Quantitative Trait Transcripts Mapping Coupled with Expression Quantitative Trait Loci Mapping Reveal the Molecular Network Regulating the Apetalous Characteristic in Brassica napus L.

Abstract

The apetalous trait of rapeseed (Brassica napus, AACC, 2n = 38) is important for breeding an ideal high-yield rapeseed with superior klendusity to Sclerotinia sclerotiorum. Currently, the molecular mechanism underlying the apetalous trait of rapeseed is unclear. In this study, 14 petal regulators genes were chosen as target genes (TGs), and the expression patterns of the 14 TGs in the AH population, containing 189 recombinant inbred lines derived from a cross between apetalous “APL01” and normal “Holly,” were analyzed in two environments using qRT-PCR. Phenotypic data of petalous degree (PDgr) in the AH population were obtained from the two environments. Both quantitative trait transcript (QTT)-association mapping and expression QTL (eQTL) analyses of TGs expression levels were performed to reveal regulatory relationships among TGs and PDgr. QTT mapping for PDgr determined that PLURIPETALA (PLP) was the major negative QTT associated with PDgr in both environments, suggesting that PLP negatively regulates the petal development of line “APL01.” The QTT mapping of PLP expression levels showed that CHROMATIN-REMODELING PROTEIN 11 (CHR11) was positively associated with PLP expression, indicating that CHR11 acts as a positive regulator of PLP expression. Similarly, QTT mapping for the remaining TGs identified 38 QTTs, associated with 13 TGs, and 31 QTTs, associated with 10 TGs, respectively, in the first and second environments. Additionally, eQTL analyses of TG expression levels showed that 12 and 11 unconditional eQTLs were detected in the first and second environment, respectively. Based on the QTTs and unconditional eQTLs detected, we presented a hypothetical molecular regulatory network in which 14 petal regulators potentially regulated the apetalous trait in “APL01” through the CHR11-PLP pathway. PLP acts directly as the terminal signal integrator negatively regulating petal development in the CHR11-PLP pathway. These findings will aid in the understanding the molecular mechanism underlying the apetalous trait of rapeseed.

Quantitative Trait Locus Mapping Combined with RNA Sequencing Reveals the Molecular Basis of Seed Germination in Oilseed Rape

“…The genotypes of this population and two parents were analyzed using simple sequence repeat (SSR) markers and the Illumina (San Diego, CA, USA) Brassica 60 K Infinium array by DNA Landmarks (Saint-Jean-sur-Richelieu, QC, Canada) in a previous study [ 75 ]. A high-density single nucleotide polymorphism (SNP) linkage map incorporating 2755 bins (involving 11,458 SNPs) and 57 SSRs, covering 2027.53 cM with an average marker interval of 0.72 cM was developed for QTL mapping of the apetalous trait [ 75 , 76 ], seed fatty acid composition [ 77 ], flowering time [ 78 ], and stem mechanical strength [ 79 ].…”

Integrated multi‐omics analyses and genome‐wide association studies reveal prime candidate genes of metabolic and vegetative growth variation in canola

“…Most previous GWAS studies in rapeseed focused on a limited number of phenotypic traits and/or only a single omics level. Some recent studies integrated at least two omics levels, such as Li et al (2023) who studied the seed oil content in rapeseed using a marker metabolite-based multi-omics analysis, Li, Yao, et al (2018) who integrated QTL and eQTL mapping to study fatty acid content, flowering time and growth-related traits, Yu et al (2018) who coupled QTL and eQTL mapping focusing on the apetalous characteristic or Zhang et al (2022) who dissected the genetic architecture of seed coat content in B. napus using a multi-omics analysis. Schaefer et al (2018) demonstrated in maize that integrating co-expression networks with GWAS can be a powerful approach to prioritise candidate genes.…”

“…(2018) who integrated QTL and eQTL mapping to study fatty acid content, flowering time and growth‐related traits, Yu et al. (2018) who coupled QTL and eQTL mapping focusing on the apetalous characteristic or Zhang et al. (2022) who dissected the genetic architecture of seed coat content in B. napus using a multi‐omics analysis.…”

The trifecta of disease avoidance, silique shattering resistance and flowering period elongation achieved by theBnaIDAediting inBrassica napus

“…For instance, apetalous rapeseed decreased the infections (D. I. Jamaux, and Spire, D., 1999; K. Yu et al, 2018).…”