QTL Analysis of Five Silique-Related Traits in Brassica napus L. Across Multiple Environments

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.

Genome-wide association study and transcriptome analysis dissect the genetic control of silique length in Brassica napus L.

Background Rapeseed is the third-largest oilseed crop after soybeans and palm that produces vegetable oil for human consumption and biofuel for industrial production. Silique length (SL) is an important trait that is strongly related to seed yield in rapeseed. Although many studies related to SL have been reported in rapeseed, only a few candidate genes have been found and cloned, and the genetic mechanisms regulating SL in rapeseed remain unclear. Here, we dissected the genetic basis of SL by genome-wide association studies (GWAS) combined with transcriptome analysis. Results We identified quantitative trait locus (QTL) for SL using a recombinant inbred line (RIL) population and two independent GWAS populations. Major QTLs on chromosomes A07, A09, and C08 were stably detected in all environments from all populations. Several candidate genes related to starch and sucrose metabolism, plant hormone signal transmission and phenylpropanoid biosynthesis were detected in the main QTL intervals, such as BnaA9.CP12-2, BnaA9.NST2, BnaA7.MYB63, and BnaA7.ARF17. In addition, the results of RNA-seq and weighted gene co-expression network analysis (WGCNA) showed that starch and sucrose metabolism, photosynthesis, and secondary cell wall biosynthesis play an important role in the development of siliques. Conclusions We propose that photosynthesis, sucrose and starch metabolism, plant hormones, and lignin content play important roles in the development of rapeseed siliques.

Expression Profile And Genome-Wide Association Analyze of Silique Length In Brassica Napus L.

Background: Silique length (SL) is an important trait tightly related to seed yield in Brassica napus (B. napus). Many studies related to SL have been reported in B. napus, but only a few candidate genes have been found and cloned, and the regulatory mechanism of SL is not clear. Results: We identified QTL for SL by using a RIL population and two independent GWAS populations. Major QTL on A07, A09, and C08 chromosome were stably detected in all environments from all populations. As important candidate genes, several genes related to starch and sucrose metabolism, plant hormone signal transmission and phenylpropanoid biosynthesis were detected in the main QTL interval. Such as, BnaA9.CP12-2, BnaA9.NST2, BnaA7.MYB63, BnaA7.ARF17, etc. At the same time, the results of RNA-seq and WGCNA showed that starch and sucrose metabolism, photosynthesis, and secondary cell wall biosynthesis played an important role in the development of siliques. Conclusions: we propose that photosynthesis, sucrose and starch metabolism, plant hormones, and lignin content play an important role in the development of rapeseed silique.

BnaC7.ROT3, the causal gene of cqSL-C7, mediates silique length by affecting cell elongation in Brassica napus

Siliques are a major carbohydrate source of energy for later seed development in rapeseed (Brassica napus). Thus, silique length (SL) has received great attention from breeders. We previously detected a novel quantitative trait locus cqSL-C7 that controls SL in B. napus. Here, we further validated the cqSL-C7 locus and isolated its causal gene (BnaC7.ROT3) by map-based cloning. In Zhongshuang11 (parent line with long siliques), BnaC7.ROT3 encodes the potential cytochrome P450 monooxygenase CYP90C1, whereas in G120 (parent line with short siliques), a single nucleotide deletion in the fifth exon of BnaC7.ROT3 results in a loss-of-function truncated protein. Subcellular localization and expression pattern analysis revealed that BnaC7.ROT3 is a membrane-localized protein mainly expressed in leaves, flowers and siliques. Cytological observation showed that the cells in silique wall of BnaC7.ROT3-transformed positive plants were longer than those of transgene-negative plants in the background of G120, suggesting that BnaC7.ROT3 affects cell elongation. Haplotype analysis demonstrated that most of the alleles of BnaC7.ROT3 are favorable alleles in B. napus germplasms and its homologs may also be involved in SL regulation. Our findings provide novel insights into the regulatory mechanisms of natural SL variations and valuable genetic resources for the improvement of SL in B. napus.

Fine Mapping and Candidate Gene Analysis of a Major Locus Controlling Ovule Abortion and Seed Number Per Silique in Brassica Napus L.

Key message A major QTL controlling ovule abortion and SN was fine-mapped to a 80.1-kb region on A8 in rapeseed, and BnaA08g07940D and BnaA08g07950D are the most likely candidate genes.Abstact The seed number per silique (SN), an important yield determining trait of rapeseed, is the final consequence of a complex developmental process including ovule initiation and the subsequent ovule/seed development. To elucidate the genetic mechanism regulating the natural variation of SN and its related components, quantitative trait locus (QTL) mapping was conducted using a doubled haploid (DH) population derived from the cross between C4-146 and C4-58B, which showed significant differences in SN and aborted ovule number (AON), but no obvious differences in ovule number (ON). QTL analysis identified 19 consensus QTLs for six SN-related traits across three environments. A novel QTL on chromosome A8, un.A8, which pleiotropically controls all these traits except for ON, was stably detected across the three environments.This QTL explained more than 50% of the SN, AON and percentage of aborted ovule (PAO) variations as well as a moderate contribution on silique length (SL) and thousand seed weight (TSW). The C4-146 allele at the locus increases SN and SL but decreases AON, PAO and TSW. Further fine mapping narrowed down this locus into a 80.1-kb interval flanked by markers BM1668 and BM1672, and six predicted genes were annotated in the delimited region. Expression analyses and DNA sequencing showed that two homologs of Arabidopsis photosystem I subunit F (BnaA08g07940D) and zinc transporter 10 precursor (BnaA08g07950D) were the most promising candidate genes underlying this locus. These results provide a solid basis for cloning un.A8 to reduce the ovule abortion and increase SN in the yield improvement of rapeseed.

Orchid Bsister gene PeMADS28 displays conserved function in ovule integument development

The ovules and egg cells are well developed to be fertilized at anthesis in many flowering plants. However, ovule development is triggered by pollination in most orchids. In this study, we characterized the function of a Bsister gene, named PeMADS28, isolated from Phalaenopsis equestris, the genome-sequenced orchid. Spatial and temporal expression analysis showed PeMADS28 predominantly expressed in ovules between 32 and 48 days after pollination, which synchronizes with integument development. Subcellular localization and protein–protein interaction analyses revealed that PeMADS28 could form a homodimer as well as heterodimers with D-class and E-class MADS-box proteins. In addition, ectopic expression of PeMADS28 in Arabidopsis thaliana induced small curled rosette leaves, short silique length and few seeds, similar to that with overexpression of other species’ Bsister genes in Arabidopsis. Furthermore, complementation test revealed that PeMADS28 could rescue the phenotype of the ABS/TT16 mutant. Together, these results indicate the conserved function of BsisterPeMADS28 associated with ovule integument development in orchid.

Estimation of heterosis for yield-related traits for single cross and three-way cross hybrids of oilseed rape (Brassica napus L.)

Rapeseed breeding programs are focused mainly on improving plant potential and seed yield. One of the ways to improve seed yield in oilseed rape is heterosis, which is hybrid vigor that results in a greater biomass, increased seed yield, and faster development. The purpose of this study was to estimate yield-related trait heterosis for single cross and three-way cross hybrids of winter oilseed rape (Brassica napus L.). A population of 60 doubled-haploid (DH) lines and two generations of hybrids were evaluated in field trials to assess six yield-related traits: plant height, number of branches per plant, number of siliques per plant, silique length, number of seeds per silique, and thousand seed weight. Heterosis effects for each trait were estimated by a comparison of the particular hybrid with: (1) the trait mean over both parents—mid-parent heterosis and (2) to the value of better parent—best-parent heterosis. Traits with clear positive heterosis and traits with varied heterosis were observed in this study. For the first group, we include plant height, silique length, and the number of seeds per silique—a large number of hybrids expressed significant positive heterosis for these traits, independent from the year of observations and the type of hybrid. For the second group, with varied heterosis, we can include the number of branches and siliques per plant and thousand seed weight. For these traits, hybrids exhibited both positive and negative significant heterosis, without a clear pattern for the years and types of hybrids.