Genome-wide association study (GWAS) of leaf cuticular wax components in Camelina sativa identifies genetic loci related to intracellular wax transport

Abstract

Background It is important to explore renewable alternatives (e.g. biofuels) that can produce energy sources to help reduce reliance on fossil oils, and reduce greenhouse gases and waste solids resulted from fossil oils consumption. Camelina sativa is an oilseed crop which has received increasing attention due to its short life cycle, broader adaptation regions, high oil content, high level of omega-3 unsaturated fatty acids, and low-input requirements in agriculture practices. To expand its Camelina production areas into arid regions, there is a need to breed for new drought-tolerant cultivars. Leaf cuticular wax is known to facilitate plant development and growth under water-limited conditions. Dissecting the genetic loci underlying leaf cuticular waxes is important to breed for cultivars with improved drought tolerance. Results Here we combined phenotypic data and single nucleotide polymorphism (SNP) data from a spring C. sativa diversity panel using genotyping-by-sequencing (GBS) technology, to perform a large-scale genome-wide association study (GWAS) on leaf wax compositions. A total of 42 SNP markers were significantly associated with 15 leaf wax traits including major wax components such as total primary alcohols, total alkanes, and total wax esters as well as their constituents. The vast majority of significant SNPs were associated with long-chain carbon monomers (carbon chain length longer than C 28 ), indicating the important effects of long-chain carbon monomers on leaf total wax biosynthesis. These SNP markers are located on genes directly or indirectly related to wax biosynthesis such as maintaining endoplasmic reticulum (ER) morphology and enabling normal wax secretion from ER to plasma membrane or Golgi network-mediated transport. Conclusions These loci could potentially serve as candidates for the genetic control involved in intracellular wax transport that might directly or indirectly facilitate leaf wax accumulation in C. sativa and can be used in future marker-assisted selection (MAS) to breed for the cultivars with high wax content to improve drought tolerance.

Metabolic Engineering a Model Oilseed Camelina sativa for the Sustainable Production of High-Value Designed Oils

“…For example, a GWAS using 391 wild Arabidopsis accessions revealed four to nineteen genomic regions responsible for FA composition in seed oil, showing that the most regions identified contained candidate genes that had never before been implicated in lipid metabolism (Branham et al, 2015). This tool was also used to examine a number of loci containing candidate genes involved in wax biosynthesis in camelina (Luo et al, 2019). By mining sequence data, the candidate enzymes for target FAs were identified, and subsequently used to manipulate C. sativa oil composition towards a superior biofuel and bio-based lubricant oil (Kim et al, 2015;Nguyen et al, 2015).…”

Genome-Wide Association Study (GWAS) Analysis of Camelina Seedling Germination under Salt Stress Condition

“…The resulting SNPs in VCF file were converted to HAPMAP format using TASSEL [31]. Detailed procedures of population genetics analyses using STRUCTURE v2.3.4 [32] were provided by Luo et al [20]. Population genetics analyses identified two subpopulations based on the results from Structure Harvester [33].…”

“…The rapid development of next-generation sequencing (NGS) technologies enables the utilization of marker-assisted selection (MAS) as a tool to accelerate genetic gains in a more cost-effective way. Genome-wide association studies (GWAS) could overcome the limitations of traditional quantitative trait loci (QTL) mapping and can be used to dissect minor genetic factors underlying complex traits in crop species [20]. The identified QTLs can be used in MAS to improve genetic gains in a more efficient manner.…”

Genome-wide SNP detection in Darjeeling tea: unravelling genetic structure, functional impact and trait associations

“…With the advent of molecular genetic approaches, efficient genotyping with high throughput markers has led to an in-depth understanding of crop genetic resources, their management, and utilization in breeding programs (Basak et al, 2019;Sudan et al, 2019). Development of SNP markers along with the determination of their genomic position assisted the trait association analyses in plants and their diversity at an individual, community as well as species level (Guajardo et al, 2020;Huq et al, 2016;Luo et al, 2019;Mammadov et al, 2012). In the present study, ddRAD based genotyping by sequencing approach was adopted for genome-wide SNP discovery and their diversity assessment in 23 Darjeeling tea cultivars.…”