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Stem mechanical strength (SMS) plays an important role in resisting stem dislodging. However, the genetic regulatory mechanisms underlying SMS in rapeseed remain unclear. In this study, a recombinant inbred line population containing 189 lines was used to investigate four SMS-related traits, namely stem breaking force (SBF), stem diameter (SD), stem weight (SW) and stem breaking strength (SBS). Accordingly, four conditional traits were also generated, namely SBF|SD, SBF|SW, SW|SD and SBS|SW. Quantitative trait locus (QTL) mapping for four unconditional SMS-related traits detected seven major QTLs, four of which were novel loci, with phenotypic contributions ranging from 10.41 to 27.22%. QTL mapping of conditional traits detected five major QTLs (including four novel loci), which explained 11.57 to 38.73% of the phenotypic variation. Comparative analyses between unconditional and conditional QTLs revealed that all 63 QTLs potentially govern biological processes (BPs) or unknown traits (UTs), which then influence SMS-related traits via 12 pathways. SBF was regulated by 13 unconditional QTLs via the QTL-BP-SD-SBF, QTL-BP-UTSD-SW-SBF, QTL-BP-SD-SW-SBF, and QTL-BP-UTSD&SW-SBF pathways, and by six conditional QTLs via the QTL-BP-SBF|SD-SBF and QTL-BP-SBF|SW-SBF pathways. SD was regulated by 18 unconditional QTLs via the QTL-BP-SD pathway, and SW by three regulatory pathways including QTL-BP-SD-SW, QTL-BP-UTSD-SW and QTL-BP-SW|SD-SW pathways. Finally, SBF potentially influences SMS via the SBF-SMS and SBF-SBS-SMS pathways. There were two additional regulatory pathways for SBS, namely QTL-BP-UTSW-SBS and QTL-BP-SBS|SW-SBS. In addition, 12 promising candidate genes were identified through multiple methods. These results contribute to our knowledge about the genetic regulatory mechanisms underlying SMS in Brassica napus.

Brassica juncea is used as a condiment, as vegetables and as an oilseed crop, especially in semiarid areas. In the present study, we constructed a genetic map using one recombinant inbred line (RIL) of B. juncea. A total of 304 ILP (intron length polymorphism) markers were mapped to 18 linkage groups designated LG01-LG18 in B. juncea. The constructed map covered a total genetic length of 1671.13 cM with an average marker interval of 5.50 cM. The QTLs for 2-propenyl glucosinolates (GSLs) colocalized with the QTLs for 3-butenyl GSLs between At1g26180 and BnapPIP1580 on LG08 in the field experiments of 2016 and 2017. These QTLs accounted for an average of 42.3% and 42.6% phenotypic variation for 2-propenyl and 3-butenyl GSLs, respectively. Furthermore, the Illumina RNA-sequencing technique was used to excavate the genes responsible for the synthesis of GSLs in the siliques of the parental lines of the RIL mapping population, because the bulk of the seed GSLs might originate from the siliques. Comparative analysis and annotation by gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) revealed that 324 genes were involved in GSL metabolism, among which only 24 transcripts were differentially expressed genes (DEGs). Among those DEGs, 15 genes were involved in the biosynthesis and transport of aliphatic GSLs, and their expression patterns were further validated by qRT-PCR analysis. Joint QTL mapping and RNA-sequencing analyses reveal one candidate gene of IIL1 (LOC106416451) for GSL metabolism in B. juncea. These results will be helpful for further fine mapping, gene cloning and genetic mechanisms of 2-propenyl and 3-butenyl GSLs in B. juncea.

Increasing leaf chlorophyll content in crops through genetic improvement is a feasible way to increase crop yield. However, the genetic mechanism that regulates the chlorophyll content of rapeseed leaves is not clear, which is not conducive to improving it through genetic pathways. In this study, a population of 189 recombinant inbred lines of Brassica napus was used to identify quantitative trait loci (QTLs) that regulate leaf chlorophyll content. A total of 12 QTLs were identified, of which two QTLs, qCHC.A6-2 and qCHC.C5-1 , explained 10.19% and 13.70% of the phenotypic variations in chlorophyll content, respectively, and were considered to be major QTLs. Furthermore, five of the 12 QTLs were inherited from APL01, while seven were inherited from Holly. Comparative transcriptomic analysis revealed that the differential expression of genes associated with the response to light stimulation, chloroplast organization, and glutathione peroxidase activity is the molecular basis for the difference in leaf chlorophyll content between APL01 and Holly. Further combining the variation analysis of the genomic DNA sequence and the functional annotation of homologous genes, four promising candidate genes ( BnaA06g37690D , BnaA06g37710D , BnaC05g00280D, and BnaC05g00300D ) were obtained, all of which are potentially involved in the response to light stimulation and/or chloroplast organization. These results help to clarify the genetic mechanism of chlorophyll content in B. napus leaves.

As an important physiological and reproductive organ, the silique is a determining factor of seed yield and a breeding target trait in rapeseed ( Brassica napus L.). Genetic studies of silique-related traits are helpful for rapeseed marker-assisted high-yield breeding. In this study, a recombinant inbred population containing 189 lines was used to perform a quantitative trait loci (QTLs) analysis for five silique-related traits in seven different environments. As a result, 120 consensus QTLs related to five silique-related traits were identified, including 23 for silique length, 25 for silique breadth, 29 for silique thickness, 22 for seed number per silique and 21 for silique volume, which covered all the chromosomes, except C5. Among them, 13 consensus QTLs, one, five, two, four and one for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively, were repeatedly detected in multiple environments and explained 4.38–13.0% of the phenotypic variation. On the basis of the functional annotations of Arabidopsis homologous genes and previously reported silique-related genes, 12 potential candidate genes underlying these 13 QTLs were screened and found to be stable in multiple environments by analyzing the re-sequencing results of the two parental lines. These findings provide new insights into the gene networks affecting silique-related traits at the QTL level in rapeseed.

Background The fatty acid composition of B. napus ’ seeds determines the oil’s nutritional and industrial values, and affects seed germination. Many studies have reported correlations among C16:0, C18:0, C18:1, C18:2 and C18:3 based on phenotypic data; however, the genetic basis of the fatty acid composition in B. napus is still not well understood. Results In this study, unconditional and conditional quantitative trail locus (QTL) mapping analyses were conducted using a recombinant inbred line in six environments. In total, 21 consensus QTLs each for C16:0, C18:0 and C18:2, 16 for C18:1 and 22 for C18:3 were detected by unconditional mapping. The QTLs with overlapping confidence intervals were integrated into 71 pleiotropically unique QTLs by meta-analysis. Two major QTLs, uuqA5–6 and uuqA5–7 , simultaneously affected the fatty acids, except C18:0, in most of environments, with the homologous genes fatty acid desaturase 2 ( FAD2 ) and glycerol-3-phosphate sn-2-acyltransferase 5 ( GPAT5 ) occurring in the confidence interval of uuqA5–6 , while phosphatidic acid phosphohydrolase 1 ( PAH1 ) was assigned to uuqA5–7 . Moreover, 49, 30, 48, 60 and 45 consensus QTLs were detected for C16:0, C18:0, C18:1, C18:2 and C18:3, respectively, by the conditional mapping analysis. In total, 128 unique QTLs were subsequently integrated from the 232 conditional consensus QTLs. A comparative analysis revealed that 63 unique QTLs could be identified by both mapping methodologies, and 65 additional unique QTLs were only identified in conditional mapping. Conclusions Thus, conditional QTL mapping for fatty acids may uncover numerous additional QTLs that were inhibited by the effects of other traits. These findings provide useful information for better understanding the genetic relationships among fatty acids at the QTL level.

Rapid and uniform seed germination improves mechanized oilseed rape production in modern agricultural cultivation practices. However, the molecular basis of seed germination is still unclear in Brassica napus. A population of recombined inbred lines of B. napus from a cross between the lower germination rate variety ‘APL01’ and the higher germination rate variety ‘Holly’ was used to study the genetics of seed germination using quantitative trait locus (QTL) mapping. A total of five QTLs for germination energy (GE) and six QTLs for germination percentage (GP) were detected across three seed lots, respectively. In addition, six epistatic interactions between the QTLs for GE and nine epistatic interactions between the QTLs for GP were detected. qGE.C3 for GE and qGP.C3 for GP were co-mapped to the 28.5–30.5 cM interval on C3, which was considered to be a novel major QTL regulating seed germination. Transcriptome analysis revealed that the differences in sugar, protein, lipid, amino acid, and DNA metabolism and the TCA cycle, electron transfer, and signal transduction potentially determined the higher germination rate of ‘Holly’ seeds. These results contribute to our knowledge about the molecular basis of seed germination in rapeseed.

Rapeseed is a globally important economic crop that can be severely impacted by aphids. However, our understanding of rapeseed resistance to aphid stress is very limited. In this study, we analyzed the resistance characteristics of the low aphid-susceptible variety APL01 and the highly aphid-susceptible variety Holly in response to aphid stress. APL01 had a more significant inhibitory effect on aphid proliferation compared with Holly during the early stage of inoculation, whereas Holly showed stronger tolerance to aphid stress compared with APL01 during the later stage of inoculation. Through transcriptome, physiological, and gene expression analyses, it was revealed that chitinase activity, catalase activity, calcium signal transduction, and activation of systemic acquired resistance might be involved in aphid resistance in B. napus. The degree of inhibition of photosynthesis in plants under aphid stress directly determines the tolerance of B. napus to aphid stress. Furthermore, four promising candidate genes were screened from eight genes related to rapeseed response to biotic stress through RT-qPCR analysis of gene expression levels. These research findings represent an important step forward in understanding the resistance of rapeseed to aphid stress and provide a solid foundation for the cloning of genes responsible for this resistance.

Agronomic traits are usually determined by multiple quantitative trait loci (QTLs) that can have pleiotropic effects. A multiparent advanced generation intercross (MAGIC) population is well suited for genetically analysing the effects of multiple QTLs on the traits of interest because it contains more QTL alleles than a biparental population and can overcome the problem of confounding the population structure of the natural germplasm population. We previously developed the B. juncea MAGIC population, derived from eight B. juncea lines with great diversity in agronomic and quality traits. In this study, we show that the B. juncea MAGIC population is also effective for the evaluation of multiple QTLs for complex agronomic traits in B. juncea. A total of twenty-two QTLs for nine seed-related traits were identified, including one QTL for each oil content, seed number per silique and thousand-seed weight; two QTLs for each acid detergent lignin and neutral detergent fibre; three QTLs for each acid detergent fibre and protein content; four QTLs for the seed maturity time; and five QTLs for the white index. Some of these QTLs overlapped. These results should be helpful for further fine mapping, gene cloning, plant breeding and marker-assisted selection (MAS) in B. juncea.

The apetalous trait of rapeseed ( , AACC, 2 = 38) is important for breeding an ideal high-yield rapeseed with superior klendusity to . 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 ( ) was the major negative QTT associated with PDgr in both environments, suggesting that negatively regulates the petal development of line \"APL01.\" The QTT mapping of expression levels showed that ( ) was positively associated with expression, indicating that acts as a positive regulator of 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 pathway. acts directly as the terminal signal integrator negatively regulating petal development in the pathway. These findings will aid in the understanding the molecular mechanism underlying the apetalous trait of rapeseed.

Leaf shape diversity in Brassica napus provides critical insights into the molecular basis of leaf complexity and its evolutionary implications in rapeseed. Two predominant leaf morphotypes were characterized in B. napus : serrated-margin and deeply lobed leaves. Serrated leaves were further subdivided based on the presence or absence of petiolar lobes, establishing a novel phenotypic classification system. Through QTL mapping of the APL01/Holly recombinant inbred line population ( n  = 2,755 markers) across three environments, we identified 10 consensus loci associated with non-lobed petioles. A major-effect QTL ( qNLP.C9-3 ) spanning a 951-kb interval on chromosome C9 accounted for 9.43–21.66% of phenotypic variation in the APL01 genetic background. Within this interval, 148 annotated genes were identified, among which BnC09.LMI1 was prioritized as a candidate gene regulating petiole lobe formation and leaf complexity based on phylogenetic analysis and differential expression. These results advance our understanding of leaf morphological diversity in B. napus and provide a molecular framework for dissecting the genetic architecture of leaf complexity.