i) To characterise a collection of S. officinarum clones for important phenotypic traits and for genetic diversity using DNA markers and identify a set of these for future breeding efforts; (ii) Using case study populations, to assess the value of using DNA marker assisted selection in introgression breeding in sugarcane. A range of candidate S. officinarum x commercial parent crosses were made at the start of the project using a random sample of S. officinarum clones not previously used in our breeding breeding program. From these a “case study” population was chosen for detailed investigation using DNA markers. Two of the progeny were subsequently chosen for “backcrossing” again to proven commercial parents to produce two other “backcross” populations. Concurrently, the collection of 282 S. officinarum clones in the Australian collection was also characterised using DNA markers, along with 147 parent clones in the Australian core breeding program. A subset of 158 S. officinarum clones, recently imported from overseas, was also evaluated in a field trial for CCS and cane yield across a plant and two ratoon crops.
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    Effect of far-red radiation on flowering of Saccharum spp. hybrids : SRDC Final report BS1S
    (1990) Berding, N; Moore, PH
    Many tropical sugarcane clones (Saccharum spp. hybrids) are unavailable for hybridization because of poor flowering. Methods are required to improve the flowering of such clones. This study was conducted to determine whether far-red radiation (> 700 nm) at end-of day would improve flowering. Three treatments in a photoperiod facility (PPF) were compared to an external control (EC) under natural photoperiod. A basic treatment known as modified Florida (MF) was used in all PPF treatments and served as the internal control. This was altered to provide a far-red (FR) treatment, by addition of either 5 or 10 min of far-red radiation at end-of-day, and a day interrupt (Dr) treatment, by imposition of 2 hr of darkness in mid afternoon. Percent flowering as harvested panicles was 21.0, 24.2, 24.6, and 9.5 for FR, Dr, MF, and EC, respectively. Total flowering was 23.4, 28.9, 27.0, and 10.7, respectively. The PPF treatments did not differ significantly for either measure. All were highly significantly greater than EC. The far-red treatments did not differ for harvested panicles. Treatments differed significantly for time of flowering. The flowering sequence was EC, MF, FR, and then DI. There were significant differences among clones in all treatments for emergence day, initiation day, elapsed days, and pollen test. Correlations among these measures were varied, with some being significant. Far red at end-of-day neither stimulated nor inhibited flowering in the PPF treatments. The FR and Dr treatments delayed emergence of flowering.
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    Optimisation of experimental design and analysis for variety trials to maximise genetic gain : SRDC final report UQ023
    (2001) Basford, K; Hogarth, M
    The analysis of field experimental data usually assumes independent observations. This method is often inappropriate if the data contain strong spatial trends. Methods of analysis (commonly used in cereal trials) which account for the spatial variability existing within a field were shown to improve the precision of the estimates of clonal effects in sugarcane variety trials. As inter-plot competition was a major contributing factor biasing clonal estimates, a model which accounted for the competitive interaction between neighbouring clones was developed. Both factors could be incorporated into a more general model that jointly assessed inter-plot interference and fertility gradients. Two different estimation procedures (marginal likelihood and profile likelihood) for the parameters in the underlying models were investigated in a simulation study. Based on the criteria of average bias and mean-squared error, there was a slight preference for the marginal likelihood estimators. An empirical investigation of the relative efficiency of the augmented randomised complete block design versus the spatial unreplicated design in early generation sugarcane breeding programs was also undertaken. This indicated that the spatial design was to be preferred with respect to the bias in the parameter estimates, but using other criteria for design evaluation there were very few advantages in choosing the more complicated spatial design.
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    Optimal plot size and replication for testing clones in early stages of selection : SRDC final report CSR017
    (1998) Jackson, P; McRae, TA
    The aim of CSRO 17 was to identifY optimal plot design, replication and selection criteria for testing and selecting clones in small plots in early stages of selection in sugarcane breeding programs. Problems associated with the use of small plots are well known in field experimentation. This is particularly so in variety selection trials where measurements in small plots are subject to possible bias due to competition effects when there are significant differences in height between genotypes being compared. In sugarcane breeding programs, small, single row or two row plots are usually used extensively for the first two stages of selection within seedling populations. The reasons for this include the desire to screen large populations of clones within available resource constraints to identifY rare, elite recombinants, and the necessity to bulk up planting material from original seedlings before planting to larger plots. Given the level of resources usually devoted to early stage selection trials, it is important that optimal procedures are used so that selection is effective and efficient. The overall approach used in the project was to obtain estimates of key genetic parameters from field experimentation and then to use these to predict gains from selection among relatively unselected clonal populations in sugarcane breeding programs using different selection options. The clones used in this study were representative of those directly derived from hybridisation in two different sugarcane breeding programs, and were unbiased by any previous selection. As such, the genetic parameters are useful for other studies that may simulate and assess different options for selection from the first stages of selection in sugarcane breeding programs.
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    Genotype X environment interaction for clones and crosses planted in Southern Queensland and Northern New South Wales : SRDC final report BS15S
    (1997) Bull, JK
    The main aims of this project were to assess whether original seedling families produced for south Queensland would be suitable for the New South Wales sugar industry and to determine whether clones selected at the Bundaberg Sugar Experiment Station would perform similarly under northern New South Wales cropping conditions.
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    Seasonal distribution of growth and sugar accumulation in sugarcane : SRDC project BS5S Final report
    (1995) Cox, MC
    At existing levels of cane yield, an extra unit of sugar content during May, June and July represented 47 6000 tonnes of sugar worth $13.3m at 1987 prices when this project was initiated. The situation now, with annual crops of greater than 30m tonnes and higher sugar prices, would provide greater returns. The potential for increasing early sugar through breeding and selectio has been demonstrated (see BS25S Final Report). Selection for high early sugar content may change the seasonal pattern of yield accumulation and affect regional adaptation.
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    Genotype X environment interaction and selection of sugarcane families for the Burdekin River irrigation area : SRDC final report BS57S
    (1995) McRae, TA; Jackson, PA
    The arable lands being developed for sugarcane production in the Burdekin River Irrigation Area (BRIA) are on markedly different soil types and, as a consequence, may present environmental challenges different to those influencing sugarcane production on the more established alluvial soils of the Burdekin delta and levee areas.