Abstract
Brassica napus (B. napus, AACC), is an economically important allotetraploid crop species that resulted from hybridization between two diploid species, Brassica rapa (AA) and Brassica olereacea (CC). We have created one new synthetic B. napus genotype Da-Ae (AACC) and one introgression line Da-Ol-1 (AACC), which were used to generate an F2 mapping population. Plants in this F2 mapping population varied in fatty acid content, flowering time, and growth-related traits. Using quantitative trait locus (QTL) mapping, we aimed to determine if Da-Ae and Da-Ol-1 provided novel genetic variation beyond what has already been found in B. napus. Making use of the genotyping information generated from RNA-seq data of these two lines and their F2 mapping population of 166 plants, we constructed a genetic map consisting of 2,021 single nucleotide polymorphism markers that spans 2,929 cM across 19 linkage groups. Besides the known major QTL identified, our high resolution genetic map facilitated the identification of several new QTL contributing to the different fatty acid levels, flowering time, and growth-related trait values. These new QTL probably represent novel genetic variation that existed in our new synthetic B. napus strain. By conducting genome-wide expression variation analysis in our F2 mapping population, genetic regions that potentially regulate many genes across the genome were revealed. A FLOWERING LOCUS C gene homolog, which was identified as a candidate regulating flowering time and multiple growth-related traits, was found underlying one of these regions. Integrated QTL and expression QTL analyses also helped us identified candidate causative genes associated with various biological traits through expression level change and/or possible protein function modification.
Highlights
Rapeseed, Brassica napus (B. napus), is one of the most important oilseed crops worldwide producing multi-purpose oil for food and biofuel
The results suggested that these phenotypic differences might be reflected in gene expression changes; for example, differentially expressed genes were enriched in Gene ontology (GO) terms related to lipid and fatty acid (FA) processes (Supplementary Figure 3)
We found that BnaA10g22080D expression was regulated by a cis-Expression QTL (eQTL), with the allele from Da-Ol-1 decreasing the gene expression level, and this cis-eQTL co-localized with quantitative trait locus (QTL) for flowering/bolting time and multiple growthrelated traits (Figure 8 and Supplementary Table 8)
Summary
Brassica napus (B. napus), is one of the most important oilseed crops worldwide producing multi-purpose oil for food and biofuel. As the global requirements for rapeseed oil are growing rapidly, it becomes important to understand the control of B. napus oil content, oil composition, and growth including flowering time, plant height, etc., so that different varieties can be bred to meet the agricultural demand in different areas. As a source of edible oil, canola seeds must contain less than 2% erucic acid and less than 35 μmol/g glucosinolates. Besides erucic acid and glucosinolate content, the composition of various FAs in the seed oil determines the economic value of rapeseed, including saturated FA palmitic (C16:0) and stearic (C18:0), monounsaturated FA palmitoleic (C16:1), oleic (C18:1) and eicosenoic (C20:1), and polyunsaturated FA: linoleic (C18:2) and linolenic (C18:3)
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