Enhancing the efficiency of disease resistance breeding in cotton using marker technology

23 November, 2020

Key Researchers: Iain Wilson, Qian-Hao Zhu, Danny Llewellyn

Brief Summary of Project Objectives:
This disease marker project aim is to find markers linked to resistance for three important diseases affecting the cotton industry in Australia, Black Root Rot (BRR), Verticillium Wilt (VW), and Fusarium Wilt (FW) that will be used by the Core Breeding and Core Biotech projects for marker assisted selection to more rapidly produce resistant conventional and GM varieties.    

Executive Summary

The disease marker group, in close cooperation with our Cotton breeders has made considerable progress, which moves us closer to developing disease resistant elite germplasm for a number of important diseases.

For Black Root Rot the pathway towards elite varieties with strong levels of resistance is becoming clearer. A major resistance locus obtained from the D-genome donor was found to produce excellent resistance to BRR in the Narrabri Bioassay, better than the regions from the A-genome donor. Originally this introgressed region was very large (~ 38 million bases) and appears to have significant yield drag associated with it. However, through careful marker screening, individual plants were isolated that were still strongly resistant, but only had less than 4 million bases derived from the D-genome . It is hoped that these lines will not suffer from linkage drag and are now our main avenue for improving BRR resistance in Australian varieties. Field trials will be performed in 2020/2021 to gauge the agronomic performance, and if possible field BRR resistance of these lines as well as other BRR resistance regions derived from the A-genome, to see if they need to be further cleaned up before they can be used in breeding new cultivars.

Verticillium Wilt field trials by Dr Trapero over the last three years have indicated that a line selected with the assistance of the molecular markers linked to our identified VW resistance regions from Sicot F-1 has good field resistance to the non-defoliating (ND) pathotype of this disease. This line has been used in a further round of backcrossing and marker selection. Several lines from this next generation were found to have significantly higher ND Verticillium Wilt resistance than current varieties in a 2019/2020 field trial. These lines provide the best means for adding increased levels of ND Verticillium Wilt resistance to our commercial GM varieties in the immediate future. Other sources of promising resistance have been identified from Pima cotton and diploids, but these are further back in the pipeline.

Potential genomic regions from an A-genome diploid cotton associated with resistance to Fusarium wilt have been identified and are being advanced in synthetic tetraploid derived lines, but these lines cannot be validated until a successful Fusarium Wilt field trial can be performed. However, bioassay data indicate that the most advanced synthetic-based lines have excellent Fusarium Wilt resistance.

An alternative source of Bacterial Blight resistance from diploid cotton species is progressing but since this is a low priority, this work has been temporarily stopped, with more emphasis being put on bioinformatic analysis to help determine which genomic locations may be involved in conferring resistance.