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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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.
Development and testing of a SNP marker platform in sugarcane : final report 2012/025
(Sugar Research Australia Limited, 2016) Aitken, K
Marker assisted selection is being used in many industries to develop new and improved crops. This project sought to develop a selection tool for the Australian sugarcane industry by developing a set of DNA markers that could be used to enhance rates of genetic gain in the Sugarcane Breeding Program when compared to phenotypic selection alone. This was a collaborative project between CSIRO, Syngenta and SRA and has been proven successful in combining the skills of each organisation to achieve the best outcome. The extensive experience within Syngenta on other crops was used in combination with the sugarcane genetic knowledge within CSIRO to select the Affymetrix Axiom array system as the platform most likely to generate results on such a complex polyploid as sugarcane. This is the first time that this technology has been utilised on a species that has a complex high ploidy genome.
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.