Browsing by Author "Piperidis, G"

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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.
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.
Exploiting Erianthus diversity to enhance sugarcane cultivars : ASSCT peer-reviewed paper
(ASSCT, 2019) Piperidis, N; Tom, C; Aitken, KS; Atkin, FC; Piperidis, G
Introgression of Erianthus arundinaceus into the SRA sugarcane-breeding program has been a goal for researchers for many years. The Erianthus genome was finally accessible to sugarcane breeders with the identification in 2005 of the first Saccharum/Erianthus fertile hybrids, developed in China. Today, Saccharum/Erianthus BC3 and BC4 clones are available in Australia, and Erianthus-sugarcane hybrids have been characterised by cytogenetics and investigated for their potential resistance against pachymetra root rot, sugarcane smut and nematodes. Some clones have shown potential as new sources of resistance for incorporation into the SRA breeding program. These hybrids were created from Erianthus clones indigenous to China and their reaction to the above diseases is unknown in Australian conditions. In Meringa we also have access to many Erianthus clones of Indonesian origin. Some of these Erianthus clones have previously shown immunity to pachymetra root rot. In the late 1990s, these Indonesian Erianthus clones were used in crossing but no fertile hybrids were ever produced due to an incompatibility between the Saccharum and the Erianthus genomes. We revisited this untapped source of resistance by utilising the fertile Erianthus hybrids derived from China to cross with the Indonesian Erianthus of known resistance to pachymetra root rot. Here we report on the early stage results of introgressing Indonesian Erianthus into the SRA breeding program.
Field evaluation of selected introgression clones for their resistance to root-knot nematodes : ASSCT peer-reviewed paper
(ASSCT, 2019) Bhuiyan, SA; Piperidis, G; Hu, F; Parfitt, R; Garlick, K; Quinn, B; Jakins, A
Sugarcane nematodes, root-knot (RKN) and root-lesion (RLN), cause an estimated loss of over $80 million per year to the Australian sugar industry. In particular, RKN is a major problem if sugarcane is planted in sandy soil. No effective control method is available for sugarcane nematodes in Australia. Crop rotation and fallowing provide only short-term control and nematode populations usually bounce back within 12 months after these control methods. The use of nematicides is restricted due to inconsistent results, difficulty in application and the highly toxic nature of the chemicals to humans and the environment. No commercial cultivars are resistant to sugarcane nematodes. Recent glasshouse trials in Australia suggested that clones from introgression populations, originating from crossing between commercial canes and Saccharum spontaneum or Erianthus arundinaceus, possessed good resistance to root knot nematodes. Field trials were established to determine the reliability of glasshouse resistance-screening results. Eight introgression clones that showed resistance to RKN in glasshouse trials were evaluated in a field in Wallaville, north of Childers. Test clones were planted in plots with high and low nematode populations and maintained up to the second ratoon crop. Trial plots were assessed for nematodes each year 6 weeks after planting and ratooning. Three years of results showed that 7 of 8 introgression clones consistently maintained low numbers of RKN until the end of the trial period, and significantly (P
Genomic organisation of sugarcane cultivars revealed by chromosome-specific oligonucleotide probes : ASSCT peer-reviewed paper
(ASSCT, 2021) Piperidis, N; Piperidis, G; D’Hont, A
Sugarcane (Saccharum spp.) is probably the crop with the most complex genome. Modern cultivars (2n=100-120) are derived from interspecific hybridization between the noble cane S. officinarum (2n=80) and the wild cane S. spontaneum (2n=40-128). We investigated the genome organization of important sugarcane cultivars and their parental species using chromosomespecific probes combined with genomic in situ hybridization (GISH). This allowed the genomic and genetic characterisation of Australian sugarcane cultivars and one of the major contributing parental clones, Mandalay. The S. spontaneum clone Mandalay follows the classical organization of S. spontaneum clones with x=8 with a major discrepancy related to an extra six chromosomes compared to the previously reported 2n=96 for Mandalay’s clone. Our previous results reported the rearrangements between the S. officinarum (x=10) and S. spontaneum (x=8) chromosomes, with a most likely scenario of a two-step process leading to x= 9 and then x=8, where each step involved three chromosomes that were rearranged into two. Further polyploidization led to the wide geographical dispersion of S. spontaneum clones with x= 8. In modern cultivars, the 13-20% of the S. spontaneum contribution originated from cytotypes with x=8. Modern cultivars have mainly 12 copies of each of the first four basic chromosomes and a more variable number for those basic chromosomes whose structure differs between the two parental species. These new insights and cytogenetic tools substantially improve our understanding of the extreme level of complexity of modern sugarcane cultivar genomes and could lead to guiding breeding strategies in the development of new improved varieties for the Australian industry.
Introgression of erianthus germplasm into the saccharum gene pool & Investigation of the saccharum spontaneum contribution to commercial clones by genomic DNA In SITU hybridisation : SRDC Final reports BS115 & BS139
(1999) Piperidis, G; D'Hont, A; Berding, N
Project objectives:
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.
Optimisation of the initial stages of the New South Wales selection program : SRDC final project report BS96S
(2002) Piperidis, G
The main aim of this project was to obtain the basic information required to implement an efficient and effective breeding and selection program in NSW. However, the project suffered major difficulties that affected the delivery of the proposed objectives. In spite of this, useful information that will have impact on the NSW selection program was obtained from the available data. In areas where two-year crops predominate, selection from Stage 1 and Stage 2 trials should be applied based on the data from two-year old crops. In addition, there was a strong correlation between the estimated net merit grade (NMGVol) and calculated net merit grade (NMG) in both the one-year and two-year Stage 2 crops at Broadwater. The correlation between the one-year NMGVol and the two-year NMG, however, was not significant. The results also show that family selection combined with visual selection in Stage 2 was generally more effective to identify elite clones in Stage 3 than family selection alone. Additionally, when the Brix of clones was taken into account the efficiency of identifying elite clones was increased even further.
Seed-based in vitro propagation to accelerate variety development : ASSCT peer-reviewed paper
(ASSCT, 2021) Zhao, L; Bolton, C; Piperidis, G; Eglinton, J
To shorten the current lengthy selection process in sugarcane breeding and to accelerate genetic gain, Sugar Research Australia is implementing a range of novel breeding strategies and selection tactics. One strategy is to rapidly evaluate the progeny of elite crosses in replicated trials without passing through the traditional Stage 1 trials. However, insufficient planting material hinders its adoption. A seed-based in vitro propagation system has been developed for sugarcane in which sodium hypochlorite (bleach) and plant preservative mixture (PPMTM) were used in the sterilisation of seeds and seedlings, as well as in the treatment of infected seedlings. The system had been successfully implemented to propagate over 1000 clones of the elite cross Q208A x CP74-2005, for a Stage 2 selection trial. The new system, a first for sugarcane, is more cost efficient, providing three times the number of clones as in the seedling-based micropropagation system with the same input of resources. This innovation will shorten the selection cycle of proven elite crosses by up to 3 years, accelerating the delivery of new varieties.
SRA's Improved Disease Rating System
(Sugar Research Australia Limited, 2021) Piperidis, G
Disease screening of varieties in the selection program is an important part of the decision-making process for advancement of clones through the program and release of new varieties to industry. For many years, disease ratings were given on a 1-to-9 scale based on the recommended International Society of Sugarcane Technologists method for assigning disease resistance ratings. This 1-to-9 scale can be further categorised as Resistant (1-3), Intermediate (4-6) and susceptible (7-9). However, this system didn’t take into account the precision of the rating for any given clone or variety.