Flax (Linum usitatissimum L., 2n = 30), also known as flax or linseed, is an annual and self-pollinated species.

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Flax (Linum usitatissimum L., 2n = 30), also known as flax or linseed, is an annual and self-pollinated species. It has been propagated for its seed oil or stem fibres and for dual purpose since several 1,000 years (Dillman1953; Zohary1999). It is a versatile crop cultivated in diverse environments for fibre, food, industrial, feed and possibly pharmaceutical uses. Flax was a potential commercial crop before the discovery of petroleum and vast use of cotton (McHughen1990).The bast or phloem fibres have remarkable mechanical properties (Ferna´ndez2016) with flexibility and strength. Because of the multipurpose uses and sustainability, there is revived interest in its breeding and cultivation. Further information on the genetic basis of variation is needed to enable modern breeding manipulating the biodiversity in the species and its wild relatives (McKenzie et al. 2008; Kurt and Evans 1998). Utilization and characterization of flax genetic resources and analysing of flax genetic diversity are piovital for flax germplasm management and breeding. Molecular or DNA markers have been used since almost half a century, and more than 20 types of DNA markers systems have since been established (Agarwal et al.2008). Among the different kinds of markers accessible, Simple Sequence Repeats (SSRs) are designated as the best preferred for different research because of their high variability and ubiquitous occurrence (Powell et al. 1996). The high variability of these microsatellites is mainly due to the differing numbers of repeats in the region of the repeated motif, and also due to short insertion/deletion events (Kalia et al. 2011). Presently, SSR markers have been used for the analysis of genetic diversity, the construction of linkage maps, and for QTL mapping in many plant species (Dettoriet al. 2015; Qin et al. 2015; Bohra et al. 2017; Luo et al.2017; Mohamed et al. 2019). Most recently, some SSR markers have also been developed in flax (Cloutier et al. 2009, 2011, 2012;Soto-Cerda et al. 2011; Wu et al. 2017). Researchers have developed a cost-effective method to identify SSRs using bioinformatics to mine sequences in public databases. For example, Cloutier et al. (2009) identified 851 putative SSRs and designed 662 primer pairsbased on a set of 146,611 expressed sequence tags generated from 10 flax cDNA libraries, and Soto-Cerda et al. (2011) evaluated a total of 3242 flax genomic sequences to identify SSRs. Further, Wuet al. (2017) screened 1574 microsatellites using reduced representation genome sequencing (RRGS) to systematically identify SSR markers and evaluate marker sensitivity and specificity based on 48 flax isolate samples. Nonetheless, in connection with the density of SSR markers in rice, wheat, and other crops (Collard et al. 2008; Bracci et al. 2011; Waqas et al.2014), the number of SSR markers in flax is meager, and information on these SSR markers is still a lacuna, making it cumbersome to meet the needs of molecular analyses. Furthermore, no earlier studies have characterized SSRs throughout the flax genome. The possibility of the flax genome sequence (Wang et al. 2012; You et al. 2018) has permitted the scanning of the whole genome heading to the identification of microsatellites that can be used for molecular analysis. With contemporary improvements in the sequencing of the flax genome (You et al. 2018), SSR markers can now be precisely assigned to particular locations on flax chromosomes, this further improves the accuracy of molecular analyses. Starting with strategic crop improvement programs, knowledge and concept about the extent of genetic variability and population structure of the crop concern laid an important mile stone. Knowledge on population structure has important significance because population structure is the main source of spurious associations (Chaoet al. 2010; Flint-Garcia et al. 2003). As L. usitatissimum has a long and complex domestication, divergent breeding history, and considering its limited gene flow, it is assumed that flax seed populations display complex population structures. Association Mapping  (AM) takes the favour of a large range of germplasm including natural populations and collections of varieties and breeding lines to map traits by linkage disequilibrium (LD), that is the non-random association of alleles at different loci (Myles et al. 2009). The main recognition of AM is its high resolution in determining the correlation between polymorphisms and QTL based on thousands of meiotic events aggregated during the shared history of the individuals in a population. Hence, population structure must be inspected to determine the ability for association analyses (Song et al.2009). Crop species studied till date do not fit the demographic supposition of the standard equilibrium neutral model, and thus despair from neutral expectation is relatively common, providing  proof of the existence of stratification, specifically in self pollinated species (Maccaferri et al. 2005; Song et al.2009). Further, assessing the genetic similarity among the accessions of the targeted population is an important necessity for the identification of nonredundant core collections suitable for optimizing LD estimation and association studies (Maccaferri et al.2005). Novel advances in DNA sequencing have facilitated the rapid development of genomic SSR (gSSR; Deng et al. 2010; Roose-Amsaleg et al.2006; Soto-Cerda et al. 2011a) and expressed sequence tag SSR markers in flax (EST-SSR; Cloutier et al. 2009; Soto-Cerda et al. 2011b). Seeing that SSR markers are dispersed throughout the genome, occur in both protein-coding and non-coding regions, show co-dominant inheritance and high information content, they have become the marker of choice for population genetic studies (Ellis and Burke 2007) and to investigate patterns of LD (Flint-Garcia et al. 2003). Quantitative trait loci (QTL) and association mapping (AM) are integral approaches for the identification of marker-trait association studies (MTA). Association Mapping can accomplish higher mapping resolution through high numbers of historical recombination events in germplasm collections. An quintessential association panel should dock the broadest genetic diversity because this is often correlated with a rapid LD decay essential to resolve complex trait variation(s) to single gene or nucleotide []. Null or weak population structure and a low level of relatedness among individuals of the germplasm collection are also alluring. Thus, genetic diversity, population structure, familial relatedness and LD patterns are pivotal features to be assessed prior to AM analyses to fully escapade their advantages for flax genetic improvement. In this study we genotyped 264 flax accessions using 28 microsatellite loci. The overall goal of the study was to evaluate the usefulness of this flax world collection for AM studies. Our specific goals were: (1) to investigate the genetic diversity; (2) to estimate the levels of population structure and assess familial relatedness; (3) to detect the patterns of LD; and (4) to identify non-neutral genomic regions potentially underlying divergent selection between fiber and linseed types. Our study will provide a useful tool for the molecular analysis of flax in the future.


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