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

Liu, H., Pan, Y., Cui, R., Hammond, J. P. ORCID: https://orcid.org/0000-0002-6241-3551, White, P. J., Zhang, Y., Zou, M., Ding, G., Wang, S., Cai, H., Xu, F. and Shi, L. ORCID: https://orcid.org/0000-0002-5312-8521 (2023) Integrating genome-wide association studies with selective sweep reveals genetic loci associated with tolerance to low phosphate availability in Brassica napus. Molecular Breeding, 43 (7). 53. ISSN 1380-3743 doi: 10.1007/s11032-023-01399-9

Abstract/Summary

Oilseed rape ( L.; ) is an important oil crop worldwide. However, the genetic mechanisms of 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 and 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 and between P-efficient and -inefficiency varieties at LP. SY_LP had a significant positive correlation with the gene expression level of both and . and could directly bind the promoters of and , respectively. Selective sweep analysis was conducted between ancient and derived , 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. The online version contains supplementary material available at 10.1007/s11032-023-01399-9.

Item Type	Article
URI	https://reading-clone.eprints-hosting.org/id/eprint/112422
Identification Number/DOI	10.1007/s11032-023-01399-9
Refereed	Yes
Divisions	Life Sciences > School of Agriculture, Policy and Development > Department of Crop Science
Uncontrolled Keywords	Phosphorus efficiency, Genome-wide association study, BnaC09.PHT1;2, Brassica napus, BnaC07.ARF9, Selective sweep
Publisher	Springer Verlag
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