Low Phytic Acid Mutants Research Articles

Study of Seed Ageing in lpa1-1 Maize Mutant and Two Possible Approaches to Restore Seed Germination.

Phytic acid (PA) is a strong anti-nutritional factor with a key antioxidant role in countering reactive oxygen species. Despite the potential benefits of low phytic acid (lpa) mutants, the reduction of PA causes pleiotropic effects, e.g., reduced seed germination and viability loss related to seed ageing. The current study evaluated a historical series of naturally aged seeds and showed that lpa1-1 seeds aged faster as compared to wildtype. To mimic natural ageing, the present study set up accelerated ageing treatments at different temperatures. It was found that incubating the seeds at 57 °C for 24 h, the wildtype germinated at 82.4% and lpa1-1 at 40%. The current study also hypothesized two possible solutions to overcome these problems: (1) Classical breeding was used to constitute synthetic populations carrying the lpa1-1 mutation, with genes pushing anthocyanin accumulation in the embryo (R-navajo allele). The outcome showed that the presence of R-navajo in the lpa1-1 genotype was not able to improve the germinability (-20%), but this approach could be useful to improve the germinability in non-mutant genotypes (+17%). (2) In addition, hydropriming was tested on lpa1-1 and wildtype seeds, and germination was improved by 20% in lpa1-1, suggesting a positive role of seed priming in restoring germination. Moreover, the data highlighted metabolic differences in the metabolome before and after hydropriming treatment, suggesting that the differences in germination could also be mediated by differences in the metabolic composition induced by the mutation.

The Potential of Low Phytic Acid1-1 Mutant in Maize (Zea mays L.): A Sustainable Solution to Non-Renewable Phosphorus.

Phosphorus is an essential component of fertilizers and feed and in recent decades has become one of the main sustainability issues as a non-renewable resource. In plant seeds, the main reserve of phosphorus is phytic acid, a strong anti-nutritional factor for monogastrics and a pollutant of cultivated lands. The reduction of phytic acid in cereal seeds has become a major challenge in breeding programs to increase the nutritional quality of foods and feeds and to improve the environmental phosphorus sustainability in agriculture. In maize (Zea mays L.), four low phytic acid (lpa) mutations have been isolated and lpa1-1 is the most promising. However, the reduction of phytic acid in lpa1-1 leads to many adverse pleiotropic effects on the seed and in general on plant performance. A seed weight reduction and a consequent yield loss were previously described in this mutant. In this work, a field experiment to study seed weight and yield was conducted for two years in two different genetic backgrounds (B73 and B73/Mo17). Furthermore, the greater susceptibility of lpa1-1 to drought stress was also investigated: a dedicated field experiment was set up and measurements were carried out under optimal water conditions and moderate drought stress. From the first experiment it emerges that under high-input conditions, lpa1-1 seems to have comparable or even better yield than the relative control. The main problem of this mutant remains the reduced field emergence (~40%). In the study of drought stress it was found that the increased sensitivity in the mutant is mainly caused by an altered stomatal regulation, but not by a less developed root system, as previously reported. When the stress occurred, the parameters measured did not significantly change in the wild-type, while they dropped in the mutant: the net photosynthesis decreased by 58%, the transpiration rate by 63% and the stomatal conductance by 67%. Some possible solutions have been proposed, with the aim of developing a commercial variety, which remains the main goal to exploit the nutritional benefits of low phytic acid mutants.

Introgression of the low phytic acid locus (lpa2) into elite maize (Zea mays L.) inbreds through marker-assisted backcross breeding (MABB)

Phytic acid (PA) is an important antinutritional component in maize that affects the availability of major micro-nutrients like di- and multi-valent mineral cations like iron (Fe) and zinc (Zn). The long-term consumption of maize as a staple food crop leads to micronutrient malnutrition especially iron and zinc deficiency in the human population. In addition, it also acts as a storehouse of a major part of mineral phosphorous (P), approximately 80% of the total P stored as phytate P is not available to mono-gastric animals like humans and poultry birds, and it gets excreted as such, leading to one of the major environmental pollution called eutrophication. Of the various low phytic acid (lpa) mutants, lpa2-2 generated through mutagenesis reduces PA by 30%. BML 6 and BML 45, the parents of the popular maize hybrid DHM 121 with high PA were selected to introgress lpa2-2 through marker-assisted backcross breeding (MABB). The percent recurrent parental genome (RPG) in the selected BC2F2 plants ranged from 88.68 to 91.04% and 90.09–91.51% in the genetic background of BML 6 and BML 45, respectively. Based on the highest percentage of RPG, best five BC2F2 plants, viz., #3190, #3283, #3230, #3263 and #3292 with RPG 88.68–91.04% in the genetic background of BML 6 and #3720, #3776, #3717, #3828 and #3832 with RPG 90.09–91.51% in the genetic background of BML 45 were advanced to BC2F3. The newly developed near-isogenic lines (NILs) possessed low phytate content (2.37 mg/g in BML 6 and 2.40 mg/g in BML 45) compared to 3.59 mg/g and 3.16 mg/g in recurrent parents BML 6 and BML 45, respectively thereby reducing the phytate by an average of 34 and 24 per cent, respectively. These newly developed progenies were similar to their recurrent parents for various morphological traits. These inbreds assume great significance in alleviating Fe and Zn deficiencies in worldwide.

Genetic and molecular characterisation of subtropically adapted low-phytate genotypes for utilisation in mineral biofortification of maize (

Phytic acid (PA) is a major anti-nutritional factor in maize grains and significantly reduces the bioavailability of minerals such as iron and zinc in humans. Reduction of PA in maize (Zea mays L.) thus assumes great significance. Despite the availability of low phytic-acid (lpa) mutants in maize, their utilisation in breeding has been limited because of non-availability of well adapted lpa-based inbreds. A set of 24 subtropically adapted lpa1-1-based maize inbreds derived through molecular breeding was evaluated along with seven wild-type inbreds at multilocation. The lpa1-1 inbreds possessed 35.8% lower PA (1.68 mg/g) than the wild-type inbreds (2.61 mg/g). Mean proportion of PA was lower in the lpa1-1-based inbreds (62.8%) than in the wild-type inbreds (91.6%). The lpa1-1 inbreds showed similar performance for plant- and ear-height besides flowering behaviour as did wild types. Average grain yield among lpa1-1 inbreds (2735.9 kg/ha) was at par with the original versions (2907.3 kg/ha). Molecular profiling of these lpa1-1 inbreds using 60 genome-wide single-sequence repeats generated 172 alleles, with a mean of 2.87 alleles per locus. Mean polymorphism information content and mean gene diversity were 0.41 and 0.48 respectively. Genetic dissimilarity ranged from 0.23 to 0.81, with an average of 0.64. Cluster analyses grouped 24 lpa1-1 genotypes into three major clusters, and principal-coordinate analysis depicted the diverse nature of genotypes. The study also identified a set of potential hybrid combinations with low PA for their direct utilisation in biofortification program. This is the first study on comprehensive characterisation of lpa1-1-based inbreds adapted to subtropical conditions.

Combination of High Zn Density and Low Phytic Acid for Improving Zn Bioavailability in Rice (Oryza stavia L.) Grain

BackgroundZn deficiency is one of the leading public health problems in the world. Staple food crop, such as rice, cannot provide enough Zn to meet the daily dietary requirement because Zn in grain would chelate with phytic acid, which resulted in low Zn bioavailability. Breeding new rice varieties with high Zn bioavailability will be an effective, economic and sustainable strategy to alleviate human Zn deficiency.ResultsThe high Zn density mutant LLZ was crossed with the low phytic acid mutant Os-lpa-XS110–1, and the contents of Zn and phytic acid in the brown rice were determined for the resulting progenies grown at different sites. Among the hybrid progenies, the double mutant always displayed significantly higher Zn content and lower phytic acid content in grain, leading to the lowest molar ratio of phytic acid to Zn under all environments. As assessed by in vitro digestion/Caco-2 cell model, the double mutant contained the relatively high content of bioavailable Zn in brown rice.ConclusionsOur findings suggested pyramiding breeding by a combination of high Zn density and low phytic acid is a practical and useful approach to improve Zn bioavailability in rice grain.

An Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase 1 Mutant with a 33-nt Deletion Showed Enhanced Tolerance to Salt and Drought Stress in Rice.

OsIPK1 encodes inositol 1,3,4,5,6-pentakisphosphate 2-kinase, which catalyzes the conversion of myo-inositol-1,3,4,5,6-pentakisphosphate to myo-inositol-1,2,3,4,5,6-hexakisphosphate (IP6) in rice. By clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas9)-mediated mutagenesis in the 3rd exon of the gene, three OsIPK1 mutations, i.e., osipk1_1 (a 33-nt deletion), osipk1_2 (a 1-nt deletion), and osipk1_3 (a 2-nt deletion) were identified in T0 plants of the rice line Xidao #1 (wild type, WT). A transfer DNA free line with the homozygous osipk1_1 mutation was developed; however, no homozygous mutant lines could be developed for the other two mutations. The comparative assay showed that the osipk1_1 mutant line had a significantly lower level of phytic acid (PA, IP6; −19.5%) in rice grain and agronomic traits comparable to the WT. However, the osipk1_1 mutant was more tolerant to salt and drought stresses than the WT, with significantly lower levels of inositol triphosphate (IP3), reactive oxygen species (ROS) and induced IP6, and higher activities of antioxidant enzymes in seedlings subjected to these stresses. Further analyses showed that the transcription of stress response genes was significantly upregulated in the osipk1_1 mutant under stress. Thus, the low phytic acid mutant osipk1_1 should have potential applications in rice breeding and production.

Genetic Analysis and Molecular Mapping of the Quantitative Trait Loci Governing Low Phytic Acid Content in a Novel LPA Rice Mutant, PLM11.

Breeding rice varieties with a low phytic acid (LPA) content is an effective strategy to overcome micronutrient deficiency in a population which consume rice as a staple food. An LPA mutant, Pusa LPA Mutant 11 (PLM11), was identified from an ethyl methane sulfonate (EMS)-induced population of Nagina 22. The present study was carried out to map the loci governing the LPA trait in PLM11 using an F2:3 population derived from a cross between a high phytic acid rice variety, Pusa Basmati 6, with PLM11. The genotyping of the F2 population with 78 polymorphic SSR markers followed by the estimation of phytic acid content in the seeds harvested from 176 F2 plants helped in mapping a major QTL, qLPA8.1, explaining a 22.2% phenotypic variation on Chromosome 8. The QTL was delimited to a 1.96 cM region flanked by the markers RM25 and RM22832. Since there are no previous reports of a QTL/gene governing the LPA content in rice in this region, the QTL qLPA8.1 is a novel QTL. In silico analysis based on the annotated physical map of rice suggested the possible involvement of a locus, Os08g0274775, encoding for a protein similar to a phosphatidylinositol 3- and 4-kinase family member. This needs further validation and fine mapping. Since this QTL is currently specific to PLM11, the linked markers can be utilized for the development of rice varieties with reduced phytic acid (PA) content using PLM11 as the donor, thus enhancing the bioavailability of mineral micronutrients in humans.

MRP Transporters and Low Phytic Acid Mutants in Major Crops: Main Pleiotropic Effects and Future Perspectives.

Phytic acid (PA) represents the major storage form of seed phosphate (P). During seed maturation, it accumulates as phytate salts chelating various mineral cations, therefore reducing their bioavailability. During germination, phytase dephosphorylates PA releasing both P and cations which in turn can be used for the nutrition of the growing seedling. Animals do not possess phytase, thus monogastric animals assimilate only 10% of the phytate ingested with feed, whilst 90% is excreted and may contribute to cause P pollution of the environment. To overcome this double problem, nutritional and environmental, in the last four decades, many low phytic acid (lpa) mutants (most of which affect the PA-MRP transporters) have been isolated and characterized in all major crops, showing that the lpa trait can increase the nutritional quality of foods and feeds and improve P management in agriculture. Nevertheless, these mutations are frequently accompanied by negative pleiotropic effects leading to agronomic defects which may affect either seed viability and germination or plant development or in some cases even increase the resistance to cooking, thus limiting the interest of breeders. Therefore, although some significant results have been reached, the isolation of lpa mutants improved for their nutritional quality and with a good field performance remains a goal so far not fully achieved for many crops. Here, we will summarize the main pleiotropic effects that have been reported to date in lpa mutants affected in PA-MRP transporters in five productive agronomic species, as well as addressing some of the possible challenges to overcome these hurdles and improve the breeding efforts for lpa mutants.

Knockout of MULTI-DRUG RESISTANT PROTEIN 5 Genes Lead to Low Phytic Acid Contents in Oilseed Rape.

Understanding phosphate uptake and storage is interesting to optimize the plant performance to phosphorus fluctuations. Phytic acid (PA) is the major source of inorganic phosphorus (Pi) in plants. Genetic analyses of PA pathway transporter genes (BnMRP5) and their functional characterization might provide clues in better utilizing the available phosphate resources. Furthermore, the failure to assimilate PA by monogastric animals results in its excess accumulation in manure, which ultimately causes groundwater eutrophication. As a first step toward breeding low PA mutants in oilseed rape (Brassica napus L.), we identified knockout mutants in PA biosynthesis and transporter genes. The obtained M3 single mutants of Bn.MRP5.A10 and Bn.MRP5.C09 were combined by crossing to produce double mutants. Simultaneously, crosses were performed with the non-mutagenized EMS donor genotype to reduce the background mutation load. Double mutants identified from the F2 progeny of direct M3 crosses and BC1 plants showed 15% reduction in PA contents with no significant differences in Pi. We are discussing the function of BnMRP5 paralogs and the benefits for breeding Bnmrp5 mutants in respect to low PA, yield, and stress tolerances.

Gene editing of three BnITPK genes in tetraploid oilseed rape leads to significant reduction of phytic acid in seeds.

SummaryCommercialization of Brassica napus. L (oilseed rape) meal as protein diet is gaining more attention due to its well‐balanced amino acid and protein contents. Phytic acid (PA) is a major source of phosphorus in plants but is considered as anti‐nutritive for monogastric animals including humans due to its adverse effects on essential mineral absorption. The undigested PA causes eutrophication, which potentially threatens aquatic life. PA accounts to 2‐5% in mature seeds of oilseed rape and is synthesized by complex pathways involving multiple enzymes. Breeding polyploids for recessive traits is challenging as gene functions are encoded by several paralogs. Gene redundancy often requires to knock out several gene copies to study their underlying effects. Therefore, we adopted CRISPR‐Cas9 mutagenesis to knock out three functional paralogs of BnITPK. We obtained low PA mutants with an increase of free phosphorus in the canola grade spring cultivar Haydn. These mutants could mark an important milestone in rapeseed breeding with an increase in protein value and no adverse effects on oil contents.

Phytic Acid and Transporters: What Can We Learn from low phytic acid Mutants.

Phytic acid has two main roles in plant tissues: Storage of phosphorus and regulation of different cellular processes. From a nutritional point of view, it is considered an antinutritional compound because, being a cation chelator, its presence reduces mineral bioavailability from the diet. In recent decades, the development of low phytic acid (lpa) mutants has been an important goal for nutritional seed quality improvement, mainly in cereals and legumes. Different lpa mutations affect phytic acid biosynthetic genes. However, other lpa mutations isolated so far, affect genes coding for three classes of transporters: A specific group of ABCC type vacuolar transporters, putative sulfate transporters, and phosphate transporters. In the present review, we summarize advances in the characterization of these transporters in cereals and legumes. Particularly, we describe genes, proteins, and mutants for these different transporters, and we report data of in silico analysis aimed at identifying the putative orthologs in some other cereal and legume species. Finally, we comment on the advantage of using such types of mutants for crop biofortification and on their possible utility to unravel links between phosphorus and sulfur metabolism (phosphate and sulfate homeostasis crosstalk).

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.

Quantitative proteomic analyses of two soybean low phytic acid mutants to identify the genes associated with seed field emergence

BackgroundSeed germination is essential to crop growth and development, and ultimately affects its harvest. It is difficult to breed soybeans low in phytic acid with a higher seed field emergence. Although additional management and selection could overcome the phytate reduction, the mechanisms of seed germination remain unknown.ResultsA comparative proteomic analysis was conducted between two low phytic acid (LPA) soybean mutants (TW-1-M and TW-1), both of which had a deletion of 2 bp in the GmMIPS1 gene. However, the TW-1 seeds showed a significantly lower field emergence compared to the TW-1-M. There were 282 differentially accumulated proteins (DAPs) identified between two mutants at the three stages. Among these DAPs, 80 were down-accumulated and 202 were up-accumulated. Bioinformatic analysis showed that the identified proteins were related to functional categories of oxidation reduction, response to stimulus and stress, dormancy and germination processes and catalytic activity. KEGG analysis showed that these DAPs were mainly involved in energy metabolism and anti-stress pathways. Based upon the conjoint analysis of DAPs with the differentially expressed genes (DEGs) previously published among three germination stages in two LPA mutants, 30 shared DAPs/DEGs were identified with different patterns, including plant seed protein, beta-amylase, protein disulfide-isomerase, disease resistance protein, pyrophosphate-fructose 6-phosphate 1-phosphotransferase, cysteine proteinase inhibitor, non-specific lipid-transfer protein, phosphoenolpyruvate carboxylase and acyl-coenzyme A oxidase.ConclusionsSeed germination is a very complex process in LPA soybean mutants. The TW-1-M and TW-1 showed many DAPs involved in seed germination. The differential accumulation of these proteins could result in the difference of seed field emergence between the two mutants. The high germination rate in the TW-1-M might be strongly attributed to reactive oxygen species-related and plant hormone-related genes. All these findings would help us further explore the germination mechanisms in LPA crops.

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.

Registration of Great Plains–Adapted Reduced Phytate Winter Wheat Germplasm

Reduced or low phytic acid (LPA) mutants of wheat (Triticum aestivum L.) increase the bioavailability and, subsequently, the gut absorption of minerals in monogastric animals, including humans. The USDA–ARS in cooperation with the University of Nebraska developed and released eight low phytate (LPA) winter wheat lines (N16MD9012 [Reg. No. GP‐1024, PI 682715], N16MD9140 [Reg. No. GP‐1025, PI 682717], N16MD9275 [Reg. No., GP‐1026, PI 682718], N16MD9268 [Reg. No. GP‐1027, PI 682719], N16MD9046 [Reg. No. GP‐1028, PI 682720], N16MD9204 [Reg. No. GP‐1029, PI 682722], N16MD9074 [Reg. No. GP‐1030, PI 682723], and N16MD9153 [Reg. No. GP‐1031, PI 682724]) adapted to the Great Plains of North America. The highest‐yielding LPA line was not significantly different in grain yield from the adapted controls ‘Anton’ and ‘Intrada’, was significantly higher in grain yield than ‘Big Sky’ and ‘Siouxland’, but was significantly lower than the two highest‐yielding controls, ‘Freeman’ and ‘Ruth’. Overall, there were no significant differences in grain yield, grain volume weight, and grain protein concentration (GPC) between the LPA lines and the mean values of the adapted controls. On average, the LPA lines had 18% more zinc than the adapted controls. Six of the eight LPA lines contain the Lr37/Sr38/Yr17 genes combination, which provides resistance for leaf, stem, and yellow/stripe rust. Grain yield data obtained in diverse environments in Nebraska indicated no grain yield reduction associated with the low phytate trait.

Characterization of the Symbiotic Nitrogen-Fixing Common Bean Low Phytic Acid (lpa1) Mutant Response to Water Stress.

The common bean (Phaseolus vulgaris L.) low phytic acid (lpa1) biofortified genotype produces seeds with improved nutritional characteristics and does not display negative pleiotropic effects. Here we demonstrated that lpa1 plants establish an efficient nitrogen-fixing symbiosis with Rhizobium etli CE3. The lpa1 nodules showed a higher expression of nodule-function related genes than the nodules of the parental wild type genotype (BAT 93). We analyzed the response to water stress of lpa1 vs. BAT 93 plants grown under fertilized or under symbiotic N2-fixation conditions. Water stress was induced by water withholding (up to 14% soil moisture) to fertilized or R. etli nodulated plants previously grown with normal irrigation. The fertilized lpa1 plants showed milder water stress symptoms during the water deployment period and after the rehydration recovery period when lpa1 plants showed less biomass reduction. The symbiotic water-stressed lpa1 plants showed decreased nitrogenase activity that coincides with decreased sucrose synthase gene expression in nodules; lower turgor weight to dry weight (DW) ratio, which has been associated with higher drought resistance index; downregulation of carbon/nitrogen (C/N)-related and upregulation of stress-related genes. Higher expression of stress-related genes was also observed in bacteroids of stressed lpa1 plants that also displayed very high expression of the symbiotic cbb3 oxidase (fixNd).

Phytic acid transport in Phaseolus vulgaris: A new low phytic acid mutant in the PvMRP1 gene and study of the PvMRPs promoters in two different plant systems

Phytic acid (InsP6) is the main storage form of phosphate in seeds. In the plant it plays an important role in response to environmental stress and hormonal changes. InsP6 is a strong chelator of cations, reducing the bioavailability of essential minerals in the diet. Only a common bean low phytic acid (lpa1) mutant, affected in the PvMRP1 gene, coding for a putative tonoplastic phytic acid transporter, was described so far. This mutant is devoid of negative pleiotropic effects normally characterising lpa mutants. With the aim of isolating new common bean lpa mutants, an ethyl methane sulfonate mutagenized population was screened, resulting in the identification of an additional lpa1 allele. Other putative lpa lines were also isolated. The PvMRP2 gene is probably able to complement the phenotype of mutants affected in the PvMRP1 gene in tissues other than the seed. Only the PvMRP1 gene is expressed at appreciable levels in cotyledons. Arabidopsis thaliana and Medicago truncatula transgenic plants harbouring 1.5 kb portions of the intergenic 5′ sequences of both PvMRP genes, fused upstream of the GUS reporter, were generated. GUS activity in different organs suggests a refined, species-specific mechanisms of regulation of gene expression for these two PvMRP genes.

Selection of Novel Non-lethal, Low Phytic Acid Mutants and Evaluation of their Agronomic Traits/Mineral Compositions in Rice (<i>Oryza sativa</i>)

Selection of Novel Non-lethal, Low Phytic Acid Mutants and Evaluation of their Agronomic Traits/Mineral Compositions in Rice (<i>Oryza sativa</i>)

Inference of Transcription Regulatory Network in Low Phytic Acid Soybean Seeds.

A dominant loss of function mutation in myo-inositol phosphate synthase (MIPS) gene and recessive loss of function mutations in two multidrug resistant protein type-ABC transporter genes not only reduce the seed phytic acid levels in soybean, but also affect the pathways associated with seed development, ultimately resulting in low emergence. To understand the regulatory mechanisms and identify key genes that intervene in the seed development process in low phytic acid crops, we performed computational inference of gene regulatory networks in low and normal phytic acid soybeans using a time course transcriptomic data and multiple network inference algorithms. We identified a set of putative candidate transcription factors and their regulatory interactions with genes that have functions in myo-inositol biosynthesis, auxin-ABA signaling, and seed dormancy. We evaluated the performance of our unsupervised network inference method by comparing the predicted regulatory network with published regulatory interactions in Arabidopsis. Some contrasting regulatory interactions were observed in low phytic acid mutants compared to non-mutant lines. These findings provide important hypotheses on expression regulation of myo-inositol metabolism and phytohormone signaling in developing low phytic acid soybeans. The computational pipeline used for unsupervised network learning in this study is provided as open source software and is freely available at https://lilabatvt.github.io/LPANetwork/.

Genetic architecture of grain chalk in rice and interactions with a low phytic acid locus

Grain quality characteristics have a major impact on the value of the harvested rice crop. In addition to grain dimensions which determine rice grain market classes, translucent milled kernels are also important for assuring the highest grain quality and crop value. Over the last several years, there has been increasing concern by the rice industry regarding prevalence of chalky grains which are resulting in a loss of some markets. This study was conducted to identify genetic markers associated with grain chalk that could be used by breeders to develop new varieties that have translucent grains across different environments. A mapping population developed from KBNT-1-1, a translucent, low phytic acid (LPA) mutant derived from the US long grain variety Kaybonnet, crossed with Zhe733, a chalky, long grain variety developed in China, was evaluated in replicated trials conducted across two years and two planting dates that differed by one month. The progeny were evaluated for days to flowering in the field. Grain was harvested at maturity and brown or milled rice were used to determine grain length, width, and percent chalk using an image analysis system. The 187 F12 progeny were evaluated using 174 genome-wide microsatellite markers and one SNP marker, and QTL analysis was performed. A large effect QTL was co-located with the LPA gene, and the mutated KBNT-1-1 LPA allele was associated with increased chalk suggesting that low phytic acid may be one cause of chalk in this cross. Nine additional QTL were detected with the KBNT-1-1 allele associated with reduced chalk and one with increased chalk. Overlaps were identified between chalk QTL, candidate genes for chalk, and QTL for other traits such as grain width. Measures of night temperature and humidity experienced during grain filling were positively correlated with increased chalk. Year and planting time were also shown to significantly affect chalk. However there was no interaction with the pattern of QTL detected and any of the environmental differences, indicating that these QTL are robust across diverse growing conditions.