Genome-wide signatures in flax pinpoint to adaptive evolution along its ecological gradient
Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
Department of Agriculture and Agri-Food, Ottawa Research and Development Center, Ottawa, ON K1A 0C6, Canada
Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK S7N 5C2, Canada
19 August 2021
11 November 2021
22 November 2021
30 December 2021
Background: Flax is one of the eight founder crops of agriculture. It is believed to have been domesticated as a long-day plant that has since spread to survive in a wide range of eco-geographic regions extending from the warm Indian subcontinent to the low latitude east African highlands and to the cool and high-latitude Eurasia. Understanding the genetic basis underlying its adaptation and selection events throughout its dispersion is essential to develop cultivars adapted to local environmental conditions. Methods: Here we detected genetic signatures of local adaptation and selection events of flax based on 385 accessions from all major flax growing regions of the world using genome scan methods and three genomic datasets: (1) a genome-wide dataset of more than 275K single nucleotide polymorphisms (SNPs), (2) a filtered dataset of 23K SNPs with minor allele frequency >10% and, (3) a 34K exon-derived SNP dataset. Results: Principal component (PC) and fixation index (FST)-based genome scans yielded consistent outlier SNP loci on chromosomes 1, 8, 9 and 12. Additional loci on chromosomes 3, 7, 8, 10, 11, 13 and 14 were detected using both the PC and FST methods in two of the three datasets. A genome-environment association (GEA) analysis using the 23K dataset and the first PC of cropping season temperature, day-length and latitude identified significant SNPs on chromosomes 3, 7, 9 and 13. Conclusions: Most of the loci detected by the three methods harbored relevant genes for local adaptation, including some that play roles in day-length, light and other biotic and abiotic stresses responses. Such genetic signatures may help to select pre-breeding materials potentially adapted to specific growing niches prior to field performance trials. Given the current low genotyping cost and freely available environmental data, the genome scans along with GEA can readily provide opportunity to sort out materials suitable to various environmental conditions from large set of germplasm in gene banks and/or in situ, thereby assisting the breeding and genetic conservation efforts.
GWAS; FST ; Principal component; Adaptive loci; Genetic signatures; Candidate genes
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Demissew Sertse, Frank M. You, Sylvie Cloutier. Genome-wide signatures in flax pinpoint to adaptive evolution along its ecological gradient. Frontiers in Bioscience-Landmark. 2021. 26(12); 1559-1571.