QTL Mapping of Fiber-Related Traits Based on a High-Density Genetic Map in Flax (Linum usitatissimum L.)

Abstract

A genetic map is an important and valuable tool for quantitative trait locus (QTL) mapping, marker-assisted selection (MAS)-based breeding, and reference-assisted chromosome assembly. In this study, 112 F2 plants from a cross between Linum usitatissimum L. “DIANE” and “NY17” and parent plants were subjected to high-throughput sequencing and specific-locus amplified fragment (SLAF) library construction. After preprocessing, 61.64 Gb of raw data containing 253.71 Mb paired-end reads, each 101 bp in length, were obtained. A total of 192,797 SLAFs were identified, of which 23,115 were polymorphic, with a polymorphism rate of 11.99%. Finally, 2,339 SLAFs were organized into a linkage map consisting of 15 linkage groups (LGs). The total length of the genetic map was 1483.25 centimorgans (cM) and the average distance between adjacent markers was 0.63 cM. Combined with flax chromosome-scale pseudomolecules, 12 QTLs associating with 6 flax fiber-related traits were mapped on the chromosomal scaffolds. This high-density genetic map of flax should serve as a foundation for flax fine QTL mapping, draft genome assembly, and MAS-guided breeding. Ultimately, the genomic regions identified in this research could potentially be valuable for improving flax fiber cultivars, as well as for identification of candidate genes involved in flax fiber formation processes.Significance statementA high-density genetic map of flax was constructed, and QTLs were identified on the sequence scaffolds to be interrelated with fiber-related traits. The results of this study will not only provide a platform for gene/QTL fine mapping, map-based gene isolation, and molecular breeding for flax, but also provide a reference to help position sequence scaffolds on the physical map and assist in the process of assembling the flax genome sequence.

Genetic Mapping of Prince Rupprecht’s Larch (Larix principis-rupprechtii Mayr) by Specific-Locus Amplified Fragment Sequencing

“…Different from previously published genetic maps in other larch species, the molecular markers used here were SNP markers detected by SLAF-seq, which enables identification and genotyping of SNPs in species with or without reference genomes [25]. Compared to conventional methods for developing markers, SLAF-seq yields higher-density and more uniform and efficacious markers at lower cost, due to its use of a predesigned scheme, reduced representation strategy, NGS-based deep sequencing, and strict filtering criteria [43,44]. To date, SLAF-seq technology has been applied in studies of several tree species.…”

QTL Mapping for Growth-Related Traits by Constructing the First Genetic Linkage Map in Simao pine

“…After linkage grouping, the maximum likelihood method was used to order the SLAFs markers in all LGs (Van Ooijen 2011;Luo et al, 2016), and SMOOTH algorithm was utilized to be put right the errors of genotyping (Van et al, 2005). To evaluate the quality of constructed Simao pine genetic map, the analysis of mapped markers integrity, and construction of haplotype maps and heat maps for each LG were carried out (West et al, 2006;Liu et al, 2017;Wu et al, 2018).…”

QTL mapping for growth-related traits by constructing the first genetic linkage map in Simao pine

“…The SMOOTH algorithm was utilized to put correct genotyping errors (Van et al, 2005). To evaluate the quality of the constructed Simao pine genetic map, mapped markers integrity and construction of haplotype maps and heat maps for each LG were carried out (West et al, 2006;Liu et al, 2017;Wu et al, 2018).…”