Rapeseed (Brassica napus L.) meal is an important source of protein, but the presence of anti-nutritional compounds, such as fibre and glucosinolates, still limits its use as a livestock feed. Understanding the genetic basis of seed fibre biosynthesis would help to manipulate its content in seeds of oilseed rape. Here, we applied high-resolution skim genotyping by sequencing (SkimGBS) and characterised 187,835 single-nucleotide polymorphism (SNP) markers across a mapping population subsequently used for a genetic mapping study (R/qtl). This approach allowed the identification of 11 stable QTL related to seed quality traits and led to the identification of potential functional genes underlying these traits. Among these, key genes with a known role in carbohydrate metabolic process, cell wall, lignin, and flavonoid biosynthesis, including cellulase GH5, TT10/LAC15, TT4, and SUC2, were found. This study furthers the understanding of the molecular mechanisms underlying seed fibre content and provides new markers for molecular breeding in B. napus.

The identification of markers responsible for regulating important agronomic traits in rapeseed supports breeding and increases the seed yield. Microsatellite (SSR) markers are mainly used as ‘neutral’ genetic markers but are also linked with many biological functions. The objective of this study was identification of microsatellite markers associated with important agronomic traits affecting the seed yield of winter oilseed rape and with the heterosis effect for these traits. The plant material consists of four parental lines, 60 doubled haploid (DH) lines, 60 single cross hybrids, and 60 three-way cross hybrids. The association between molecular markers and observed traits was estimated using regression analysis. Among 89 SSR markers, 43 were polymorphic, and 15 were selected for mapping because they demonstrated stability in both years of observation. These markers were physically mapped in the rapeseed reference genomes and their immediate vicinity was searched to identify candidate genes associated with the studied traits. Six markers (BrGMS3837, BnEMS1119, BrGMS2901, BnGMS0509, BrGMS3688, BrGMS4057), which showed a positive estimation effect in our association analysis, and thus increased the value of a given trait or heterosis effect, turned out to be linked with genes that could be responsible for the development and growth of plants.

Limited genetic variability is a major problem in rapeseed breeding, whose strict selection, limited geographical range and a short period of domestication has led to a reduction in genetic and phenotypic diversity. Assessing specific populations for the greatest genetic diversity for many traits simultaneously, requires the evaluation of multi-feature characteristics. The aim of this study was to estimate the variability of DH (doubled haploid) lines and two generations of winter oilseed rape hybrids. In addition, the relationship between the Mahalanobis distances of parental forms and the effect of heterosis in hybrids was investigated. The results of MANOVA showed that the genotypes and years as well as genotype × year interaction were significantly different (p < 0.001) for all eight observed traits. The first (V₁) and the second (V₂) canonical variate explained 38.57% and 27.55% of the total variation in 2015, and 50.19% and 31.84% in 2016, respectively Canonical variate analysis showed that the traits, flowering time and number of branches per plant had a very large influence on the differentiation of genotypes. Graphs demonstrated that the tested DH lines and hybrids are characterized by a similar, wide range of variability. It was observed, that when using a diverse population of DH lines for crossbreeding with only one CMS/Rfo line, there was no significant reduction of variation in hybrid generations and between these generations. The phenotypic distance values determined by the results of Mahalanobis analysis were similar in both years, but slightly wider in 2016. The observed minimum and maximum ranged from 1.324 to 22.356 in 2015, and from 1.105 to 27.792 in 2016, respectively. No significant correlation was observed between the hybrid heterosis effect and the Mahalanobis distance of the parental lines.

A crucial aim for rapeseed breeders is increasing the seed yield through improving yield- and silique-related traits. In this research, traits including the number of seeds per silique, silique length, silique width, and thousand-seed weight combined with seed coat color were investigated. Yellow-seeded lines of oilseed rape have a thinner seed coat, lower fiber content, and higher protein and oil content than traditional varieties. Hybrids of yellow- and black-seeded Brassica napus, which combine the advantages of both types of seeds, are tested for their suitability in breeding. Therefore, the aim of this study was to assess a population of 78 doubled haploid lines with different seed coat colors to select genotypes connecting a light color of seeds with good yielding characteristics. Multivariate methods such as analysis of variance, correlation analysis, regression analysis, canonical variate analysis, Mahalanobis distances, and estimation of gene effects were used. The results showed that all tested genotypes were significantly different regarding all five studied traits. The multidimensional analyses gave an accurate overview of the relationship between the examined features. The color and weight of seeds were considered the most important for breeding rapeseed with better seed properties. Although a negative correlation between these two characteristics occurs quite commonly, it was not present in our plant material, which allowed us to select lines with a-light seed color and high thousand-seed weight, which is a significant achievement. As a result, two doubled haploid lines were chosen as valuable breeding material for creating oilseed rape varieties with improved biochemical characteristics of seeds.

Seed biochemical composition critically influences the quality and industrial value of oilseed rape (Brassica napus L.). Understanding the genetic basis of seed oil, protein, and fiber content is essential for breeding improved cultivars. Here we conducted a genome-wide association study (GWAS) on 350 diverse winter oilseed rape lines over three years, using near-infrared reflectance spectroscopy (NIRS) to measure seed traits and SNP genotyping for association mapping. We identified numerous SNP markers significantly associated with seed oil, protein, acid detergent fiber (ADF), and neutral detergent fiber (NDF) content. From 18,566 detected SNPs, 3782 met stringent criteria and were used for association mapping, resulting in 3189 significant associations across three years. The highest number of associations was observed for protein (3480), followed by NDF (3662), ADF (3422), and oil (2046). Individual markers explained up to 35% of phenotypic variation, indicating strong genetic control of these traits. Gene ontology enrichment analyses linked candidate genes to key metabolic and regulatory pathways influencing these traits: protein biosynthesis and post-translational modification, lipid metabolism regulated by phosphorylation, and transcriptional control of cell wall polysaccharide synthesis. These findings provide valuable molecular markers that can be validated for further use in marker-assisted selection, supporting the development of rapeseed cultivars with optimized seed quality for food, feed, and industrial applications.