Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

Abstract

Quantitative trait loci (QTL) are genomic regions associated with phenotype variation of quantitative traits. To date, a total of 313 QTL for 31 quantitative traits have been reported in 14 studies on flax. Of these, 200 QTL from 12 studies were identified based on genetic maps, the scaffold sequences, or the pre-released chromosome-scale pseudomolecules. Molecular markers for QTL identification differed across studies but the most used ones were simple sequence repeats (SSRs) or single nucleotide polymorphisms (SNPs). To uniquely map the SSR and SNP markers from different references onto the recently released chromosome-scale pseudomolecules, methods with several scripts and database files were developed to locate PCR- and SNP-based markers onto the same reference, co-locate QTL, and scan genome-wide candidate genes. Using these methods, 195 out of 200 QTL were successfully sorted onto the 15 flax chromosomes and grouped into 133 co-located QTL clusters; the candidate genes that co-located with these QTL clusters were also predicted. The methods and tools presented in this article facilitate marker re-mapping to a new reference, genome-wide QTL analysis, candidate gene scanning, and breeding applications in flax and other crops.

Genomic Regions Associated with Fusarium Wilt Resistance in Flax

“…A function of the candidate genes containing the identified QTNs was inferred from the function of their Arabidopsis orthologs in the TAIR database, from flax genome annotations kindly provided by Cloutier group (Ottawa Research and Development Centre, Canada) [65], as well as from the function of the homologous genes in other plant species, as described in the literature. We also searched for candidate genes within a window surrounding detected QTNs, where width was defined as proceeding from the LD decay estimated for each chromosome (Figure S4).…”

The Genetic Landscape of Fiber Flax

“…In addition, 11 candidate selection sweep regions on seven chromosomes overlapped with known Quantitative Trait Loci (QTL)s ( Figure 5A and Supplementary Table 12 ), associated with fatty acid content, plant height, and seed mucilage content ( You and Cloutier, 2020 ). The functional repertoire of genes associated with these regions was quite diverse ( Supplementary Tables 7 – 10 ), encompassing response to stress, protein kinase activity, cell wall biogenesis, protein ubiquitination, fatty acid biogenesis and transport, hormone signaling, embryo and flower development, disease resistance, and finally transcription.…”

“…Cloutier Group (Ottawa Research and Development Centre) for sharing the latest version of flax genome annotation (You and Cloutier, 2020).…”

“…Variant calling was run using NGSEP ( Tello et al, 2019 ) version 4.0. Flax genome annotation ( You and Cloutier, 2020 ) was kindly provided by the Cloutier group (Ottawa Research and Development Centre).…”

Genome Sequencing of Fiber Flax Cultivar Atlant Using Oxford Nanopore and Illumina Platforms

“…Scaffold-level genome assemblies of linseed cultivar Longya-10, fiber cultivar Heiya-14, and pale flax were generated in 2020, based on Illumina sequencing, Hi-C technology, and genetic mapping (Zhang et al, 2020b ). These results are extremely important for further progress in molecular studies of flax, the development of genome editing, and marker-assisted and genomic selection (Saha et al, 2019 ; Morello et al, 2020 ; You and Cloutier, 2020 ). A high-quality genome can be used as a reference for genome and transcriptome assemblies of different flax cultivars/lines, and the identification of polymorphisms and differences in gene expression within L. usitatissimum genotypes (Dmitriev et al, 2019 , 2020b ; Guo et al, 2019 ; Wu et al, 2019 ).…”