Genomic Selection for fast-tracking cotton breeding

Principal Researchers

Philippe Moncuquet, Washy Gapare, Qian-Hao Zhu, Iain Wilson, Shiming Liu, Warren Conaty and Warwick Stiller.

Executive Summary

This is a long term project that aims to develop and evaluate in cotton a new molecular based breeding approach called Genomic Selection (GS) that is now being widely used in livestock breeding and increasingly in crop breeding.

The objective is to be able to predict the phenotypic potential (for example, yield, fibre quality or other agronomic properties) of breeding selections or populations based on the combinations of large numbers of single nucleotide polymorphisms (SNPs) markers present in individual plants.

GS, if validated, will eventually be used by our breeders as an aid to help select parents in crossing, to identify progenies in segregating populations with the best genetic make-up, and will reduce the amount of field based screening required to generate elite cultivars.

Procedures have been established to enable breeding lines to be sampled each year for genotyping and the collection of phenotype data for the GS statistical model development. Weather stations have been established at breeding sites to enable long term integration of environmental data with genetic data to improve the GS models. Using the 63K Cotton SNP Chip genotyping platform and models developed specifically for cotton breeding, a training population consisting of all historical varieties for which seeds (and hence DNA) are available, year 2014 and year 2015 breeding lines (a total of 922 lines) was used to predict year 2016/2017 phenotypes (validation population) (a total of 347 breeding lines). Prediction accuracies for fibre length averaged 0.37 and for fibre strength averaged 0.28. It is hoped that with the addition of further field data these predictions will increase and become of value for selection.

To enable GS to be applied to cotton breeding once predictions becomes informative, genotyping needs to become cheaper and preferably applied to seeds. A pilot genotyping experiment with DArT has indicated they have the potential to deliver a genotyping system capable of being applied to cotton breeding. Experiments are currently under way to determine whether it possible for this system to be applied to seed genotyping.