Genome-wide signatures in flax pinpoint to adaptive evolution along its ecological gradient

Abstract

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 (FS⁢T)-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 FS⁢T 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.

Genetic diversity analysis of drought tolerant flax varieties based on genome-wide SNP

“…The results of phylogenetic analysis of 385 materials from major flax producing areas in the world also showed that the clustering situation was not completely consistent with the flax source countries [28]. So we speculated that this is related to the different sources of the parent and maternal origin selected by each breed during breeding.For example, Baya 13 (GroupⅢ) from Hebei province, the mother selected during breeding is Jinya 7 from Shanxi province, also in GroupⅢ [44], So on the evolutionary tree these two varietise are in the same clade of GroupⅢ.…”

“…Ahasanul et al [27] used 6,200 SNP markers to cluster 350 flax genotypes into 7 subpopulations (P1~P7) and considered that the wide geographic distance hindered gene flow. Demissew et al [28] used genome scanning and three SNP data sets to detect 385 germplasms from all major flax planting areas in the world. Through genome environment association analysis (GEA), they identified important SNPs on chromosomes 3, 7, 9 and 13 related to the temperature, day length and latitude of the planting season, which assisted flax breeding and genetic protection.…”

Identified Resilient Flax Genotypes With Improved Agronomic Characteristics for Pre-Breeding

“…The availability of diverse germplasm, characterization and evaluation data is of the greatest importance to realize the full potential of flax in agriculture [5] - [7]. Furthermore, plant breeders are continuously challenged to develop flax cultivars adapted to changing market needs and environments [8], [9].…”

Historical Selection, Adaptation Signatures, and Ambiguity of Introgressions in Wheat

“…Current advances in genome technologies, and in computational and statistical methods in handling big data, have created opportunities to explore historical adaptive signatures and to reconstruct the past selection, hybridization, and other evolutionary events of several species [19,20], including those with complex genomes, such as wheat [18,21,22]. Genome scans, based on FST and principal components, have pinpointed genetic signatures of past selection and hybridization events, as well as the genomic regions underlying adaptation to environmental factors [23,24]. Using whole genome exome capture data, He et al [22] delimited a large introgression segment on chromosome 4A, between positions 174,725,311 and 485,745,837 bps, and postulated that its origin was wild emmer wheat.…”