Browsing by Author "Jackson, P"

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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.
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.
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.
More crop per drop : SRDC final report BSS305
(2011) Basnayake, J; Jackson, P; Inman-Bamber, G; Lakshmanan, P
Water stress is the major constraint to productivity in the Australian sugar industry, with an estimated cost of $260 million/annum (CSE014 Milestone Report 3.5). In 2003 and 2004, the losses exceeded $140 million in Mackay alone. This impact may increase with climate change. About 40% of the Australian sugarcane production is rain-fed with or without supplementary irrigation. With the erratic rainfall and the increasing cost and restrictions on water use, efficient use of available water is an increasingly important priority in irrigated production systems as well.Varieties that adapt well to drought and use water efficiently are becoming increasingly important for sustainable sugarcane production. Australian sugarcane breeding programs, however, do not explicitly address selection for response to dry conditions. To effectively address this issue there is a need to understand the main physiological mechanisms underlying genetic variation in response to different types of water stress environments in sugarcane. Hence, this project was initiated to determine the potential of Australian sugarcane germplasm for developing water use-efficient and drought tolerant commercial cultivars.In this project the phenotypic and genetic variations of traits that confer or linked to drought tolerance and water use efficiency (WUE) and their contribution towards productivity were studied in a genetically diverse sugarcane population. Field experiments were conducted for 3 years under rainfed, fully irrigated and managed drought conditions at three locations in the Northern Queensland. The experiment sites were in Home Hill in the Burdekin shire, Crystal Creek in the Herbert Shire and Dalbeg in the upper Burdekin. All trials were conducted in commercial sugarcane farms and followed the best crop management practices. A genetically diverse population (131 genotypes) comprising S. officinarum crosses with wild relatives, commercial cultivars including foreign clones, advanced lines in the selection program and some parental clones in the BSES breeding program was used as test clones. Clone performance was evaluated under rainfed, irrigated and managed drought conditions adopting most appropriate statistical field designs for the respective sites. The agronomic and cane yield characteristics, fibre, sugar and sugar quality characteristics and physiological traits related to drought tolerance were collected during the crop growth period and at harvest. Appropriate statistical methodologies were used to analyse and interpret the results at the end of the project.
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.
Provision of improved varieties and pathology services for the Ord Sugar Industry : final report CTA043
(2003) Jackson, P
This project was established to introduce and evaluate new sugarcane varieties into the Ord River Irrigation Area (ORIA), and to provide advice on pathology issues relating to the ORIA. Cultivars in the ORIA currently are old (introduced in 1980 or before) and it is believed that newer varieties bred since then could provide improved productivity and profitability for the ORIA industry. Varieties were initially chosen for introduction to the ORIA based mostly on commercial performance in north Queensland. They were transferred to the ORIA via a three to four year process that aimed to reduce the risk of inadvertently introducing important diseases present in Queensland but which are not present in the ORIA. Professional pathology advice was provided in supervising this process and ensuring plant material was apparently disease free at various points in the process. Pathology related advice was also provided to Agriculture Western Australia staff and growers on specific crop management matters in the ORIA throughout the project. The directions taken in this project were greatly impacted on by the discovery of smut disease in the ORIA in 1998. This was the first time this disease had been found in Australia. It has a potentially devastating effect on productivity of susceptible varieties. The environmental conditions in the ORIA are highly favourable to smut infection, and a high level of resistance is required in cultivars for sustainable production. It was very fortunate that three cultivars in the ORIA at the time of the outbreak were resistant, and this enabled the industry to maintain productivity levels much better than it otherwise would have. However, in 1998 little was known about the relative smut resistance of most Australian varieties. As testing for smut resistance proceeded in the next few years in Indonesia by BSES (through BSS214) and by the CTA043 project team in the ORIA, it became apparent that around 80% of varieties from Australian breeding programs were too susceptible to smut to be grown commercially in the ORIA.
Provision of improved varieties and pathology services for the Ord Sugar Industry : Final report CTA043
(2012) Jackson, P
This project was established to introduce and evaluate new sugarcane varieties into the Ord river Irrigation Area (ORIA), and to provide advice on pathology issues relating to the ORIA. Cultivars in the ORIA currently are old (introduced in 1980 or before) and it is believed that newer varieties bred since then could provide improved productivity and profitability for the ORIA industry.
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.
Sugarcane for future climates : final report 2013/029
(Sugar Research Australia Limited, 2017) Stokes, C; Jackson, P; Basnayake, J; Inman-Bamber, G; Lakshmanan, P; Natarajan, S
Increasing costs of irrigation in irrigated production regions, and seasonal periods of water deficits in rain-fed production regions are impacting greatly on profitability, sustainability, and expansion of the Australian sugarcane industry. Improving crop transpiration efficiency (TE, defined as growth per unit of water used) is one strategy to help address these issues.