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
(F)-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 F 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.