Genome-wide association study dissects the genetic control of plant height and branch number in response to low-phosphorus stress in Brassica napus |
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| Authors: | Haijiang Liu Jingchi Wang Bingbing Zhang Xinyu Yang John P Hammond Guangda Ding Sheliang Wang Hongmei Cai Chuang Wang Fangsen Xu Lei Shi |
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| Institution: | 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. Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia |
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| Abstract: | Background and AimsOilseed rape (Brassica napus) is one of the most important oil crops worldwide. Phosphorus (P) deficiency severely decreases the plant height and branch number of B. napus. However, the genetic bases controlling plant height and branch number in B. napus under P deficiency remain largely unknown. This study aims to mine candidate genes for plant height and branch number by genome-wide association study (GWAS) and determine low-P-tolerance haplotypes.MethodsAn association panel of B. napus was grown in the field with a low P supply (P, 0 kg ha−1) and a sufficient P supply (P, 40 kg ha−1) across 2 years and plant height and branch number were investigated. More than five million single-nucleotide polymorphisms (SNPs) were used to conduct GWAS of plant height and branch number at two contrasting P supplies.Key ResultsA total of 2127 SNPs were strongly associated (P < 6·25 × 10−07) with plant height and branch number at two P supplies. There was significant correlation between phenotypic variation and the number of favourable alleles of associated loci on chromosomes A10 (chrA10_821671) and C08 (chrC08_27999846), which will contribute to breeding improvement by aggregating these SNPs. BnaA10g09290D and BnaC08g26640D were identified to be associated with chrA10_821671 and chrC08_27999846, respectively. Candidate gene association analysis and haplotype analysis showed that the inbred lines carrying ATT at BnaA10g09290Hap1 and AAT at BnaC08g26640Hap1 had greater plant height than lines carrying other haplotype alleles at low P supply.ConclusionOur results demonstrate the power of GWAS in identifying genes of interest in B. napus and provided insights into the genetic basis of plant height and branch number at low P supply in B. napus. Candidate genes and favourable haplotypes may facilitate marker-based breeding efforts aimed at improving P use efficiency in B. napus. |
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| Keywords: | Oilseed rape genome wide association study plant height branch number low phosphorus supply haplotype analysis |
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