Genome-wide association study dissects the genetic control of plant height and branch number in response to low-phosphorus stress in Brassica napus

Abstract

Background and aims: 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.

Methods: 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.

Key results: 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.

Conclusion: 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.

Keywords: Oilseed rape; branch number; genome wide association study; haplotype analysis; low phosphorus supply; plant height.

Fig. 1.

The co-localized locus and haplotypes on chromosome A10 associated with PH_LP and PHr of B. napus. (A) Manhattan plot of co-localized locus for PH_LP and PHr in Trial 2_R2 and Trial 2_BLUP. (B) Significant SNPs associated with PH_LP and PHr on chromosome A10. The big red dots represent the significant SNPs. (C) Candidate gene association analysis of BnaA10g09290D with PH_LP. Association of the three alleles in chrA10_8216680 (D), chrA10_8216711 (E) and chrA10_8216756 (F) with PH_LP, respectively. (G) Two haplotypes of BnaA10g09290D. (H) Candidate gene association analysis of BnaA10g09290D with PHr. Association of the three alleles in chrA10_8216680 (I), chrA10_8216711 (J) and chrA10_8216756 (K) with PHr, respectively. (L) Two haplotypes of BnaA10g09290D. The number of inbred lines harbouring the corresponding allele is shown in brackets at the bottom.

Fig. 2.

The co-localized locus and haplotypes on chromosome C08 associated with PHr of B. napus. (A) Manhattan plot of co-localized locus for PHr in Trial 1_R2, Trial 1_R3, Trial 1_BLUP and Trial 2_BLUP. (B) Significant SNP associated with PHr on chromosome C08. The big red dots represent the significant SNPs. (C) Candidate gene association analysis of BnaC08g26640D with PHr. Association of the three alleles in chrC08_27999709 (D), chrC08_27999778 (E) and chrC08_27999846 (F) with PHr, respectively. (G) Two haplotypes of BnaC08g26640D. The number of inbred lines harbouring the corresponding allele is shown in brackets at the bottom.

Fig. 3.

Co-localized locus on chromosome A02 for PH of B. napus at LP. (A) QTL detected for PH in the BnaTNDH population linkage analysis (Shi et al., 2013). (B) Manhattan plot of PH_LP (Trial 2_R1). (C) Peak SNP for PH_LP (Trial 2_R1). (D) Association of the co-localized locus with PH at LP. (E) Candidate gene association analysis of BnaA02g33340D. (F) Association of the five alleles in chrA02_23899623, chrA02_23899654, chrA02_23899669, chrA02_23899686 and chrA02_23899688 with PH at LP, respectively. (G) Two haplotypes of BnaA02g33340D. The number of inbred lines harbouring the corresponding allele is shown in brackets at the bottom. R1, replication 1.