Characterization of the quantitative trait locus OilA1 for oil content in Brassica napus

Fine mapping and candidate gene analysis of a major QTL for oil content in the seed of Brassica napus

KEY MESSAGE

By integrating QTL fine mapping and transcriptomics, a candidate gene responsible for oil content in rapeseed was identified. The gene is anticipated to primarily function in photosynthesis and photosystem metabolism pathways. Brassica napus is one of the most important oil crops in the world, and enhancing seed oil content is an important goal in its genetic improvement. However, the underlying genetic basis for the important trait remains poorly understood in this crop. We previously identified a major locus, OILA5 responsible for seed oil content on chromosome A5 through genome-wide association study. To better understand the genetics of the QTL, we performed fine mapping of OILA5 with a double haploid population and a BC3F2 segregation population consisting of 6227 individuals. We narrowed down the QTL to an approximate 43 kb region with twelve annotated genes, flanked by markers ZDM389 and ZDM337. To unveil the potential candidate gene responsible for OILA5, we integrated fine mapping data with transcriptome profiling using high and low oil content near-isogenic lines. Among the candidate genes, BnaA05G0439400ZS was identified with high expression levels in both seed and silique tissues. This gene exhibited homology with AT3G09840 in Arabidopsis that was annotated as cell division cycle 48. We designed a site-specific marker based on resequencing data and confirmed its effectiveness in both natural and segregating populations. Our comprehensive results provide valuable genetic information not only enhancing our understanding of the genetic control of seed oil content but also novel germplasm for advancing high seed oil content breeding in B. napus and other oil crops.

Phenotypic Characterization and Fine Mapping of a Major-Effect Fruit Shape QTL FS5.2 in Cucumber, Cucumis sativus L., with Near-Isogenic Line-Derived Segregating Populations

Cucumber (Cucumis sativus L.) fruit size/shape (FS) is an important yield and quality trait that is quantitatively inherited. Many quantitative trait loci (QTLs) for fruit size/shape have been identified, but very few have been fine-mapped or cloned. In this study, through marker-assisted foreground and background selections, we developed near-isogenic lines (NILs) for a major-effect fruit size/shape QTL FS5.2 in cucumber. Morphological and microscopic characterization of NILs suggests that the allele of fs5.2 from the semi-wild Xishuangbanna (XIS) cucumber (C. s. var. xishuangbannesis) reduces fruit elongation but promotes radial growth resulting in shorter but wider fruit, which seems to be due to reduced cell length, but increased cellular layers. Consistent with this, the NIL carrying the homozygous XIS allele (fs5.2) had lower auxin/IAA contents in both the ovary and the developing fruit. Fine genetic mapping with NIL-derived segregating populations placed FS5.2 into a 95.5 kb region with 15 predicted genes, and a homolog of the Arabidopsis CRABS CLAW (CsCRC) appeared to be the most possible candidate for FS5.2. Transcriptome profiling of NIL fruits at anthesis identified differentially expressed genes enriched in the auxin biosynthesis and signaling pathways, as well as genes involved in cell cycle, division, and cell wall processes. We conclude that the major-effect QTL FS5.2 controls cucumber fruit size/shape through regulating auxin-mediated cell division and expansion for the lateral and longitudinal fruit growth, respectively. The gibberellic acid (GA) signaling pathway also plays a role in FS5.2-mediated fruit elongation.

Construction of a Quantitative Genomic Map, Identification and Expression Analysis of Candidate Genes for Agronomic and Disease-Related Traits in Brassica napus

Rapeseed is the second most important oil crop in the world. Improving seed yield and seed oil content are the two main highlights of the research. Unfortunately, rapeseed development is frequently affected by different diseases. Extensive research has been made through many years to develop elite cultivars with high oil, high yield, and/or disease resistance. Quantitative trait locus (QTL) analysis has been one of the most important strategies in the genetic deciphering of agronomic characteristics. To comprehend the distribution of these QTLs and to uncover the key regions that could simultaneously control multiple traits, 4,555 QTLs that have been identified during the last 25 years were aligned in one unique map, and a quantitative genomic map which involved 128 traits from 79 populations developed in 12 countries was constructed. The present study revealed 517 regions of overlapping QTLs which harbored 2,744 candidate genes and might affect multiple traits, simultaneously. They could be selected to customize super-rapeseed cultivars. The gene ontology and the interaction network of those candidates revealed genes that highly interacted with the other genes and might have a strong influence on them. The expression and structure of these candidate genes were compared in eight rapeseed accessions and revealed genes of similar structures which were expressed differently. The present study enriches our knowledge of rapeseed genome characteristics and diversity, and it also provided indications for rapeseed molecular breeding improvement in the future.

Mapping of seed quality traits in the C genome of Brassica napus by using a population carrying genome content of B. oleracea and their effect on other traits

Increasing seed oil and protein contents and reducing the content of seed glucosinolates (GSLs) in Brassica oilseed crops are important objectives in breeding. By using an oilseed rape (B. napus L.) doubled-haploid (DH) population carrying genome content introgressed from Chinese kale (B. oleracea L.), we mapped quantitative trait loci (QTL) for these seed quality traits and investigated their effect on other traits including seed yield. A stable QTL for seed oil content was identified on chromosome C5 at 40-42 Mb position and a QTL for seed GSL content was identified on C9 at 7-8 Mb position. The C5 and C9 QTL alleles for high oil and GSL contents were derived from Chinese kale, demonstrating that high-oil QTL allele can be found in the parental species of oilseed rape. The low-GSL QTL allele of C9 exerted a significant positive effect on seed protein content, demonstrating that selection for this QTL allele contributed to higher protein content in canola seed. These two QTL were not affected by field environmental conditions and did not exert a significant effect on days to flowering and seed yield. Thus, the genomic regions and the molecular markers identified in this study should be useful in molecular breeding of the seed quality traits in oilseed rape.

Stable and novel QTL identification and new insights into the genetic networks affecting seed fiber traits in Brassica napus

QTL mapping for fiber-related traits and elucidation of a stable and novel QTL affecting seed lignin content, cellulose content and seed oil content. Dissection of the genetic networks for fiber biosynthesis is important for improving the seed oil content and meal value of Brassica napus. In this study, the genetic basis of seed fiber biosynthesis in B. napus was investigated via quantitative trait locus (QTL) analysis using a doubled haploid population derived from 'KenC-8' crossed with 'N53-2.' Seed lignin content (LC), cellulose content (CC) and hemicellulose content (HC) were significantly negatively correlated with seed oil content (OC). Co-localization QTLs among LC, CC, HC and OC on A09 were found with contributions ranging from 9.87 to 48.50%. Seven co-localization QTLs involved in the fiber component and OC were further verified by bulked segregant analysis (BSA). The unique QTL uqA9-12 might be a real and new QTL that was commonly identified by QTL mapping and BSA and simultaneously affected LC, CC and OC with opposite additive effects. A potential regulatory network controlling seed fiber biosynthesis was constructed to dissect the complex mechanism of seed fiber and oil accumulation, and numerous candidate genes were identified in the fiber-related QTL regions. These results provided an enrichment of QTLs and potential candidates for fiber biosynthesis, as well as useful new information for understanding the complex genetic mechanism underlying rapeseed seed fiber accumulation.

Synteny analysis of genes and distribution of loci controlling oil content and fatty acid profile based on QTL alignment map in Brassica napus

Background

Deciphering the genetic architecture of a species is a good way to understand its evolutionary history, but also to tailor its profile for breeding elite cultivars with desirable traits. Aligning QTLs from diverse population in one map and utilizing it for comparison, but also as a basis for multiple analyses assure a stronger evidence to understand the genetic system related to a given phenotype.

Results

In this study, 439 genes involved in fatty acid (FA) and triacylglycerol (TAG) biosyntheses were identified in Brassica napus. B. napus genome showed mixed gene loss and insertion compared to B. rapa and B. oleracea, and C genome had more inserted genes. Identified QTLs for oil (OC-QTLs) and fatty acids (FA-QTLs) from nine reported populations were projected on the physical map of the reference genome “Darmor-bzh” to generate a map. Thus, 335 FA-QTLs and OC-QTLs could be highlighted and 82 QTLs were overlapping. Chromosome C3 contained 22 overlapping QTLs with all trait studied except for C18:3. In total, 218 candidate genes which were potentially involved in FA and TAG were identified in 162 QTLs confidence intervals and some of them might affect many traits. Also, 76 among these candidate genes were found inside 57 overlapping QTLs, and candidate genes for oil content were in majority (61/76 genes). Then, sixteen genes were found in overlapping QTLs involving three populations, and the remaining 60 genes were found in overlapping QTLs of two populations. Interaction network and pathway analysis of these candidate genes indicated ten genes that might have strong influence over the other genes that control fatty acids and oil formation.

Conclusion

The present results provided new information for genetic basis of FA and TAG formation in B. napus. A map including QTLs from numerous populations was built, which could serve as reference to study the genome profile of B. napus, and new potential genes emerged which might affect seed oil. New useful tracks were showed for the selection of population or/and selection of interesting genes for breeding improvement purpose.

Electronic supplementary material

The online version of this article (10.1186/s12864-017-4176-6) contains supplementary material, which is available to authorized users.

Genetic dissection of seed oil and protein content and identification of networks associated with oil content in Brassica napus

High-density linkage maps can improve the precision of QTL localization. A high-density SNP-based linkage map containing 3207 markers covering 3072.7 cM of the Brassica napus genome was constructed in the KenC-8 × N53-2 (KNDH) population. A total of 67 and 38 QTLs for seed oil and protein content were identified with an average confidence interval of 5.26 and 4.38 cM, which could explain up to 22.24% and 27.48% of the phenotypic variation, respectively. Thirty-eight associated genomic regions from BSA overlapped with and/or narrowed the SOC-QTLs, further confirming the QTL mapping results based on the high-density linkage map. Potential candidates related to acyl-lipid and seed storage underlying SOC and SPC, respectively, were identified and analyzed, among which six were checked and showed expression differences between the two parents during different embryonic developmental periods. A large primary carbohydrate pathway based on potential candidates underlying SOC- and SPC-QTLs, and interaction networks based on potential candidates underlying SOC-QTLs, was constructed to dissect the complex mechanism based on metabolic and gene regulatory features, respectively. Accurate QTL mapping and potential candidates identified based on high-density linkage map and BSA analyses provide new insights into the complex genetic mechanism of oil and protein accumulation in the seeds of rapeseed.

Seed Quality Traits Can Be Predicted with High Accuracy in Brassica napus Using Genomic Data

Improving seed oil yield and quality are central targets in rapeseed (Brassica napus) breeding. The primary goal of our study was to examine and compare the potential and the limits of marker-assisted selection and genome-wide prediction of six important seed quality traits of B. napus. Our study is based on a bi-parental population comprising 202 doubled haploid lines and a diverse validation set including 117 B. napus inbred lines derived from interspecific crosses between B. rapa and B. carinata. We used phenotypic data for seed oil, protein, erucic acid, linolenic acid, stearic acid, and glucosinolate content. All lines were genotyped with a 60k SNP array. We performed five-fold cross-validations in combination with linkage mapping and four genome-wide prediction approaches in the bi-parental population. Quantitative trait loci (QTL) with large effects were detected for erucic acid, stearic acid, and glucosinolate content, blazing the trail for marker-assisted selection. Despite substantial differences in the complexity of the genetic architecture of the six traits, genome-wide prediction models had only minor impacts on the prediction accuracies. We evaluated the effects of training population size, marker density and phenotyping intensity on the prediction accuracy. The prediction accuracy in the independent and genetically very distinct validation set still amounted to 0.14 for protein content and 0.17 for oil content reflecting the utility of the developed calibration models even in very diverse backgrounds.

Identification of QTLs associated with oil content in a high-oil Brassica napus cultivar and construction of a high-density consensus map for QTLs comparison in B. napus

Increasing seed oil content is one of the most important goals in breeding of rapeseed (B. napus L.). To dissect the genetic basis of oil content in B. napus, a large and new double haploid (DH) population containing 348 lines was obtained from a cross between 'KenC-8' and 'N53-2', two varieties with >10% difference in seed oil content, and this population was named the KN DH population. A genetic linkage map consisting of 403 markers was constructed, which covered a total length of 1783.9 cM with an average marker interval of 4.4 cM. The KN DH population was phenotyped in eight natural environments and subjected to quantitative trait loci (QTL) analysis for oil content. A total of 63 identified QTLs explaining 2.64-17.88% of the phenotypic variation were identified, and these QTLs were further integrated into 24 consensus QTLs located on 11 chromosomes using meta-analysis. A high-density consensus map with 1335 marker loci was constructed by combining the KN DH map with seven other published maps based on the common markers. Of the 24 consensus QTLs in the KN DH population, 14 were new QTLs including five new QTLs in A genome and nine in C genome. The analysis revealed that a larger population with significant differences in oil content gave a higher power detecting new QTLs for oil content, and the construction of the consensus map provided a new clue for comparing the QTLs detected in different populations. These findings enriched our knowledge of QTLs for oil content and should be a potential in marker-assisted breeding of B. napus.