Genome wide association study (GWAS) of early vigour and flowering time in canola (Brassica napus)

Mr Kianoush Nikoumanesh1, Dr Harsh Raman2, Professor Wallace Cowling3, Dr  Li Li1

1Animal Genetics and Breeding Unit (a joint venture of NSW Department of Primary Industries and the University of New England), University of New England, Armidale, Australia,
2NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, Australia,
3School of Agriculture and Environment and The UWA Institute of Agriculture, The University of Western Australia, Perth, Australia

Canola is one of the most agronomically important members of the Brassicaceae family with an approximately 1 billion USD export value for the Australian agriculture industry. However, this crop requires more efficient plant breeding strategies to satisfy its market dynamics and problems resulted from its limited genetic diversity. Therefore, accurate identification of genomic regions (QTLs) controlling the genetic architecture of important traits (e.g. early vigour and flowering time) and the estimation of their effects are of crucial priorities for a sustainable plant breeding program in canola. In this study we have used genome wide association study (GWAS) to find statistically significant associations between early vigour and flowering time and more than 13,000 Illumina Infinium™ Single Nucleotide Polymorphisms (SNPs) in a canola germplasm. For days to 50% flowering, we found significant associations in genomic regions, particularly chromosomes A02 and A03, that seem to be associated in controlling the flowering time. We compared the results from three different methods for our analysis: 1) general linear model, 2) mixed model using kinship matrix (K), and 3) a unified Mixed Model that incorporates both K and population structure (Q). Consistent QTLs were located in similar chromosome regions in the three different methods across three trial locations. Similar methods were employed to assess QTLs for early vigour in the glasshouse and field. Potential epistatic interactions between genes controlling early vigour and flowering time were explored. The study will also identify SNP molecular markers for these traits for use in the Australian canola breeding industry.


My ultimate career goal is to help Australian growers gain a competitive edge in this world’s turbulent economy.



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