• ISSN 1008-505X
  • CN 11-3996/S
刘海疆, 李晓娟, 谢毅文, 吴海亚, 鲁明星, 丁广大, 徐芳森, 石磊. 正常供磷及低磷胁迫下油菜种子植酸浓度与含量的全基因组关联分析[J]. 植物营养与肥料学报, 2021, 27(10): 1692-1702. DOI: 10.11674/zwyf.2021135
引用本文: 刘海疆, 李晓娟, 谢毅文, 吴海亚, 鲁明星, 丁广大, 徐芳森, 石磊. 正常供磷及低磷胁迫下油菜种子植酸浓度与含量的全基因组关联分析[J]. 植物营养与肥料学报, 2021, 27(10): 1692-1702. DOI: 10.11674/zwyf.2021135
LIU Hai-jiang, LI Xiao-juan, XIE Yi-wen, WU Hai-ya, LU Ming-xing, DING Guang-da, XU Fang-sen, SHI Lei. Genome wide association study of seed phytate concentration and content in Brassica napus under contrasting phosphate conditions[J]. Journal of Plant Nutrition and Fertilizers, 2021, 27(10): 1692-1702. DOI: 10.11674/zwyf.2021135
Citation: LIU Hai-jiang, LI Xiao-juan, XIE Yi-wen, WU Hai-ya, LU Ming-xing, DING Guang-da, XU Fang-sen, SHI Lei. Genome wide association study of seed phytate concentration and content in Brassica napus under contrasting phosphate conditions[J]. Journal of Plant Nutrition and Fertilizers, 2021, 27(10): 1692-1702. DOI: 10.11674/zwyf.2021135

正常供磷及低磷胁迫下油菜种子植酸浓度与含量的全基因组关联分析

Genome wide association study of seed phytate concentration and content in Brassica napus under contrasting phosphate conditions

  • 摘要:
    目的 鉴定不同磷水平油菜种子植酸浓度 (PA_Conc)和含量 (PA_Cont) 显著关联的 SNP 位点,挖掘候选基因及其优异单倍型,为油菜低植酸品种的培育提供遗传基础和优异基因资源。
    方法 采用田间试验,测定正常供磷(施磷,P2O5 90 kg/hm2)及低磷(不施磷,P2O5 0 kg/hm2)条件下403个甘蓝型油菜品种种子中的PA_Conc和PA_Cont,利用基于全基因组重测序技术获得的530多万个高质量SNP (single nucleotide polymorphism)标记,用 TASSEL 5.0 软件中的一般线性模型(general linear model,GLM)和混合线性模型(mixed linear model,MLM)进行全基因组关联分析(genome-wide association study, GWAS),鉴定种子植酸浓度和含量显著关联的SNP位点及其候选基因。采用Bcftools提取BnaA07.MRP13基因的SNP,利用Haploview 4.2软件进行单倍型分析。
    结果 关联群体正常供磷处理PA_Conc变异范围为17.52~81.32 mg/g,PA_Cont变异范围为0.30~0.99 mg/5粒种子;低磷处理PA_Conc变异范围为17.47~49.05 mg/g,PA_Cont变异范围为0.33~0.85 mg/5粒种子。与正常供磷相比,关联群体低磷胁迫下的PA_Conc和PA_Cont均值分别降低13.5%和10.8%。GLM模型检测到56个与油菜种子植酸浓度和含量显著关联的SNP位点,分布在除A08和C03外的17条染色体上,它们对表型变异的解释率为7.33%~14.28%。其中A03染色体上含有最多的SNP (9个)。MLM模型共检测到23个与油菜种子植酸浓度和含量显著关联的SNP位点,分布在A03、A05、A06、A07、A09、C01、C02、C04、C05、C06和C07等11条染色体上,它们对表型变异的解释率为9.6%~14.28%。其中A03染色体上含有8个SNP。对显著SNP位点上下游300 kb范围内的基因进行分析,挖掘出可能与种子中植酸合成相关的14个候选基因,其中包括拟南芥植酸合成通路中的MRPPLCPIP5KSULTR4等同源基因。对BnaA07.MRP13进行候选基因关联及单倍型分析,鉴定出高植酸单倍型“BnaA07.MRP13ContHap1”(TTTA)和低植酸单倍型“BnaA07.MRP13ContHap2”(CCCT)。自然群体中18%的品种(72/403)为低植酸单倍型,种子平均植酸含量为 0.56 mg/5粒种子,极显著低于高植酸单倍型 (平均植酸含量为0.62 mg/5粒种子)。
    结论 正常供磷和低磷胁迫下,油菜种子植酸浓度和含量均具有广泛的遗传变异。GLM模型和MLM模型分别检测到56和23个与油菜种子植酸浓度和含量显著关联的SNP位点,预测的与油菜种子植酸含量相关的候选基因有14个,发现的BnaA07.MRP13的高和低植酸单倍型为后续油菜种子植酸含量的遗传改良奠定了基础。

     

    Abstract:
    Objectives The study was conducted to unravel the significant SNP (single nucleotide polymorphism) loci, candidate genes and favorable haplotypes affecting the seed phytate concentration (PA_Conc) and seed phytate content (PA_Cont) in oilseed rape (Brassica napus L.) under contrasting phosphorus (P) application rates, in order to provide elite genes for the breeding of low phytate varieties of B. napus.
    Methods Field experiments were conducted to determine the PA_Conc and PA_Cont in the seed of an association panel of 403 B. napus accessions under sufficient (P2O5, 90 kg/hm2) and deficient (P2O5, 0 kg/hm2) P conditions. The whole genome sequencing (WGS) technology was used to develop more than 5.3 million SNPs in the association panel. The genome-wide association study was conducted to identify the significant SNPs associated with seed PA_Conc and PA_Cont by GLM (general linear model) and MLM (mixed linear model) using TASSEL 5.0 software, and the candidate genes were predicted. Bcftools was used to extract the SNP in the BnaA07.MRP13, and Haploview 4.2 was used for haplotype analysis.
    Results In the association panel, the PA_Conc varied from 17.52–81.32 mg/g and PA_Cont in 5 seeds varied from 0.30–0.99 mg at sufficient P supply, while the two parameters varied from 17.47–49.05 mg/g and from 0.33–0.85 mg at P deficient supply. Compared with those at the sufficient P supply, the average seed PA_Conc and PA_Cont of the association panel at deficient P supply reduced by 13.5% and 10.8%, respectively. Fifty-six SNPs were identified to be significantly associated with seed PA_Conc and seed PA_Cont in B. napus by GLM, which were distributed on 17 of the 19 chromosomes (excluding A08 and C03) and explained the phenotypic variation of 7.33% to 14.28%. Chromosome A03 had the largest number of significant SNPs (9). Twenty-three SNPs were identified to be significantly associated with PA_Conc and PA_Cont in the seed of B. napus by MLM, and they were distributed on eleven chromosomes including A03, A05, A06, A07, A09, C01, C02, C04, C05, C06, and C07, and they explained the phenotypic variation of 9.60% to 14.28%. Among them, 8 SNPs were identified on chromosome A03. Fourteen candidate genes, such as MRP, PLC, PIP5K, SULTR4, in phytate synthesis pathway of Arabidopsis, were identified by the analysis of the genes in the interval between 300 kb up and downstream of the significant SNP. Candidate gene association study and haplotype analysis of BnaA07.MRP13 determined a high phytate haplotype “BnaA07.MRP13ContHap1” (TTTA) and a low phytate haplotype “BnaA07.MRP13ContHap2” (CCCT). Eighteen percent of the varieties (72/403) in the association panel were low phytic acid haplotypes, with an average PA_Cont in 5 seeds of 0.56 mg, which was significantly lower than that of high phytate haplotypes (0.62 mg).
    Conclusions Seed PA_Conc and seed PA_Cont in the association panel of B. napus under both sufficient and deficient phosphorus supplies had extensive genetic variation. The GLM and MLM models detected 56 and 23 SNPs significantly associated with seed PA_Conc and PA_Cont in B. napus, respectively, and 14 candidate genes were predicted to be associated with the PA_Conc and PA_Cont. The high and low phytate haplotypes associated with BnaA07.MRP13 gene will be helpful for the genetic improvement of the seed PA_Conc and PA_Cont in B. napus.

     

/

返回文章
返回