Mapping loci controlling fatty acid profiles, oil and protein content by genome-wide association study in Brassica napus

Optimizing the profile and quantity of fatty acids in rapeseed(Brassica napus L.) is critical for maximizing the value of edible oil and biodiesel. However, selection of these complex seed quality traits is difficult before haplotypes controlling their contents are identified. To efficiently identify genetic loci influencing these traits and underlying candidate genes and networks, we performed a genome-wide association study(GWAS) of eight seed quality traits(oil and protein content, palmitic, stearic, oleic, linoleic, eicosenoic and erucic acids content). The GWAS population comprised 370 diverse accessions, which were phenotyped in five environments and genotyped using 60K SNP arrays. The results indicated that oil and protein contents generally showed negative correlations, while fatty acid contents showed positive or negative correlations,with palmitic and erucic acid contents directly affecting oil content. Seven SNPs on five chromosomes were associated with both seed oil and protein content, and five genes orthologous to genes in Arabidopsis thaliana were predicted as candidates. From resequencing data, besides known haplotypes in Bna A.FAE1.a and Bna C.FAE1.a, three accessions harboring a new haplotype conferring moderate erucic acid content were identified. Interestingly, in a haplotype block, one haplotype was associated with high palmitic acid content and low oil content, while the others showed the reverse effects. This finding was consistent with a negative correlation between palmitic acid and oil contents, suggesting historical selection for high oil content. The identification by this study of genetic variation and complex correlations of eight seed quality traits may be beneficial for crop selection strategies.

Development and application of molecular markers for TSW(thousand-seed weight)related gene BnaGRF7.C02 in Brassica napus

Brassica napus L(rapeseed)is one of the most important oil crops with large cultivated area in China.Seed size and seed weight play crucial roles for yield and harvest.In this study,a type of 15 bp-deletion in BnaGRF7.CO2 coding region was identified through sequence alignment of BnaGRF7.C02 in 42 rapeseed varieties,and associ-ation analysis indicated that the 15 bp-deletion was related to the rapeseed Thousand-Seed Weight(TSW)phenotype.Furthermore,we developed two InDel markers to identify this 15 bp InDel.The tissue-specific expression patterns showed that BnaGRF7.C02 prominently expressed in the late stage of seed development.These findings may assist in InDel markers-based breeding efforts to select higher TWS varieties and improve the crop yield of B.nqpus.

BnaOmics:A comprehensive platform combining pan-genome and multi-omics data from Brassica napus

Dear Editor,Brassica napus was originally formed7500 years ago by the interspecific hybridization of B.rapa and B.oleracea(Chalhoub et al.,2014).It accounts for approximately 13%–16%of global vegetable oil production and provides an excellent model for polyploid genomics and evolutionary research in plants.Currently,the Brassicaceae Database(BRAD V3.0;Chen et al.,2022),Genoscope(https://www.genoscope.cns.fr/brassicanapus/),and Ensembl Plants(https://plants.ensembl.org)are used for genomic research pertaining to B.napus.However,they only provide genome browsers for research into the B.napus cultivar Darmorbzh.The B.napus pan-genome information resource(BnPIR)also provides eight B.napus reference genomes(Song et al.,2021),gene information,and resequencing data.The B.napus variation information resource(BnVIR)provides information on genetic variation,including single-nucleotide polymorphisms(SNPs),insertions or deletions(INDELs),and structural variations(SVs)(Yang et al.,2022).

Syntenic quantitative trait loci and genomic divergence for Sclerotinia resistance and ?owering time in Brassica napus

Oilseed rape(Brassica napus) is an allotetraploid with two subgenomes descended from a common ancestor. Accordingly, its genome contains syntenic regions with many duplicate genes, some of which may have retained their original functions, whereas others may have diverged. Here, we mapped quantitative trait loci(QTL) for stem rot resistance(SRR), a disease caused by the fungus Sclerotinia sclerotiorum, and flowering time(FT) in a recombinant inbred line population. The population was genotyped using B.napus 60 K single nucleotide polymorphism arrays and phenotyped in six(FT) and nine(SSR) experimental conditions or environments. In total, we detected 30 SRR QTL and 22 FT QTL and show that some of the major QTL associated with these two traits were co-localized,suggesting a genetic linkage between them. Two SRR QTL on chromosome A2 and two on chromosome C2 were shown to be syntenic, suggesting the functional conservation of these regions. We used the syntenic properties of the genomic regions to exclude genes for selection candidates responsible for QTL-associated traits. For example, 152 of the 185 genes could be excluded from a syntenic A2–C2 region. These findings will help to elucidate polyploid genomics in future studies, in addition to providing useful information for B. napus breeding programs.