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) 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.

Trade‐offs between root‐secreted acid phosphatase and root morphology traits, and their contribution to phosphorus acquisition in Brassica napus

“…RFW, SAP and total SAP were used to cluster genotypes into three different classes: (1) high RFW but low SAP, (2) high SAP but low RFW, and (3) low RFW and SAP (Figure 1A). In addition, the differences in seed yield under P‐deficient soil among the three classes were compared according to the data provided by Liu et al (2023).…”

“…Seeds were germinated for six days and then transferred to a nutrient solution without Pi for five days. The SY data were provided by Liu et al (2023). Significant difference based on Duncan's post‐hoc analysis at P < 0.05.…”

“…A total of 54 plants were grown in each pot containing 11 L nutrient solution and all the plants were cultivated in a greenhouse with a 16 h / 8 h (light/dark) at 22 C. RFW, SAP and total SAP were used to cluster genotypes into three different classes: (1) high RFW but low SAP, (2) high SAP but low RFW, and (3) low RFW and SAP (Figure 1A). In addition, the differences in seed yield under P-deficient soil among the three classes were compared according to the data provided by Liu et al (2023). Significant difference based on Duncan's post-hoc analysis at P < 0.05.…”

“…Brassica napus is one of the most important and profitable oil crops in the world (Angelovič et al, 2013), but it is sensitive to low soil P availability (Ding et al, 2012; Duan et al, 2020; Shi et al, 2013; Yuan et al, 2016). Root morphology traits of B. napus in response to low P availability have been well studied (Duan et al, 2021; Li et al, 2022; Wang et al, 2017; Xu et al, 2022; Xu et al, 2023; Yang et al, 2010), and wide genotype variations in root morphology traits and seed yield (SY) are reported among a large association panel of B. napus with diverse genetic backgrounds under P‐deficient conditions (Wang et al, 2017; Liu et al, 2023). Recently, Duan et al (2020) report that rhizosphere APase activity of B. napus increased from the leaf development stage to pod development in soils with low P availability, especially during the leaf development stage.…”

“…Total SAP, total root secreted APase activity per plant; SAP, root secreted APase activity per root fresh weight; RFW, root fresh weight; SY, seed yield. The SY data were provided by Liu et al (2023). Table S2.…”