Carotenoid composition and expression of biosynthetic genes in yellow and white foxtail millet [Setaria italica (L.) Beauv]

Gene mapping and identification of candidate genes controlling carotenoid accumulation of yellow kernels in foxtail millet

BACKGROUND

Kernel color is an important characteristic of foxtail millet (Setaria italica) associated with its market ability, quality, and nutritional value, which is mainly due to the accumulation of carotenoids. Despite its importance, the genetic basis of carotenoid variation in foxtail millet remains largely unexplored. Herein, the molecular mechanisms governing carotenoid accumulation in the kernel of foxtail millet were investigated by an exhaustive methodology encompassing Genome-Wide Association Study (GWAS), Bulk Segregant Analysis sequencing (BSA-seq), and integrated transcriptomic and metabolomic analyses.

RESULTS

The total carotenoid content in kernels across 201 foxtail millet germplasms showed a spectrum of variations, which indicated that the kernel color is a quantitative genetic trait controlled by multiple genes. Using GWAS on these germplasms and BSA-seq on an F6 generation Recombinant Inbred Line (RIL) population derived from the GBS (yellow kernel) and NMB (white kernel) cross, we identified genome regions linked with total carotenoid content in foxtail millet kernels. Integrated transcriptomic and metabolomic profiling during grain filling in both yellow and white varieties pinpointed SiPSY1 and SiCCD1 as key genes controlling carotenoid accumulation. Notably, the SNP (G/A) at 364 bp and the Indel (29 bp insertion) at 856 bp within the SiPSY1 promoter predominantly contributed to the variance in promoter activity. These variations markedly affected SiPSY1 expression levels, ultimately determining the phenotypic difference between yellow and white kernels.

CONCLUSIONS

These findings provide crucial genetic insights for the molecular mechanisms involved in carotenoid metabolism and lay a solid foundation for millet color breeding in foxtail millet.

Foxtail millet research in supporting climate change resilience efforts: Bibliometric analysis and focused literature review

Foxtail millet is part of the millet group but is less popular than sorghum and pearl millet. Nevertheless, the potential of this plant is considered promising for diversifying food nutrition, health products, feed, biofuel, and several other uses, as indicated by various publications, including review articles. However, studies, analyses, and development trends of foxtail millet are lacking, and the current development status of foxtail millet and future projections cannot be systematically identified. Bibliometric analysis offers a method to clarify the current state of the development and interaction of a study topic for systematic analysis. Therefore, this study conducted a bibliometric review to examine the development, interaction, and projections of foxtail millet research regarding publication trends, countries involved, and keywords. Publications related to foxtail millet were first mined from the Scopus database and analyzed using Biblioshiny R Studio and VOSviewer software, with 2091 Scopus documents identified as being associated with the topic of foxtail millet. A significant development occurred in 2012 when the entire foxtail millet genome was explored. The main countries that focus on developing foxtail millet are China and India. The development of foxtail millet is focused on optimizing omics-based approaches to support the use of its potential, especially in research efforts involving climate change tolerance systems. Therefore, innovation, exploration, and potential use of foxtail millet in the future will continue to develop along with submarginal land and public health problems, including in Indonesia, which has the fourth largest population globally.

Integrating dynamic high-throughput phenotyping and genetic analysis to monitor growth variation in foxtail millet

BACKGROUND

Foxtail millet [Setaria italica (L.) Beauv] is a C4 graminoid crop cultivated mainly in the arid and semiarid regions of China for more than 7000 years. Its grain highly nutritious and is rich in starch, protein, essential vitamins such as carotenoids, folate, and minerals. To expand the utilisation of foxtail millet, efficient and precise methods for dynamic phenotyping of its growth stages are needed. Traditional foxtail millet monitoring methods have high labour costs and are inefficient and inaccurate, impeding the precise evaluation of foxtail millet genotypic variation.

RESULTS

This study introduces a high-throughput imaging system (HIS) with advanced image processing techniques to enhance monitoring efficiency and data quality. The HIS can accurately extract a range of key growth feature parameters, such as plant height (PH), convex hull area (CHA), side projected area (SPA) and colour distribution, from foxtail millet images. Compared with traditional manual measurements, this HIS improved data quality and phenotyping of the key foxtail millet growth traits. High-throughput phenotyping combined with a genome-wide association study (GWAS) revealed genetic loci associated with dynamic growth traits, particularly plant height (PH), in foxtail millet. The loci were linked to genes involved in the gibberellic acid (GA) synthesis pathway related to PH.

CONCLUSION

The HIS developed in this study enables the efficient and dynamic monitoring of foxtail millet phenotypic traits. It significantly improves the quality of data obtained for phenotyping key growth traits. The integration of high-throughput phenotyping with GWAS provides new insights into the genetic underpinnings of dynamic growth traits, particularly plant height, by identifying associated genetic loci in the GA synthesis pathway. This methodological advancement opens new avenues for the precise phenotyping and exploration of genetic resources in foxtail millet, potentially enhancing its utilisation.

The Role of Alternative Crops in an Upcoming Global Food Crisis: A Concise Review

Achieving Food Security (FS) is perhaps our most challenging aspiration. Despite our best efforts, millions of people around the globe are malnourished or live with hunger. The state of the geo-political scene, as well as the COVID-19 pandemic, have recently brought forth fears of a Global Food Crisis (GFC). Here, we present the factors that threaten FS and could trigger a GFC, examine the potential of alternative crops (ACs) as a measure against an upcoming GFC, and highlight the key aspects of the ACs introduction process in new regions. ACs could enhance FS, yet their success is premised on the adoption of sustainable practices and the implementation of food strategies that aim to promote healthy consumer behaviours.

Carotenoid Cleavage Dioxygenase 1 Catalyzes Lutein Degradation To Influence Carotenoid Accumulation and Color Development in Foxtail Millet Grains

Foxtail millet is a minor but economically important crop in certain regions of the world. Millet color is often used to judge grain quality, yet the molecular determinants of millet coloration remain unclear. Here, we explored the relationship between SiCCD1 and millet coloration in yellow and white millet varieties. Carotenoid levels declined with grain maturation and were negatively correlated with SiCCD1 expression, which was significantly higher in white millet as compared to yellow millet during the color development stage. Cloning of the SiCCD1 promoter and CDS sequences from these different millet varieties revealed the presence of two additional cis-regulatory elements within the SiCCD1 promoter in white millet varieties, including an enhancer-like GC motif element associated with anoxic specific inducibility and a GCN4-motif element associated with endosperm expression. Dual-luciferase reporter assays confirmed that SiCCD1 promoter fragments containing these additional cis-acting elements derived from white millet varieties were significantly more active than those from yellow millet varieties, consistent with the observed SiCCD1 expression patterns. Further in vitro enzyme detection assays confirmed that SiCCD1 primarily targets and degrades lutein. Together, these data suggest that SiCCD1 promoter variation was a key factor associated with the observed differences in SiCCD1 expression, which in turn led to the difference in millet coloration.

Comparative metabolomic and transcriptomic analysis reveals a coexpression network of the carotenoid metabolism pathway in the panicle of Setaria italica

BACKGROUND

The grains of foxtail millet are enriched in carotenoids, which endow this plant with a yellow color and extremely high nutritional value. However, the underlying molecular regulation mechanism and gene coexpression network remain unclear.

METHODS

The carotenoid species and content were detected by HPLC for two foxtail millet varieties at three panicle development stages. Based on a homologous sequence BLAST analysis, these genes related to carotenoid metabolism were identified from the foxtail millet genome database. The conserved protein domains, chromosome locations, gene structures and phylogenetic trees were analyzed using bioinformatics tools. RNA-seq was performed for these samples to identify differentially expressed genes (DEGs). A Pearson correlation analysis was performed between the expression of genes related to carotenoid metabolism and the content of carotenoid metabolites. Furthermore, the expression levels of the key DEGs were verified by qRT-PCR. The gene coexpression network was constructed by a weighted gene coexpression network analysis (WGCNA).

RESULT

The major carotenoid metabolites in the panicles of DHD and JG21 were lutein and β-carotene. These carotenoid metabolite contents sharply decreased during the panicle development stage. The lutein and β-carotene contents were highest at the S1 stage of DHD, with values of 11.474 μg /100 mg and 12.524 μg /100 mg, respectively. Fifty-four genes related to carotenoid metabolism were identified in the foxtail millet genome. Cis-acting element analysis showed that these gene promoters mainly contain 'plant hormone', 'drought stress resistance', 'MYB binding site', 'endosperm specific' and 'seed specific' cis-acting elements and especially the 'light-responsive' and 'ABA-responsive' elements. In the carotenoid metabolic pathways, SiHDS, SiHMGS3, SiPDS and SiNCED1 were more highly expressed in the panicle of foxtail millet. The expression of SiCMT, SiAACT3, SiPSY1, SiZEP1/2, and SiCCD8c/8d was significantly correlated with the lutein content. The expression of SiCMT, SiHDR, SiIDI2, SiAACT3, SiPSY1, and SiZEP1/2 was significantly correlated with the content of β-carotene. WGCNA showed that the coral module was highly correlated with lutein and β-carotene, and 13 structural genes from the carotenoid biosynthetic pathway were identified. Network visualization revealed 25 intramodular hub genes that putatively control carotenoid metabolism.

CONCLUSION

Based on the integrative analysis of the transcriptomics and carotenoid metabonomics, we found that DEGs related to carotenoid metabolism had a stronger correlation with the key carotenoid metabolite content. The correlation analysis and WGCNA identified and predicted the gene regulation network related to carotenoid metabolism. These results lay the foundation for exploring the key target genes regulating carotenoid metabolism flux in the panicle of foxtail millet. We hope that these target genes could be used to genetically modify millet to enhance the carotenoid content in the future.

Genotypic diversity of quality traits in Chinese foxtail millet (Setaria italica L.) and the establishment of a quality evaluation system

Foxtail millet (Setaria italica L.) is an important reserve cereal crop, and its nutritional and medicinal properties have seen its demand increase in recent years. Therefore, it is important to establish an evaluation system for the comprehensive assessment of its quality. We assessed 90 accessions of foxtail millet from China for 23 quality traits. The results showed that the 23 quality traits had diverse coefficients of variation, with the greatest variation in a*, phosphorus content, and potassium contents, at 37.71, 28.81, and 20.18%, respectively. Cluster analysis defined five categories that were consistent with the geographical origins of the accessions. Seven principal components were also extracted from the 23 traits using principal component analysis. A comprehensive quality evaluation system was established, and 8 high-quality accessions were identified. The findings of the present study could facilitate the breeding of high-quality foxtail millet and enhance quality evaluation activities.

Carotenoid Pigment Content in Durum Wheat (Triticum turgidum L. var durum): An Overview of Quantitative Trait Loci and Candidate Genes

Carotenoid pigment content is an important quality trait as it confers a natural bright yellow color to pasta preferred by consumers (whiteness vs. yellowness) and nutrients, such as provitamin A and antioxidants, essential for human diet. The main goal of the present review is to summarize the knowledge about the genetic regulation of the accumulation of pigment content in durum wheat grain and describe the genetic improvements obtained by using breeding approaches in the last two decades. Although carotenoid pigment content is a quantitative character regulated by various genes with additive effects, its high heritability has facilitated the durum breeding progress for this quality trait. Mapping research for yellow index and yellow pigment content has identified quantitative trait loci (QTL) on all wheat chromosomes. The major QTL, accounting for up to 60%, were mapped on 7L homoeologous chromosome arms, and they are explained by allelic variations of the phytoene synthase (PSY) genes. Minor QTL were detected on all chromosomes and associated to significant molecular markers, indicating the complexity of the trait. Despite there being currently a better knowledge of the mechanisms controlling carotenoid content and composition, there are gaps that require further investigation and bridging to better understand the genetic architecture of this important trait. The development and the utilization of molecular markers in marker-assisted selection (MAS) programs for improving grain quality have been reviewed and discussed.

Effect of Foliar Spray Application of Zinc Oxide Nanoparticles on Quantitative, Nutritional, and Physiological Parameters of Foxtail Millet (Setaria italica L.) under Field Conditions

It has been shown that the foliar application of inorganic nano-materials on cereal plants during their growth cycle enhances the rate of plant productivity by providing a micro-nutrient source. We therefore studied the effects of foliarly applied ZnO nanoparticles (ZnO NPs) on Setaria italica L. foxtail millet's quantitative, nutritional, and physiological parameters. Scanning electron microscopy showed that the ZnO NPs have an average particle size under 20 nm and dominant spherically shaped morphology. Energy dispersive X-ray spectrometry then confirmed ZnO NP homogeneity, and X-ray diffraction verified their high crystalline and wurtzite-structure symmetry. Although plant height, thousand grain weight, and grain yield quantitative parameters did not differ statistically between ZnO NP-treated and untreated plants, the ZnO NP-treated plant grains had significantly higher oil and total nitrogen contents and significantly lower crop water stress index (CWSI). This highlights that the slow-releasing nano-fertilizer improves plant physiological properties and various grain nutritional parameters, and its application is therefore especially beneficial for progressive nanomaterial-based industries.