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

Haijiang Liu; Yuan Pan; Rui Cui; John P Hammond; Philip J White; Yuting Zhang; Maoyan Zou; Guangda Ding; Sheliang Wang; Hongmei Cai; Fangsen Xu; Lei Shi

doi:10.1007/s11032-023-01399-9

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

Mol Breed. 2023 Jun 16;43(7):53. doi: 10.1007/s11032-023-01399-9. eCollection 2023 Jul.

Authors

Haijiang Liu^{1

2}, Yuan Pan^{1

2}, Rui Cui^{1

2}, John P Hammond³, Philip J White^{1

4}, Yuting Zhang¹, Maoyan Zou^{1

2}, Guangda Ding^{1

2}, Sheliang Wang^{1

2}, Hongmei Cai², Fangsen Xu^{1

2}, Lei Shi^{1

2}

Affiliations

¹ National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070 China.
² Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan, 430070 China.
³ School of Agriculture, Policy and Development, University of Reading, Reading, RG6 6AR UK.
⁴ The James Hutton Institute, Dundee, UK.

PMID: 37333997
PMCID: PMC10275852 (available on 2024-06-16)
DOI: 10.1007/s11032-023-01399-9

Abstract

Oilseed rape (Brassica napus L.; B. napus) is an important oil crop worldwide. However, the genetic mechanisms 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, and 7 SNPs significantly associated with phosphorus efficiency coefficient (PEC) 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 combining 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.

Supplementary information: The online version contains supplementary material available at 10.1007/s11032-023-01399-9.

Keywords: BnaC07.ARF9; BnaC09.PHT1;2; Brassica napus; Genome-wide association study; Phosphorus efficiency; Selective sweep.

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