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

Abstract

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) identi ed 68 SNPs signi cantly 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 identi ed as candidate genes of them, respectively, by combine GWAS with quantitative reverse-transcription PCR (qRT-PCR). There were signi cant differences in the gene expression level of BnaC07.ARF9 and BnaC09.PHT1;2 between P -e cient and -ine ciency varieties at LP. SY_LP had a signi cant 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 ndings provide novel insights into the molecular targets for breeding P e ciency varieties in B. napus.