Association mapping of seed quality traits using the Canadian flax (Linum usitatissimum L.) core collection

Abstract

Key messageThe identification of stable QTL for seed quality traits by association mapping of a diverse panel of linseed accessions establishes the foundation for assisted breeding and future fine mapping in linseed.AbstractLinseed oil is valued for its food and non-food applications. Modifying its oil content and fatty acid (FA) profiles to meet market needs in a timely manner requires clear understanding of their quantitative trait loci (QTL) architectures, which have received little attention to date. Association mapping is an efficient approach to identify QTL in germplasm collections. In this study, we explored the quantitative nature of seed quality traits including oil content (OIL), palmitic acid, stearic acid, oleic acid, linoleic acid (LIO) linolenic acid (LIN) and iodine value in a flax core collection of 390 accessions assayed with 460 microsatellite markers. The core collection was grown in a modified augmented design at two locations over 3 years and phenotypic data for all seven traits were obtained from all six environments. Significant phenotypic diversity and moderate to high heritability for each trait (0.73–0.99) were observed. Most of the candidate QTL were stable as revealed by multivariate analyses. Nine candidate QTL were identified, varying from one for OIL to three for LIO and LIN. Candidate QTL for LIO and LIN co-localized with QTL previously identified in bi-parental populations and some mapped nearby genes known to be involved in the FA biosynthesis pathway. Fifty-eight percent of the QTL alleles were absent (private) in the Canadian cultivars suggesting that the core collection possesses QTL alleles potentially useful to improve seed quality traits. The candidate QTL identified herein will establish the foundation for future marker-assisted breeding in linseed.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-014-2264-4) contains supplementary material, which is available to authorized users.

Genetic diversity, population structure and association analysis in linseed (Linum usitatissimum L.)

“…Association mapping in linseed have been carried out for various agronomic and seed quality traits (Soto-Cerda et al 2013 using SSR markers. Soto-Cerda et al (2013) identified 12 QTLs for six agronomic traits while 9 QTLs were identified for seed quality traits (Soto-Cerda et al 2014). In the present investigation only 1 QTL was potentially identified for days to 50% flowering.…”

A method of estimating broad-sense heritability for quantitative traits in the type 2 modified augmented design

“…The same MAD2 design was employed with the same population in all environments but the designs differed across populations. The experimental designs and phenotyping for the 22 traits in CC, 14 in BM, 19 in EV, and 11 in SU over six to eight environments have been previously described (Cloutier et al, 2010;Soto-Cerda et al, 2014b;Kumar et al, 2015;You et al, 2016b). The adjusted observations in each environment were used for estimation and evaluation.…”

“…Heritability estimation varies depending on the experimental design (Holland et al, 2003). The modified augment design (MAD) has been proposed for square plots (Type 1) (Lin and Poushinsky, 1983) and specifically for rectangular plots (Type 2 -MAD2) (Lin and Poushinsky, 1985) for field evaluation of a large number of breeding lines and used in many crops such as flax (Soto-Cerda et al, 2014a;Soto-Cerda et al, 2014b;Kumar et al, 2015), wheat (Golparvar et (Schaalje et al, 1987), soybean (Lin and Voldeng, 1989), and barley (May et al, 1989;May and Kozub, 1995). This design can accommodate a large number of unreplicated test genotypes with typically only three control genotypes for error control (You et al, 2013).…”

Environmental and varietal impact on linseed composition and on oil unidirectional expression process

“…As for other plant species, the flax cultivars tend to maintain their rank in regard to oil content and fatty acid composition whatever the culture conditions (Ghamkhar et al, 2010;McGregor and Carson, 1961;Rahimi et al, 2011). Thus, the flax variability is specifically exploited to identify common molecular markers linked to oil content and fatty acids in order to establish efficient strategies for marker-assisted breeding of flax (Chandrawati et al, 2014;Soto-Cerda et al, 2014).…”