A set of additive loci for seed oil content were identified using association mapping and one of the novel loci on the chromosome A5 was validated by linkage mapping. Increasing seed oil content is one of the most important goals in the breeding of oilseed crops including Brassica napus, yet the genetic basis for variations in this important trait remains unclear. By genome-wide association study of seed oil content using 521 B. napus accessions genotyped with the Brassica 60K SNP array, we identified 50 loci significantly associated with seed oil content using three statistical models, the general linear model, the mixed linear model and the Anderson-Darling test. Together, the identified loci could explain approximately 80 % of the total phenotypic variance, and 29 of these loci have not been reported previously. Furthermore, a novel locus on the chromosome A5 that could increase 1.5-1.7 % of seed oil content was validated in an independent bi-parental linkage population. Haplotype analysis showed that the favorable alleles for seed oil content exhibit cumulative effects. Our results thus provide valuable information for understanding the genetic control of seed oil content in B. napus and may facilitate marker-based breeding for a higher seed oil content in this important oil crop.

Stem rot caused by Sclerotinia sclerotiorum in many important dicotyledonous crops, including oilseed rape (Brassica napus), is one of the most devastating fungal diseases and imposes huge yield loss each year worldwide. Currently, breeding for Sclerotinia resistance in B. napus, as in other crops, can only rely on germplasms with quantitative resistance genes. Thus, the identification of quantitative trait locus (QTL) for S. sclerotiorum resistance/tolerance in this crop holds immediate promise for the genetic improvement of the disease resistance. In this study, ten QTLs for stem resistance (SR) at the mature plant stage and three QTLs for leaf resistance (LR) at the seedling stage in multiple environments were mapped on nine linkage groups (LGs) of a whole genome map for B. napus constructed with SSR markers. Two major QTLs, LRA9 on LG A9 and SRC6 on LG C6, were repeatedly detected across all environments and explained 8.54–15.86% and 29.01%–32.61% of the phenotypic variations, respectively. Genotypes containing resistant SRC6 or LRA9 allele showed a significant reduction in disease lesion after pathogen infection. Comparative mapping with Arabidopsis and data mining from previous gene profiling experiments identified that the Arabidopsis homologous gene of IGMT5 (At1g76790) was related to the SRC6 locus. Four copies of the IGMT5 gene in B. napus were isolated through homologous cloning, among which, only BnaC.IGMT5.a showed a polymorphism between parental lines and can be associated with the SRC6. Furthermore, two parental lines exhibited a differential expression pattern of the BnaC.IGMT5.a gene in responding to pathogen inoculation. Thus, our data suggested that BnaC.IGMT5.a was very likely a candidate gene of this major resistance QTL.

Seed weight is an important component of grain yield in oilseed rape (Brassica napus L.), but the genetic basis for the important quantitative trait is still not clear. In order to identify the genes for seed weight in oilseed rape, QTL mapping for thousand seed weight (TSW) was conducted with a doubled haploid (DH) population and an F(2) population. A complete linkage map of the DH population was constructed using 297 simple sequence repeat (SSR) markers. Among nine TSW QTLs detected, two major QTLs, TSWA7a and TSWA7b, were stably identified across years and collectively explained 27.6-37.9% of the trait variation in the DH population. No significant epistatic interactions for TSW detected in the DH population indicate that the seed weight variation may be primarily attributed to additive effects. The stability and significance of TSWA7a and TSWA7b were further validated in the F(2) population with different genetic backgrounds. By cloning BnMINI3a and BnTTG2a, two B. napus homologous genes to Arabidopsis thaliana, allele-specific markers were developed for TSWA5b and TSWA5c, two TSW QTLs on A5, respectively. The importance of the major and minor QTLs identified was further demonstrated by analysis of the allelic effects on TSW in the DH population.

Sclerotinia stem rot (SSR) caused by the necrotrophic fungus Sclerotinia sclerotiorum is a major disease in rapeseed (Brassica napus) worldwide. Breeding for SSR resistance in B. napus, as in other crops, relies only on germplasms with quantitative resistance genes. A better understanding of the genetic basis for SSR resistance in B. napus thus holds promise for the genetic improvement of disease resistance. In the present study, a genome-wide association study (GWAS) for SSR resistance in B. napus were performed using an association panel of 448 accessions genotyped with the Brassica 60K Infinium® single-nucleotide polymorphism (SNP) array. A total of 26 SNPs corresponding to three loci, DSRC4, DSRC6, and DSRC8 were associated with SSR resistance. Haplotype analysis showed that the three favorable alleles for SSR resistance exhibited cumulative effects. After aligning SSR resistance quantitative trait loci (QTL) identified in the present and previous studies to the B. napus reference genome, one locus (DSRC6) was found to be located within the confidence interval of a QTL identified in previous QTL mapping studies and another two loci (DSRC4 and DSRC8) were considered novel loci for SSR resistance. A total of 39 candidate genes were predicted for the three loci based on the GWAS combining with the differentially expressed genes identified in previous transcriptomics analyses.

An optimized plant architecture (PA) is fundamental for high-yield breeding but the genetic control of the important trait is largely unknown in rapeseed. Here plant architecture factors (PAFs) were proposed to consist of main inflorescence length proportion (MILP), branch height proportion (BHP), and branch segment proportion (BSP). Comparison of different genotypes in a DH population grown in diverse environments showed that an optimized PAF performance with MILP and BHP between 0.3–0.4 was important for high yield potential. In total, 163 unique quantitative trait loci (QTLs) for PA- and plant yield (PY)-related traits were mapped onto a high-density genetic map. Furthermore, 190 PA-related candidate genes for 91 unique PA QTLs and 2350 PY epistatic interaction loci-pairs were identified, which explain 2.8–51.8% and 5.2–23.6% of phenotypic variation, respectively. Three gene categories, transcription factor, auxin/IAA, and gibberellin, comprise the largest proportions of candidate genes for PA-related QTLs. The effectiveness of QTL candidate genes prediction was demonstrated by cloning of three candidate genes, Bna.A02.CLV2, Bna.A09.SLY2, and Bna.C07.AHK4. The study thus outlines a gene network for control of PA-related traits and provides novel information for understanding the establishment of ideal PA and for developing effective breeding strategies for yield improvement in rapeseed and other crops.

No abstract

BackgroundMap-based cloning of quantitative trait loci (QTLs) in polyploidy crop species remains a challenge due to the complexity of their genome structures. QTLs for seed weight in B. napus have been identified, but information on candidate genes for identified QTLs of this important trait is still rare.ResultsIn this study, a whole genome genetic linkage map for B. napus was constructed using simple sequence repeat (SSR) markers that covered a genetic distance of 2,126.4 cM with an average distance of 5.36 cM between markers. A procedure was developed to establish colinearity of SSR loci on B. napus with its two progenitor diploid species B. rapa and B. oleracea through extensive bioinformatics analysis. With the aid of B. rapa and B. oleracea genome sequences, the 421 homologous colinear loci deduced from the SSR loci of B. napus were shown to correspond to 398 homologous loci in Arabidopsis thaliana. Through comparative mapping of Arabidopsis and the three Brassica species, 227 homologous genes for seed size/weight were mapped on the B. napus genetic map, establishing the genetic bases for the important agronomic trait in this amphidiploid species. Furthermore, 12 candidate genes underlying 8 QTLs for seed weight were identified, and a gene-specific marker for BnAP2 was developed through molecular cloning using the seed weight/size gene distribution map in B. napus.ConclusionsOur study showed that it is feasible to identify candidate genes of QTLs using a SSR-based B. napus genetic map through comparative mapping among Arabidopsis and B. napus and its two progenitor species B. rapa and B. oleracea. Identification of candidate genes for seed weight in amphidiploid B. napus will accelerate the process of isolating the mapped QTLs for this important trait, and this approach may be useful for QTL identification of other traits of agronomic significance.

Polyploidy plays a crucial role in plant evolution. Brassica napus (2n = 38, AACC), the most important oil crop in the Brassica genus, is an allotetraploid that originated through natural doubling of chromosomes after the hybridization of its progenitor species, B. rapa (2n = 20, AA) and B. oleracea (2n = 18, CC). A better understanding of the evolutionary relationship between B. napus and B. rapa, B. oleracea, as well as Arabidopsis, which has a common ancestor with these three species, will provide valuable information about the generation and evolution of allopolyploidy. Based on a high-density genetic map with single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers, we performed a comparative genomic analysis of B. napus with Arabidopsis and its progenitor species B. rapa and B. oleracea. Based on the collinear relationship of B. rapa and B. oleracea in the B. napus genetic map, the B. napus genome was found to consist of 70.1% of the skeleton components of the chromosomes of B. rapa and B. oleracea, with 17.7% of sequences derived from reciprocal translocation between homoeologous chromosomes between the A- and C-genome and 3.6% of sequences derived from reciprocal translocation between non-homologous chromosomes at both intra- and inter-genomic levels. The current study thus provides insights into the formation and evolution of the allotetraploid B. napus genome, which will allow for more accurate transfer of genomic information from B. rapa, B. oleracea and Arabidopsis to B. napus.