The genetics underlying metabolic signatures in a brown rice diversity panel and their vital role in human nutrition.

Brown rice (Oryza sativa) possesses various nutritionally dense bioactive phytochemicals exhibiting a wide range of antioxidant, anti-cancer, and anti-diabetic properties known to promote various human health benefits. However, despite the wide claims made about the importance of brown rice for human nutrition the underlying metabolic diversity has not been systematically explored. Non-targeted metabolite profiling of developing and mature seeds of a diverse genetic panel of 320 rice cultivars allowed quantification of 117 metabolites. The metabolite genome-wide association study (mGWAS) detected genetic variants influencing diverse metabolic targets in developing and mature seeds. We further interlinked genetic variants on chromosome 7 (6.06-6.43 Mb region) with complex epistatic genetic interactions impacting multi-dimensional nutritional targets, including complex carbohydrate starch quality, the glycemic index, antioxidant catechin, and rice grain color. Through this nutrigenomics approach rare gene bank accessions possessing genetic variants in bHLH and IPT5 genes were identified through haplotype enrichment. These variants were associated with a low glycemic index, higher catechin levels, elevated total flavonoid contents, and heightened antioxidant activity in the whole grain with elevated anti-cancer properties being confirmed in cancer cell lines. This multi-disciplinary nutrigenomics approach thus allowed us to discover the genetic basis of human health-conferring diversity in the metabolome of brown rice.

Nutritional and genetic variation in a core set of Ethiopian Tef (Eragrostis tef) varieties.

BACKGROUND: Tef (Eragrostis tef) is a tropical cereal domesticated and grown in the Ethiopian highlands, where it has been a staple food of Ethiopians for many centuries. Food insecurity and nutrient deficiencies are major problems in the country, so breeding for enhanced nutritional traits, such as Zn content, could help to alleviate problems with malnutrition. RESULTS: To understand the breeding potential of nutritional traits in tef a core set of 24 varieties were sequenced and their mineral content, levels of phytate and protein, as well as a number of nutritionally valuable phenolic compounds measured in grain. Significant variation in all these traits was found between varieties. Genome wide sequencing of the 24 tef varieties revealed 3,193,582 unique SNPs and 897,272 unique INDELs relative to the tef reference var. Dabbi. Sequence analysis of two key transporter families involved in the uptake and transport of Zn by the plant led to the identification of 32 Zinc Iron Permease (ZIP) transporters and 14 Heavy Metal Associated (HMA) transporters in tef. Further analysis identified numerous variants, of which 14.6% of EtZIP and 12.4% of EtHMA variants were non-synonymous changes. Analysis of a key enzyme in flavanol synthesis, flavonoid 3'-hydroxylase (F3'H), identified a T-G variant in the tef homologue Et_s3159-0.29-1.mrna1 that was associated with the differences observed in kaempferol glycoside and quercetin glycoside levels. CONCLUSION: Wide genetic and phenotypic variation was found in 24 Ethiopian tef varieties which would allow for breeding gains in many nutritional traits of importance to human health.

The Role of the Wheat Reduced height (Rht)-DELLA Mutants and Associated Hormones in Infection by Claviceps purpurea, the Causal Agent of Ergot.

Partial resistance to the biotrophic fungal pathogen Claviceps purpurea, causal agent of ergot, has been found that colocates with mutant alleles of the wheat Reduced height (Rht) loci on chromosomes 4B and 4D. These Rht loci represent the wheat orthologs of the Arabidopsis Della genes. To investigate the role of the Rht mutant DELLA proteins in ergot resistance, we assessed C. purpurea infection in wheat near-isogenic lines (NILs) carrying the gibberellic acid (GA)-insensitive semidwarf alleles Rht-B1b and Rht-D1b and the severe dwarf alleles Rht-B1c and Rht-D1c. NILs of the GA-sensitive alleles Rht8 (chromosome 2D) and Rht12 (chromosome 5A) were also included. A general trend toward increased resistance to C. purpurea, with smaller and lighter sclerotia, was observed on the NILs Rht-B1b, Rht-D1b, Rht-B1c, and Rht-D1c, and also on Rht8. Levels of the bioactive GA4 and the auxin indole-3-acetic acid increased after inoculation with C. purpurea, following similar patterns and implicating a potential auxin-mediated induction of GA biosynthesis. In contrast, jasmonic acid (JA) levels fell in the parental lines 'Mercia' and 'Maris Huntsman' after inoculation with C. purpurea, but increased in all the Rht-mutant NILs. Inoculation with C. purpurea did not show any informative changes in the levels of salicylic acid. Our results suggest that GA-mediated degradation of the DELLA proteins and down-regulation of JA-signaling pathways supports infection of wheat by C. purpurea. As these responses are generally associated with necrotrophic fungal pathogens, we propose that the biotroph C. purpurea may have a necrotrophic growth stage.

Distribution of Puccinia striiformis f. sp. tritici Races and Virulence in Wheat Growing Regions of Kenya from 1970 to 2014.

Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, is a major threat to wheat (Triticum spp.) production worldwide. The objective of this study was to determine the virulence of P. striiformis f. sp. tritici races prevalent in the main wheat growing regions of Kenya, which includes Mt. Kenya, Eastern Kenya, and the Rift Valley (Central, Southern, and Northern Rift). Fifty P. striiformis f. sp. tritici isolates collected from 1970 to 1992 and from 2009 to 2014 were virulence phenotyped with stripe rust differential sets, and 45 isolates were genotyped with sequence characterized amplified region (SCAR) markers to differentiate the isolates and identify aggressive strains PstS1 and PstS2. Virulence corresponding to stripe rust resistance genes Yr1, Yr2, Yr3, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, and Yr27 and the seedling resistance in genotype Avocet S were detected. Ten races were detected in the P. striiformis f. sp. tritici samples obtained from 1970 to 1992, and three additional races were detected from 2009 to 2014, with a single race being detected in both periods. The SCAR markers detected both Pst1 and Pst2 strains in the collection. Increasing P. striiformis f. sp. tritici virulence was found in the Kenyan P. striiformis f. sp. tritici population, and different P. striiformis f. sp. tritici race groups were found to dominate different wheat growing regions. Moreover, recent P. striiformis f. sp. tritici races in East Africa indicated possible migration of some race groups into Kenya from other regions. This study is important in elucidating P. striiformis f. sp. tritici evolution and virulence diversity and useful in breeding wheat cultivars with effective resistance to stripe rust.

Reprogramming of the wheat transcriptome in response to infection with Claviceps purpurea, the causal agent of ergot.

BACKGROUND: Ergot, caused by the fungal pathogen Claviceps purpurea, infects the female flowers of a range of cereal crops, including wheat. To understand the interaction between C. purpurea and hexaploid wheat we undertook an extensive examination of the reprogramming of the wheat transcriptome in response to C. purpurea infection through floral tissues (i.e. the stigma, transmitting and base ovule tissues of the ovary) and over time. RESULTS: C. purpurea hyphae were observed to have grown into and down the stigma at 24 h (H) after inoculation. By 48H hyphae had grown through the transmitting tissue into the base, while by 72H hyphae had surrounded the ovule. By 5 days (D) the ovule had been replaced by fungal tissue. Differential gene expression was first observed at 1H in the stigma tissue. Many of the wheat genes differentially transcribed in response to C. purpurea infection were associated with plant hormones and included the ethylene (ET), auxin, cytokinin, gibberellic acid (GA), salicylic acid and jasmonic acid (JA) biosynthetic and signaling pathways. Hormone-associated genes were first detected in the stigma and base tissues at 24H, but not in the transmitting tissue. Genes associated with GA and JA pathways were seen in the stigma at 24H, while JA and ET-associated genes were identified in the base at 24H. In addition, several defence-related genes were differential expressed in response to C. purpurea infection, including antifungal proteins, endocytosis/exocytosis-related proteins, NBS-LRR class proteins, genes involved in programmed cell death, receptor protein kinases and transcription factors. Of particular interest was the identification of differential expression of wheat genes in the base tissue well before the appearance of fungal hyphae, suggesting that a mobile signal, either pathogen or plant-derived, is delivered to the base prior to colonisation. CONCLUSIONS: Multiple host hormone biosynthesis and signalling pathways were significantly perturbed from an early stage in the wheat - C. purpurea interaction. Differential gene expression at the base of the ovary, ahead of arrival of the pathogen, indicated the potential presence of a long-distance signal modifying host gene expression.

Genetic and transcriptional dissection of resistance to Claviceps purpurea in the durum wheat cultivar Greenshank.

KEY MESSAGE: Four QTL for ergot resistance (causal pathogen Claviceps purpurea) have been identified in the durum wheat cultivar Greenshank. Claviceps purpurea is a pathogen of grasses that infects flowers, replacing the seed with an ergot sclerotium. Ergot presents a significant problem to rye, barley and wheat, in particular hybrid seed production systems. In addition, there is evidence that the highly toxic alkaloids that accumulate within sclerotia can cross-contaminate otherwise healthy grain. Host resistance to C. purpurea is rare, few resistance loci having been identified. In this study, four ergot resistance loci are located on chromosomes 1B, 2A, 5A and 5B in the durum wheat cv. Greenshank. Ergot resistance was assessed through analysis of phenotypes associated with C. purpurea infection, namely the number of inoculated flowers that produced sclerotia, or resulted in ovary death but no sclerotia, the levels of honeydew produced, total sclerotia weight and average sclerotia weight and size per spike. Ergot testing was undertaken in Canada and the UK. A major effect QTL, QCp.aafc.DH-2A, was detected in both the Canadian and UK experiments and had a significant effect on honeydew production levels. QCp.aafc.DH-5B had the biggest influence on total sclerotia weight per spike. QCp.aafc.DH-1B was only detected in the Canadian experiments and QCp.aafc.DH-5A in the UK experiment. An RNASeq analysis, undertaken to identify wheat differentially expressed genes associated with different combinations of the four ergot resistance QTL, revealed a disproportionate number of DEGs locating to the QCp.aafc.DH-1B, QCp.aafc.DH-2A and QCp.aafc.DH-5B QTL intervals.

Outlook for coeliac disease patients: towards bread wheat with hypoimmunogenic gluten by gene editing of α- and γ-gliadin gene families.

BACKGROUND: Wheat grains contain gluten proteins, which harbour immunogenic epitopes that trigger Coeliac disease in 1-2% of the human population. Wheat varieties or accessions containing only safe gluten have not been identified and conventional breeding alone struggles to achieve such a goal, as the epitopes occur in gluten proteins encoded by five multigene families, these genes are partly located in tandem arrays, and bread wheat is allohexaploid. Gluten immunogenicity can be reduced by modification or deletion of epitopes. Mutagenesis technologies, including CRISPR/Cas9, provide a route to obtain bread wheat containing gluten proteins with fewer immunogenic epitopes. RESULTS: In this study, we analysed the genetic diversity of over 600 α- and γ-gliadin gene sequences to design six sgRNA sequences on relatively conserved domains that we identified near coeliac disease epitopes. They were combined in four CRISPR/Cas9 constructs to target the α- or γ-gliadins, or both simultaneously, in the hexaploid bread wheat cultivar Fielder. We compared the results with those obtained with random mutagenesis in cultivar Paragon by γ-irradiation. For this, Acid-PAGE was used to identify T1 grains with altered gliadin protein profiles compared to the wild-type endosperm. We first optimised the interpretation of Acid-PAGE gels using Chinese Spring deletion lines. We then analysed the changes generated in 360 Paragon γ-irradiated lines and in 117 Fielder CRISPR/Cas9 lines. Similar gliadin profile alterations, with missing protein bands, could be observed in grains produced by both methods. CONCLUSIONS: The results demonstrate the feasibility and efficacy of using CRISPR/Cas9 to simultaneously edit multiple genes in the large α- and γ-gliadin gene families in polyploid bread wheat. Additional methods, generating genomics and proteomics data, will be necessary to determine the exact nature of the mutations generated with both methods.

Genetic Characterization of Leaf and Stripe Rust Resistance in the Brazilian Wheat Cultivar Toropi.

Leaf and stripe rust are major threats to wheat production worldwide. The effective, multiple rust resistances present in the Brazilian cultivar Toropi makes it an excellent choice for a genetic study of rust resistance. Testing of DNA from different seed lots of Toropi with 2,194 polymorphic 90K iSelect single nucleotide polymorphism markers identified significant genetic divergence, with as much as 35% dissimilarity between seed lots. As a result, further work was conducted with a single plant line derived from Toropi variant Toropi-6.4. A double haploid population with 168 lines derived from the cross Toropi-6.4 × Thatcher was phenotyped over multiple years and locations in Canada, New Zealand, and Kenya, with a total of seven field trials undertaken for leaf rust and nine for stripe rust. Genotyping with the 90K iSelect array, simple sequence repeat and Kompetitive allele-specific polymerase chain reaction markers resulted in a genetic map of 3,043 cM, containing 1,208 nonredundant markers. Significant quantitative trait loci (QTL) derived from Toropi-6.4 were identified in multiple environments on chromosomes 1B (QLr.crc-1BL/QYr.crc-1BL), 3B (QLr.crc-3BS), 4B (QYr.crc-4BL), 5A (QLr.crc-5AL and QYr.crc-5AL), and 5D (QLr.crc-5DS). The QTL QLr.crc-1BL/QYr.crc-1BL colocated with the multi-rust resistance locus Lr46/Yr29, while the QTL QLr.crc-5DS located to the Lr78 locus previously found in a wheat backcross population derived from Toropi. Comparisons of QTL combinations showed QLr.crc-1BL to contribute a significantly enhanced leaf rust resistance when combined with QLr.crc-5AL or QLr.crc-5DS, more so than when QLr.crc-5AL and QLr.crc-5DS were combined. A strong additive effect was also seen when the stripe rust resistance QTL QYr.crc-1BL and QYr.crc-5AL were combined.

Quantitative Trait Loci Conferring Leaf Rust Resistance in Hexaploid Wheat.

Leaf rust, caused by the fungal pathogen Puccinia triticina, is a major threat to wheat production in many wheat-growing regions of the world. The introduction of leaf rust resistance genes into elite wheat germplasm is the preferred method of disease control, being environmentally friendly and crucial to sustained wheat production. Consequently, there is considerable value in identifying and characterizing new sources of leaf rust resistance. While many major, qualitative leaf rust resistance genes have been identified in wheat, a growing number of valuable sources of quantitative resistance have been reported. Here we review the progress made in the genetic identification of quantitative trait loci (QTL) for leaf rust resistance detected primarily in field analyses, i.e., adult plant resistance. Over the past 50 years, leaf rust resistance loci have been assigned to genomic locations through chromosome analyses and genetic mapping in biparental mapping populations, studies that represent 79 different wheat leaf rust resistance donor lines. In addition, seven association mapping studies have identified adult plant and seedling leaf rust resistance marker trait associations in over 4,000 wheat genotypes. Adult plant leaf rust resistance QTL have been found on all 21 chromosomes of hexaploid wheat, with the B genome carrying the greatest number of QTL. The group 2 chromosomes are also particularly rich in leaf rust resistance QTL. The A genome has the lowest number of QTL for leaf rust resistance. Copyright © 2018 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

A comparative analysis of nonhost resistance across the two Triticeae crop species wheat and barley.

BACKGROUND: Nonhost resistance (NHR) protects plants against a vast number of non-adapted pathogens which implicates a potential exploitation as source for novel disease resistance strategies. Aiming at a fundamental understanding of NHR a global analysis of transcriptome reprogramming in the economically important Triticeae cereals wheat and barley, comparing host and nonhost interactions in three major fungal pathosystems responsible for powdery mildew (Blumeria graminis ff. ssp.), cereal blast (Magnaporthe sp.) and leaf rust (Puccinia sp.) diseases, was performed. RESULTS: In each pathosystem a significant transcriptome reprogramming by adapted- or non-adapted pathogen isolates was observed, with considerable overlap between Blumeria, Magnaporthe and Puccinia. Small subsets of these general pathogen-regulated genes were identified as differentially regulated between host and corresponding nonhost interactions, indicating a fine-tuning of the general pathogen response during the course of co-evolution. Additionally, the host- or nonhost-related responses were rather specific for each pair of adapted and non-adapted isolates, indicating that the nonhost resistance-related responses were to a great extent pathosystem-specific. This pathosystem-specific reprogramming may reflect different resistance mechanisms operating against non-adapted pathogens with different lifestyles, or equally, different co-option of the hosts by the adapted isolates to create an optimal environment for infection. To compare the transcriptional reprogramming between wheat and barley, putative orthologues were identified. Within the wheat and barley general pathogen-regulated genes, temporal expression profiles of orthologues looked similar, indicating conserved general responses in Triticeae against fungal attack. However, the comparison of orthologues differentially expressed between host and nonhost interactions revealed fewer commonalities between wheat and barley, but rather suggested different host or nonhost responses in the two cereal species. CONCLUSIONS: Taken together, our results suggest independent co-evolutionary forces acting on host pathosystems mirrored by barley- or wheat-specific nonhost responses. As a result of evolutionary processes, at least for the pathosystems investigated, NHR appears to rely on rather specific plant responses.

Plant-pathogen interactions: disease resistance in modern agriculture.

The growing human population will require a significant increase in agricultural production. This challenge is made more difficult by the fact that changes in the climatic and environmental conditions under which crops are grown have resulted in the appearance of new diseases, whereas genetic changes within the pathogen have resulted in the loss of previously effective sources of resistance. To help meet this challenge, advanced genetic and statistical methods of analysis have been used to identify new resistance genes through global screens, and studies of plant-pathogen interactions have been undertaken to uncover the mechanisms by which disease resistance is achieved. The informed deployment of major, race-specific and partial, race-nonspecific resistance, either by conventional breeding or transgenic approaches, will enable the production of crop varieties with effective resistance without impacting on other agronomically important crop traits. Here, we review these recent advances and progress towards the ultimate goal of developing disease-resistant crops.

The identification of QTL controlling ergot sclerotia size in hexaploid wheat implicates a role for the Rht dwarfing alleles.

KEY MESSAGE: Four QTL conferring resistance to ergot were identified in the UK winter wheat varieties 'Robigus' and 'Solstice'. Two QTL co-located with semi-dwarfing alleles at the Rht loci Rht - 1B and Rht - 1D implicating a role of these DELLA proteins in infection success of Claviceps purpurea. The fungal pathogen Claviceps purpurea infects ovaries of a broad range of temperate grasses and cereals, including hexaploid wheat, causing a disease commonly known as ergot. Sclerotia produced in place of seed carry a cocktail of harmful alkaloid compounds that result in a range of symptoms in humans and animals, causing ergotism. Following a field assessment of C. purpurea infection in winter wheat, two varieties 'Robigus' and 'Solstice' were selected which consistently produced the largest differential effect on ergot sclerotia weights. They were crossed to produce a doubled haploid mapping population, and a marker map, consisting of 714 genetic loci and a total length of 2895 cM was produced. Four ergot reducing QTL were identified using both sclerotia weight and size as phenotypic parameters; QCp.niab.2A and QCp.niab.4B being detected in the wheat variety 'Robigus', and QCp.niab.6A and QCp.niab.4D in the variety 'Solstice'. The ergot resistance QTL QCp.niab.4B and QCp.niab.4D peaks mapped to the same markers as the known reduced height (Rht) loci on chromosomes 4B and 4D, Rht-B1 and Rht-D1, respectively. In both cases, the reduction in sclerotia weight and size was associated with the semi-dwarfing alleles, Rht-B1b from 'Robigus' and Rht-D1b from 'Solstice'. Two-dimensional, two-QTL scans identified significant additive interactions between QTL QCp.niab.4B and QCp.niab.4D, and between QCp.niab.2A and QCp.niab.4B when looking at sclerotia size, but not between QCp.niab.2A and QCp.niab.4D. The two plant height QTL, QPh.niab.4B and QPh.niab.4D, which mapped to the same locations as QCp.niab.4B and QCp.niab.4D, also displayed significant genetic interactions.

Changes in gene expression profiles as they relate to the adult plant leaf rust resistance in the wheat cv. Toropi.

Leaf rust, caused by the foliar pathogen Puccinia triticina is a major disease of wheat in the southern region of Brazil and invariably impacts on production, being responsible for high yield losses. The Brazilian wheat cultivar Toropi has proven, durable adult plant resistance (APR) to leaf rust, which uniquely shows a pre-haustorial resistance phenotype. In this study we aimed to understand the interaction between P. triticina and the pre-haustorial APR in Toropi by quantitatively evaluating the temporal transcription profiles of selected genes known to be related to infection and defense in wheat. The expression profiles of 15 selected genes varied over time, grouping into six expression profile groups. The expression profiles indicated the induction of classical defence pathways in response to pathogen development, but also the potential modification of Toropi's cellular status for the benefit of the pathogen. Classical defence genes, including peroxidases, ß-1,3-glucanases and an endochitinase were expressed both early (pre-haustorial) and late (post-haustorial) over the 72 h infection time course, while induction of transcription of other infection-related genes with a potential role in defence, although variable was maintained through-out. These genes directly or indirectly had a role in plant lignification, oxidative stress, the regulation of energy supply, water and lipid transport, and cell cycle regulation. The early induction of transcription of defence-related genes supports the pre-haustorial resistance phenotype in Toropi, providing a valuable source of genes controlling leaf rust resistance for wheat breeding.

A change in temperature modulates defence to yellow (stripe) rust in wheat line UC1041 independently of resistance gene Yr36.

BACKGROUND: Rust diseases are of major importance in wheat production worldwide. With the constant evolution of new rust strains and their adaptation to higher temperatures, consistent and durable disease resistance is a key challenge. Environmental conditions affect resistance gene performance, but the basis for this is poorly understood. RESULTS: Here we show that a change in day temperature affects wheat resistance to Puccinia striiformis f. sp tritici (Pst), the causal agent of yellow (or stripe) rust. Using adult plants of near-isogenic lines UC1041 +/- Yr36, there was no significant difference between Pst percentage uredia coverage in plants grown at day temperatures of 18°C or 25°C in adult UC1041 + Yr36 plants. However, when plants were transferred to the lower day temperature at the time of Pst inoculation, infection increased up to two fold. Interestingly, this response was independent of Yr36, which has previously been reported as a temperature-responsive resistance gene as Pst development in adult UC1041 -Yr36 plants was similarly affected by the plants experiencing a temperature reduction. In addition, UC1041 -Yr36 plants grown at the lower temperature then transferred to the higher temperature were effectively resistant and a temperature change in either direction was shown to affect Pst development up to 8 days prior to inoculation. Results for seedlings were similar, but more variable compared to adult plants. Enhanced resistance to Pst was observed in seedlings of UC1041 and the cultivar Shamrock when transferred to the higher temperature. Resistance was not affected in seedlings of cultivar Solstice by a temperature change in either direction. CONCLUSIONS: Yr36 is effective at 18°C, refining the lower range of temperature at which resistance against Pst is conferred compared to previous studies. Results reveal previously uncharacterised defence temperature sensitivity in the UC1041 background which is caused by a change in temperature and independently of Yr36. This novel phenotype is present in some cultivars but absent in others, suggesting that Pst defence may be more stable in some cultivars than others when plants are exposed to varying temperatures.

Unravelling marker trait associations linking nutritional value with pigmentation in rice seed.

While considerable breeding effort has focused on increasing the yields of staple crops such as rice and the levels of micronutrients such as iron and zinc, breeding to address the problems of the double-burden of malnutrition has received less attention. Pigmented rice has higher nutritional value and greater health benefits compared to white rice. However, the genetic associations underlying pericarp coloration and accumulation of nutritionally valuable compounds is still poorly understood. Here we report the targeted genetic analysis of 364 rice accessions, assessing the genetic relationship between pericarp coloration (measured using multi-spectral imaging) and a range of phenolic compounds with potential nutritional and health-promoting characteristics. A genome-wide association study resulted in the identification of over 280 single nucleotide polymorphisms (SNPs) associated with the traits of interest. Many of the SNPs were associated with more than one trait, colocalization occurring between nutritional traits, and nutritional and color-related traits. Targeted association analysis identified 67 SNPs, located within 52 candidate genes and associated with 24 traits. Six haplotypes identified within the genes Rc/bHLH17 and OsIPT5 indicated that these genes have an important role in the regulation of a wide range of phenolic compounds, and not only those directly conferring pericarp color. These identified genetic linkages between nutritionally valuable phenolic compounds and pericarp color present not only a valuable resource for the enhancement of the nutritional value of rice but an easy method of selection of suitable genotypes.

Assessing nutritional and genetic variations within foxtail millet (Setaria italica) landraces collected from indigenous communities across the Philippines.

Unknown to many, the Philippines is host to a few remaining accessions of the underutilised and understudied cereal foxtail millet (Setaria italica (L.) P. Beauv.). We collected together accessions of this crop from different eco-geographical locations within the Philippines, along with a few accessions from Lanyu, Taiwan, to undertake a study of their nutritional value and genetic diversity. All accessions were field-grown in 2022, dry season (DS) at the Institute of Plant Breeding (IPB) Experiment Station, Los Baños, Laguna, Philippines. The accessions were tested for micronutrients, including Zn and Fe, nitrogen as a proxy for protein, ß-carotene, phytic acid, and a number of phenolic compounds with known nutritional potential. Of the 20 accessions tested, the accessions Bayaras and GB61438 had the highest level of Zn (107.1 mg/kg) and Fe (70.52 mg/kg), respectively, higher than levels found in traditional rice varieties. For ß-carotene the highest concentration was found in the accession Balles (∼10 µg/g). Twelve phenolic compounds were detected, with catechin, syringic acid, ferulic acid and kaempferol having the highest concentrations. To assess the genetic diversity, we sequenced a set of eight samples selected from among the accessions to a depth of at least 25-fold using whole-genome re-sequencing. Analysis of the population structure, using genome-wide, high-quality SNPs, showed modest diversity among the accessions, with two unadmixed groups. The accessions are monophyletic relative to their earliest common ancestor, with the very light brown accessions emerging earlier than the light brown and reddish-brown varieties. Analysis of zinc-regulated, iron-regulated transporter-like protein (ZIP) transporters within the foxtail millet reference sequence, var. Yugu1 identified 17 putative ZIP transporters. Variant calling identified SNPs primarily within 3' and 5' regions, and introns, indicating variation between foxtail millet accessions within regulatory gene regions rather than in structural proteins. The local foxtail millet accessions, therefore, represent a potential alternative source of nutrients which may help in addressing malnutrition in the Philippines.

Mathematical modeling to predict rice's phenolic and mineral content through multispectral imaging.

Over half the world population relies on rice for energy, but being a carbohydrate-based crop, it offers limited nutritional benefits. To achieve nutritional security targets in Asia, we must understand the genetic variation in multi-nutritional properties with therapeutic properties and deploy this knowledge to future rice breeding. High throughput, VideometerLAB spectral imaging data has been effective in estimating total anthocyanin content, particularly bound anthocyanin content, using the high prediction power of partial least square (PLS) regression models. Multi-pronged nutritional properties of phenolic compounds and minerals, together with videometerLAB features, were utilized to develop models to classify a collection of black rice varieties into three distinct nutritional quality ideotypes. These derived models for black rice diversity panels were created utilizing videometerLAB data (L, A, B parameters), selected phenolic types (total phenolics, total anthocyanins, and bound flavonoids), and minerals (Molybdenum and Phosphorous). Random forest and artificial neural network models depicted the multi-nutritional features of black rice with 85.35 and 99.9% accuracy, respectively. These prediction algorithms would help rice breeders strategically breed nutritionally valuable genotypes based on simple, high-through-put videometerLAB readings and a small number of nutritional assays.

Multi-Layer Biosensor for Pre-Symptomatic Detection of Puccinia strifformis, the Causal Agent of Yellow Rust.

The yellow rust of wheat (caused by Puccinia striiformis f. sp. tritici) is a devastating fungal infection that is responsible for significant wheat yield losses. The main challenge with the detection of this disease is that it can only be visually detected on the leaf surface between 7 and 10 days after infection, and by this point, counter measures such as the use of fungicides are generally less effective. The hypothesis of this study is to develop and use a compact electrochemical-based biosensor for the early detection of P. striiformis, thus enabling fast countermeasures to be taken. The biosensor that was developed consists of three layers. The first layer mimics the wheat leaf surface morphology. The second layer consists of a sucrose/agar mixture that acts as a substrate and contains a wheat-derived terpene volatile organic compound that stimulates the germination and growth of the spores of the yellow rust pathogen P. s. f. sp. tritici. The third layer consists of a nonenzymatic glucose sensor that produces a signal once invertase is produced by P. striiformis, which comes into contact with the second layer, thereby converting sucrose to glucose. The results show the proof that this innovative biosensor can enable the detection of yellow rust spores in 72 h.

Genetic variation within and between winter wheat genotypes from Turkey, Kazakhstan, and Europe as determined by nucleotide-binding-site profiling.

The genetic diversity within wheat breeding programs across Turkey and Kazakhstan was compared with a selection of European cultivars that represented the genetic diversity across eight European countries and six decades of wheat breeding. To focus the measure of genetic diversity on that relevant to disease-resistant phenotypes, nucleotide-binding-site (NBS) profiling was used to detect polymorphisms associated with the NBS motifs found within the NBS--leucine-rich repeat (LRR) class of resistance (R) genes. Cereal-specific NBS primers, designed specifically to the conserved NBS motifs found within cereal R-genes, provided distinct NBS profiles. Although the genetic diversity associated with NBS motifs was only slightly higher within the Eastern wheat genotypes, the NBS profiles produced by Eastern and European wheat lines differed considerably. Structure analysis divided the wheat genotypes into four groups, which compared well with the origin of the wheat genotypes. The highest levels of genetic diversity were seen for the wheat genotypes from the Genetic Resource Collection held in Ankara, Turkey, as wheat genotypes within breeding programs were genetically more similar. The wheat genotypes from Kazakhstan were the most similar to the European cultivars, reflecting the significant number of eastern European cultivars used in the breeding program in Kazakhstan. In general, the NBS profiles suggested that NBS-LRR R-gene usage in winter wheat breeding in Turkey and Kazakhstan differed from that deployed in European cultivars.

The Genetic Basis and Nutritional Benefits of Pigmented Rice Grain.

Improving the nutritional quality of rice grains through modulation of bioactive compounds and micronutrients represents an efficient means of addressing nutritional security in societies which depend heavily on rice as a staple food. White rice makes a major contribution to the calorific intake of Asian and African populations, but its nutritional quality is poor compared to that of pigmented (black, purple, red orange, or brown) variants. The compounds responsible for these color variations are the flavonoids anthocyanin and proanthocyanidin, which are known to have nutritional value. The rapid progress made in the technologies underlying genome sequencing, the analysis of gene expression and the acquisition of global 'omics data, genetics of grain pigmentation has created novel opportunities for applying molecular breeding to improve the nutritional value and productivity of pigmented rice. This review provides an update on the nutritional value and health benefits of pigmented rice grain, taking advantage of both indigenous and modern knowledge, while also describing the current approaches taken to deciphering the genetic basis of pigmentation.