Elucidating the Genetic Architecture of Fiber Quality in Hemp (Cannabis sativa L.) Using a Genome-Wide Association Study

Abstract

Hemp (Cannabis sativa L.) is a bast-fiber crop with a great potential in the emerging bio-based economy. Yet, hemp breeding for fiber quality is restricted and that is mainly due to the limited knowledge of the genetic architecture of its fiber quality. A panel of 123 hemp accessions, with large phenotypic variability, was used to study the genetic basis of seven cell wall and bast fiber traits relevant to fiber quality. These traits showed large genetic variance components and high values of broad sense heritability in this hemp panel, as concluded from the phenotypic evaluation across three test locations with contrasting environments. The hemp panel was genotyped using restriction site associated DNA sequencing (RAD-seq). Subsequently, a large set (> 600,000) of selected genome-wide single nucleotide polymorphism (SNP) markers was used for a genome-wide association study (GWAS) approach to get insights into quantitative trait loci (QTLs) controlling fiber quality traits. In absence of a complete hemp genome sequence, identification of QTLs was based on the following characteristics: (i) association level to traits, (ii) fraction of explained trait variance, (iii) collinearity between QTLs, and (iv) detection across different environments. Using this approach, 16 QTLs were identified across locations for different fiber quality traits, including contents of glucose, glucuronic acid, mannose, xylose, lignin, and bast fiber content. Among them, six were found across the three environments. The genetic markers composing the QTLs that are common across locations are valuable tools to develop novel genotypes of hemp with improved fiber quality. Underneath the QTLs, 12 candidate genes were identified which are likely to be involved in the biosynthesis and modification of monosaccharides, polysaccharides, and lignin. These candidate genes were suggested to play an important role in determining fiber quality in hemp. This study provides new insights into the genetic architecture of fiber traits, identifies QTLs and candidate genes that form the basis for molecular breeding for high fiber quality hemp cultivars.

Genetic Architecture of Flowering Time and Sex Determination in Hemp (Cannabis sativa L.): A Genome-Wide Association Study

“…The genotyping of the GWAS panel was performed using restriction-site associated DNA sequencing (RAD-seq), essentially as previously described by Petit et al (2020a). DNA was extracted from plants at the juvenile stage before sex was differentiated.…”

“…DNA was extracted from plants at the juvenile stage before sex was differentiated. Briefly, high quality genomic DNA (2.5 to 5 µg at a concentration ≥25 ng/µl) of the plants was extracted following a modified CTAB method (Petit et al, 2020a). As the sex of the plants was unknown, to cover all allelic variation within accessions and sexes, the genomic DNA of eight randomly selected plants per accessions were pooled in equimolar amounts, resulting in 123 samples.…”

“…SNP marker selection was performed in R version 3.4.3 statistical software. In total, 621.452 SNP markers were selected for the genetic analysis (Petit et al, 2020a). The genotypic data of these SNP markers from the GWAS panel were used in the present study.…”

“…First, a linear mixed model was used to identify significant associations between genotypes and flowering/sex traits (significant QTL-markers), using a kinship correction (VanRaden, 2008) and following the same approach as in Yu et al (2006); Huang et al (2010), Malosetti et al (2011); 1 https://doi.org/10.4121/12826832 Zhou and Stephens (2012), Kruijer et al (2015), and Petit et al (2020a). The effects of the SNP markers on the phenotypic variation were studied with the fixed effects of the model.…”

Bibliometric and Scientometric Analysis of Scopus-Indexed Literature on Hemp (Cannabis sativa) Breeding

“…The most commonly used index keywords were 'Cannabis', Cannabis sativa', 'Hemp' and 'Cultivar'. The sampled papers also reported on research themes such as genetic diversity [29][30][31][32][33], fibre quality [34,35], pollen quantification and sex genetics [36,37], cannabinoid content [38], seed oil [39] and pulp yield [40].…”