Unlocking the potential of Kodo millet: reviving an indigenous super grain for tomorrow's nutrition

Kodo millet (Paspalum scrobiculatum L.) is an underutilized crop that encompasses nutritional benefits and climate resilience, making it a viable option for future crop development with nutraceutical properties. The cultivation of this crop has ancient roots, where it was revered for its ability to thrive in times of famine and was a vital companion crop to rice. Dishes made with Kodo millet are highly palatable and can be easily integrated into mainstream rice-based dishes. Among all cereals, Kodo millet is distinguished by its gluten-free composition, high phosphorus content, and significant antioxidant potential, which contributes to a diet that may reduce cardiovascular disease risk. Often grown in rainfed zones by marginal farmers, Kodo millet is valued for its grain and fodder. This less demanding crop can tolerate both biotic and abiotic stress, allowing it to thrive in soils with low organic matter and with minimal inputs, making it an ideal dual-purpose crop for rainfed areas. Despite its nutritional and agricultural benefits, Kodo millet's popularity is hindered by challenges such as low yield, market demand, lodging at harvest, and poor dehulling recovery, which necessitate the development of high-yielding varieties through the latest breeding advancements. Systematic investment and concerted breeding efforts are essential to harness the full potential of this nutrient-dense crop. The absence of whole genome sequence for Kodo millet poses a barrier to uncovering novel genetic traits. Consequently, there is an imperative to establish a millet-based value chain that elevates these underutilized crops, shaping smart cropping patterns and enhancing nutritional profiles for sustainable diets. Accordingly, this review highlights the significance of Kodo millet and the impact of breeding to establish it as a smart food choice for the future.

Nourishing the Cognition with Millets: A Comprehensive Review of Their Nutritional Impact and Potential as Cognitive Enhancers

Cognition is the mental processes and abilities involved in acquiring, storing, retrieving and using it for decision making. Cognitive decline due to aging, lifestyle factor, chronic health conditions, genetic, and environmental factors are rising global concern and propose a potential threat to the cognitive health. The nutritional imbalance has led to increase in cognitive disorders around the world. Millets can be a nutritional intervention for promoting cognitive health and preventing cognitive decline. Millets has abundant phenolic compounds, flavonoids, and antioxidants to protect against oxidative stress-induced cognitive impairment. Millets exert neuroprotective effects by modulating pathways involved in neuronal-survival, synaptic-plasticity, and release of brain-derived neurotrophic factor. Millets demonstrates anti-inflammatory properties by regulating inflammatory-pathways and suppressing cytokines associated with cognitive impairment. Millets maintain healthy gut microbiota by producing metabolites such as short-chain fatty acids, which influence brain function and cognition. However, further research is needed to elucidate the underlying mechanisms and on optimizing the proportion do exploit its potential. Implementing millet-based dietary strategies through public health initiatives and educational programs can be a practical approach to support cognitive health across populations. Harnessing the potential of millets as a nutritional intervention offers a promising avenue for promoting cognitive health and improving the quality of life.

Ancient genomes reveal millet farming-related demic diffusion from the Yellow River into southwest China

The study of southwest China is vital for understanding the dispersal and development of farming because of the coexistence of millet and rice in this region since the Neolithic period.1,2 However, the process of the Neolithic transition in southwest China is largely unknown, mainly due to the lack of ancient DNA from the Neolithic period. Here, we report genome-wide data from 11 human samples from the Gaoshan and Haimenkou sites with mixed farming of millet and rice dating to between 4,500 and 3,000 years before present in southwest China. The two ancient groups derived approximately 90% of their ancestry from the Neolithic Yellow River farmers, suggesting a demic diffusion of millet farming to southwest China. We inferred their remaining ancestry to be derived from a Hòabìnhian-related hunter-gatherer lineage. We did not detect rice farmer-related ancestry in the two ancient groups, which indicates that they likely adopted rice farming without genetic assimilation. We, however, observed rice farmer-related ancestry in the formation of some present-day Tibeto-Burman populations. Our results suggested the occurrence of both demic and cultural diffusion in the development of Neolithic mixed farming in some parts of southwest China.

Milletdb: a multi-omics database to accelerate the research of functional genomics and molecular breeding of millets

Millets are a class of nutrient-rich coarse cereals with high resistance to abiotic stress; thus, they guarantee food security for people living in areas with extreme climatic conditions and provide stress-related genetic resources for other crops. However, no platform is available to provide a comprehensive and systematic multi-omics analysis for millets, which seriously hinders the mining of stress-related genes and the molecular breeding of millets. Here, a free, web-accessible, user-friendly millets multi-omics database platform (Milletdb, http://milletdb.novogene.com) has been developed. The Milletdb contains six millets and their one related species genomes, graph-based pan-genomics of pearl millet, and stress-related multi-omics data, which enable Milletdb to be the most complete millets multi-omics database available. We stored GWAS (genome-wide association study) results of 20 yield-related trait data obtained under three environmental conditions [field (no stress), early drought and late drought] for 2 years in the database, allowing users to identify stress-related genes that support yield improvement. Milletdb can simplify the functional genomics analysis of millets by providing users with 20 different tools (e.g., 'Gene mapping', 'Co-expression', 'KEGG/GO Enrichment' analysis, etc.). On the Milletdb platform, a gene PMA1G03779.1 was identified through 'GWAS', which has the potential to modulate yield and respond to different environmental stresses. Using the tools provided by Milletdb, we found that the stress-related PLATZs TFs (transcription factors) family expands in 87.5% of millet accessions and contributes to vegetative growth and abiotic stress responses. Milletdb can effectively serve researchers in the mining of key genes, genome editing and molecular breeding of millets.

Comprehensive physiological, transcriptomic, and metabolomic analysis of the key metabolic pathways in millet seedling adaptation to drought stress

Drought is one of the leading environmental constraints that affect the growth and development of plants and, ultimately, their yield and quality. Foxtail millet (Setaria italica) is a natural stress-resistant plant and an ideal model for studying plant drought resistance. In this study, two varieties of foxtail millet with different levels of drought resistance were used as the experimental material. The soil weighing method was used to simulate drought stress, and the differences in growth, photosynthetic physiology, metabolite metabolism, and gene transcriptional expression under drought stress were compared and analyzed. We aimed to determine the physiological and key metabolic regulation pathways of the drought-tolerant millet in resistance to drought stress. The results showed that drought-tolerant millet exhibited relatively stable growth and photosynthetic parameters under drought stress while maintaining a relatively stable level of photosynthetic pigments. The metabolomic, transcriptomic, and gene co-expression network analysis confirmed that the key to adaptation to drought by millet was to enhance lignin metabolism, promote the metabolism of fatty acids to be transformed into cutin and wax, and improve ascorbic acid circulation. These findings provided new insights into the metabolic regulatory network of millet adaptation to drought stress.

5M approach to decipher starch-lipid interaction in minor millets

The 5M approach can be applied to understand genetic complexity underlying nutritional traits of minor millets. It will help to systematically identify genomic regions/candidate genes imprinting metabolite profiles.

Alternative Strategies for Multi-Stress Tolerance and Yield Improvement in Millets

Millets are important cereal crops cultivated in arid and semiarid regions of the world, particularly Africa and southeast Asia. Climate change has triggered multiple abiotic stresses in plants that are the main causes of crop loss worldwide, reducing average yield for most crops by more than 50%. Although millets are tolerant to most abiotic stresses including drought and high temperatures, further improvement is needed to make them more resilient to unprecedented effects of climate change and associated environmental stresses. Incorporation of stress tolerance traits in millets will improve their productivity in marginal environments and will help in overcoming future food shortage due to climate change. Recently, approaches such as application of plant growth-promoting rhizobacteria (PGPRs) have been used to improve growth and development, as well as stress tolerance of crops. Moreover, with the advance of next-generation sequencing technology, genome editing, using the clustered regularly interspaced short palindromic repeats (CRISPR/Cas9) system are increasingly used to develop stress tolerant varieties in different crops. In this paper, the innate ability of millets to tolerate abiotic stresses and alternative approaches to boost stress resistance were thoroughly reviewed. Moreover, several stress-resistant genes were identified in related monocots such as rice (Oryza sativa), wheat (Triticum aestivum), and maize (Zea mays), and other related species for which orthologs in millets could be manipulated by CRISPR/Cas9 and related genome-editing techniques to improve stress resilience and productivity. These cutting-edge alternative strategies are expected to bring this group of orphan crops at the forefront of scientific research for their potential contribution to global food security.

What do "barbarians" eat? Integrating ceramic use-wear and residue analysis in the study of food and society at the margins of Bronze Age China

The Siwa archaeological culture (ca. 3350 and 2650 cal yr BP) has often been associated with the tribes referenced in textual sources as Qiang and Rong: prized captives commonly sacrificed by the Shang and marauding hordes who toppled the Western Zhou dynasty. In early Chinese writings, food plays a key role in accentuating the 'sino-barbarian' dichotomy believed to have taken root over 3000 years ago, with the Qiang and Rong described as nomadic pastoralists who consumed more meat than grain and knew little of proper dining etiquette. To date, however, little direct archaeological evidence has allowed us to reconstruct the diet and foodways of the groups who occupied the Loess Plateau during this pivotal period. Here we present the results of the first ceramic use-wear study performed on the Siwa ma'an jars from the site of Zhanqi, combined with the molecular and isotopic characterization of lipid residues from foodcrusts, and evidence from experimental cooking. We report molecular data indicating the preparation of meals composed of millet and ruminant dairy among the Siwa community of Zhanqi. Use-wear analysis shows that Zhanqi community members were sophisticated creators of ceramic equipment, the ma'an cooking pot, which allowed them to prepare a wide number of dishes with limited fuel. These findings support recent isotope studies at Zhanqi as well as nuance the centrality of meat in the Siwa period diet.

A genome resource for green millet Setaria viridis enables discovery of agronomically valuable loci

Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (Setaria viridis), a model species for studies of C4 grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a 'loss of shattering' trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR-Cas9 genome editing, we validated Less Shattering1 (SvLes1) as a gene whose product controls seed shattering. In S. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.

Genetic Variation of Physicochemical Properties and Digestibility of Foxtail Millet (Setaria italica) Landraces of Taiwan

Foxtail millet is considered a 'smart food' because of nutrient richness and resilience to environments. A diversity panel of 92 foxtail millet landraces preserved by Taiwan indigenous peoples containing amylose content (AC) in the range of 0.7% to 16.9% exhibited diverse physiochemical properties revealed by a rapid viscosity analyzer (RVA). AC was significantly correlated with 5 RVA parameters, and some RVA parameters were also highly correlated with one another. In comparison to rice, foxtail millet contained less starch (65.9-73.1%) and no significant difference in totals of resistant starch (RS), slowly digestible starch (SDS), hydrolysis index (HI), and expected glycemic index (eGI) according to in vitro digestibility assays of raw flour with similar AC. RS was significantly positively correlated with AC and four RVA parameters, cold paste viscosity (CPV), setback viscosity (SBV), peak time (PeT), and pasting temperature (PaT), implying that suitable food processing to alter physicochemical properties of foxtail millet might mitigate hyperglycemia. This investigation of pasting properties and digestibility of diverse foxtail millet germplasm revealed much variation and showed potential for multi-dimensional utilizations in daily staple food and food industries.

Phosphate supply influenced the growth, yield and expression of PHT1 family phosphate transporters in seven millets

Phosphate starvation altered the root morphology and phosphate uptake with the induction of PHT1 family transporter genes in root and shoot tissues of seven millets. Millets are nutrient-rich cereals majorly cultivated in Asia and Africa. Foxtail millet (FoxM), pearl millet (PeaM), finger millet (FinM), kodo millet (KodM), little millet (LitM), proso millet (ProM), and barnyard millet (BarM) were examined for the influence of external phosphorous (P) supply on phenotypic traits, P uptake, yield, and PHosphate Transporter1 (PHT1) family gene expression. Millet seedlings grown under low Pi condition (LPC) produced significantly lower mean values for all traits except for lateral root length (LRL) and lateral root number (LRN) which were increased under LPC. Under LPC, seed weight (SW) also reduced by > 75% and had significantly lower levels of total P (TP) and Pi contents in leaf and root tissues. Expression dynamics of 12 PHT1 family (PHT1;1-1;12) transporters genes were analyzed in 7 millets. PHT1;2 has been found to be a constitutive transporter gene in all millets. Under LPC, root tissues showed the overexpression of PHT1;2, 1;3, 1;4 and 1;9 in FoxM, PHT1;1, 1;2, 1;3, 1;4, 1;8 and 1;10 in PeaM, PHT1;2 and 1;3 in FinM and ProM and PHT1;3, 1;6 and 1;11 in BarM. In leaf, LPC induced the expression of PHT1;3, 1;4 and 1;6 in FoxM, PHT1;2, 1;3, 1;4 and 1;8 in PeaM, PHT1;2, 1;3 and 1;4 in FinM and KodM, PHT1;2 in LitM and PHT1;4 in ProM and BarnM. This comprehensive study on the influence of P in phenotype, physiology, and molecular responses may help to improve the P uptake and its use efficiency of millets in future.

Genome-Wide Population Structure Analyses of Three Minor Millets: Kodo Millet, Little Millet, and Proso Millet

Developed genome-wide SNP marker data for kodo, proso, and little millet Marker data used to analyze genetic diversity Heritability results of various traits used to validate genetic data Millets are a diverse group of small-seeded grains that are rich in nutrients but have received relatively little advanced plant breeding research. Millets are important to smallholder farmers in Africa and Asia because of their short growing season, good stress tolerance, and high nutritional content. To advance the study and use of these species, we present genome-wide marker datasets and population structure analyses for three minor millets: kodo millet (Paspalum scrobiculatum L.), little millet (Panicum sumatrense Roth), and proso millet (Panicum miliaceum L.).We generated genome-wide marker data sets for 190 accessions of each species with genotyping-by-sequencing (GBS). After filtering, we retained between 161 and 165 accessions of each species, with 3461, 2245, and 1882 single-nucleotide polymorphisms (SNPs) for kodo, little, and proso millet, respectively. Population genetic analysis revealed seven putative subpopulations of kodo millet and eight each of proso millet and little millet. To confirm the accuracy of this genetic data, we used public phenotype data on a subset of these accessions to estimate the heritability of various agronomically relevant phenotypes. Heritability values largely agree with the prior expectation for each phenotype, indicating that these SNPs provide an accurate genome-wide sample of genetic variation. These data represent one of first genome-wide population genetics analyses-and the most extensive-in these species and the first genomic analyses of any sort for little millet and kodo millet. These data will be a valuable resource for researchers and breeders trying to improve these crops for smallholder farmers.

Genome-wide Identification and in silico Analysis of PHT1 Family Genes and Proteins in Setaria viridis: The Best Model to Study Nutrient Transport in Millets

Millets are small-seeded cereals predominantly cultivated and consumed by millions of poor people living in developing countries in Asia and Africa. Limited availability of genomic resources hinders studies of nutrient transport in millets. Two species, foxtail millet [ (L.) P. Beauv.] and its wild relative green foxtail [ (L.) P. Beauv.], are considered to be suitable models to study the genomics of other millets. Understanding the nutrient mobilization of millets is essential for improving nutrient use efficiency and biofortification in millets and other cereal crops. Millets are adapted for low-input agriculture, so understanding and improving the phosphate use efficiency of these plants is important because (i) subsistence farmers cannot afford to buy expensive phosphate fertilizers and (ii) the phosphate rock used for phosphate fertilizer production is depleting quickly. In this minireview, I discuss various studies on nutrient transport in millets and highlight phosphate transport studies. I report the identification and phylogenetic and multiple sequence analyses of 12 PHosphate Transporter1 (PHT1) family genes and proteins of green foxtail for the first time. With the exception of PHT1;5, all other green foxtail PHT1 transporters are closely clustered with foxtail millet PHT1 transporters. The multiple sequence analysis of SvPHT1s revealed that the key residues involved in phosphate and H-binding and transport are well conserved, as in other PHT1 transporters. Efforts need to be undertaken to understand and improve phosphate uptake and utilization in millets to strengthen food security in the developing world.

Application of protoplast technology to CRISPR/Cas9 mutagenesis: from single-cell mutation detection to mutant plant regeneration

Plant protoplasts are useful for assessing the efficiency of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) mutagenesis. We improved the process of protoplast isolation and transfection of several plant species. We also developed a method to isolate and regenerate single mutagenized Nicotianna tabacum protoplasts into mature plants. Following transfection of protoplasts with constructs encoding Cas9 and sgRNAs, target gene DNA could be amplified for further analysis to determine mutagenesis efficiency. We investigated N. tabacum protoplasts and derived regenerated plants for targeted mutagenesis of the phytoene desaturase (NtPDS) gene. Genotyping of albino regenerants indicated that all four NtPDS alleles were mutated in amphidiploid tobacco, and no Cas9 DNA could be detected in most regenerated plants.

Review: Shaping a sustainable food future by rediscovering long-forgotten ancient grains

Genetic erosion of crops has been determined way back in the 1940s and accelerated some twenty years later by the inception of the Green Revolution. Claims that the revolution was a complete triumph remain specious, especially since the massive production boost in the global big three grain crops; wheat, maize, and rice that happened back then is unlikely to recur under current climate irregularities. Presently, one of the leading strategies for sustainable agriculture is by unlocking the genetic potential of underutilized crops. The primary focus has been on a suite of ancient cereals and pseudo-cereals which are riding on the gluten-free trend, including, among others, grain amaranth, buckwheat, quinoa, teff, and millets. Each of these crops has demonstrated tolerance to various stress factors such as drought and heat. Apart from being the centuries-old staple in their native homes, these crops have also been traditionally used as forage for livestock. This review summarizes what lies in the past and present for these underutilized cereals, particularly concerning their potential role and significance in a rapidly changing world, and provides compelling insights into how they could one day be on par with the current big three in feeding a booming population.

Identification of putative QTLs for seedling stage phosphorus starvation response in finger millet (Eleusine coracana L. Gaertn.) by association mapping and cross species synteny analysis

A germplasm assembly of 128 finger millet genotypes from 18 countries was evaluated for seedling-stage phosphorus (P) responses by growing them in P sufficient (Psuf) and P deficient (Pdef) treatments. Majority of the genotypes showed adaptive responses to low P condition. Based on phenotype behaviour using the best linear unbiased predictors for each trait, genotypes were classified into, P responsive, low P tolerant and P non-responsive types. Based on the overall phenotype performance under Pdef, 10 genotypes were identified as low P tolerants. The low P tolerant genotypes were characterised by increased shoot and root length and increased root hair induction with longer root hairs under Pdef, than under Psuf. Association mapping of P response traits using mixed linear models revealed four quantitative trait loci (QTLs). Two QTLs (qLRDW.1 and qLRDW.2) for low P response affecting root dry weight explained over 10% phenotypic variation. In silico synteny analysis across grass genomes for these QTLs identified putative candidate genes such as Ser-Thr kinase and transcription factors such as WRKY and basic helix-loop-helix (bHLH). The QTLs for response under Psuf were mapped for traits such as shoot dry weight (qHSDW.1) and root length (qHRL.1). Putative associations of these QTLs over the syntenous regions on the grass genomes revealed proximity to cytochrome P450, phosphate transporter and pectin methylesterase inhibitor (PMEI) genes. This is the first report of the extent of phenotypic variability for P response in finger millet genotypes during seedling-stage, along with the QTLs and putative candidate genes associated with P starvation tolerance.

Rates of return to sorghum and millet research investments: A meta-analysis

Sorghum and millet grow in some of the most heterogeneous and austere agroecologies around the world. These crops are amongst the top five cereal sources of food and feed. Yet, few studies document the impact of sorghum and millet genetic enhancement. The Internal Rate of Return (ROR) is one of the most popular metrics used to measure the economic return on investment on agricultural research and development (R&D). This study conducted a meta-analysis of 59 sorghum and millet ROR estimates obtained from 25 sources published between 1958 and 2015. The average rate of return to sorghum and millet R&D investment is between 54-76 percent per year. All studies computed social rather than private RORs because the technologies were developed using public funds originating from host country National Agricultural Research Systems (NARS) and international organizations such as the INTSORMIL CRSP, ICRISAT and others. Nearly three quarter of the studies focused only on sorghum (72 percent) and around one tenth of the studies (8 percent) on millet. Regression models analyzed the determinants of variation in the reported RORs. Results show that ex-ante type and self-evaluated type of analyses are positively and significantly associated with the ROR estimates. Compared to estimates conducted by a university, results from international institutions and other mixed organizations provided significantly smaller estimates. Estimates conducted at national level also are significantly lower than those conducted at sub-national levels. The ROR is higher for studies conducted in the United States and for those conducted more recently. The study also reconstructed modified internal rate of return (MIRR) for a sub-sample of the reported RORs following recent methods from the literature. These results show that the MIRR estimates are significantly smaller than the reported ROR estimates. Both results indicate that investment in sorghum and millet research generates high social rates of return.

Exploration of millet models for developing nutrient rich graminaceous crops

Protein-energy malnutrition and micronutrient deficiencies contribute to high mortality among considerable proportion of the current 7.2 billion global populations, especially children. Although poverty and diets poor in nutrition are prime reasons for prevalence of malnutrition, nutritionally dense crops offer an inexpensive and sustainable solution to the problem of malnutrition. Remarkably, millets are nutritionally superior to major non-millet cereals. They especially are rich in dietary fibers, antioxidants, phytochemicals and polyphenols, which contribute broad-spectrum positive impacts to human health. However, millets have received lesser research attention universally, and considering this, the present review was planned to summarize the reports available on nutrition profile of millets and non-millet cereals to provide a comparative insight on importance of millets. It also emphasizes the need for research on deciphering nutritional traits present in millets and to develop strategies for introgressing these traits into other conventional staple crops using germplasm and 'omics' technologies. In some millet species, excellent 'omics' and germplasm panels have started to get available which can act as a starting point for understanding as well as of introgressing healthful traits across millets and non-millet cereals.

Nucleotide Sequence Diversity and Linkage Disequilibrium of Four Nuclear Loci in Foxtail Millet (Setaria italica)

Foxtail millet (Setaria italica (L.) Beauv) is one of the earliest domesticated grains, which has been cultivated in northern China by 8,700 years before present (YBP) and across Eurasia by 4,000 YBP. Owing to a small genome and diploid nature, foxtail millet is a tractable model crop for studying functional genomics of millets and bioenergy grasses. In this study, we examined nucleotide sequence diversity, geographic structure, and levels of linkage disequilibrium at four nuclear loci (ADH1, G3PDH, IGS1 and TPI1) in representative samples of 311 landrace accessions across its cultivated range. Higher levels of nucleotide sequence and haplotype diversity were observed in samples from China relative to other sampled regions. Genetic assignment analysis classified the accessions into seven clusters based on nucleotide sequence polymorphisms. Intralocus LD decayed rapidly to half the initial value within ~1.2 kb or less.