Food crops low in seed-phytate improve human and other non-ruminant animals’ health.

Background: Low phytic acid crops may offer improved nutrition for human population that largely depend upon on cereals- and legume-based staple foods, reduce the risk of eutrophication, but may compromise crops productivity and nutritional quality. Methods: Google search was conducted for the period between 2000 to 2021 to search for published literature in high impact factor journals focusing key words/phrases such as ‘genes and diagnostic markers’, ‘genetically modified low-seed phytate crops’, ‘high-seed phytase activity’, ‘low-seed phytate mutants’, ‘phytate and minerals bioavailability and absorption’, ‘phytate and stress tolerance’, ‘phytate-human-nonruminant livestock’s health’, ‘seed phytate, plant growth, development and yield’, ‘seed phytate and germination & seedling establishment’, ‘seed phytate and nutritional quality’, and ‘seed phytate and baking and nutritional quality’. Results: Low phytate mutants (except with few exceptions in barley and common bean) often carry negative pleiotropic effects in grain crops. Oil and protein contents in soybean lpa mutants were not affected, but some mutants relative to the wild type (WT) had greater sucrose and isoflavone and lower raffinose. Predominance of crossing parents on the metabolite profile and imprinting of a specific mutation induced metabolites—consistently expressed in the homozygous lpa mutant offspring—were noted across generations and environments. A few functionally characterized genes and many putative candidate genes associated with low seed phytate or seed phytase have been discovered in grain crops. Both crossbreeding and biotechnology-led genetic improvement with lpa led to offspring combining high yield and low seed phytate in maize, rice, soybean, and wheat. Crossbreeding has shown that it is possible to combine lower seed phytate with greater iron and zinc in the offspring. A few lpa cultivars are commercially grown in USA and Canada, while such developments are yet to occur in the developing world. A fine balance between yield-nutrition-stress tolerance may be achieved by deploying modern biotechnology. Accumulated evidence suggests more bioavailable iron in biofortified and lpa grains than normal phytate grains. The lack of phytic acid however perturb Ca distribution, which as a consequence may alter cooking time and stability of storage proteins, thereby causing serious gastrointestinal discomfort, and should be factored while developing biofortified or lpa beans. The low phytate-based products by and large were not associated with detrimental effects on nutritional and baking quality or retention of nutrients in the food. A long-term assessment may be necessary to assess bioavailability and absorption of minerals from diets differing in phytate concentrations and its effect on human health. Low-phytate-based feed has demonstrated substantial health and productivity benefits to nonruminant animals. Enabling policy for taxing high phytate animal waste may encourage more investments on private agricultural research programs to deal with excess phytate in food and feedstocks. Conclusions: This review highlights advances regarding seed phytate or phytase activity in cultigen gene pools and suggests how to organize cost-effective breeding programs for developing low seed phytate cultivars. The use of modern biotechnology effectively untangled negative pleiotropic effects associated with low phytate grains. A moderate reduction of seed phytate should be achievable to combining crops productivity and adaptation across environments. Effects of low phytate diet on human and nonruminant livestock’s health are also highlighted

Genomic-based root plasticity to enhance abiotic stress adaptation and edible yield in grain crops

Phenotypic plasticity refers to changes expressed by a genotype across different environments and is one of the major means by which plants cope with environmental variability. Multi-fold differences in phenotypic plasticity have been noted across crops, with wild ancestors and landraces being more plastic than crops when under stress. Plasticity in response to abiotic stress adaptation, plant architecture, physio-reproductive and quality traits are multi-genic (QTL). Plasticity QTL (pQTL) were either collocated with main effect QTL and QEI (QTL × environment interaction) or located independently from the main effect QTL. For example, variations in root plasticity have been successfully introgressed to enhance abiotic stress adaptation in rice. The independence of genetic control of a trait and of its plasticity suggests that breeders may select for high or low plasticity in combination with high or low performance of economically important traits. Trait plasticity in stressful environments may be harnessed through breeding stress-tolerant crops. There exists a genetic cost associated with plasticity, so a better understanding of the trade-offs between plasticity and productivity is warranted prior to undertaking breeding for plasticity traits together with productivity in stress environments.Phenotypic plasticity refers to changes expressed by a genotype across different environments and is one of the major means by which plants cope with environmental variability. Mull-fold differences in phenotypic plasticity have been noted across crops, with wild ancestors and landraces being more plastic than crops when under stress. Plasticity in response to abiotic stress adaptation, plant architecture, physio-reproductive and quality traits are multi-genic (QTL). Plasticity QTL (pQTL) were either collocated with main effect QTL and QEI (QTL x environment interaction) or located independently from the main effect QTL. For example, variations in root plasticity have been successfully introgressed to enhance abiotic stress adaptation in rice. The independence of genetic control of a trait and of its plasticity suggests that breeders may select for high or low plasticity in combination with high or low performance of economically important traits. Trait plasticity in stressful environments may be harnessed through breeding stress-tolerant crops. There exists a genetic cost associated with plasticity, so a better understanding of the trade-offs between plasticity and productivity is warranted prior to undertaking breeding for plasticity traits together with productivity in stress environments.Peer reviewe

Mitigating tradeoffs in plant breeding

Tradeoffs among plant traits help maintain relative fitness under unpredictable conditions and maximize reproductive success. However, modifying tradeoffs is a breeding challenge since many genes of minor effect are involved. The intensive crosstalk and fine-tuning between growth and defense responsive phytohormones via transcription factors optimizes growth, reproduction, and stress tolerance. There are regulating genes in grain crops that deploy diverse functions to overcome tradeoffs, e.g., miR-156-IPA1 regulates crosstalk between growth and defense to achieve high disease resistance and yield, while OsALDH2B1 loss of function causes imbalance among defense, growth, and reproduction in rice. GNI-A1 regulates seed number and weight in wheat by suppressing distal florets and altering assimilate distribution of proximal seeds in spikelets. Knocking out ABA-induced transcription repressors (AITRs) enhances abiotic stress adaptation without fitness cost in Arabidopsis. Deploying AITRs homologs in grain crops may facilitate breeding. This knowledge suggests overcoming tradeoffs through breeding may expose new ones

Anthocyanin-Rich Vegetables for Human Consumption—Focus on Potato, Sweetpotato and Tomato

Malnutrition, unhealthy diets, and lifestyle changes have become major risk factors for non-communicable diseases while adversely impacting economic growth and sustainable development. Anthocyanins, a group of flavonoids that are rich in fruits and vegetables, contribute positively to human health. This review focuses on genetic variation harnessed through crossbreeding and biotechnology-led approaches for developing anthocyanins-rich fruit and vegetable crops. Significant progress has been made in identifying genes involved in anthocyanin biosynthesis in various crops. Thus, the use of genetics has led to the development and release of anthocyanin-rich potato and sweet potato cultivars in Europe and the USA. The purple potato ’Kufri Neelkanth’ has been released for cultivation in northern India. In Europe, the anthocyanin-rich tomato cultivar ‘Sun Black’ developed via the introgression of Aft and atv genes has been released. The development of anthocyanin-rich food crops without any significant yield penalty has been due to the use of genetic engineering involving specific transcription factors or gene editing. Anthocyanin-rich food ingredients have the potential of being more nutritious than those devoid of anthocyanins. The inclusion of anthocyanins as a target characteristic in breeding programs can ensure the development of cultivars to meet the nutritional needs for human consumption in the developing world

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses

Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted

Developing germplasm and promoting consumption of anthocyanin-rich grains for health benefits

Malnutrition, unhealthy diets, and lifestyle changes are the major risk factors for overweight and obesity-linked chronic diseases in humans adversely impact achieving sustainable development goals. Colored grains are a source of anthocyanins, a group of flavonoids, that contribute positively to human health. This review focuses on genetic variation harnessed through breeding and biotechnology tools for developing anthocyanin-rich grain crops. Agronomic practices, genotype × environment interactions, different stresses, seed development and seed maturity are factors that impact the content and composition of anthocyanins. Significant progress has been made in characterizing genes associated with anthocyanin biosynthesis in cereal and other crops. Breeding has led to the development and release of grain anthocyanin-rich crop cultivars in Europe, America and in some countries in Asia. Notably, genetic engineering utilizing specific transcription factors and gene editing has led to the development of anthocyanin-rich genetic variants without any significant yield penalty. A variety of food products derived from colored grains or flours are now available in grocery stores and supermarkets worldwide. The public perception about anthocyanin-rich food is positive, but availability, affordability, and willingness to pay a higher price than before limit consumption. Together with other seed nutrition traits in breeding programs the inclusion of anthocyanins can ensure the development of cultivars that meet nutrition needs of humans, especially in the developing world

Alternative Splicing Variation: Accessing and Exploiting in Crop Improvement Programs

Alternative splicing (AS) is a gene regulatory mechanism modulating gene expression in multiple ways. AS is prevalent in all eukaryotes including plants. AS generates two or more mRNAs from the precursor mRNA (pre-mRNA) to regulate transcriptome complexity and proteome diversity. Advances in next-generation sequencing, omics technology, bioinformatics tools, and computational methods provide new opportunities to quantify and visualize AS-based quantitative trait variation associated with plant growth, development, reproduction, and stress tolerance. Domestication, polyploidization, and environmental perturbation may evolve novel splicing variants associated with agronomically beneficial traits. To date, pre-mRNAs from many genes are spliced into multiple transcripts that cause phenotypic variation for complex traits, both in model plant Arabidopsis and field crops. Cataloguing and exploiting such variation may provide new paths to enhance climate resilience, resource-use efficiency, productivity, and nutritional quality of staple food crops. This review provides insights into AS variation alongside a gene expression analysis to select for novel phenotypic diversity for use in breeding programs. AS contributes to heterosis, enhances plant symbiosis (mycorrhiza and rhizobium), and provides a mechanistic link between the core clock genes and diverse environmental clues

Genetic relationships among seven sections of genus Arachis studied by using SSR markers

<p>Abstract</p> <p>Background</p> <p>The genus <it>Arachis</it>, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the <it>Arachis </it>species are diploids (2<it>n </it>= 2<it>x </it>= 20) and the tetraploid species (2<it>n </it>= 2<it>x </it>= 40) are found in sections <it>Arachis</it>, <it>Extranervosae </it>and <it>Rhizomatosae</it>. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of <it>Arachis </it>by using simple sequence repeat (SSR) markers developed from <it>Arachis hypogaea </it>genomic library and gene sequences from related genera of <it>Arachis</it>.</p> <p>Results</p> <p>The average transferability rate of 101 SSR markers tested to section <it>Arachis </it>and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, <it>Arachis pusilla </it>exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (<it>A. duranensis</it>) and the B-genome accession ICG 8206 (<it>A. ipaënsis</it>) were found most closely related to <it>A. hypogaea</it>.</p> <p>Conclusion</p> <p>A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of <it>Arachis</it>, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of <it>A. monticola </it>and <it>A. hypogaea </it>as well as on the most probable donor of A and B-genomes of cultivated groundnut.</p

Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)

<p>Abstract</p> <p>Background</p> <p>Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program <url>http://www.generationcp.org</url> conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions.</p> <p>Results</p> <p>The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild <it>Cicer</it>; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild <it>Cicer </it>shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild <it>Cicer </it>accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection.</p> <p>Conclusion</p> <p>The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.</p

Exploiting genetic and genomic resources to enhance productivity and abiotic stress adaptation of underutilized pulses

Underutilized pulses and their wild relatives are typically stress tolerant and their seeds are packed with protein, fibers, minerals, vitamins, and phytochemicals. The consumption of such nutritionally dense legumes together with cereal-based food may promote global food and nutritional security. However, such species are deficient in a few or several desirable domestication traits thereby reducing their agronomic value, requiring further genetic enhancement for developing productive, nutritionally dense, and climate resilient cultivars. This review article considers 13 underutilized pulses and focuses on their germplasm holdings, diversity, crop-wild-crop gene flow, genome sequencing, syntenic relationships, the potential for breeding and transgenic manipulation, and the genetics of agronomic and stress tolerance traits. Recent progress has shown the potential for crop improvement and food security, for example, the genetic basis of stem determinacy and fragrance in moth bean and rice bean, multiple abiotic stress tolerant traits in horse gram and tepary bean, bruchid resistance in lima bean, low neurotoxin in grass pea, and photoperiod induced flowering and anthocyanin accumulation in adzuki bean have been investigated. Advances in introgression breeding to develop elite genetic stocks of grass pea with low β-ODAP (neurotoxin compound), resistance to Mungbean yellow mosaic India virus in black gram using rice bean, and abiotic stress adaptation in common bean, using genes from tepary bean have been carried out. This highlights their potential in wider breeding programs to introduce such traits in locally adapted cultivars. The potential of de-domestication or feralization in the evolution of new variants in these crops are also highlighted