A single nucleotide substitution in the SPDT transporter gene reduced phytic acid and increased mineral bioavailability from Rice grain ( Oryza sativa L.)

Abstract

Phosphorus (P) flow in agricultural land depends on the P taken off from harvested product, its losses through runoff and fertilizer applied to balance the removed P. Phytic acid (PA), the major storage form of phosphorus (P) in cereal grains is a key anti‐nutrient for human and non‐ruminants leads to eutrophication of waterways. As the natural non‐renewable P reserves are limited, enhancing P use efficiency is needed for field crops. SULTR‐like phosphorus distribution transporter (SPDT) is a novel rice transporter transfer P to the grain. Any alteration in transporter gene reduce grain P with concomitant rise in the leaves. A low PA (3.0 g/kg) rice Khira was identified where a single nucleotide mutation in LOC_Os06g05160 gene encoding SPDT showed low P transportation to grain. An amino acid change was detected as Valine‐330 to Alanine at the 3′ end of fifth exon. Highest expression of SPDT was observed in node I of rice as compared to low PA genotype. The mutation in SPDT could significantly affect P and PA accumulation in the grains with increased mineral bioavailability. Practical applications Excessive P application in crop leads to higher production cost as well as rapid depletion of limited rock phosphate. Alteration of P transporter function in the rice lower PA and total P accumulation in the grains with increased mineral bioavailability. The re‐distributed P in the straw can be applied as manure to the rice field. Thus, less P will be removed from the field, result in the decreased requirement for P fertilizer.

Understanding natural genetic variation for grain phytic acid content and functional marker development for phytic acid-related genes in rice

“…Researchers from throughout the globe are concentrating their efforts on reducing grain PA levels without compromising grain production. For identification of superior donors and development of superior cultivars through breeding, it is necessary to: (i) understand natural genetic variation for grain PA content and effect of environment on accumulation of PA in grains, (ii) have varieties and natural variants with low-PA content for different rice ecologies, (iii) analyse the genetic nature of the low-PA trait, and (iv) have surrogate molecular markers available for deployment in genomic assisted breeding programmes [ 2 ].…”

“…Since those markers were specific to mutant regions, they did not find wide application in applied breeding. In our previous study, a non-synonymous SNP (T to C) in the fifth exon of SPDT gene was found responsible for the natural variation for grain PA content between rice varieties Khira and Phalguni [ 2 ]. However, due to lack of restriction site polymorphism, we could not develop an allele specific CAPS marker.…”

“…Up to 85 percent of the phosphate (P) in rice grains and other plants is stored as phytic acid (PA) (myo-inositol-1,2,3,4,5,6-hexakisphosphate) [ 1 ]. PA chelates cations and limits digestive enzyme activity by binding to certain amino acid residues [ 2 ]. As a result, the bioavailability of minerals such as iron, zinc, potassium, calcium, and magnesium is reduced [ 3 ].…”

“…Alternatively, genomic resources developed for the purpose of identifying naturally occurring genetic variants for grain PA are limited [ 14 ]. Recent study [ 2 ] reported a single nucleotide substitution in the SPDT gene that is associated with the low PA phenotype and increased mineral bioavailability in the rice variety Khira. Similarly, an increase of zinc bioavailability (up to 12.51 mg/kg) was reported in natural low-PA variants of rice lines [ 15 ].…”

“…Knowledge of the allelic diversity in low PA candidate genes and their effects would be helpful for genetic improvement towards reduction of PA content in rice. We [ 2 ] reported that a T-C mutation in the fifth exon of the SPDT gene causes spontaneous variation in grain PA content in rice as well as enhanced mineral nutrient bioavailability. However, a single SNP in the SPDT gene may not be sufficient to account for the entire diversity in grain PA level found in rice germplasm.…”