The rice OsLpa1 gene encodes a novel protein involved in phytic acid metabolism

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

Breeding low phytic acid (lpa) crops is a strategy that has potential to both improve the nutritional quality of food and feed and contribute to the sustainability of agriculture. Here, we review the lipid-independent and -dependent pathways of phytate synthesis and their regulatory mechanisms in plants. We compare the genetic variation of the phytate concentration and distribution in seeds between dicot and monocot species as well as the associated temporal and spatial expression patterns of the genes involved in phytate synthesis and transport. Quantitative trait loci or significant single nucleotide polymorphisms for the seed phytate concentration have been identified in different plant species by linkage and association mapping, and some genes have been cloned from lpa mutants. We summarize the effects of various lpa mutations on important agronomic traits in crop plants and propose SULTR3;3 and SULTR3;4 as optimal target genes for lpa crop breeding.

Phytic acid accumulation in plants: Biosynthesis pathway regulation and role in human diet

Phytate or phytic acid (PA), is a phosphorus (P) containing compound generated by the stepwise phosphorylation of myo-inositol. It forms complexes with some nutrient cations, such as Ca, Fe and Zn, compromising their absorption and thus acting as an anti-nutrient in the digestive tract of humans and monogastric animals. Conversely, PAs are an important form of P storage in seeds, making up to 90% of total seed P. Phytates also play a role in germination and are related to the synthesis of abscisic acid and gibberellins, the hormones involved in seed germination. Decreasing PA content in plants is desirable for human dietary. Therefore, low phytic acid (lpa) mutants might present some negative pleiotropic effects, which could impair germination and seed viability. In the present study, we review current knowledge of the genes encoding enzymes that function in different stages of PA synthesis, from the first phosphorylation of myo-inositol to PA transport into seed reserve tissues, and the application of this knowledge to reduce PA concentrations in edible crops to enhance human diet. Finally, phylogenetic data for PA concentrations in different plant families and distributed across several countries under different environmental conditions are compiled. The results of the present study help explain the importance of PA accumulation in different plant families and the distribution of PA accumulation in different foods.

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

Brassica napus (oilseed rape) is an important oil crop in temperate regions, which originated from hybridization of Brassica oleracea and Brassica rapa. Owing to its polyploidy, the functional study of single genes is cumbersome. Phytic acid is considered as an antinutritive compound, and we aimed to knock out the underlying synthesis and transporter genes to identify low phytic acid mutants. We implemented a high-throughput next-generation sequencing screening protocol for an ethylmethane sulfonate population of 7680 plants in six gene families (BnMIPS, BnMIK, Bn2-PGK, BnIPK1, BnIPK2, and BnMRP5) with two paralogues for each gene. A total of 1487 mutations were revealed, and the vast majority (96%) were confirmed by Sanger sequencing. Furthermore, the characterization of double mutants of Bn.2-PGK2 showed a significant reduction of phytic acid contents. We propose to use three-dimensional pooling combined with amplicon stacking and next-generation sequencing to identify mutations in polyploid oilseed rape in a fast and cost-effective manner for complex metabolic pathways. Furthermore, the mutants identified in Bn2-PGK2 might be a very valuable resource for industrial production of oilseed rape protein for human consumption.

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

The low phytic acid (lpa), or "low-phytate" seed trait can provide numerous potential benefits to the nutritional quality of foods and feeds and to the sustainability of agricultural production. Major benefits include enhanced phosphorus (P) management contributing to enhanced sustainability in non-ruminant (poultry, swine, and fish) production; reduced environmental impact due to reduced waste P in non-ruminant production; enhanced "global" bioavailability of minerals (iron, zinc, calcium, magnesium) for both humans and non-ruminant animals; enhancement of animal health, productivity and the quality of animal products; development of "low seed total P" crops which also can enhance management of P in agricultural production and contribute to its sustainability. Evaluations of this trait by industry and by advocates of biofortification via breeding for enhanced mineral density have been too short term and too narrowly focused. Arguments against breeding for the low-phytate trait overstate the negatives such as potentially reduced yields and field performance or possible reductions in phytic acid's health benefits. Progress in breeding or genetically-engineering high-yielding stress-tolerant low-phytate crops continues. Perhaps due to the potential benefits of the low-phytate trait, the challenge of developing high-yielding, stress-tolerant low-phytate crops has become something of a holy grail for crop genetic engineering. While there are widely available and efficacious alternative approaches to deal with the problems posed by seed-derived dietary phytic acid, such as use of the enzyme phytase as a feed additive, or biofortification breeding, if there were an interest in developing low-phytate crops with good field performance and good seed quality, it could be accomplished given adequate time and support. Even with a moderate reduction in yield, in light of the numerous benefits of low-phytate types as human foods or animal feeds, should one not grow a nutritionally-enhanced crop variant that perhaps has 5% to 10% less yield than a standard variant but one that is substantially more nutritious? Such crops would be a benefit to human nutrition especially in populations at risk for iron and zinc deficiency, and a benefit to the sustainability of agricultural production.

Expression regulation of myo-inositol 3-phosphate synthase 1 (INO1) in determination of phytic acid accumulation in rice grain

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.

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

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.

Locating QTLs controlling overwintering seedling rate in perennial glutinous rice 89-1 (Oryza sativa L.)

A new cold tolerant germplasm resource named glutinous rice 89-1 (Gr89-1, Oryza sativa L.) can overwinter using axillary buds, with these buds being ratooned the following year. The overwintering seedling rate (OSR) is an important factor for evaluating cold tolerance. Many quantitative trait loci (QTLs) controlling cold tolerance at different growth stages in rice have been identified, with some of these QTLs being successfully cloned. However, no QTLs conferring to the OSR trait have been located in the perennial O. sativa L. To identify QTLs associated with OSR and to evaluate cold tolerance. 286 F₁₂ recombinant inbred lines (RILs) derived from a cross between the cold tolerant variety Gr89-1 and cold sensitive variety Shuhui527 (SH527) were used. A total of 198 polymorphic simple sequence repeat (SSR) markers that were distributed uniformly on 12 chromosomes were used to construct the linkage map. The gene ontology (GO) annotation of the major QTL was performed through the rice genome annotation project system. Three main-effect QTLs (qOSR2, qOSR3, and qOSR8) were detected and mapped on chromosomes 2, 3, and 8, respectively. These QTLs were located in the interval of RM14208 (35,160,202 base pairs (bp))-RM208 (35,520,147 bp), RM218 (8,375,236 bp)-RM232 (9,755,778 bp), and RM5891 (24,626,930 bp)-RM23608 (25,355,519 bp), and explained 19.6%, 9.3%, and 11.8% of the phenotypic variations, respectively. The qOSR2 QTL displayed the largest effect, with a logarithm of odds score (LOD) of 5.5. A total of 47 candidate genes on the qOSR2 locus were associated with 219 GO terms. Among these candidate genes, 11 were related to cell membrane, 7 were associated with cold stress, and 3 were involved in response to stress and biotic stimulus. OsPIP1;3 was the only one candidate gene related to stress, biotic stimulus, cold stress, and encoding a cell membrane protein. After QTL mapping, a total of three main-effect QTLs-qOSR2, qOSR3, and qOSR8-were detected on chromosomes 2, 3, and 8, respectively. Among these, qOSR2 explained the highest phenotypic variance. All the QTLs elite traits come from the cold resistance parent Gr89-1. OsPIP1;3 might be a candidate gene of qOSR2.

Manipulating the Phytic Acid Content of Rice Grain Toward Improving Micronutrient Bioavailability

Myo-inositol hexaphosphate, also known as phytic acid (PA), is the most abundant storage form of phosphorus in seeds. PA acts as a strong chelator of metal cations to form phytate and is considered an anti-nutrient as it reduces the bioavailability of important micronutrients. Although the major nutrient source for more than one-half of the global population, rice is a poor source of essential micronutrients. Therefore, biofortification and reducing the PA content of rice have arisen as new strategies for increasing micronutrient bioavailability in rice. Furthermore, global climate change effects, particularly rising atmospheric carbon dioxide concentration, are expected to increase the PA content and reduce the concentrations of most of the essential micronutrients in rice grain. Several genes involved in PA biosynthesis have been identified and characterized in rice. Proper understanding of the genes related to PA accumulation during seed development and creating the means to suppress the expression of these genes should provide a foundation for manipulating the PA content in rice grain. Low-PA rice mutants have been developed that have a significantly lower grain PA content, but these mutants also had reduced yields and poor agronomic performance, traits that challenge their effective use in breeding programs. Nevertheless, transgenic technology has been effective in developing low-PA rice without hampering plant growth or seed development. Moreover, manipulating the micronutrient distribution in rice grain, enhancing micronutrient levels and reducing the PA content in endosperm are possible strategies for increasing mineral bioavailability. Therefore, a holistic breeding approach is essential for developing successful low-PA rice lines. In this review, we focus on the key determinants for PA concentration in rice grain and discuss the possible molecular methods and approaches for manipulating the PA content to increase micronutrient bioavailability.

Engineering crop nutrient efficiency for sustainable agriculture

Increasing crop yields can provide food, animal feed, bioenergy feedstocks and biomaterials to meet increasing global demand; however, the methods used to increase yield can negatively affect sustainability. For example, application of excess fertilizer can generate and maintain high yields but also increases input costs and contributes to environmental damage through eutrophication, soil acidification and air pollution. Improving crop nutrient efficiency can improve agricultural sustainability by increasing yield while decreasing input costs and harmful environmental effects. Here, we review the mechanisms of nutrient efficiency (primarily for nitrogen, phosphorus, potassium and iron) and breeding strategies for improving this trait, along with the role of regulation of gene expression in enhancing crop nutrient efficiency to increase yields. We focus on the importance of root system architecture to improve nutrient acquisition efficiency, as well as the contributions of mineral translocation, remobilization and metabolic efficiency to nutrient utilization efficiency.

Analysis of Lysophospholipid Content in Low Phytate Rice Mutants

As a fundamental component of nucleic acids, phospholipids, and adenosine triphosphate, phosphorus (P) is critical to all life forms, however, the molecular mechanism of P translocation and distribution in rice grains are still not understood. Here, with the use of five different low phytic acid (lpa) rice mutants, the redistribution in the main P-containing compounds in rice grain, phytic acid (PA), lysophospholipid (LPL), and inorganic P (Pi), was investigated. The lpa mutants showed a significant decrease in PA and phytate-phosphorus (PA-P) concentration with a concomitant increase in Pi concentration. Moreover, defects in the OsST and OsMIK genes result in a great reduction of specific LPL components and LPL-phosphorus (LPL-P) contents in rice grain. In contrast, defective OsMRP5 and Os2-PGK genes led to a significant increase in individual LPL components. The effect of the Os2-PGK gene on the LPL accumulation was validated using breeding lines derived from a cross between KBNT-lpa (Os2-PGK mutation) and Jiahe218. This study demonstrates that these rice lpa mutants lead to the redistribution of Pi in endosperm and modify LPL biosynthesis. Increase LPLs in the endosperm in the lpa mutants may have practical applications in rice breeding to produce "healthier" rice.

Tissue-specific expression, developmentally and spatially regulated alternative splicing, and protein subcellular localization of OsLpa rice

The OsLpa1 gene (LOC_Os57400) was identified to be involved in phytic acid (PA) metabolism because its knockout and missense mutants reduce PA content in rice grain. However, little is known about the molecular characteristics of OsLpa rice and of its homologues in other plants. In the present study, the spatial pattern of OsLpa1 expression was revealed using OsLpa1 promoter::GUS transgenic plants (GUS: β-glucuronidase); GUS histochemical assay showed that OsLpa1 was strongly expressed in stem, leaf, and root tissues, but in floral organ it is expressed mainly and strongly in filaments. In seeds, GUS staining was concentrated in the aleurone layers; a few blue spots were observed in the outer layers of embryo, but no staining was observed in the endosperm. Three OsLpa1 transcripts (OsLpa1.1, OsLpa1.2, OsLpa1.3) are produced due to alternative splicing; quantitative reverse-transcriptase polymerase chain reaction (RT-PCR) analysis revealed that the abundance of OsLpa1.3 was negligible compared with OsLpa1.1 and OsLpa all tissues. OsLpa1.2 is predominant in germinating seeds (about 5 times that of OsLpa1.1), but its abundance decreases quickly with the development of seedlings and plants, whereas the abundance of OsLpa1.1 rises and falls, reaching its highest level in 45-d-old plants, with abundance greater than that of OsLpa both leaves and roots. In seeds, the abundance of OsLpa1 continuously increases with seed growth, being 27.5 and 15 times greater in 28-DAF (day after flowering) seeds than in 7-DAF seeds for OsLpa1.1 and OsLpa1.2, respectively. Transient expression of chimeric genes with green fluorescence protein (GFP) in rice protoplasts demonstrated that all proteins encoded by the three OsLpa1 transcripts are localized to the chloroplast.

Analysis of weighted co-regulatory networks in maize provides insights into new genes and regulatory mechanisms related to inositol phosphate metabolism

BACKGROUND

D-myo-inositol phosphates (IPs) are a series of phosphate esters. Myo-inositol hexakisphosphate (phytic acid, IP6) is the most abundant IP and has negative effects on animal and human nutrition. IPs play important roles in plant development, stress responses, and signal transduction. However, the metabolic pathways and possible regulatory mechanisms of IPs in maize are unclear. In this study, the B73 (high in phytic acid) and Qi319 (low in phytic acid) lines were selected for RNA-Seq analysis from 427 inbred lines based on a screening of IP levels. By integrating the metabolite data with the RNA-Seq data at three different kernel developmental stages (12, 21 and 30 days after pollination), co-regulatory networks were constructed to explore IP metabolism and its interactions with other pathways.

RESULTS

Differentially expressed gene analyses showed that the expression of MIPS and ITPK was related to differences in IP metabolism in Qi319 and B73. Moreover, WRKY and ethylene-responsive transcription factors (TFs) were common among the differentially expressed TFs, and are likely to be involved in the regulation of IP metabolism. Six co-regulatory networks were constructed, and three were chosen for further analysis. Based on network analyses, we proposed that the GA pathway interacts with the IP pathway through the ubiquitination pathway, and that Ca(2+) signaling functions as a bridge between IPs and other pathways. IP pools were found to be transported by specific ATP-binding cassette (ABC) transporters. Finally, three candidate genes (Mf3, DH2 and CB5) were identified and validated using Arabidopsis lines with mutations in orthologous genes or RNA interference (RNAi)-transgenic maize lines. Some mutant or RNAi lines exhibited seeds with a low-phytic-acid phenotype, indicating perturbation of IP metabolism. Mf3 likely encodes an enzyme involved in IP synthesis, DH2 encodes a transporter responsible for IP transport across organs and CB5 encodes a transporter involved in IP co-transport into vesicles.

CONCLUSIONS

This study provides new insights into IP metabolism and regulation, and facilitates our development of a better understanding of the functions of IPs and how they interact with other pathways involved in plant development and stress responses. Three new genes were discovered and preliminarily validated, thereby increasing our knowledge of IP metabolism.

Seed Biofortification and Phytic Acid Reduction: A Conflict of Interest for the Plant?

Most of the phosphorus in seeds is accumulated in the form of phytic acid (myo-inositol-1,2,3,4,5,6-hexakisphosphate, InsP₆). This molecule is a strong chelator of cations important for nutrition, such as iron, zinc, magnesium, and calcium. For this reason, InsP₆ is considered an antinutritional factor. In recent years, efforts to biofortify seeds through the generation of low phytic acid (lpa) mutants have been noteworthy. Moreover, genes involved in the biosynthesis and accumulation of this molecule have been isolated and characterized in different species. Beyond its role in phosphorus storage, phytic acid is a very important signaling molecule involved in different regulatory processes during plant development and responses to different stimuli. Consequently, many lpa mutants show different negative pleitotropic effects. The strength of these pleiotropic effects depends on the specific mutated gene, possible functional redundancy, the nature of the mutation, and the spatio-temporal expression of the gene. Breeding programs or transgenic approaches aimed at development of new lpa mutants must take into consideration these different aspects in order to maximize the utility of these mutants.

A decrease in phytic acid content substantially affects the distribution of mineral elements within rice seeds

Phytic acid (myo-inositol hexakisphosphate; InsP6) is the storage compound of phosphorus and many mineral elements in seeds. To determine the role of InsP6 in the accumulation and distribution of mineral elements in seeds, we performed fine mappings of mineral elements through synchrotron-based X-ray microfluorescence analysis using developing seeds from two independent low phytic acid (lpa) mutants of rice (Oryza sativa L.). The reduced InsP6 in lpa seeds did not affect the translocation of mineral elements from vegetative organs into seeds, because the total amounts of phosphorus and the other mineral elements in lpa seeds were identical to those in the wild type (WT). However, the reduced InsP6 caused large changes in mineral localization within lpa seeds. Phosphorus and potassium in the aleurone layer of lpa greatly decreased and diffused into the endosperm. Zinc and copper, which were broadly distributed from the aleurone layer to the inner endosperm in the WT, were localized in the narrower space around the aleurone layer in lpa mutants. We also confirmed that similar distribution changes occurred in transgenic rice with the lpa phenotype. Using these results, we discussed the role of InsP6 in the dynamic accumulation and distribution patterns of mineral elements during seed development.

Overexpression of a Gene Involved in Phytic Acid Biosynthesis Substantially Increases Phytic Acid and Total Phosphorus in Rice Seeds

The manipulation of seed phosphorus is important for seedling growth and environmental P sustainability in agriculture. The mechanism of regulating P content in seed, however, is poorly understood. To study regulation of total P, we focused on phytic acid (inositol hexakisphosphate; InsP₆) biosynthesis-related genes, as InsP₆ is a major storage form of P in seeds. The rice (Oryza sativa L.) low phytic acid mutant lpa1-1 has been identified as a homolog of archael 2-phosphoglycerate kinase. The homolog might act as an inositol monophosphate kinase, which catalyzes a key step in InsP₆ biosynthesis. Overexpression of the homolog in transgenic rice resulted in a significant increase in total P content in seed, due to increases in InsP₆ and inorganic phosphates. On the other hand, overexpression of genes that catalyze the first and last steps of InsP₆ biosynthesis could not increase total P levels. From the experiments using developing seeds, it is suggested that the activation of InsP₆ biosynthesis in both very early and very late periods of seed development increases the influx of P from vegetative organs into seeds. This is the first report from a study attempting to elevate the P levels of seed through a transgenic approach.

Seed-specific silencing of OsMRP5 reduces seed phytic acid and weight in rice

Phytic acid (PA) is poorly digested by humans and monogastric animals and negatively affects human/animal nutrition and the environment. Rice mutants with reduced PA content have been developed but are often associated with reduced seed weight and viability, lacking breeding value. In the present study, a new approach was explored to reduce seed PA while attaining competitive yield. The OsMRP5 gene, of which mutations are known to reduce seed PA as well as seed yield and viability, was down-regulated specifically in rice seeds by using an artificial microRNA driven by the rice seed specific promoter Ole18. Seed PA contents were reduced by 35.8-71.9% in brown rice grains of transgenic plants compared to their respective null plants (non-transgenic plants derived from the same event). No consistent significant differences of plant height or number of tillers per plant were observed, but significantly lower seed weights (up to 17.8% reduction) were detected in all transgenic lines compared to null plants, accompanied by reductions of seed germination and seedling emergence. It was observed that the silencing of the OsMRP5 gene increased the inorganic P (Pi) levels (up to 7.5 times) in amounts more than the reduction of PA-P in brown rice. This indicates a reduction in P content in other cellular compounds, such as lipids and nucleic acids, which may affect overall seed development. Put together, the present study demonstrated that seed specific silencing of OsMRP5 could significantly reduce the PA content and increase Pi levels in seeds; however, it also significantly lowers seed weight in rice. Discussions were made regarding future directions towards producing agronomically competitive and nutritionally valuable low PA rice.

Induction of phytic acid synthesis by abscisic acid in suspension-cultured cells of rice

A pathway of phytic acid (PA) synthesis in plants has been revealed via investigations of low phytic acid mutants. However, the regulation of this pathway is not well understood because it is difficult to control the environments of cells in the seeds, where PA is mainly synthesized. We modified a rice suspension culture system in order to study the regulation of PA synthesis. Rice cells cultured with abscisic acid (ABA) accumulate PA at higher levels than cells cultured without ABA, and PA accumulation levels increase with ABA concentration. On the other hand, higher concentrations of sucrose or inorganic phosphorus do not affect PA accumulation. Mutations in the genes RINO1, OsMIK, OsIPK1 and OsLPA1 have each been reported to confer low phytic acid phenotypes in seeds. Each of these genes is upregulated in cells cultured with ABA. OsITPK4 and OsITPK6 are upregulated in cells cultured with ABA and in developing seeds. These results suggest that the regulation of PA synthesis is similar between developing seeds and cells in this suspension culture system. This system will be a powerful tool for elucidating the regulation of PA synthesis.

Characterization of OsMIK in a rice mutant with reduced phytate content reveals an insertion of a rearranged retrotransposon

The rice low phytic acid (lpa) mutant Os-lpa-XS110-1(XS-lpa) has ~45 % reduction in seed phytic acid (PA) compared with the wild-type cultivar Xiushui 110. Previously, a single recessive gene mutation was shown to be responsible for the lpa phenotype and was mapped to a region of chromosome 3 near OsMIK (LOC_Os03g52760) and OsIPK1 (LOC_Os03g51610), two genes involved in PA biosynthesis. Here, we report the identification of a large insert in the intron of OsMIK in the XS-lpa mutant. Sequencing of fragments amplified through TAIL-PCRs revealed that the insert was a derivative of the LINE retrotransposon gene LOC_Os03g56910. Further analyses revealed the following characteristics of the insert and its impacts: (1) the inserted sequence of LOC_Os03g56910 was split at its third exon and rejoined inversely, with its 5' and 3' flanking sequences inward and the split third exon segments outward; (2) the LOC_Os03g56910 remained in its original locus in XS-lpa, and the insertion probably resulted from homologous recombination repair of a DNA double strand break; (3) while the OsMIK transcripts of XS-lpa and Xiushui 110 were identical, substantial reductions of the transcript abundance (~87 %) and the protein level (~60 %) were observed in XS-lpa, probably due to increased methylation in its promoter region. The above findings are discussed in the context of plant mutagenesis, epigenetics and lpa breeding.

Identification and characterization of the soybean IPK1 ortholog of a low phytic acid mutant reveals an exon-excluding splice-site mutation

Phytic acid (myo-inositol 1, 2, 3, 4, 5, 6 hexakisphosphate) is an important constituent of soybean meal. Since phytic acid and its mineral salts (phytates) are almost indigestible for monogastrics, their abundance in grain food/feed causes nutritional and environmental problems; interest in breeding low phytic acid has therefore increased considerably. Based on gene mapping and the characteristics of inositol polyphosphates profile in the seeds of a soybean mutant line Gm-lpa-ZC-2, the soybean ortholog of inositol 1,3,4,5,6 pentakisphosphate (InsP(5)) 2-kinase (IPK1), which transforms InsP(5) into phytic acid, was first hypothesized as the candidate gene responsible for the low phytic acid alteration in Gm-lpa-ZC-2. One IPK1 ortholog (Glyma14g07880, GmIPK1) was then identified in the mapped region on chromosome 14. Sequencing revealed a G → A point mutation in the genomic DNA sequence and the exclusion of the entire fifth exon in the cDNA sequence of GmIPK1 in Gm-lpa-ZC-2 compared with its wild-type progenitor Zhechun No. 3. The excluded exon encodes 37 amino acids that spread across two conserved IPK1 motifs. Furthermore, complete co-segregation of low phytic acid phenotype with the G → A mutation was observed in the F(2) population of ZC-lpa x Zhexiandou No. 4 (a wild-type cultivar). Put together, the G → A point mutation affected the pre-mRNA splicing and resulted in the exclusion of the fifth exon of GmIPK1 which is expected to disrupt the GmIPK1 functionality, leading to low phytic acid level in Gm-lpa-ZC-2. Gm-lpa-ZC-2, would be a good germplasm source in low phytic acid soybean breeding.

Iron biofortification in rice: it's a long way to the top

Rice and most staple cereals contain low iron (Fe) levels, most of which is lost during grain processing. Populations with monotonous diets consisting mainly of cereals are especially prone to Fe deficiency, which affects about two billion people. Supplementation or food fortification programs have not always been successful. Crop Fe fertilization is also not very effective due to Fe soil insolubility. An alternative solution is Fe biofortification by generating cultivars that efficiently mobilize, uptake and translocate Fe to the edible parts. Here, we review the strategies used for the Fe biofortification of rice, including conventional breeding and directed genetic modification, which offer the most rapid way to develop Fe-rich rice plants. While classical breeding is able to modify the contents of inhibitors of Fe absorption, transgenic approaches have focused on enhanced Fe uptake from soil, xylem and phloem loading and grain sink strength. A comprehensive table is provided in which the percentages of the recommended dietary Fe intake reached by independently developed transgenic plants are calculated. In this review we also emphasize that the discovery of new QTLs and genes related to Fe biofortification is extremely important, but interdisciplinary research is needed for future success in this area.

A defective ABC transporter of the MRP family, responsible for the bean lpa1 mutation, affects the regulation of the phytic acid pathway, reduces seed myo-inositol and alters ABA sensitivity

• We previously identified the lpa1 (low phytic acid) 280-10 line that carries a mutation conferring a 90% reduction in phytic acid (InsP(6) ) content. In contrast to other lpa mutants, lpa1(280-10) does not display negative pleiotropic effects. In the present paper, we have identified the mutated gene and analysed its impact on the phytic acid pathway. • Here, we mapped the lpa1(280-10) mutation by bulk analysis on a segregating F(2) population, an then, by comparison with the soybean genome, we identified and sequenced a candidate gene. The InsP(6) pathway was analysed by gene expression and quantification of metabolites. • The mutated Pvmrp1(280-10) cosegregates with the lpa1(280-10) mutation, and the expression level of several genes of the InsP(6) pathway are reduced in the lpa1(280-10) mutant as well as the inositol and raffinosaccharide content. PvMrp2, a very similar paralogue of PvMrp1 was also mapped and sequenced. • The lpa1 mutation in beans is likely the result of a defective Mrp1 gene (orthologous to the lpa genes AtMRP5 and ZmMRP4), while its Mrp2 paralog is not able to complement the mutant phenotype in the seed. This mutation appears to down-regulate the InsP(6) pathway at the transcriptional level, as well as altering inositol-related metabolism and affecting ABA sensitivity.

Identification of genes necessary for wild-type levels of seed phytic acid in Arabidopsis thaliana using a reverse genetics approach

The majority of phosphorus (P) in seeds is found in phytic acid (InsP(6)) which accumulates as the mixed salt phytate. InsP(6) is generally considered to be an anti-nutrient and the development of low phytic acid (lpa) seed crops is of significant interest. We have employed a reverse genetics approach to examine the impact of disrupting genes involved in inositol phosphate metabolism on Arabidopsis seed InsP(6) levels. Our analysis revealed that knockout mutations in three genes (AtITPK1, AtITPK4, and AtMIK/At5g58730) reduced seed InsP(6) in addition to knockouts of four previously reported genes (AtIPK1, AtIPK2β, AtMRP5, and At5g60760). Seeds of these lpa mutants also exhibited reduced germination under various stress conditions. The greatest reduction in InsP(6) (>70%) was observed in atmrp5 seeds which were also among the least sensitive to the stresses examined. Expression analysis of the lpa genes revealed three distinct patterns in developing siliques consistent with their presumed roles. Disruption of each lpa gene resulted in changes in the expression in some of the other lpa genes indicating that transcription of lpa genes is modulated by other constituents of InsP(6) metabolism. While all the lpa genes represent possible targets for genetic engineering of low phytate seed crops, mutations in AtMRP5, AtMIK, and At5g60760 may be most successful for conventional approaches such as mutation breeding.

Identification of genes necessary for wild-type levels of seed phytic acid in Arabidopsis thaliana using a reverse genetics approach

The majority of phosphorus (P) in seeds is found in phytic acid (InsP(6)) which accumulates as the mixed salt phytate. InsP(6) is generally considered to be an anti-nutrient and the development of low phytic acid (lpa) seed crops is of significant interest. We have employed a reverse genetics approach to examine the impact of disrupting genes involved in inositol phosphate metabolism on Arabidopsis seed InsP(6) levels. Our analysis revealed that knockout mutations in three genes (AtITPK1, AtITPK4, and AtMIK/At5g58730) reduced seed InsP(6) in addition to knockouts of four previously reported genes (AtIPK1, AtIPK2β, AtMRP5, and At5g60760). Seeds of these lpa mutants also exhibited reduced germination under various stress conditions. The greatest reduction in InsP(6) (>70%) was observed in atmrp5 seeds which were also among the least sensitive to the stresses examined. Expression analysis of the lpa genes revealed three distinct patterns in developing siliques consistent with their presumed roles. Disruption of each lpa gene resulted in changes in the expression in some of the other lpa genes indicating that transcription of lpa genes is modulated by other constituents of InsP(6) metabolism. While all the lpa genes represent possible targets for genetic engineering of low phytate seed crops, mutations in AtMRP5, AtMIK, and At5g60760 may be most successful for conventional approaches such as mutation breeding.

A nonsense mutation in a putative sulphate transporter gene results in low phytic acid in barley

Low phytic acid grains can provide a solution to dietary micronutrient deficiency and environmental pollution. A low phytic acid 1-1 (lpa1-1) barley mutant was identified using forward genetics and the mutant gene was mapped to chromosome 2HL. Comparative genomic analysis revealed that the lpa1-1 gene was located in the syntenic region of the rice Os-lpa-MH86-1 gene on chromosome 4. The gene ortholog of rice Os-lpa-MH86-1 (designated as HvST) was isolated from barley using polymerase chain reaction and mapped to chromosome 2HL in a doubled haploid population of Clipper×Sahara. The results demonstrate the collinearity between the rice Os-lpa-MH86-1 gene and the barley lpa1-1 region. Sequence analysis of HvST revealed a single base pair substitution (C→T transition) in the last exon of the gene in lpa1-1 (M422), which resulted in a nonsense mutation. These results will facilitate our understanding of the molecular mechanisms controlling the low phytic acid phenotype and assist in the development of a diagnostic marker for the selection of the lpa1-1 gene in barley.

Genetic analysis of two OsLpa1-like genes in Arabidopsis reveals that only one is required for wild-type seed phytic acid levels

Phytic acid (inositol-1,2,3,4,5,6-hexakisphosphate or InsP(6)) is the primary storage form of phosphorus in plant seeds. The rice OsLpa1 encodes a novel protein required for wild-type levels of seed InsP(6) and was identified from a low phytic acid (lpa) mutant exhibiting a 45-50% reduction in seed InsP(6). OsLpa1 is highly conserved in plants and Arabidopsis contains two OsLpa1-like genes, At3g45090 and At5g60760. Analysis of homozygous T-DNA insertion mutants of At5g60760 revealed significantly reduced levels of seed InsP(6) while no changes were observed in seeds of At3g45090 mutants. A double knockout mutant of At5g60760 and At3g45090 was created and its seed InsP(6) content was similar to that of the At5g60760 mutant indicating that At3g45090 does not provide functional redundancy. OsLpa1 was confirmed to be the ortholog of At5g60760 by complementation of a knockout mutant with a cDNA clone corresponding to the largest of three alternative transcripts of OsLpa1. The spatial and temporal expression of At5g60760 during seed development is consistent with its involvement in seed InsP(6) biosynthesis.

Mutations in genes controlling the biosynthesis and accumulation of inositol phosphates in seeds

Most of the phosphorus in the resting seed is stored inside protein storage vacuoles as PA (phytic acid; InsP(6)). The biosynthesis and accumulation of PA can be detected beginning from a few days after anthesis and seem to continue during seed development until maturation. The first step in PA biosynthesis is the formation of Ins3P by conversion of glucose 6-phosphate. This is then followed by a sequential and ordered phosphorylation of the remaining five positions of the inositol ring by a number of kinases, resulting in PA. Identification of low-PA mutants in cereals, legumes and Arabidopsis is instrumental for resolving the biosynthetic pathway and identification of genes controlling the accumulation of PA. Mutations in seven genes involved in the metabolism of PA have been identified and characterized among five plant species using induced mutagenesis and insertion elements. Understanding the biosynthetic pathway and genes controlling the accumulation of PA in plant seeds and how PA may balance the free phosphate is of importance for molecular breeding of crop plants, particularly cereals and legumes.

Mutations of the multi-drug resistance-associated protein ABC transporter gene 5 result in reduction of phytic acid in rice seeds

Phytic acid (PA, myo-inositol 1,2,3,4,5,6-hexakisphosphate) is important to the nutritional quality of cereal and legume seeds. PA and its salts with micronutrient cations, such as iron and zinc, cannot be digested by humans and non-ruminant animals, and hence may affect food/feed nutritional value and cause P pollution of groundwater from animal waste. We previously developed a set of low phytic acid (LPA) rice mutant lines with the aim of increasing the nutritional quality of rice. Two of these lines, Os-lpa-XS110-2 (homozygous non-lethal) Os-lpa-XS110-3 (homozygous lethal), contain two mutant alleles of a LPA gene (hereafter XS-lpa2-1 and XS-lpa2-2, respectively). In this study, we mapped the XS-lpa2-1 gene to a region on chromosome 3 between microsatellite markers RM14360 and RM1332, where the rice orthologue (OsMRP5) of the maize lpa1 gene is located. Sequence analysis of the OsMRP5 gene revealed a single base pair change (C/G-T/A transition) in the sixth exon of XS-lpa2-1 and a 5-bp deletion in the first exon of XS-lpa2-2. OsMRP5 is expressed in both vegetative tissues and developing seeds, and the two mutations do not change the level of RNA transcription. A T-DNA insertion line, 4A-02500, in which OsMRP5 was disrupted, also showed the same high inorganic phosphorus phenotype as Os-lpa-XS110-3 and appeared to be homozygous lethal. PA is significantly reduced in Os-lpa-XS110-2 (~20%) and in 4A-02500 (~90%) seeds compared with their wild type lines, and no PA was detected in Os-lpa-XS110-3 using HPLC analysis. This evidence indicates that the OsMRP5 gene plays an important role in PA metabolism in rice seeds.

Isolation and characterization of a low phytic acid rice mutant reveals a mutation in the rice orthologue of maize MIK

Using a forward genetics approach, we isolated two independent low phytic acid (lpa) rice mutants, N15-186 and N15-375. Both mutants are caused by single gene, recessive non-lethal mutations, which result in approximately 75% (N15-186) and 43% (N15-375) reductions in seed phytic acid (inositol hexakisphosphate). High-performance liquid chromatography and GC-MS analysis of seed extracts from N15-186 indicated that, in addition to phytic acid, inositol monophosphate was significantly reduced whereas inorganic phosphorus and myo-inositol were greatly increased when compared with wild-type. The changes observed in N15-186 resemble those previously described for the maize lpa3 mutant. Analysis of N15-375 revealed changes similar to those observed in previously characterized rice lpa1 mutants (i.e. significant reduction in phytic acid and corresponding increase in inorganic phosphorus with little or no change in inositol phosphate intermediates or myo-inositol). Further genetic analysis of the N15-186 mutant indicated that the mutation, designated lpa N15-186, was located in a region on chromosome 3 between the microsatellite markers RM15875 and RM15907. The rice orthologue of maize lpa3, which encodes a myo-inositol kinase, is in this interval. Sequence analysis of the N15-186 allele of this orthologue (Os03g52760) revealed a single base pair change (C/G to T/A) in the first exon of the gene, which results in a nonsense mutation. Our results indicate that lpa N15-186 is a mutant allele of the rice myo-inositol kinase (OsMIK) gene. Identification and characterization of lpa mutants, such as N15-186, will facilitate studies on the regulation of phytic acid biosynthesis and accumulation and help address questions concerning the contribution of the inositol lipid-dependent and independent biosynthetic pathways to the production of seed phytic acid.