National Key Lab of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China.
Key Lab of Cultivated Land Conservation, Ministry of Agriculture and Rural Affairs/Microelement Research Centre, Huazhong Agricultural University, Wuhan 430070, China.
Ann Bot. 2021 Nov 9;128(7):919-930. doi: 10.1093/aob/mcab115.
Oilseed 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.
An 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.
A 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.
Our 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.
油菜（甘蓝型油菜）是全球最重要的油料作物之一。磷（P）缺乏严重降低油菜的株高和分枝数。然而，P 缺乏下控制油菜株高和分枝数的遗传基础在很大程度上仍然未知。本研究旨在通过全基因组关联研究（GWAS）挖掘与株高和分枝数相关的候选基因，并确定低 P 耐性的单倍型。
利用油菜关联群体在田间进行低 P 供应（P，0 kg ha-1）和高 P 供应（P，40 kg ha-1）的两年试验，调查株高和分枝数。利用超过 500 万个单核苷酸多态性（SNP）对两个不同 P 供应下的株高和分枝数进行 GWAS。
共发现 2127 个 SNP 与两个 P 供应下的株高和分枝数显著相关（P < 6.25 × 10-07）。在染色体 A10（chrA10_821671）和 C08（chrC08_27999846）上与关联位点的有利等位基因数量的表型变异之间存在显著相关性，这将有助于通过聚集这些 SNP 来进行育种改良。鉴定出 BnaA10g09290D 和 BnaC08g26640D 与 chrA10_821671 和 chrC08_27999846 相关。候选基因关联分析和单倍型分析表明，在低 P 供应下，携带 BnaA10g09290Hap1 上的 ATT 和 BnaC08g26640Hap1 上的 AAT 的自交系比携带其他单倍型等位基因的系具有更高的株高。
本研究结果表明 GWAS 能够在油菜中鉴定出感兴趣的基因，并为油菜在低 P 供应下株高和分枝数的遗传基础提供了新的见解。候选基因和有利单倍型可能有助于旨在提高油菜 P 利用效率的标记辅助育种工作。
