Abstract
Phytic acid (PA) is the primary phosphorus (P) storage compound in the seeds of cereals and legumes. Low PA crops, which are considered an effective way to improve grain nutrient availability and combat environmental issues relating to seed P have been developed using mutational and reverse genetics approaches. Here, we identify molecular mechanism regulating PA content among natural rice variants. First, we performed genome-wide association (GWA) mapping of world rice core collection (WRC) accessions to understand the genetic determinants underlying PA trait in rice. Further, a comparative study was undertaken to identify the differences in PA accumulation, protein profiles, and gene expression in low (WRC 5) and high PA (WRC 6) accessions. GWA results identified myo-inositol 3-phosphate synthase 1 (INO1) as being closely localized to a significant single nucleotide polymorphism. We found high rates of PA accumulation 10 days after flowering, and our results indicate that INO1 expression was significantly higher in WRC 6 than in WRC 5. Seed proteome assays found that the expression of INO1 was significantly higher in WRC 6. These results suggest that not only the gene itself but regulation of INO1 gene expression at early developmental stages is important in determining PA content in rice.
Highlights
In cereal crops, phytic acid (PA), or myo-inositol 1,2,3,4,5,6-hexakisphosphate, is the primary phosphorous (P) storage molecule and accounts for 65–85% of total P in seeds[1]
We used four models, each using different kinship matrix (K) and population structure (Q) combinations, in genome-wide association (GWA) analyses to reveal significant nucleotide polymorphism (SNP) significantly associated with Phytic acid (PA) content
The world rice core collection (WRC) accessions used in this study have been developed based on a restricted fragment length polymorphism (RFLP) investigation and possess 91% of the alleles detected in the original rice collection[30]
Summary
Phytic acid (PA), or myo-inositol 1,2,3,4,5,6-hexakisphosphate, is the primary phosphorous (P) storage molecule and accounts for 65–85% of total P in seeds[1]. Several genes responsible for PA biosynthesis and accumulation have been identified in rice Among these genes, 8 genes, which are expressed in developing rice grains have been identified, including myo-inositol 3-phosphate synthase 1 (INO1), inositol 1,3,4-triskisphosphate 5/6-kinase 1 (ITPK1), Multidrug resistance-associated protein 13 (MRP13), inositol 1, 3, 4-trisphosphate 5/6-kinase 2 (ITPK6), myo-inositol kinase (MIK), inositol-pentakisphosphate 2-kinase 1 (IPK1), low phytic acid 1 (lpa1) and inositol 1, 3, 4-trisphosphate 5/6-kinase 2 (ITPK2)[16,17,18]. We determined the PA contents of natural rice variants using GWAS17, but, to the best of our knowledge, this is the first report of an association mapping study using both candidate gene identification and comparative proteomics to understand functional variation among low and high PA accessions during rice grain development. Comparisons of gene-expression profiles and comparative proteomics analyses were carried out during the primary developmental stage, during which PA is accumulated, in both low and high PA accessions to develop the deeper understanding of the PA accumulation in rice grain
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