Eight high-quality genomes reveal pan-genome architecture and ecotype differentiation of Brassica napus

Abstract

Rapeseed (Brassica napus) is the second most important oilseed crop in the world but the genetic diversity underlying its massive phenotypic variations remains largely unexplored. Here, we report the sequencing, de novo assembly and annotation of eight B. napus accessions. Using pan-genome comparative analysis, millions of small variations and 77.2–149.6 megabase presence and absence variations (PAVs) were identified. More than 9.4% of the genes contained 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), demonstrating that PAV-GWAS was complementary to SNP-GWAS in identifying associations to traits. Further analysis showed that PAVs in three FLOWERING LOCUS C genes were closely related to flowering time and ecotype differentiation. This study provides resources to support a better understanding of the genome architecture and acceleration of the genetic improvement of B. napus.

Comparison of Read Mapping and Variant Calling Tools for the Analysis of Plant NGS Data

“…To allow for a consistent comparison of baseline performance, we used default parameters for all tools as these parameters are frequently chosen in plant science applications [4,5,9]. Sequence read datasets from different sequencing platforms, with different read lengths, and different sizes were processed to ensure a realistic benchmarking of tools.…”

“…As the number of high-quality reference genome sequences rises continuously, the number of re-sequencing projects increases as well [2]. There are pangenome projects for various species focusing on the genome evolution [3][4][5] and mapping-by-sequencing projects which focus on agronomically important traits of crops [6][7][8][9].…”

The impact of transposable elements on tomato diversity

“…While genomics-enabled genetics has revolutionized our ability to identify loci underlying domestication and improvement traits in virtually any crop [4][5][6] , our understanding of the genetic basis of crop diversity is still limited. This situation stems in part from the fact that, with few notable exceptions [7][8][9][10][11] , most genome wide association studies (GWAS) consider only single nucleotide polymorphisms (SNPs) and short indels 12,13 , when structural variants, which include gene presence/absence variants, account for the largest amount of DNA sequence differences between individuals and cultivars 3,10,11,14 . Furthermore, the majority of structural variants result from the mobilization of transposable elements (TEs), which by themselves are potentially an important source of large effect alleles 15 .…”

Comparison of read mapping and variant calling tools for the analysis of plant NGS data

“…To allow for a consistent comparison of baseline performance, we used default parameters for all tools as these parameters are frequently chosen in plant science applications 4,5,9 . Sequence read data sets from different sequencing platforms, with different read lengths, and different sizes were processed to ensure a realistic benchmarking of tools.…”