Integrating a genome-wide association study with transcriptomic data to predict candidate genes and favourable haplotypes influencing Brassica napus seed phytate

Abstract

Phytate is the storage form of phosphorus in angiosperm seeds and plays vitally important roles during seed development. However, in crop plants phytate decreases bioavailability of seed-sourced mineral elements for humans, livestock and poultry, and contributes to phosphate-related water pollution. However, there is little knowledge about this trait in oilseed rape (Brassica napus). Here, a panel of 505 diverse B. napus accessions was screened in a genome-wide association study (GWAS) using 3.28 × 106 single-nucleotide polymorphisms (SNPs). This identified 119 SNPs significantly associated with phytate concentration (PA_Conc) and phytate content (PA_Cont) and six candidate genes were identified. Of these, BnaA9.MRP5 represented the candidate gene for the significant SNP chrA09_5198034 (27 kb) for both PA_Cont and PA_Conc. Transcription of BnaA9.MRP5 in a low-phytate variety (LPA20) was significantly elevated compared with a high-phytate variety (HPA972). Association and haplotype analysis indicated that inbred lines carrying specific SNP haplotypes within BnaA9.MRP5 were associated with high- and low-phytate phenotypes. No significant differences in seed germination and seed yield were detected between low and high phytate cultivars examined. Candidate genes, favourable haplotypes and the low phytate varieties identified in this study will be useful for low-phytate breeding of B. napus.

Genetic Control of Seed Phytate Accumulation and the Development of Low-Phytate Crops: A Review and Perspective

“…The QTL identified by Bentsink et al 80 is not only associated with seed phytate but also with the seed P i concentration, leaf phytate, and P i concentrations. In addition, this QTL and a QTL affecting the seed phytate concentration in oilseed rape detected by Liu et al 84 were colocated in a syntenic region between Arabidopsis and oilseed rape (Figure S1). This major locus was further fine-mapped to a 99 kb region in which 13 open reading frames are located, with a vacuolar membrane ATPase subunit G1 (At3g01390) predicted as a promising candidate gene.…”

“…In addition to traditional linkage mapping using biparental recombinant populations, GWAS has also been used to uncover the genetic basis of the seed phytate accumulation in oilseed rape and rice (Table ). , Additional QTLs within a narrower mapping interval can be detected by GWAS using natural populations that contain extensive genetic diversity and have undergone numerous recombination events under selection . In oilseed rape, Liu et al identified 31 QTLs associated with the seed phytate concentration by GWAS using a panel of 404 diverse oilseed rape accessions.…”

“… , Additional QTLs within a narrower mapping interval can be detected by GWAS using natural populations that contain extensive genetic diversity and have undergone numerous recombination events under selection . In oilseed rape, Liu et al identified 31 QTLs associated with the seed phytate concentration by GWAS using a panel of 404 diverse oilseed rape accessions. A MRP5 gene BnaA09.MRP5 has been proposed as the candidate gene for a QTL harboring the significant SNP chrA09_5198034 on chromosome A09.…”

“…This gene shows a significant differential expression in developing seeds between low- and high-phytate varieties. In addition, a significant difference has been observed in the seed phytate concentration between two major haplotypes within BnaA9.MRP5 , suggesting that this gene is a promising candidate for the target QTL. In rice, a total of nine QTLs have been identified that affect the seed phytate concentration by GWAS using a panel of 62 world rice core collection accessions .…”

Deciphering the Genetic Basis of Root and Biomass Traits in Rapeseed (Brassica napus L.) through the Integration of GWAS and RNA-Seq under Nitrogen Stress

“…Transcriptome analysis is a robust approach that helps the identification of differentially expressed genes with their expression level and regulatory mechanisms [ 48 ]. The present study identified 245 and 540 DEGs specific to HN/LN and HNCK/LNCK, respectively, while 399 DEGs were considered common DEGs for HN/LN/HNCK/LNCK-T1T2 ( Table S3 , Figure 3 B).…”