Distinct expression and function of carotenoid metabolic genes and homoeologs in developing wheat grains

An intronic SNP in the Carotenoid Cleavage Dioxygenase 1 (CsCCD1) controls yellow flesh formation in cucumber fruit (Cucumis sativus L.)

Vitamin A is a crucial yet scarce vitamin essential for maintaining normal metabolism and bodily functions in humans and can only be obtained from food. Carotenoids represent a diverse group of functional pigments that act as precursors for vitamins, hormones, aroma volatiles and antioxidants. As a vital vegetable in the world, elevated carotenoid levels in cucumber fruit produce yellow flesh, enhancing both visual appeal and nutritional value. However, the genetic mechanisms and regulatory networks governing yellow flesh in cucumbers remain inadequately characterized. In this study, we employed map-based cloning to identify a Carotenoid Cleavage Dioxygenase 1 (CsCCD1) as a key genetic factor influencing yellow flesh in cucumbers. A causal single nucleotide polymorphism (SNP) in the eighth intron of CsCCD1 led to aberrant splicing, resulting in a truncated transcript. The truncated protein has significantly decreased enzyme activity and increased carotenoid accumulation in the fruit. CRISPR/Cas9-generated CsCCD1 knockout mutants exhibited yellow flesh and significantly higher carotenoid content compared to wild-type cucumbers. Metabolic profiling indicated a marked accumulation of β-cryptoxanthin in the flesh of these knockout mutants. The intronic SNP was shown to perfectly segregate with yellow flesh in 159 diverse cucumber germplasms, particularly within the semi-wild ecotype Xishuangbanna, known for its substantial carotenoid accumulation. Furthermore, transient overexpression of CsCCD1 in yellow-fleshed Xishuangbanna cucumbers restored a white flesh phenotype, underscoring the critical role of CsCCD1 in determining flesh colour in both cultivated and semi-wild cucumbers. These findings lay a theoretical foundation for breeding high-nutrient yellow-fleshed cucumber varieties.

Pyramiding of mutations in lycopene ε-cyclase and β-hydroxylase 1 increases β-carotene content and modifies carotenoid metabolism in durum wheat

Carotenoids are essential pigments in plants, playing critical roles in photosynthesis, photoprotection, and stress tolerance, particularly under environmental conditions such as high light intensity and drought. To enhance β-carotene content in durum wheat (Triticum durum Desf.), a TILLING approach was used to generate null mutants for the lycopene ε-cyclase (LCYE) and β-hydroxylases 1 (HYD1) genes, which are key players in carotenoid biosynthesis. Homozygous mutants for both genes were obtained by crossing single homeoallelic mutant lines, resulting in three distinct mutant lines (LxH_1, LxH_2, LxH_3). Carotenoid metabolism and antioxidant-related genes expression were analyzed during seed ripening, revealing significantly reduced expression of LCYE and HYD1, while violaxanthin de-epoxidase (VDE) gene was upregulated at later stages. The mutant lines also showed significantly higher β-carotene accumulation in seeds, with an increase of up to 245 % compared to the control, while lutein content was reduced by over 99 %. In leaves, β-carotene levels remained unchanged, but zeaxanthin and violaxanthin accumulated at significantly higher levels compared to the control plants. Chlorophyll content was reduced in the mutant leaves, leading to altered chlorophyll a/b ratios and an overall decrease in total carotenoid levels. Although photosynthetic efficiency was lower in the mutants, gas exchange parameters remained unaffected, suggesting that primary carbon assimilation was not severely compromised. Phenotypic analysis revealed a reduction in plant height, spike length, and spikelet number; however, key yield traits were largely preserved. Notably, the mutant lines exhibited albinism under cold acclimation conditions, a phenotype absent in the control plants, likely due to the crucial role of lutein in photoprotection at low temperatures. These findings demonstrate that the pyramiding of mutations in LCYE and HYD1 effectively alters carotenoid composition, impacts photosynthesis-related traits, and influences plant responses to environmental stresses. This study provides valuable insights for breeding programs aimed at enhancing carotenoid content in wheat, with potential applications in improving both nutritional quality and stress resilience in cereal crops.

Genome-wide analysis and identification of Carotenoid Cleavage Oxygenase (CCO) gene family in coffee (coffee arabica) under abiotic stress

The coffee industry holds importance, providing livelihoods for millions of farmers globally and playing a vital role in the economies of coffee-producing countries. Environmental conditions such as drought and temperature fluctuations can adversely affect the quality and yield of coffee crops.Carotenoid cleavage oxygenases (CCO) enzymes are essential for coffee plants as they help break down carotenoids contributing to growth and stress resistance. However, knowledge about the CCO gene family in Coffee arabica was limited. In this study identified 21 CCO genes in Coffee arabica (C. arabica) revealing two subfamilies carotenoid cleavage dioxygenases (CCDs) and 9-cis-epoxy carotenoid dioxygenases (NCED) through phylogenic analysis. These subfamilies exhibited distribution patterns in terms of gene structure, domains, and motifs. The 21 CaCCO genes, comprising 5 NCED and 16 CCD genes were found across chromosomes. Promoter sequencing analysis revealed cis-elements that likely interact with plant stress-responsive, growth-related, and phytohormones, like auxin and abscisic acid. A comprehensive genome-wide comparison, between C. arabica and A. thaliana was conducted to understand the characteristics of CCO genes. RTqPCR data indicated that CaNCED5, CaNCED6, CaNCED12, and CaNCED20 are target genes involved in the growth of drought coffee plants leading to increased crop yield, in a conditions, with limited water availability. This reveals the role of coffee CCOs in responding to abiotic stress and identifies potential genes useful for breeding stress-resistant coffee varieties.

Identification of Novel Loci Precisely Modulating Pre-Harvest Sprouting Resistance and Red Color Components of the Seed Coat in T. aestivum L

The association between pre-harvest sprouting (PHS) and seed coat color has long been recognized. Red-grained wheats generally exhibit greater PHS resistance compared to white-grained wheat, although variability in PHS resistance exists within red-grained varieties. Here, we conducted a genome-wide association study on a panel consisting of red-grained wheat varieties, aimed at uncovering genes that modulate PHS resistance and red color components of seed coat using digital image processing. Twelve loci associated with PHS traits were identified, nine of which were described for the first time. Genetic loci marked by SNPs AX-95172164 (chromosome 1B) and AX-158544327 (chromosome 7D) explained approximately 25% of germination index variance, highlighting their value for breeding PHS-resistant varieties. The most promising candidate gene for PHS resistance was TraesCS6B02G147900, encoding a protein involved in aleurone layer morphogenesis. Twenty-six SNPs were significantly associated with grain color, independently of the known Tamyb10 gene. Most of them were related to multiple color characteristics. Prioritization of genes within the revealed loci identified TraesCS1D03G0758600 and TraesCS7B03G1296800, involved in the regulation of pigment biosynthesis and in controlling pigment accumulation. In conclusion, our study identifies new loci associated with grain color and germination index, providing insights into the genetic mechanisms underlying these traits.

Analysis of Carotenoids and Gene Expression in Apple Germplasm Resources Reveals the Role of MdCRTISO and MdLCYE in the Accumulation of Carotenoids

Carotenoids play an important role in the coloring and nutritional value of apple (Malus spp.) fruits. Here, six carotenoids, including lutein, zeaxanthin, β-carotene, β-cryptoxanthin, violaxanthin, and neoxanthin, were detected in 105 fruits of apple germplasm resources, which showed a skewed distribution in both the peel and pulp. There were more carotenoids in the peel than in the pulp, and lutein and β-carotene were the primary carotenoids that were present. The expression levels of most carotenoid pathway genes in germplasm fruits during fruit development were higher in the fruits that had an abundance of carotenoids. A linear relationship analysis showed that the expression levels of MdCRTISO and MdLCYE were highly correlated with the content of carotenoids. The leaves accumulated the greatest number of carotenoids, while the roots had the lowest amount. MdCRTISO and MdLCYE were highly expressed in the fruits compared to other tissues. Transgenic calli and transiently transformed fruits confirmed that MdCRTISO and MdLCYE affected the biosynthesis of carotenoids owing to their effects on the expression of other genes for enzymes in the carotenoid pathway. Our findings will extend the understanding of carotenoid biosynthesis in apple and excavate apple germplasm resources with rich carotenoids to breed high-quality apples.

Temporal transcriptome and metabolite analyses provide insights into the biochemical and physiological processes underlying endodormancy release in pistachio (Pistacia vera L.) flower buds

Pistachio (Pistacia vera L.), an economically and nutritionally important tree crop, relies on winter chill for bud endodormancy break and subsequent blooming and nut production. However, insufficient winter chill poses an increasing challenge in pistachio growing regions. To gain a better understanding of the physiological and biochemical responses of endodormant pistachio buds to chilling accumulation, we investigated the global gene expression changes in flower buds of pistachio cv. Kerman that were cultivated at three different orchard locations and exposed to increasing durations of winter chill. The expression of genes encoding β-1,3-glucanase and β-amylase, enzymes responsible for breaking down callose (β-1,3-glucan) and starch (α-1,4-glucan), respectively, increased during the endodormancy break of pistachio buds. This result suggested that the breakdown of callose obstructing stomata as well as the release of glucose from starch enables symplasmic trafficking and provides energy for bud endodormancy break and growth. Interestingly, as chilling accumulation increased, there was a decrease in the expression of nine-cis-epoxycarotenoid dioxygenase (NCED), encoding an enzyme that uses carotenoids as substrates and catalyzes the rate-limiting step in abscisic acid (ABA) biosynthesis. The decrease in NCED expression suggests ABA biosynthesis is suppressed, thus reducing inhibition of endodormancy break. The higher levels of carotenoid precursors and a decrease in ABA content in buds undergoing endodormancy break supports this suggestion. Collectively, the temporal transcriptome and biochemical analyses revealed that the degradation of structural (callose) and non-structural (starch) carbohydrates, along with the attenuation of ABA biosynthesis, are critical processes driving endodormancy break in pistachio buds.

Characterization of thioredoxin gene TaTrxh9 associated with heading-time regulation in wheat

Thioredoxins (Trxs) are thiol-disulfide oxidoreductase proteins that play important roles in a spectrum of processes linking redox regulation and signaling in plants. However, little is known about Trxs and their biological functions in wheat, one of the most important food crops worldwide. This study reports the identification and functional characterization of an h-type Trx gene, TaTrxh9, in wheat. Three homoeologs of TaTrxh9 were identified and the sequences in the coding region were highly consistent among the homoeologs. Protein characterization showed that a conserved Trx_family domain, as well as a typical active site with a dithiol signature (WCGPC), was included in TaTrxh9. Structural modeling demonstrated that TaTrxh9 could fold into a canonical thioredoxin structure consisting of five-stranded antiparallel beta sheets sandwiched between four alpha helices. The insulin disulfide reduction assay demonstrated that TaTrxh9 was catalytically active in vitro. TaTrxh9 overexpression in the Arabidopsis mutant trxh9 complemented the abnormal growth phenotypes of the mutant, suggesting is functionality in vivo. The transcription level of TaTrxh9 was higher in leaf tissues and it was differentially expressed during the development of wheat plants. Interestingly, barley stripe mosaic virus-mediated suppression of TaTrxh9 shortened the seedling-heading period of wheat. Furthermore, CRISPR-Cas9 mediated gene knockout confirmed that the TaTrxh9 mutation resulted in early heading of wheat. To our knowledge, this study is the first to report that Trxh is associated with heading-time regulation, which lays a foundation for further exploring the biological function of TaTrxh9 and provides new ideas for molecular breeding focusing on early heading in wheat.

A multi-omic resource of wheat seed tissues for nutrient deposition and improvement for human health

As a globally important staple crop, wheat seeds provide us with nutrients and proteins. The trend of healthy dietary has become popular recently, emphasizing the consumption of whole-grain wheat products and the dietary benefits. However, the dynamic changes in nutritional profiles of different wheat seed regions (i.e., the embryo, endosperm and outer layers) during developmental stages and the molecular regulation have not been well studied. Here, we provide this multi-omic resource of wheat seeds and describe the generation, technical assessment and preliminary analyses. This resource includes a time-series RNA-seq dataset of the embryo, endosperm and outer layers of wheat seeds and their corresponding metabolomic dataset, covering the middle and late stages of seed development. Our RNA-seq experiments profile the expression of 63,708 genes, while the metabolomic data includes the abundance of 984 metabolites. We believe that this was the first reported transcriptome and metabolome dataset of wheat seeds that helps understand the molecular regulation of the deposition of beneficial nutrients and hence improvements for nutritional and processing quality traits.

Genetic dissection of the roles of β-hydroxylases in carotenoid metabolism, photosynthesis, and plant growth in tetraploid wheat (Triticum turgidum L.)

Functional redundancy and subfunctionalization of β-hydroxylases in tetraploid wheat tissues open up opportunities for manipulation of carotenoid metabolism for trait improvement. The genetic diversity provided by subgenome homoeologs in allopolyploid wheat can be leveraged for developing improved wheat varieties with modified chemical traits, including profiles of carotenoids, which play critical roles in photosynthesis, photoprotection, and growth regulation. Carotenoid profiles are greatly influenced by hydroxylation catalyzed by β-hydroxylases (HYDs). To genetically dissect the contribution of HYDs to carotenoid metabolism and wheat growth and yield, we isolated loss-of-function mutants of the two homoeologs of HYD1 (HYD-A1 and HYD-B1) and HYD2 (HYD-A2 and HYD-B2) from the sequenced ethyl methanesulfonate mutant population of the tetraploid wheat cultivar Kronos, and generated various mutant combinations. Although functional redundancy between HYD1 and HYD2 paralogs was observed in leaves, HYD1 homoeologs contributed more than HYD2 homoeologs to carotenoid β-ring hydroxylation in this tissue. By contrast, the HYD2 homoeologs functioned toward production of lutein, the major carotenoid in mature grains, whereas HYD1 homoeologs had a limited role. These results collectively suggested subfunctionalization of HYD genes and homoeologs in different tissues of tetraploid wheat. Despite reduced photoprotective responses observed in the triple hyd-A1 hyd-B1 hyd-A2 and the quadruple hyd-A1 hyd-B1 hyd-A2 hyd-B2 combinatorial mutants, comprehensive plant phenotyping analysis revealed that all mutants analyzed were comparable to the control for growth, yield, and fertility, except for a slight delay in anthesis and senescence as well as accelerated germination in the quadruple mutant. Overall, this research takes steps toward untangling the functions of HYDs in wheat and has implications for improving performance and consumer traits of this economically important global crop.

Genetic dissection of lutein content in common wheat via association and linkage mapping

Genetic architecture controlling grain lutein content of common wheat was investigated through an integration of genome-wide association study (GWAS) and linkage analysis. Putative candidate genes involved in carotenoid metabolism and regulation were identified, which provide a basis for gene cloning and development of nutrient-enriched wheat varieties through molecular breeding. Lutein, known as 'the eye vitamin', is an important component of wheat nutritional and end-use quality. However, the genetic manipulation of grain lutein content (LUC) in common wheat has not previously been well studied. Here, quantitative trait loci (QTL) associated with the LUC measured by high performance liquid chromatography (HPLC) were first identified by integrating a genome-wide association study (GWAS) and linkage mapping. A Chinese wheat mini-core collection (MCC) of 262 accessions and a doubled haploid (DH) population derived from Jinchun 7 and L1219 were genotyped using the 90K SNP array. A total of 124 significant marker-trait associations (MTAs) on all 21 wheat chromosomes except for 1A, 4D, and 5B that formed 58 QTL were detected. Among them, six stable QTL were identified on chromosomes 2AL, 2DS, 3BL, 3DL, 7AL, and 7BS. Meanwhile, three of the ten QTL identified in the DH population, QLuc.5A.1 and QLuc.5A.2 on chromosome 5AL and QLuc.6A.2 on 6AS, were stable and independently explained 5.58-10.86% of the phenotypic variation. The QLuc.6A.2 region colocalized with two MTAs identified by GWAS. Moreover, 71 carotenoid metabolism-related candidate genes were identified, and the allelic effects were analyzed in the MCC panel based on the 90K array. Results revealed that the genes CYP97A3 (Chr. 6B) and CCD1 (Chr. 5A) were significantly associated with LUC. Additionally, the gene PSY3 (QLuc.5A.1) and several candidate genes involved in the methylerythritol 4-phosphate (MEP) pathways colocalized with stable QTL regions. The present study provides potential targets for future functional gene exploration and molecular breeding in common wheat.

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.

Cytokinin and Its Key Role to Enrich the Plant Nutrients and Growth Under Adverse Conditions-An Update

Among the field crops, wheat is regarded as one of the most paramount cereal crops because it is widely grown, consumed as food across the world, and also known as the staple food for nearly 35 per cent of the world population. However, it is threatened by spot blotch disease causing considerable yield loss, with existing genotypes lacking the resistance and the necessary nutrients. Cytokinins (CKs) are key phytohormones that not only regulate the plant growth/development but also play an important role during stress and in the nutrient metabolic pathway of crop plants. Deficiency of important nutrients like zinc, iron, and vitamin A causes irreparable damage to the body, pressing the need to increase the accumulation of such micronutrients in the edible parts of the plant. Crop bio-fortification is one of the emerging approaches through which the quantities of these nutrients could be increased to an advisable amount. Cytokinin is observed to have a pivotal role in managing environmental stress/climate change and defense systems of plants, and apart from this, it is also found that it has an impact over Zn accumulation in cereal crops. Manipulation of the cytokine dehydrogenase (CKX) enzyme that degrades cytokinin could affect the yield, root growth, and important nutrients. Several instances revealed that an increment in the contents of Zn, S, Fe, and Mn in the seeds of cereals is a reflection of increasing the activity of CKX enzyme resulting the enhancement of the root system which not only helps in the absorption of water in a drought prone area but is also beneficial for scavenging nutrients to the deeper ends of the soil. Exploring micronutrients from the lithosphere via the root system helps in the uptake of the micronutrients and transporting them via the vascular system to the sink of crop plants, therefore, identification and incorporation of CKs/CKX linked gene(s) into targeted crop plants, exploring a bio-fortification approach including CRISPR-Cas9 through conventional and molecular breeding approaches could be the most paramount job for improving the important traits and stress management in order to enhance the plant growth, productivity, and nutritional value of the wheat crops, which would be useful for mankind.

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.

Mutant combinations of lycopene ɛ-cyclase and β-carotene hydroxylase 2 homoeologs increased β-carotene accumulation in endosperm of tetraploid wheat (Triticum turgidum L.) grains

Grains of tetraploid wheat (Triticum turgidum L.) mainly accumulate the non-provitamin A carotenoid lutein-with low natural variation in provitamin A β-carotene in wheat accessions necessitating alternative strategies for provitamin A biofortification. Lycopene ɛ-cyclase (LCYe) and β-carotene hydroxylase (HYD) function in diverting carbons from β-carotene to lutein biosynthesis and catalyzing the turnover of β-carotene to xanthophylls, respectively. However, the contribution of LCYe and HYD gene homoeologs to carotenoid metabolism and how they can be manipulated to increase β-carotene in tetraploid wheat endosperm (flour) is currently unclear. We isolated loss-of-function Targeting Induced Local Lesions in Genomes (TILLING) mutants of LCYe and HYD2 homoeologs and generated higher order mutant combinations of lcye-A, lcye-B, hyd-A2, and hyd-B2. Hyd-A2 hyd-B2, lcye-A hyd-A2 hyd-B2, lcye-B hyd-A2 hyd-B2, and lcye-A lcye-B hyd-A2 hyd-B2 achieved significantly increased β-carotene in endosperm, with lcye-A hyd-A2 hyd-B2 exhibiting comparable photosynthetic performance and light response to control plants. Comparative analysis of carotenoid profiles suggests that eliminating HYD2 homoeologs is sufficient to prevent β-carotene conversion to xanthophylls in the endosperm without compromising xanthophyll production in leaves, and that β-carotene and its derived xanthophylls are likely subject to differential catalysis mechanisms in vegetative tissues and grains. Carotenoid and gene expression analyses also suggest that the very low LCYe-B expression in endosperm is adequate for lutein production in the absence of LCYe-A. These results demonstrate the success of provitamin A biofortification using TILLING mutants while also providing a roadmap for guiding a gene editing-based approach in hexaploid wheat.

The wheat AGL6-like MADS-box gene is a master regulator for floral organ identity and a target for spikelet meristem development manipulation

The AGAMOUS-LIKE6 (AGL6)-like genes are ancient MADS-box genes and are functionally studied in a few model plants. The knowledge of these genes in wheat remains limited. Here, by studying a 'double homoeolog mutant' of the AGL6 gene in tetraploid wheat, we showed that AGL6 was required for the development of all four whorls of floral organs with dosage-dependent effect on floret fertility. Yeast two-hybrid analyses detected interactions of AGL6 with all classes of MADS-box proteins in the ABCDE model for floral organ development. AGL6 was found to interact with several additional proteins, including the G protein β and γ (DEP1) subunits. Analysis of the DEP1-B mutant showed a significant reduction in spikelet number per spike in tetraploid wheat, while overexpression of AGL6 in common wheat increased the spikelet number per spike and hence the grain number per spike. RNA-seq analysis identified the regulation of several meristem activity genes by AGL6, such as FUL2 and TaMADS55. Our work therefore extensively updated the wheat ABCDE model and proposed an alternative approach to improve wheat grain yield by manipulating the AGL6 gene.

Assessment of Biofortification Approaches Used to Improve Micronutrient-Dense Plants That Are a Sustainable Solution to Combat Hidden Hunger

Malnutrition causes diseases, immune system disorders, deterioration in physical growth, mental development, and learning capacity worldwide. Micronutrient deficiency, known as hidden hunger, is a serious global problem. Biofortification is a cost-effective and sustainable agricultural strategy for increasing the concentrations or bioavailability of essential elements in the edible parts of plants, minimizing the risks of toxic metals, and thus reducing malnutrition. It has the advantage of delivering micronutrient-dense food crops to a large part of the global population, especially poor populations. Agronomic biofortification and biofertilization, traditional plant breeding, and optimized fertilizer applications are more globally accepted methods today; however, genetic biofortification based on genetic engineering such as increasing or manipulating (such as CRISPR-Cas9) the expression of genes that affect the regulation of metal homeostasis and carrier proteins that serve to increase the micronutrient content for higher nutrient concentration and greater productivity or that affect bioavailability is also seen as a promising high-potential strategy in solving this micronutrient deficiency problem. Data that micronutrients can help strengthen the immune system against the COVID-19 pandemic and other diseases has highlighted the importance of tackling micronutrient deficiencies. In this study, biofortification approaches such as plant breeding, agronomic techniques, microbial fertilization, and some genetic and nanotechnological methods used in the fight against micronutrient deficiency worldwide were compiled.

Enrichment of provitamin A content in durum wheat grain by suppressing β-carotene hydroxylase 1 genes with a TILLING approach

The suppression of the HYD-1 gene by a TILLING approach increases the amount of β-carotene in durum wheat kernel. Vitamin A deficiency is a major public health problem that affects numerous countries in the world. As humans are not able to synthesize vitamin A, it must be daily assimilated along with other micro- and macronutrients through the diet. Durum wheat is an important crop for Mediterranean countries and provides a discrete amount of nutrients, such as carbohydrates and proteins, but it is deficient in some essential micronutrients, including provitamin A. In the present work, a targeting induced local lesions in genomes strategy has been undertaken to obtain durum wheat genotypes biofortified in provitamin A. In detail, we focused on the suppression of the β-carotene hydroxylase 1 (HYD1) genes, encoding enzymes involved in the redirection of β-carotene toward the synthesis of the downstream xanthophylls (neoxanthin, violaxanthin and zeaxanthin). Expression analysis of genes involved in carotenoid biosynthesis revealed a reduction of the abundance of HYD1 transcripts greater than 50% in mutant grain compared to the control. The biochemical profiling of carotenoid in the wheat mutant genotypes highlighted a significant increase of more than 70% of β-carotene compared to the wild-type sibling lines, with no change in lutein, α-carotene and zeaxanthin content. This study sheds new light on the molecular mechanism governing carotenoid biosynthesis in durum wheat and provides new genotypes that represent a good genetic resource for future breeding programs focused on the provitamin A biofortification through non-transgenic approaches.

Assessing the Role of Carotenoid Cleavage Dioxygenase 4 Homoeologs in Carotenoid Accumulation and Plant Growth in Tetraploid Wheat

The dietary needs of humans for provitamin A carotenoids arise from their inability to synthesize vitamin A de novo. To improve the status of this essential micronutrient, special attention has been given to biofortification of staple foods, such as wheat grains, which are consumed in large quantities but contain low levels of provitamin A carotenoids. However, there remains an unclear contribution of metabolic genes and homoeologs to the turnover of carotenoids in wheat grains. To better understand carotenoid catabolism in tetraploid wheat, Targeting Induced Local Lesions in Genomes (TILLING) mutants of CCD4, encoding a Carotenoid Cleavage Dioxygenase (CCD) that cleaves carotenoids into smaller apocarotenoid molecules, were isolated and characterized. Our analysis showed that ccd4 mutations co-segregated with Poltergeist-like (pll) mutations in the TILLING mutants of A and B subgenomes, hence the ccd-A4 pll-A, ccd-B4 pll-B, and ccd-A4 ccd-B4 pll-A pll-B mutants were analyzed in this study. Carotenoid profiles are comparable in mature grains of the mutant and control plants, indicating that CCD4 homoeologs do not have a major impact on carotenoid accumulation in grains. However, the neoxanthin content was increased in leaves of ccd-A4 ccd-B4 pll-A pll-B relative to the control. In addition, four unidentified carotenoids showed a unique presence in leaves of ccd-A4 ccd-B4 pll-A pll-B plants. These results suggested that CCD4 homoeologs may contribute to the turnover of neoxanthin and the unidentified carotenoids in leaves. Interestingly, abnormal spike, grain, and seminal root phenotypes were also observed for ccd-A4 pll-A, ccd-B4 pll-B, and ccd-A4 ccd-B4 pll-A pll-B plants, suggesting that CCD4 and/or PLL homoeologs could function toward these traits. Overall, this study not only reveals the role of CCD4 in cleavage of carotenoids in leaves and grains, but also uncovers several critical growth traits that are controlled by CCD4, PLL, or the CCD4-PLL interaction.

Multi-strategy engineering greatly enhances provitamin A carotenoid accumulation and stability in Arabidopsis seeds

Staple grains with low levels of provitamin A carotenoids contribute to the global prevalence of vitamin A deficiency and therefore are the main targets for provitamin A biofortification. However, carotenoid stability during both seed maturation and postharvest storage is a serious concern for the full benefits of carotenoid biofortified grains. In this study, we utilized Arabidopsis as a model to establish carotenoid biofortification strategies in seeds. We discovered that manipulation of carotenoid biosynthetic activity by seed-specific expression of Phytoene synthase (PSY) increases both provitamin A and total carotenoid levels but the increased carotenoids are prone to degradation during seed maturation and storage, consistent with previous studies of provitamin A biofortified grains. In contrast, stacking with Orange (OR ^His ), a gene that initiates chromoplast biogenesis, dramatically enhances provitamin A and total carotenoid content and stability. Up to 65- and 10-fold increases of β-carotene and total carotenoids, respectively, with provitamin A carotenoids composing over 63% were observed in the seeds containing OR ^His and PSY. Co-expression of Homogentisate geranylgeranyl transferase (HGGT) with OR ^His and PSY further increases carotenoid accumulation and stability during seed maturation and storage. Moreover, knocking-out of β-carotene hydroxylase 2 (BCH2) by CRISPR/Cas9 not only potentially facilitates β-carotene accumulation but also minimizes the negative effect of carotenoid over production on seed germination. Our findings provide new insights into various processes on carotenoid accumulation and stability in seeds and establish a multiplexed strategy to simultaneously target carotenoid biosynthesis, turnover, and stable storage for carotenoid biofortification in crop seeds.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42994-021-00046-1.

Unraveling the versatility of CCD4: Metabolic engineering, transcriptomic and computational approaches

Carotenoids are economically valuable isoprenoids synthesized by plants and microorganisms, which play a paramount role in their overall growth and development. Carotenoid cleavage dioxygenases are a vast group of enzymes that specifically cleave thecarotenoids to produce apocarotenoids. Recently, CCDs are a subject of talk because of their contributions to different aspects of plant growth and due to their significance in the production of economically valuable apocarotenoids. Among them, CCD4 stands unique because of its versatility in performing metabolic roles. This review focuses on the multiple functionalities of CCD4 like pigmentation, volatile apocarotenoid production, stress responses, etc. Interestingly, through our literature survey we arrived at a conclusion that CCD4 could perform functions of other carotenoid cleaving enzymes.The metabolic engineering, transcriptomic, and computational approaches adopted to reveal the contributions of CCD4 were also considered here for the study.Phylogenetic analysis was performed to delve into the evolutionary relationships of CCD4 in different plant groups. A tree of 81CCD genes from 64 plant species was constructed, signifying the presence of well-conserved families. Gene structures were illustrated and the difference in the number and position of exons could be considered as a factor behind functional versatility and substrate tolerance of CCD4 in different plants.

Carotenoid cleavage dioxygenases (HD-CCD1A and B) contribute as strong negative regulators of β-carotene in Indian bread wheat (cv. HD2967)

Wheat (Triticum aestivum L.) is the most common cereal crop that is considered to be deficient in provitamin A carotenoids. Carotenoids are prone to degrade into apocarotenoids by the activity of carotenoid cleavage dioxygenases (CCDs). Hence, in this study, multiple CCDs were cloned from commercial Indian wheat cultivar HD2967 to understand their role in provitamin A carotenoids degradation. The homoeolog specific expression of HD-CCD1 and HD-CCD4 at different grain filling stages revealed the higher expression of transcripts arising from the A and B subgenomes of HD-CCD1. Furthermore, the grain development stages showed a strong negative correlation of HD-CCD1A (r = - 0.969) and B (r = - 0.970) homoeologs expression to that of β-carotene accumulation. It suggested that they could be potentially involved in deciding the turn-over of β-carotene in wheat grain. Three-dimensional (3D) structures for all six homoeologs of HD-CCD1 and HD-CCD4 were predicted using maize VP14 template to gain better insight into their molecular mechanism. Ramachandran plot assessment revealed that ~ 90% of residues are in the most favoured region. Docking studies with various carotenoid substrates revealed the higher affinity of HD-CCD1A and B for β-carotene and β-cryptoxanthin. Bacterial complementation analysis validated the functional role of all six homoeologs with HD-CCD1B showing the highest activity followed by HD-CCD1A for β-carotene degradation. Results of this study provide valuable insights into the characteristics of HD-CCDs in wheat and thereby justifying them (HD-CCD1A and B) as the candidate genes for employing genome editing tools for developing β-carotene enriched wheat grains.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02775-y.

The Genetic Basis of Tomato Aroma

Tomato (Solanum lycopersicum L.) aroma is determined by the interaction of volatile compounds (VOCs) released by the tomato fruits with receptors in the nose, leading to a sensorial impression, such as "sweet", "smoky", or "fruity" aroma. Of the more than 400 VOCs released by tomato fruits, 21 have been reported as main contributors to the perceived tomato aroma. These VOCs can be grouped in five clusters, according to their biosynthetic origins. In the last decades, a vast array of scientific studies has investigated the genetic component of tomato aroma in modern tomato cultivars and their relatives. In this paper we aim to collect, compare, integrate and summarize the available literature on flavour-related QTLs in tomato. Three hundred and 5ifty nine (359) QTLs associated with tomato fruit VOCs were physically mapped on the genome and investigated for the presence of potential candidate genes. This review makes it possible to (i) pinpoint potential donors described in literature for specific traits, (ii) highlight important QTL regions by combining information from different populations, and (iii) pinpoint potential candidate genes. This overview aims to be a valuable resource for researchers aiming to elucidate the genetics underlying tomato flavour and for breeders who aim to improve tomato aroma.

Identification of Lycopene epsilon cyclase (LCYE) gene mutants to potentially increase β-carotene content in durum wheat (Triticum turgidum L.ssp. durum) through TILLING

Increasing β-carotene (a vitamin A precursor) content in Triticum turgidum L. ssp. durum (durum wheat) grains is important to improve pasta nutritional quality. Studies in other species show that altering the expression of LCYE genes increases the flux towards the β-β branch, accumulating higher β-carotene levels. Durum wheat is a tetraploid species that has two LCYE genes (LCYE-A and LCYE-B) associated to the A and B genomes. The objective of this work was to produce durum wheat LCYE mutants through EMS to potentially increase β-carotene content. The LCYE point mutations created with EMS were identified using a Kronos TILLING (Targeting Induced Local Lesion IN Genomes) mutant population. Specific primers that amplified exons 3 through 10 of the LCYE genes were designed and validated. To simplify the TILLING procedure, fragments were digested with CJE (Celery Juice Extract) and visualized on 2% agarose gels. 6X mutant pools were identified, which showed cleavage products and then made into 2X pools to identify mutant individuals. LCYE mutants were then sequenced and evaluated with BLOSUM62, SIFT and PSSM algorithms. Mutants with substitutions W437*, P334L and G368R in LCYE-A and P405L, G352R and T393I in LCYE-B predicted to affect protein function were selected. Substitution W437* increased β-carotene in 75% and overall total carotenoids content in leaves of the mutant 2426 (A1 mutant line), but no significant differences relative to the control were found in grains through HPLC. Finally, the increased levels of β-carotene on leaves have potential applications to improving plant resistance under contaminated environmental conditions.

RNAi-mediated suppression of three carotenoid-cleavage dioxygenase genes, OsCCD1, 4a, and 4b, increases carotenoid content in rice

Carotenoids of staple food crops have a high nutritional value as provitamin A components in the daily diet. To increase the levels of carotenoids, inhibition of carotenoid-cleavage dioxygenases (CCDs), which degrade carotenoids, has been considered as a promising target in crop biotechnology. In this study, suppression of the OsCCD1, OsCCD4a, and OsCCD4b genes using RNAi was verified in transgenic rice plants by quantitative RT-PCR and small RNA detection. Leaf carotenoids were significantly increased overall in OsCCD4a-RNAi lines of the T1 generation, and the highest accumulation of 1.3-fold relative to non-transgenic plants was found in a line of the T2 generation. The effects on seed carotenoids were determined via cross-fertilization between β-carotene-producing transgenic rice and one of two independent homozygous lines of OsCCD1-RNAi, OsCCD4a-RNAi, or OsCCD4b-RNAi. This showed that carotenoids were increased to a maximum of 1.4- and 1.6-fold in OsCCD1-RNAi and OsCCD4a-RNAi, respectively, with a different preference toward α-ring and β-ring carotenoids; levels could not be established in OsCCD4b-RNAi. In addition, the contents of four carotenoids decreased when OsCCD1, OsCCD4a, and OsCCD4b were overexpressed in E. coli strains accumulating phytoene, lycopene, β-carotene, and zeaxanthin. OsCCD1 and OsCCD4a had a similar high carotenoid degrading activity, followed by OsCCD4b without substrate specificity. Overall, our results suggest that suppresing OsCCD4a activity may have potential as a tool for enhancing the carotenoid content of seed endosperms and leaves in rice.

Breeding Major Cereal Grains through the Lens of Nutrition Sensitivity

Cereal grains are the common food staples that collectively provide over 50% of dietary calories and proteins for the world's population. Although the Green Revolution has greatly increased the yield of commercial cereal crops, they often lack nutrients essential for human health in the edible tissues. In developing nutrition-sensitive agriculture, the nutritional quality of cereal grains has been a major target for improvement using breeding and biotechnology approaches. This review examines recent progress on biofortification of micronutrients (provitamin A and folates) and an essential amino acid (lysine) in three major cereal grains, wheat, rice, and maize, through plant breeding. In addition, how natural variations, induced mutations, and the advanced genome-editing technologies can be applied to improving the nutrient content and stability in these cereal grains are discussed. High-yield cereal crops pyramided with improved (micro)nutrient contents hold great promise to meet the increasing demand of nutritionally limited populations and to contribute to achieving sustainable nutrition security.

Carotenoid Metabolism in Plants: The Role of Plastids

Carotenoids are indispensable to plants and critical in human diets. Plastids are the organelles for carotenoid biosynthesis and storage in plant cells. They exist in various types, which include proplastids, etioplasts, chloroplasts, amyloplasts, and chromoplasts. These plastids have dramatic differences in their capacity to synthesize and sequester carotenoids. Clearly, plastids play a central role in governing carotenogenic activity, carotenoid stability, and pigment diversity. Understanding of carotenoid metabolism and accumulation in various plastids expands our view on the multifaceted regulation of carotenogenesis and facilitates our efforts toward developing nutrient-enriched food crops. In this review, we provide a comprehensive overview of the impact of various types of plastids on carotenoid biosynthesis and accumulation, and discuss recent advances in our understanding of the regulatory control of carotenogenesis and metabolic engineering of carotenoids in light of plastid types in plants.

Characterization of Aldehyde Oxidase (AO) Genes Involved in the Accumulation of Carotenoid Pigments in Wheat Grain

Aldehyde Oxidase (AO) enzyme (EC 1.2.3.1) catalyzes the final steps of carotenoid catabolism and it is a key enzyme in the abscisic acid (ABA) biosynthesis. AO isoforms are located in the cytosolic compartment of tissues in many plants, where induce the oxidation of aldehydes into carboxylic acid, and in addition, catalyze the hydroxylation of some heterocycles. The goal of the present study was to characterize the AO genes involved in the accumulation of carotenoid pigments in wheat grain, an important quantitative trait controlled by multiple genes. The cDNAs corresponding to the four AO isoforms from Arabidopsis thaliana and five AO isoforms from Brachypodium distachyon were used as query in 454 sequence assemblies data for Triticum aestivum cv. Chinese Spring (https://urgi.versailles.inra.fr/blast/blast.php) to obtain the partial or whole orthologous wheat AO sequences. Three wheat isoforms, designated AO1, AO2, and AO3 were located on the chromosome groups 2, 5, and 7, respectively, and mapped on two consensus wheat maps by SNP markers located within the AO gene sequences. To validate the possible relationships between AO3 genes and carotenoid accumulation in wheat, the expression levels of AO-A3 and AO-B3 gene were determined during the kernel maturation stage of two durum wheat cultivars, Ciccio and Svevo, characterized by a low and high carotenoid content, respectively. Different AO-A3 gene expression values were observed between the two cultivars indicating that the AO-A3 allele present in Ciccio was more active in carotenoid degradation. A gene marker was developed and can be used for marker-assisted selection in wheat breeding programs.

Transgenic Pro-Vitamin A Biofortified Crops for Improving Vitamin A Deficiency and Their Challenges

Vitamin A Deficiency (VAD) has been a public health problem among children in developing countries. To alleviate VAD, Vitamin A Supplementation (VAS), food fortification, biofortification and nutrition education have been implemented in various degrees of success with their own merits and limits. While VAS is the most widely utilized intervention in developing countries to ease the burden of VAD, some have raised questions on VAS’ effectiveness. Biofortification, often touted as an effective alternative to VAS, has received significant attention. Among the available biofortification methods, adopting transgenic technology has not only facilitated rapid progress in science for enhanced pro-Vitamin A (pVA) levels in target crops, but drawn considerable skepticism in politics for safety issues. Additionally, VAD-afflicted target regions of transgenic pVA crops widely vary in their national stance on Genetically Modified (GM) products, which further complicates crop development and release. This paper briefly reviews VAS and its controversy which partly demanded shifts to food-based VAD interventions, and updates the current status of transgenic pVA crops. Also, this paper presents a framework to provide potential influencers for transgenic pVA crop development under politically challenging climates with GM products. The framework could be applicable to other transgenic micronutrient biofortification.

The carotenoid biosynthetic and catabolic genes in wheat and their association with yellow pigments

BACKGROUND

In plants carotenoids play an important role in the photosynthetic process and photo-oxidative protection, and are the substrate for the synthesis of abscisic acid and strigolactones. In addition to their protective role as antioxidants and precursors of vitamin A, in wheat carotenoids are important as they influence the colour (whiteness vs. yellowness) of the grain. Understanding the genetic basis of grain yellow pigments, and identifying associated markers provide the basis for improving wheat quality by molecular breeding.

RESULTS

Twenty-four candidate genes involved in the biosynthesis and catabolism of carotenoid compounds have been identified in wheat by comparative genomics. Single nucleotide polymorphisms (SNPs) found in the coding sequences of 19 candidate genes allowed their chromosomal location and accurate map position on two reference consensus maps to be determined. The genome-wide association study based on genotyping a tetraploid wheat collection with 81,587 gene-associated SNPs validated quantitative trait loci (QTLs) previously detected in biparental populations and discovered new QTLs for grain colour-related traits. Ten carotenoid genes mapped in chromosome regions underlying pigment content QTLs indicating possible functional relationships between candidate genes and the trait.

CONCLUSIONS

The availability of linked, candidate gene-based markers can facilitate breeding wheat cultivars with desirable levels of carotenoids. Identifying QTLs linked to carotenoid pigmentation can contribute to understanding genes underlying carotenoid accumulation in the wheat kernels. Together these outputs can be combined to exploit the genetic variability of colour-related traits for the nutritional and commercial improvement of wheat products.