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 (PH) and branch number (BN) of B. napus. However, the genetic bases controlling PH and BN in B. napus under P deficiency remain largely unknown. This study aims to mine candidate genes for PH and BN by genome-wide association study (GWAS) and determine low-P tolerance haplotypes. Methods An association panel of B. napus were grown in the field with a low P supply (P, 0 kg/ha) and a sufficient P supply (P, 40 kg/ha) across two years and PH and BN were investigated. More than five million single-nucleotide polymorphisms (SNPs) were used to conduct GWAS of PH and BN at two contrasting P supplies. Key Results A total of 2127 SNPs were strongly associated (P < 6.25×10 −07) with PH and BN at two P supplies. There was significant correlation between phenotypic variation and the number of favorable 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 the 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 higher PH 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 PH and BN at low P supply in B. napus. Candidate genes and favorable haplotypes may facilitate marker-based breeding efforts aimed at improving P use efficiency in B. napus.

Genome-wide association study identifies candidate genes and favorable haplotypes for seed yield in Brassica napus

“…A total of 403 B. napus accessions were used in this study. Detailed information on them and their genotypes are described in our previous study (Liu et al, 2021). All accessions were planted in sandy loam soil at Meichuan Town, Wuxue city, Hubei province, China (115.55°E, 29.85°N) during B. napus growing seasons from 2018 to 2019 (Trial 1) and from 2019 to 2020 (Trial 2).…”

“…More than 5 million high-quality SNPs of the association panel were derived from previous study Liu et al, 2021). Tassel 5.0 software was used for GWAS analysis by general linear models (GLM) and mixed linear models (MLM).…”

“…Tassel 5.0 software was used for GWAS analysis by general linear models (GLM) and mixed linear models (MLM). The threshold for this population was 6.25 × 10 −07 (Liu et al, 2021). GGplot2 (https://cran.r-project.org/web/packages/ggplot2/index.html) and CMplot (https://github.com/YinLiLin/CMplot) software were used to draw Manhattan plot and Quantile-Quantile plot, respectively.…”

“…GGplot2 (https://cran.r-project.org/web/packages/ggplot2/index.html) and CMplot (https://github.com/YinLiLin/CMplot) software were used to draw Manhattan plot and Quantile-Quantile plot, respectively. The population could be divided into ve subgroups based on the cross validation errors and the r pairwise relative kinship was close to 0 (Liu et al, 2021). The LD value of the association panel is 300 kb (Liu et al, 2021), thus the genes located within LD decay (300 kb) value up/downstream of the peak SNPs were considered as candidate genes.…”

“…The population could be divided into ve subgroups based on the cross validation errors and the r pairwise relative kinship was close to 0 (Liu et al, 2021). The LD value of the association panel is 300 kb (Liu et al, 2021), thus the genes located within LD decay (300 kb) value up/downstream of the peak SNPs were considered as candidate genes. The genotypes of BnaA01g17200D, BnaA02g08680D and BnaA09g10430D in the association panel of B. napus were obtained by vcftools software (https://vcftools.github.io/index.html).…”