Genomic regions underlying agronomic traits in linseed (Linum usitatissimum L.) as revealed by association mapping

Abstract

The extreme climate of the Canadian Prairies poses a major challenge to improve yield. Although it is possible to breed for yield per se, focusing on yield-related traits could be advantageous because of their simpler genetic architecture. The Canadian flax core collection of 390 accessions was genotyped with 464 simple sequence repeat markers, and phenotypic data for nine agronomic traits including yield, bolls per area, 1,000 seed weight, seeds per boll, start of flowering, end of flowering, plant height, plant branching, and lodging collected from up to eight environments was used for association mapping. Based on a mixed model (principal component analysis (PCA) + kinship matrix (K)), 12 significant marker-trait associations for six agronomic traits were identified. Most of the associations were stable across environments as revealed by multivariate analyses. Statistical simulation for five markers associated with 1000 seed weight indicated that the favorable alleles have additive effects. None of the modern cultivars carried the five favorable alleles and the maximum number of four observed in any accessions was mostly in breeding lines. Our results confirmed the complex genetic architecture of yield-related traits and the inherent difficulties associated with their identification while illustrating the potential for improvement through marker-assisted selection.

Genetic Variability of Morphological, Flowering, and Biomass Quality Traits in Hemp (Cannabis sativa L.)

“…As in the present study, extensive genetic studies have shown large heritability values for cell wall components (cellulose, hemicellulose, and lignin) in other fiber crops, such as poplar and eucalyptus (Raymond and Schimleck, 2002;Klasnja et al, 2003;Schimleck et al, 2004;Poke et al, 2006;Davis, 2008), miscanthus (Slavov et al, 2014;Van Der Weijde et al, 2017), switchgrass (Mclaughlin et al, 2006;Boe and Lee, 2007), and maize (Torres et al, 2015). Furthermore, similar heritability values for flowering time were reported in several plant species such as almond [reviewed in Sánchez-Pérez et al (2014)], apricot (Campoy et al, 2011), arabidopsis (Sasaki et al, 2015), cotton (Kushanov et al, 2017), flax (Soto-Cerda et al, 2014;You et al, 2017), and rice (Takahashi et al, 2001;Huang et al, 2010). It seems plausible that a large fraction of the phenotypic variation of biomass and flowering traits might be controlled by highly "robust genetic systems," although they are highly complex and polygenic traits, since respectively~4,000 (Wang et al, 2012) and~300 genes are estimated to be involved in cell wall synthesis and flowering in arabidopsis (Wang et al, 2012;Bouché et al, 2016).…”

Agronomic and Quality Assessment of Linseed Advanced Breeding Lines Varying in Seed Mucilage Content and Their Use for Food and Feed

“…The SOC yield is pivotal since higher SOC could compensate for a lower seed yield and, thus, be profitable for farmers and industry. Similar maximum SOCs (~51%) have been reported across Canadian environments (Soto-Cerda et al, 2014c). The ALAC, an omega-3 fatty acid, largely determines the industrial applications of linseed oil.…”

“…Linseed oil content and its fatty acid profile define to a large extent its market end use and value (Soto-Cerda et al, 2014c). The ABLs exhibited suitable content of SOC, SPC, and fatty acid profile.…”

Mapping Quantitative Trait Loci onto Chromosome-Scale Pseudomolecules in Flax

“…All 313 flax QTL reported in the 14 studies (Table 2) were identified from three types of markers: amplified fragment length polymorphisms (AFLPs), SSRs, and SNPs. PCR primer sequences of AFLPs and SSRs were retrieved from the literature [15,[19][20][21]23,24]. For the SNPs named based on the scaffold sequences, their scaffold names and coordinates were collected directly from the publications [17,26].…”