Genome wide association studies and transcriptome changes during acclimation and deacclimation in divergent canola varieties

Authors: Horvath, David; JIAPING, ZHANG - Zhejiang University; Chao, Wun; ASHOK, MANDAL - North Dakota State University; RAHMAN, MUKHLESUR - North Dakota State University; Anderson, James

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/23/2020
Publication Date: 11/30/2020
Citation: Horvath, D.P., Jiaping, Z., Chao, W.S., Ashok, M., Rahman, M., Anderson, J.V. 2020. Genome wide association studies and transcriptome changes during acclimation and deacclimation in divergent canola varieties. International Journal of Molecular Sciences. 21(23):9148. https://doi.org/10.3390/ijms21239148.
DOI: https://doi.org/10.3390/ijms21239148

Interpretive Summary: Canola is an important oilseed crop of the northern Great Plains, but higher yielding winter varieties are not grown in more northerly regions because they are susceptible to the extreme temperature fluctuations in the late winter and early spring. These volatile weather extremes often result in winter canola being re-sensitized (sometimes referred to as deacclimation) to freezing following brief warming spells. Scientists at the USDA-ARS in Fargo North Dakota used a combination of genetic and phenotypic analysis to determine which genes are responsive to deacclimating conditions and to identify genetic loci that can make cold acclimated (freezing tolerant) plants less susceptible to freezing following brief warm spells. This information will help breeders develop winter canola varieties that are better adapted to survive freezing and the potential impacts associated with climate change.

Technical Abstract: Information concerning the genes and signals regulating cold acclimation processes in plants is abundant; however, less is understood about genes and signals regulating the deacclimation process. Using a population of primarily winter canola varieties, both a genome wide association study and transcriptome analyses from two of the winter canola varieties with differing response to a deacclimation treatment over time were used to identify loci, candidate genes, and signaling processes impacting deacclimation. Information related to gene expression differences among the two divergent winter canola varieties during a four-week acclimation at 5C is also provided. GWAS identified polymorphisms at 5 different loci associated with freezing tolerance following deacclimation. Local linkage decay rates near these polymorphisms were used to identified 38 possible candidate genes. Several of these genes were reported as differentially regulated by cold stress in arabidopsis, and a calcium-binding EF-hand family protein (encoded by BnaCnng10250D) was also differentially expressed during deacclimation in this study. Thousands of other genes differentially expressed during the acclimation and deacclimation processes were implicated in processes involving oxidative stress, photosynthesis, light-regulated diurnal responses, and growth regulation. Generally, responses observed during acclimation were reversed within one week of deacclimation. The primary differences between the two winter canola varieties with differential deacclimation responses appeared to be protection from oxidative stress and ability to maintain photosynthesis.