Genome‐Wide Association Studies of Important Agronomic Traits in Brassica napus : What We Have Learned and Where We Are Headed

Abstract

Oilseed rape ( Brassica napus L.; B. napus ) is one of the main oil crops in China as well as in the world. Genome‐wide association studies (GWAS) have revolutionised the field of complex agronomic traits. In B. napus, these include seed yield and yield‐related traits, seed oil content, and abiotic and biotic stress‐tolerance traits over the past decade in which hundreds of thousands to millions of genetic variants across the genomes of hundreds of individuals have been tested to identify genotype–phenotype associations. In this review, we assess the current status of GWAS in terms of genotypes, phenotypes, statistical models, and candidate genes for these agronomic traits in B. napus . Post‐GWAS, the combination of QTL mapping, transcriptomics, and new statistical methods, has allowed us to identify candidate genes associated with specific agronomic traits. In addition, we can use diverse populations, increase the population size, or look for rare variants and structural variations of B. napus by whole‐genome sequencing to minimise the ‘missing heritability’ effects. These approaches are essential for uncovering the genetic mechanisms defining or regulating complex agronomic traits and the delivery of molecular marker‐assisted breeding in B. napus to breed new varieties that are higher yielding but resilient to our changing climate.

Integrating genome-wide association studies with selective sweep reveals genetic loci associated with tolerance to low phosphate availability in Brassica napus

“…Genetic architecture of LP tolerance traits Compared with linkage analysis, association analysis has the advantages of no need to construct mapping groups and high analysis accuracy (Liu et al 2022). In this study, through GWAS with highdensity SNP markers, 68 SNPs were signi cantly associated with SY_LP, which could explain 6.17%-10.55% of the phenotypic variation (Supplementary Table 3).…”

“…Compared with other crops, the LD value of B. napus is relatively large, which leads to the linkage disequilibrium region of signi cant SNPs containing hundreds of genes, making it extremely di cult to identify the real candidate genes (Zhang et al 2022). Therefore, GWAS combined with transcriptome sequencing to mine new candidate genes has become a common method (Liu et al 2022). In this study, two reliable SNP cluster (chrC07: 17114844-17116381; chrC09: 17114844-17116381) were identi ed on C07 and C09 chromosome, and two genes (BnaC07.ARF9 and BnaC09.PHT1;2) signi cantly induced by P de ciency were identi ed by GWAS combined with previous transcriptome data, respectively (Fig.…”

“…GWAS has become a common method for identifying candidate genes in B. napus (Liu et al 2022). For example, BnaTT8, a gene that controls seed coat content has been identi ed by GWAS combined with transcriptome sequencing, and the seed coat content of BnaTT8 knockout mutants was signi cantly lower than that of the wild type (Zhang et al 2022).…”

Genome-wide association study identifies new loci for 1000-seed weight in Brassica napus L

“…The physical intervals for QTLs are usually very large, which makes it di cult to identify candidate genes (Xiao et al 2017;Liu et al 2022). So far, only two genes (BnaA09.ARF18 and BnaA9.CYP78A9) controlling SW have been cloned in B. napus using linkage analysis (Liu et al 2015;Shi et al 2019).…”

Genome-wide association study identifies candidate genes and favorable haplotypes for seed yield in Brassica napus

“…Compared with linkage analysis, GWAS has the advantages of high positioning accuracy without constructing mapping population (Xiao et al, 2017;Liu et al, 2022). GWAS has been widely applied to the genetic dissection of seed (grain) yield in different crops, such as rice (Zhong et al, 2021), maize (Ma and Cao, 2021), oil palm (Kalyana et al, 2021), wheat (Garcia et al, 2019), soybean (Hu et al, 2020) and cotton (Zhu et al, 2021).…”