Rapeseed (Brassica napus L.), also known as rape, or oilseed rape, is the second most important oilseed crop in the world. It is an allotetraploid crop with a complex genome; extensive genomic and phenotypic variation exists among different accessions and ecotypes. Genome sequencing is a unique resource that provides a valuable resource for understanding the origins and improvement history of rapeseed and will help dissect the genetic basis of important agronomically complex traits. Important single nucleotide polymorphisms (SNPs) associated with favorable variants, selection signals, and candidate genes will become valuable resources to further improve the yield, seed quality, oil content, and adaptability of this latest allopolyploid crop and its relatives.

CD Genomics is a leading service provider for agricultural genomics research, offering reliable rapeseed genome sequencing services to support research and breeding efforts in the field of rapeseed genomics for clients worldwide. Our services help improve oil content and composition, resistance to pathogens, cold tolerance, yield, and even nitrogen use efficiency of rapeseed varieties.

Our rapeseed genome sequencing service

CD Genomics offers comprehensive and customizable rapeseed genome sequencing services using cutting-edge technology and expertise to characterize the rapeseed genome at the cytogenetic, genetic, and molecular levels. Our services cover all stages of the sequencing process, from library preparation to data analysis, ensuring high-quality and accurate results.

With our advanced next-generation sequencing and long-read sequencing technology platforms, as well as bioinformatics tools, we provide high-quality whole-genome sequencing data for rapeseed to meet the diverse needs of researchers and breeders. Our rapeseed genome sequencing services are designed to address the complexity of the rapeseed genome and provide researchers with valuable insights into its structure and function.

What we offer

CD Genomics can sequence, de novo assemble, and annotate the whole genome of over 500 rapeseed species. Our workflow involves several key steps:

• Sample preparation

We begin by extracting high-quality genomic DNA from rapeseed samples. This critical step ensures that the DNA is intact and free of contaminants, resulting in reliable sequencing results.

• Library construction

We generate libraries by fragmenting genomic DNA and attaching specific sequencing connectors. These libraries are quality-controlled to ensure optimal sequencing performance.

• Sequencing

The libraries are then subjected to high-throughput sequencing using state-of-the-art sequencing platforms. Our NGS technology (e.g. Illumina sequencing) generates millions of short reads covering the entire rapeseed genome.

• Data analysis

Raw sequencing data undergoes a series of bioinformatics analyses to filter out low-quality reads, perform read comparisons, and assemble the rapeseed genome. Our team of bioinformaticians utilizes cutting-edge algorithms and software tools to ensure accurate and comprehensive genome assembly.

Our experts can construct linkage maps based on recombination data from rapeseed mapping populations that show the distances between loci and their order on chromosomes. These linkage maps are based on a range of marker systems such as restriction fragment length polymorphisms (RFLP), random amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLP), simple sequence repeats (SSR), sequence tagged sites (STS), sequence-related amplified polymorphisms (SRAP), SNPs, and diversity array technology (DArT).

We also utilize the information gathered from whole genome resequencing of these breeds for genomic variation, genome-wide selection, and genome-wide association studies. We aim to help you determine which possible genes and associated loci are responsible for specific agronomic traits, including genes associated with morphological traits, stress and disease resistance, growth period, yield composition, and seed quality.

Applications of rapeseed genome sequencing

• Genetic variation and diversity analysis

Rapeseed genome sequencing can identify and analyze genetic variation within kale-type rapeseed populations. By comparing the genomes of different rapeseed varieties, researchers can identify variants such as SNPs and insertions/deletions (indel).

• Trait mapping and selection

The availability of rapeseed genome sequences has enabled researchers to map and identify genomic regions associated with important agronomic traits. By associating specific genetic markers with phenotypic traits of interest, breeders can speed up the breeding process.

• Comparative genomics

Comparative analysis between rapeseed genomes allows the identification of conserved genomic regions and evolutionary relationships.

• Gene discovery and functional annotation

Rapeseed genome sequences help researchers identify and annotate genes involved in various biological processes and metabolic pathways.

• Breeding and crop improvement

The availability of rapeseed genome sequences accelerates the identification and selection of candidate genes associated with desired genes for characterization. Breeders can use this information to develop molecular markers for marker-assisted selection, leading to more efficient and precise breeding efforts.

Case study of rapeseed genome sequencing

Rapeseed is the second most important oil crop in the world, but the genetic diversity underlying its large phenotypic variation remains largely unexplored. The researchers used advanced sequencing technologies, including PacBio SMRT, Hi-C, and BioNano data integration, to generate eight high-quality genomes. This study provides a resource for better understanding the genome structure of Brassica napus and accelerating genetic improvement.

• Using pan-genome comparative analysis, millions of small variants and 77.2-149.6 megabase presence and absence variants (PAVs) were identified. More than 9.4% of genes contain large-effect mutations or structural variations.
• PAV-based genome-wide association study (PAV-GWAS) directly identified causal structural variations for silique length, seed weight and flowering time in a nested association mapping population with ZS11 (reference line) as the donor, which were not detected by single-nucleotide polymorphisms-based GWAS (SNP-GWAS).
• Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation.

Fig. 1. Features of the B. napus genome. (Song et al., 2020)

CD Genomics offers cutting-edge rapeseed genome sequencing services to provide comprehensive genomic information to researchers and breeders for their studies. We aim to provide data to support basic research on the genetics of important rapeseed traits and to promote rapeseed improvement. If you are interested, please feel free to contact us.

Reference

1. Song, Jia-Ming, et al. Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus. Nature Plants. 6.1 (2020): 34-45.