Technology use in advancing progress in Germplasm use for the development of improved cane varieties

Thursday 7 July 2022

11 a.m. GMT

As part of the series of Webinars that are being organized by the ISSCT in 2022 for its different disciplines, the Germplasm & Breeding Section Webinar will be held on Thursday 7 July 2022 at 11 a.m. GMT.


Introduction by Goolam Badaloo, Chair ISSCT Germplasm and Breeding Section

Guest Speaker

Addressing limits to faster progress in sugarcane breeding, with special reference to using genomic data

By Phil Jackson, Honorary Fellow, CSIRO, Australia

Sugarcane breeding programmes worldwide follow a generally similar overall recurrent breeding cycle and strategy, which has been relatively stable in many programmes for many decades.  However, this cycle and strategy has some major constraints to faster gains which may becoming increasingly important, and this will be explained.   At the same time, the application of DNA markers has for at least 30 years been touted to attain faster progress in sugarcane breeding, but significant impact on actual cultivar development appears still yet to widely happen.  Problems and complications in the past in application of DNA markers to sugarcane breeding, and important lessons learnt to date, will be briefly reviewed in the presentation.  However, it will be argued that past problems have been largely overcome with on-going advances in technology and knowledge, such that obtaining and using genomic data could likely significantly, and cost effectively, now speed up gains in sugarcane breeding programmes.  This view will be detailed in relation to the constraints in the traditional sugarcane breeding cycle previously described.  Some potential future trends in genomics technologies with relevance to sugarcane breeding will also be outlined.  

Use of latest analytical tools in simplifying variety selection at advanced stages in Mauritius

By Deepack Santchurn, MSIRI, Réduit, Mauritius

With the advent of computers in the 1960s, the Mauritius Sugarcane Industry Research Institute (MSIRI) was among the first to automate data recording, statistical analysis and selection. Modules were developed that integrated ANOVA techniques to analyse advanced selection trials involving individual and combined crop cycles within locations. Those automated analyses represented a major breakthrough towards fast generation of objective statistical results. These modules are still being used in the analysis and interpretation of selection data. At the advanced variety evaluation trials, each genotype from each trial is scrutinised individually and the available t-differences compared to commercial checks to help to identify the best varieties within trials. Adaptation to different agro-climates, stability analysis of new varieties and ratooning ability are, however, determined through a synthesis of observations across trials using direct differences between individual test genotypes and the commercial controls. These approaches are lengthy, cumbersome and, generally, highly demanding in terms of manpower and assimilation capacity of breeders. In recent years, new statistical techniques involving Spatial analysis, Biplots and Linear Mixed Model (LMM) analyses have been progressively used in controlling variability in field, combining different sets of trials data and interpretation of genotype by environment interactions (GEI). At the MSIRI, attempt has been made to run combined analysis of all advanced variety trials implemented in the last decade using LMM algorithm and compare the results with the conventional approach. The preliminary models used included all pre-conceivable genetic and environmental main effects prevailing in Mauritius and all first and second order interactions. The results looked highly promising as not only the best screened promising varieties using conventional method appeared in the top list but also the ranking and genetic gain with released commercial varieties could be assessed. The analysis also provided a range of GEI outputs that would alternatively take considerable time and resources to determine. The preliminary model will be refined in due course and run in parallel with the conventional approach in the near future until the best and parsimonious model reflecting the local conditions is obtained and adopted. The new techniques available remain fundamental in further improving breeding and selection efficiency at the MSIRI.

New and old technology to improve breeding
1Sugar Research Australia, 71378 Bruce Highway, Gordonvale Qld, 2 30962 Bruce Highway, Brandon Qld, 3 26135 Peak Downs Highway, Mackay Qld, 4 B314 Pashleys Road Bundaberg North Qld

Jason Eglinton1, Felicity Atkin1, Fengduo Hu2, Xianming Wei3, George Piperidis3 and Roy Parfitt4
By George Piperidis, SRA, Australia

Plant breeding is the largest single investment made by SRA on behalf of the Australian sugarcane industry. Varieties are one of the most tangible and highly valued R&D outputs, and levy payers expect an enduring pipeline of improved varieties which make a significant contribution to increasing productivity and profitability. The market share of new varieties was 36% of commercial production in 2005 and steadily decreased to 3% in 2020. A total of 71 new varieties were released during that period. This has resulted in people thinking there is a variety adoption problem, accompanied by criticism of variety release decision making, appropriateness of variety performance information, variety marketing, and clean seed programmes. Improvements in these key parts of the adoption pipeline can (and are) being made but they are not the root cause of the low market share of new varieties. Adoption rates of Q240A in the Central and Burdekin regions, and adoption speed of Q253A in the Herbert and Northern regions demonstrate that the current system does support successful adoption for varieties with improved performance. The reality is that most of the 71 varieties released did not offer growers a better value proposition. There was no single factor responsible for the modest performance of plant breeding during this period. The incursion of smut disease had a significant impact on the germplasm pool and parent selection, and added a new breeding target, however work on incorporating smut resistance started over 20 years ago. There were important changes in personnel appointed to plant breeder positions which can impact genetic gain. The breeding programme had also operated under a highly formulaic approach that was unchanged for a very long time. A technical review in 2017 defined a significant change plan to systematically improve genetic gain and develop better varieties.  These changes will be detailed in the presentation.

The Confirmation of the Status of Elite Parents for Brix within the Variety Improvement programme at WICSCBS

By Morexa Martin-Gardiner, West Indies Central Sugar Cane Breeding Station (WICSCBS, Barbados)

With every batch of crosses made at the West Indies Central Sugar Cane Breeding Station (WICSCBS), attention is given to identifying parents which seem to show signs of high general combining ability based on the rate at which their progeny/families are identified as superior.  Parents that consistently contribute to good selections are identified as elite and are tagged as such in our database thus given priority for use in crosses. The study was designed to determine whether the elite label is a genuine indicator of superiority.  It is generally accepted that under normal circumstances, the progeny mean should be distributed about the mid-parent value.  For the purposes of this study, a parent will be considered truly elite if the distribution of the progeny is superior to the mid-parent value. A trial was planted containing crosses made using elite parents. Each batch of crosses were planted in 3 replicates, each containing 200 seedlings.  The individual parents were also planted in each block.  The seedlings and parents were Brixed for each of 3 crop cycles.   Observations on vigour were also recorded. Scatter plots were prepared for each family with a line inserted to indicate the mid-parent value.

Benefits of Mixed Models in Sugarcane Breeding
By Jean Yves Hoarau (eRcane, Réunion Island)

The use of Linear Mixed Models (LMM) and its Best Linear Unbiased Prediction (BLUP) methodology is becoming increasingly popular with a broad community of research scientists. Development of computer power and user-friendly statistical software allows them to be used more frequently. This presentation will give an overview of the benefits of the flexible LMM/BLUP framework to analyse experimental data collected in sugarcane breeding programmes to make efficient breeding and selection decisions, or to study genetic properties of traits of agronomic interest. Several applications of mixed models will be presented. Their common feature is to exploit some co-variances existing between some experimental data. Depending on applications, the nature of co-variances differs and may be related either to spatial, temporal and/or genetic considerations, with possible nested effects. In all cases, the methodology has the advantage of providing unbiased statistical inferences and predictions likely supporting objective conclusions in the scientific issues investigated.

Use of spatial variability and analysis at early selection stages in Brazil
By Danilo Eduardo Cursi1 and Luciana Gonçalves Chaves Castellani1
1Centro de Tecnologia Canavieira, CTC, Brazil

Large experimental trials in early selection stages are often needed to assess progeny and clonal performance in sugarcane breeding programmes. In these stages, spatial variability can be partly controlled by using an appropriate experimental design. Technologies that support the systematic removal of the source of variation in the residual variance have great potential for application in those stages since a small-scale detection would have great potential to improve the selection accuracy. This ability of identify of variation in the field has proved to be useful in cultivar selection experiments. In this presentation, different approaches to model the effects of spatial variability, among them the use of proximal field sensing methods, will be discussed. An increase in the selection accuracy will be presented when environmental covariates from the different approaches are employed as an adjustment method while analysing the genetic potential of each family/genotype under experimentation.

Standing on the shoulders of giants
By Anna Hale and James Todd (USDA-ARS Sugarcane Research Unit, Houma, LA)

In Louisiana, germplasm enhancement has been an integrated component of the sugarcane breeding programme since its infancy.  Through a steady and steadfast approach, incremental increases in sugar yields, disease resistance, cold tolerance, ratooning ability, and yield stability have been achieved through the incorporation of wild germplasm into newly developed parents which are actively utilised in the commercial breeding programme.   All contemporary commercial varieties in Louisiana are derived from the introgression programme, and each successive generation builds on work from the past.  The sugarcane variety HoCP 14-885 was released in 2021 by the USDA-ARS Sugarcane Research Unit in Houma, LA, The American Sugarcane League of the U.S.A., Inc., and the Louisiana State University Agricultural Center.  This variety is early maturing with excellent sugar per hectare, and a good disease package, fibre percent cane, and stalk weight.  It is aggressive with early shading ability and a good planting ratio and harvestability.  Most notable is the excellent ratooning ability of this high early sugar and high tonnage variety. The variety results from introgression events involving multiple Saccharum spontaneum accessions and represents the ongoing impact of the basic breeding programme in Louisiana.

BLUP analysis in sugarcane breeding
By Marvellous Zhou, South African Sugarcane Research Institute (SASRI), South Africa)

Best Linear Unbiased Prediction (BLUP) was first used in animal breeding to estimate breeding values in animal breeding. BLUP analysis has been used to estimate breeding values in sugarcane breeding. Sugarcane breeding stages in South Africa are Mini-Lines, Single Lines and Variety Trials. Data from Mini-Lines trials are used to determine family and breeding values while that from Single Lines and Variety Trials estimate genetic values used to select genotypes for advancement and commercial release. The objective of this presentation is to demonstrate how BLUP analysis can be applied to analyse cane yield data derived from Mini-Lines, Single Lines and Variety Trials, stages that have equivalents in other sugarcane breeding programmes. Data used for this case study were from irrigated breeding programme trials in South Africa and analysed using SAS software. The Mini Lines BLUP showed significant (P<0.0001) yield differences among families, female (P<0.001) and male parents (P=0.0006) suggesting elite families and parents with higher breeding values can be selected. For Single Lines, there were significant (P<0.0001) BLUP values indicating significant differences among genotypes. For Variety Trials, there were significant (P<0.0001) BLUP values indicating significant genotype differences. Elite families and genotypes showed significant positive values while low yielding families and genotypes produced significant negative values, providing an easy statistic to guide selection. BLUP analysis is a robust method that can be used to analyse unbalanced data due to missing values, partial replication or different number of replications or crop-years in plant breeding trials. BLUP analysis can also be used for analysing data across breeding cycles providing a mechanism to estimate cultivar genetic gains over breeding cycles.

The facilitators/organizers are:

  • Dr Goolam Badaloo, Ag Research Manager, MSIRI, Mauritius
  • Dr Danilo Cursi, CTC, Brazil
  • Dr Marvellous Zhou, SASRI, South Africa
  • Dr Jean Yves Hoarau, CIRAD/eRcane, Réunion
  • and other Germplasm & Breeding Section members


Q&A Session



The Webinar will be conducted in English.


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Further information

For further information, please contact the ISSCT Germplasm and Breeding Section Chair, Dr Goolam Badaloo ( or the ISSCT Secretariat at

Please click here to access the short biodata on the Presenters.