Identification of Quantitative Trait Loci (QTLs) and candidate genes for trichome development in Brassica villosa using genetic, genomic, and transcriptomic approaches

Abstract

Brassica villosa is characterized by its dense hairiness and high resistance against the fungal pathogen Sclerotinia sclerotiorum. Information on the genetic and molecular mechanisms governing trichome development in B. villosa is rare. Here, we analyzed an F₂ population, derived from a cross between B. villosa and the glabrous B. oleracea by QTL mapping and transcriptomic analyses. As a result, the phenotyping of 171 F₂ progenies revealed a wide range of variation in trichome development. Subsequent genotyping with the 15-k Illumina SNP array resulted in a genetic map with 970 markers and a total length of 812 cM. Four QTLs were identified, which explained phenotypic variation from 3.2% to 40.3%. Interestingly, one of these was partially co-localized with the major QTL for Sclerotinia-resistance previously detected in the same F₂ population. However, only a moderate correlation between trichomes and Sclerotinia-resistance was observed. In total, 133 differentially expressed genes (DEGs) associated with trichome development were identified, from which only BoTRY, an orthologue of Arabidopsis TRY encoding a MYB transcription factor negatively regulating trichome development, was located within the major QTL. Expression of BoTRY was tissue-specific and highly variable between the hairy and glabrous species, suggesting that BoTRY may also act as a master-switch regulator of trichome development in B. villosa. This study provides valuable data for further understanding the genetic architecture of trichome development and identifying related genes and mechanisms in Brassica species. Molecular markers can be developed to facilitate the introgression and selection of this trait in oilseed rape breeding.

Keywords: Brassica villosa; TRY; Genetic mapping; Genomics and transcriptomics of Brassica; QTL analysis; Trichomes.

Fig. 1

Exemplary representation of the trichome variation in the F₂ population from a cross between the hairy B. villosa (BRA1896) and the glabrous B. oleracea (BRA1909). The pictures show the crossover from petiole to leaf. The hairiness of petioles is representative for the hairiness of stems. A–C Representative trichome phenotypes of F₂ plants. D Trichome phenotype of the hairy B. villosa

Fig. 2

A Distribution of hairy and glabrous F₂ plants. The distribution shows a significant deviation from a monogenic 3:1 segregation (X² = 23.16, P value < 0.001). B Classification of trichome phenotypes into five trichome groups ranging from group “0” (glabrous) to group “4” (most densely haired) based on trichome density and covered tissue

Fig. 3

LOD profiles for genomic loci associated with the trichome phenotype in the F₂ population. Horizontal lines indicate significance thresholds. The QTL peaks are highlighted by the nearest SNP marker. Dark gray: LOD profile from the non-parametric single-QTL scan. Purple: LOD_av1 profile for chromosome C03 from the two-dimensional parametric QTL scan (Haley-Knott regression) with the tQTL1 on chromosome C01 at position 51 cm (Bn-scaff_15747_1-p105633) as covariate

Fig. 4

Positional overview of the co-localization of the major QTL for trichomes (t1QTL) with the major QTL for Sclerotinia-resistance (l2QTLb) from Bergmann et al. (2023). The brackets highlight the peak intervals of the QTLs. The arrow indicates the position of BoTRYc

Fig. 5

Heatmap of 133 differentially expressed genes (DEGs) related to trichome formation between the hairy B. villosa (BRA1896) and the glabrous B. oleracea (BRA1909). The genes were automatically subdivided into five clusters (Cluster I–V) based on the log₂-transformed fragments per million per kilobases (FPKM) expression profiles. The darker the blue the stronger the gene expression. The adjacent heatmap illustrates the log₂-transformed fold change of the FPKM values between both Brassica species. Here, blue means a stronger induction in the hairy B. villosa and red means a stronger induction in the glabrous B. oleracea. BR Biological replication

Fig. 6

Relative gene expression of BoTRY orthologs between the glabrous B. oleracea (BRA1909) in comparison to the hairy B. villosa (BRA1896) in leaf tissue by real-time quantitative PCR (rt-qPCR). BoTRY gene expression was normalized to BoACT2 and gene expression in B. oleracea (BRA1909) was set in relation to B. villosa (BRA1896). Error bars represent standard deviation of three biological replications. Asterisks indicate a significantly higher expression in B. oleracea compared to B. villosa calculated by a linear model using generalized least squares and multiple contrast tests. *P adj. < 0.05, ***P adj. < 0.001