Completed projects and reports

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Sugar Research Australia, Sugar Research Development Corporation and BSES reports from completed research projects and papers.

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Subject: search.filters.subject.DNA markers

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    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.
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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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    Perfect markers for sugarcane mapping
    (2001) McIntyre, L
    Sugarcane is a complex aneuploid, polyploid, interspecific hybrid. Most breeding traits are complex and molecular markers associated with these traits are a tool that may assist breeders to more efficiently identify sugarcane clones containing these desirable traits. At the start of this project, molecular mapping in sugarcane was relatively new with maps being developed in interspecific crosses or within the selfed progeny of a variety. These maps relied heavily on the use of two major marker types, namely restriction fragment length polymorphisms (RFLPs) and randomly amplified polymorphic DNA (RAPDs), both of which had major disadvantages in their ease and reliability of use. The area of genomics was also very new, and genomics studies of sugarcane were being initiated in Australia, the USA, Brazil and South Africa, generating large amounts of gene information and potential markers for mapping in many traits of interest. The major objectives of this project were, therefore, to compare genomic regions associated with traits in Australian and French sugarcane populations, to demonstrate whether “candidate genes”, derived from partial gene sequences (termed expressed sequence tags, ESTs), were a useful strategy for the identification of closely linked markers for traits of interest, and to develop methods other than the RFLP approach to enable more rapid screening of ESTs in mapping populations. Using a variety of approaches, these objectives have been met as described below. Australian sugarcane maps have now been generated from two crosses involving Australian sugarcane varieties or elite material. Each cross has been used to generate two maps, one for the male and female parent of the cross. The Q1 population is derived from a cross between Q117 and 74C42, while the Q3 population is derived from a cross between Q117 and MQ77-340. The four maps now have approximately 300-450 markers each, using mainly PCRbased markers, namely simple sequence repeat (SSRs) and amplified fragment length polymorphisms (AFLPs). Our policy of using SSRs that have been mapped in the French variety R570, currently the largest published map with approximately 1000 markers, has assisted our comparative mapping attempts between the Australian and French maps. Many of the cosegregation groups identified in the Q1 and Q3 population maps have been tentatively aligned with Linkage Groups in R570 on the basis of shared SSRs. Using this approach, we have shown that the same SSRs are linked to sugar and fibre-related traits in both R570 and Q3 populations. This observation provides additional support to the usefulness of these SSRs in markerassisted selection. In addition, novel associations were also identified for both Q3 and R570 populations. These marker-trait associations could be due to different parts of the genome being mapped in the two populations, to novel alleles in the two populations, or to fixation of this region in one of the populations. The alignment between the R570 and Q3 population maps was more difficult than anticipated because most markers on the R570 map were AFLPs and because marker sizes had not been recorded for either map. AFLPs are plentiful but are more difficult to score accurately and comparatively. In addition, the low level of genome coverage in both maps (~33% for R570 and <20% for Q3) meant that genome comparisons could 3 only be made at the homology group level as it was likely that different linkage groups within a homology group had been mapped in the two populations.