Oilseed rape (Brassica napus L.; B. napus) is an important oil crop around the world. However, the genetic mechanism of B. napus adaptations to low phosphate (P) stress are largely unknown. In this study, a genome-wide association study (GWAS) identified 68 SNPs significantly associated with seed yield (SY) under low P (LP) availability in two trials. Among these SNPs, two, chrC07__39807169 and chrC09__14194798, were co-detected in two trials, and BnaC07.ARF9 and BnaC09.PHT1;2 were identified as candidate genes of them, respectively, by combine GWAS with quantitative reverse-transcription PCR (qRT-PCR). There were significant differences in the gene expression level of BnaC07.ARF9 and BnaC09.PHT1;2 between P -efficient and -inefficiency varieties at LP. SY_LP had a significant positive correlation with the gene expression level of both BnaC07.ARF9 and BnaC09.PHT1;2. BnaC07.ARF9 and BnaA01.PHR1 could directly bind the promoters of BnaA01.PHR1 and BnaC09.PHT1;2, respectively. Selective sweep analysis was conducted between ancient and derived B. napus, and detected 1280 putative selective signals. Within the selected region, a large number of genes related to P uptake, transport and utilization were detected, such as purple acid phosphatase (PAP) family genes and phosphate transporter (PHT) family genes. These findings provide novel insights into the molecular targets for breeding P efficiency varieties in B. napus.

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Oilseed rape (Brassica napus L.) is one of the most essential oil crops. Genetic improvement of seed yield (SY) is a major aim of B. napus breeding. Several studies have been reported the genetic mechanisms of SY of B. napus. Here, a genome-wide association study (GWAS) of SY was conducted using a panel of 403 natural accessions of B. napus, with more than ve million high-quality single nucleotide polymorphisms (SNPs). A total of 1773 signi cant SNPs were detected associated with SY and 783 signi cant SNPs were co-located with previously reported QTLs. The lead SNPs chrA01__8920351 and chrA02__4555979 were jointly detected in Trial 2_2 and Trial 2_mean value, and in Trial 1_2 and Trial 1_mean value, respectively. Subsequently, two candidate genes of BnaA01g17200D and BnaA02g08680D were identi ed by combining transcriptome, candidate gene association analysis and haplotype analysis. BnaA09g10430D detected through lead SNP chrA09__5160639 was associated with SY of B. napus. Our results provide valuable information for studying the genetic control of seed yield in B. napus and can provide valuable genes, haplotypes and cultivars resources for the breeding of high seed yield B. napus cultivars.