Developing cytogenetic and molecular tools to improve selection for soil-borne pathogen resistance in wild hybrids : final report 2013/358

Abstract

In Australia, sugarcane has been grown for more than 100 years now as a monoculture without much fallow cropping. Consequently, the heavily cultivated areas had no chance to reduce the levels of soil-borne pathogens. Soil health is a major concern for the Australian sugar industry.

Large economic losses caused by soil-borne pathogens such as nematodes and Pachymetra severely affect the Australian sugarcane industry every year. In 2013, it was estimated that the losses caused by those two pathogens reached $80 and 100 million/ annum respectively. The best way to address Pachymetra is with resistant varieties. Following the Smut outbreak in 2005/ 2006, growers were well-resourced with high yield performance/ smut resistant varieties such as Q200A , Q208A , and KQ228A ; however, these varieties have only intermediate resistance to Pachymetra. There has been a large investment in introgression projects in recent years in Australia to address these issues and introduce new resistance genes into the breeding program to produce better varieties with resistance to targeted disease.

SRA has been involved in two ACIAR projects in collaboration with CSIRO and China to characterize clones from the S. spontaneum introgression population as well as Saccharum/ Erianthus hybrids This sugarcane relative (part of the Saccharum complex), Erianthus arundinaceus, is highly drought tolerant, almost immune to Pachymetra root rot and is highly resistant to nematodes. Some advanced backcross clones retain high levels of resistance to root knot and lesion nematodes, and Pachymetra root rot. Clones from the introgression populations have been used in this project to initiate the development of molecular marker-based screening methods. The Australian Sugar Industry is looking for enhanced Pachymetra resistance., This project aimed to characterize more Erianthus hybrids for the breeders to make better-informed crosses and to find tools/ methods to improve the breeding program efficiency in combining Smut and Pachymetra resistance as well as Nematode resistance in sugarcane. ”.

This project ultimately targeted SRA breeding and molecular breeding teams as an end user to provide a marker based screening method for Pachymetra, Nematode and Smut resistance. Collaborations were formed between the cytogenetics laboratory in Mackay, two majors groups within SRA, the pathology team led by Barry Croft and the breeding team led by George Piperidis, and with Karen Aitken leading the molecular marker group at CSIRO. The rationale for this project was based on newly acquired BC3-Erianthus hybrids had less than the basic chromosome number of 10 Erianthus chromosomes as revealed by Genomic In Situ Hybridization (GISH). This implied that each of the Erianthus chromosomes within the BC3 clones studied are different from each other and are specific to one homology group (HG) of sugarcane. The main objective of this project was to develop a highly efficient and economical PCR test that could be used to identify each of the 10 basic Erianthus chromosomes.