Flax transposons: unraveling their impact on domestication and agronomic trait variation

Flax is an important agricultural crop with multifunctional uses. Diversified breeding for oil content in seeds and fiber in stems has led to the emergence of two morphotypes - fiber flax and oilseed flax. Previously, using single nucleotide polymorphisms (SNPs), we characterized the genetic diversity of 306 flax samples from the collection of the Russian Federal Research Center for Bast Crops. However, larger structural variations, such as mobile genetic elements, also play a significant role in shaping agronomically important plant traits and can be used for further flax improvement. Here, we used the same flax collection to predict sites of new transposon insertions and to assess the role of such insertions in the formation of agronomically important traits, as well as in the process of flax domestication. We discovered 588,480 new transposon insertion sites not present in the reference flax genome (NCBI assembly ASM22429v2), the majority of which were attributed to retrotransposons of the Copia and Gypsy superfamilies, while among DNA transposons, insertion sites of the MULE-MuDR, hAT, and CMC-EnSpm superfamilies were most common. Unlike SNPs, which were significantly more numerous in oilseed flax than in fiber flax, we did not find such a substantial difference in the number of insertions of different transposon families per plant among samples of different morphotypes. Analysis of genomic regions affected by recent breeding efforts revealed a total of 61 candidate regions, of which 18 regions overlapped with QTLs associated with important agronomic traits. Interestingly, 5 regions of reduced genetic diversity in kryazhs and cultivars compared to landraces were also identified as regions of reduced diversity when using single nucleotide polymorphisms as markers. A genome-wide association study (GWAS) identified 50 TE insertions associated with different phenotypic traits, with many associations confirmed by multiple models or detected in data from multiple years. Thus, transposon insertion sites are an important source of genetic diversity in flax, alongside single nucleotide polymorphisms, making them suitable for further crop improvement in breeding.