Novel allelic variant of Lpa1 gene associated with a significant reduction in seed phytic acid content in rice (Oryza sativa L.)

Abstract

In plants, myo-inositol-1,2,3,4,5,6-hexakisphosphate (InsP6), also known as phytic acid (PA), is a major component of organic phosphorus (P), and accounts for up to 85% of the total P in seeds. In rice (Oryza sativa L.), PA mainly accumulates in rice bran, and chelates mineral cations, resulting in mineral deficiencies among brown rice consumers. Therefore, considerable efforts have been focused on the development of low PA (LPA) rice cultivars. In this study, we performed genetic and molecular analyses of OsLpa1, a major PA biosynthesis gene, in Sanggol, a low PA mutant variety developed via chemical mutagenesis of Ilpum rice cultivar. Genetic segregation and sequencing analyses revealed that a recessive allele, lpa1-3, at the OsLpa1 locus (Os02g0819400) was responsible for a significant reduction in seed PA content in Sanggol. The lpa1-3 gene harboured a point mutation (C623T) in the fourth exon of the predicted coding region, resulting in threonine (Thr) to isoleucine (Ile) amino acidsubstitution at position 208 (Thr208Ile). Three-dimensional analysis of Lpa1 protein structure indicated that myo-inositol 3-monophosphate [Ins(3)P1] could bind to the active site of Lpa1, with ATP as a cofactor for catalysis. Furthermore, the presence of Thr208 in the loop adjacent to the entry site of the binding pocket suggests that Thr208Ile substitution is involved in regulating enzyme activity via phosphorylation. Therefore, we propose that Thr208Ile substitution in lpa1-3 reduces Lpa1 enzyme activity in Sanggol, resulting in reduced PA biosynthesis.

Low phytic acid Crops: Observations Based on Four Decades of Research

“…But as time goes there have been some reports of low-phytate genotypes of various crops, whether developed via conventional breeding or via genetic engineering, which have good field performance and yield [27,32,62,79]. Perhaps this attitude might slowly change as these developments become more widely known [80].…”

Can Inositol Pyrophosphates Inform Strategies for Developing Low Phytate Crops?

“…This gene product was originally categorized as a potential 2-phosphoglycerate kinase that impacts InsP 6 accumulation [41]. However, recent structural modeling indicates that InsP 3 can be accommodated in the active site of this kinase, supporting a role for it as an InsP kinase [42].…”

Identification of phytic acid mutants in oilseed rape (Brassica napus) by large‐scale screening of mutant populations through amplicon sequencing

“…It was hypothesized that this enzyme, in addition to producing 2,3-bisphosphoglycerate, uses myo-inositol monophosphate as a substrate, resulting in the synthesis of inositol bisphosphate (Raboy, 2007;Lu et al, 2016). The enzyme was initially identified in rice, and knockout mutants are available from rice and Arabidopsis, which showed a phytic acid reduction of 45% and 57%, respectively (Kim et al, 2008;Kim & Tai, 2011;Kishor et al, 2019). Paralogues of Bn2-PGK2 showed a conserved P-loop kinase domain with two conserved motifs (Walker A and Walker B; Fig.…”

“…Since the biochemical function of the 2-PGK2 protein is largely unknown in plant species (Lu et al, 2016;Kishor et al, 2019), the novel bn2-pgk2 mutants can be used to investigate its biochemical properties in the phytic acid pathway in B. napus. Since we have not seen pleiotropic effects on plant growth and thousand kernel weights between the mutants and the controls there are no adverse effects of the induced mutations (Table S4).…”