Virus-Mediated Transient Expression Techniques Enable Functional Genomics Studies and Modulations of Betalain Biosynthesis and Plant Height in Quinoa

Comparative role of betalains and other key antioxidant metabolites in the photoprotection against acute exposure to UV-B radiation in Chenopodium quinoa and C. berlandieri seedlings

Chenopodium quinoa Willd. is a betalainic crop with remarkable tolerance to extreme environmental conditions. Despite numerous varieties grow at high altitudes, where UV-B radiation is intense, research on the effects of UV-B stress on this and related species is very scarce. In the present work we aimed to determine whether UV-B radiation induces the production of betalains, and evaluated the role of these pigments and other key antioxidants in preventing oxidative damage, in seedlings of C. quinoa (ecotypes CICA and Villarrica) and its close relative C. berlandieri Moq., grown in darkness and after exposure to an acute pulse of UV-B radiation (24 h, 2.5 W m-2). UV-B significantly increased MDA accumulation and induced the production of betalains (particularly betacyanins), polyphenols and UV-B-absorbing compounds in all seedlings tested. The activity of antioxidant enzymes showed comparatively minor changes, with the exception of GPOX which consistently decreased after UV-B irradiation. The degree of oxidative damage was not correlated to the concentration of betalains present in the tissues at the end of the treatment. However, when pigment synthesis was stimulated by short white light pulses prior to UV-B irradiation, the increase in MDA levels could be prevented in C. berlandieri seedlings despite no major changes occurred in most of the remaining metabolites evaluated, suggesting that betalains have an important role in controlling oxidative damage in this species. In contrast, the presence of high levels of polyphenolic compounds rather than the accumulation of betalains contributed to improved UV-B tolerance in C. quinoa seedlings.

Global investigation into the CqCYP76AD and CqDODA families in Chenopodium quinoa: Identification, evolutionary history, and their functional roles in betalain biosynthesis

Betalains are water-soluble pigments mainly distributed in the core Caryophyllales plants. Betalains provide plant with striking colors to attract pollinators and are beneficial to human health due to the strong antioxidant activity. To date, many studies regarding to betalain biosynthesis have been exerted in sugar beet (Beta vulgaris) and four-O-clock (Mirabilis jalapa), however, the key regulators in betalain pigmentation of quinoa (Chenopodium quinoa) remain to be elucidated. CYP76AD and DODA genes encode core enzymes converting L-DOPA to cyclo-DOPA and betalamic acid, respectively, in betalain biosynthesis. In this study, 44 CqCYP76AD (5 α-clade, 6 β-clade and 33 γ-clade homologs) and 18 CqDODA (10 α-clade, 2 β-clade and 6 γ-clade homologs) members were identified in quinoa genome. Expression analysis and cis-element analysis indicated that light and ABA are involved in the regulation of CqCYP76AD and CqDODA. We found application of exogenous ABA and darkness repressed the betalain production in quinoa seedlings. Tandem duplication is the major driving force for CqCYP76AD and CqDODA family expansion. Evolutionary history analysis on the duplication events of quinoa and its close relatives, sugar beet, C. pallidicaule, C. suecicum and C. formosanum, identified the quinoa-specific tandem duplications CqCYP76AD-α2/-α3, CqDODA-α1/-α6 in Chr04, and CqCYP76AD-α1/-α4/-α5, CqDODA-α3/-α4/-α5 in Chr03, which are absent in sugar beet. The close co-location of the CqCYP76AD-α-CqDODA-α gene clusters suggests they are putative enhanced regulatory units for betalain biosynthesis in quinoa, similar to the operon BvCYP76AD1-BvDODA1 in sugar beet. The functions of α-, β- and γ-clade CqCYP76ADs and CqDODAs were investigated by transient expression system in tobacco leaves and hairy root transformation in quinoa. The results indicated that CqCYP76AD-α1, CqCYP76AD-β3, CqDODA-α1, CqDODA-α3 and CqDODA-α5 are the important positive regulators for betalain accumulation in quinoa. Correlation between pigment contents and expression levels at different developmental stages indicates their roles in pigmentation of leaf, stem and spike tissues of in betalain-enriched quinoa. Overall, this study performed genome-wide identification and functional characterization of the important functional enzymes of CqCYP76ADs and CqDODAs for betalain biosynthesis in quinoa, which will deep our understanding of the mechanisms of betalain pigmentation in quinoa.

Integrating Physiology, Transcriptome, and Metabolome Analyses Reveals the Drought Response in Two Quinoa Cultivars with Contrasting Drought Tolerance

Quinoa (Chenopodium quinoa Willd.) is an annual broadleaf plant belonging to the Amaranthaceae family. It is a nutritious food crop and is considered to be drought-tolerant, but drought is still one of the most important abiotic stress factors limiting its yield. Quinoa responses to drought are related to drought intensity and genotype. This study used two different drought-responsive quinoa cultivars, LL1 (drought-tolerant) and ZK1 (drought-sensitive), to reveal the important mechanisms of drought response in quinoa by combining physiological, transcriptomic, and metabolomic analyses. The physiological analysis indicated that Chla/Chlb might be important for drought tolerance in quinoa. A total of 1756 and 764 differentially expressed genes (DEGs) were identified in LL1 and ZK1, respectively. GO (Gene Ontology) enrichment analysis identified 52 common GO terms, but response to abscisic acid (GO:0009737) and response to osmotic stress (GO:0006970) were only enriched in LL1. KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis revealed that glycerophospholipid metabolism (ko00564) and cysteine and methionine metabolism (ko00270) ranked at the top of the list in both cultivars. A total of 1844 metabolites were identified by metabolomic analysis. "Lipids and lipid-like" molecules had the highest proportions. The DEMs in LL1 and ZK1 were mainly categorized 6 and 4 Human Metabolome Database (HMDB) superclasses, respectively. KEGG analysis revealed that the 'α-linolenic acid metabolism' was enriched in both LL1 and ZK1. Joint KEGG analysis also revealed that the 'α-linolenic acid metabolism' pathway was enriched by both the DEGs and DEMs of LL1. There were 17 DEGs and 8 DEMs enriched in this pathway, and methyl jasmonate (MeJA) may play an important role in the drought response of quinoa. This study will provide information for the identification of drought resistance in quinoa, research on the molecular mechanism of drought resistance, and genetic breeding for drought resistance in quinoa.

Chromosome-level genome assemblies for two quinoa inbred lines from northern and southern highlands of Altiplano where quinoa originated

Quinoa is emerging as a key seed crop for global food security due to its ability to grow in marginal environments and its excellent nutritional properties. Because quinoa is partially allogamous, we have developed quinoa inbred lines necessary for molecular genetic analysis. Our comprehensive genomic analysis showed that the quinoa inbred lines fall into three genetic subpopulations: northern highland, southern highland, and lowland. Lowland and highland quinoa are the same species, but have very different genotypes and phenotypes. Lowland quinoa has relatively small grains and a darker grain color, and is widely tested and grown around the world. In contrast, the white, large-grained highland quinoa is grown in the Andean highlands, including the region where quinoa originated, and is exported worldwide as high-quality quinoa. Recently, we have shown that viral vectors can be used to regulate endogenous genes in quinoa, paving the way for functional genomics to reveal the diversity of quinoa. However, although a high-quality assembly has recently been reported for a lowland quinoa line, genomic resources of the quality required for functional genomics are not available for highland quinoa lines. Here we present high-quality chromosome-level genome assemblies for two highland inbred quinoa lines, J075 representing the northern highland line and J100 representing the southern highland line, using PacBio HiFi sequencing and dpMIG-seq. In addition, we demonstrate the importance of verifying and correcting reference-based scaffold assembly with other approaches such as linkage maps. The assembled genome sizes of J075 and J100 are 1.29 and 1.32 Gb, with contigs N50 of 66.3 and 12.6 Mb, and scaffold N50 of 71.2 and 70.6 Mb, respectively, comprising 18 pseudochromosomes. The repetitive sequences of J075 and J100 represent 72.6% and 71.5% of the genome, the majority of which are long terminal repeats, representing 44.0% and 42.7% of the genome, respectively. The de novo assembled genomes of J075 and J100 were predicted to contain 65,303 and 64,945 protein-coding genes, respectively. The high quality genomes of these highland quinoa lines will facilitate quinoa functional genomics research on quinoa and contribute to the identification of key genes involved in environmental adaptation and quinoa domestication.

Leaf and shoot apical meristem transcriptomes of quinoa (Chenopodium quinoa Willd.) in response to photoperiod and plant development

Understanding the regulation of flowering time is crucial for adaptation of crops to new environment. In this study, we examined the timing of floral transition and analysed transcriptomes in leaf and shoot apical meristems of photoperiod-sensitive and -insensitive quinoa accessions. Histological analysis showed that floral transition in quinoa initiates 2-3 weeks after sowing. We found four groups of differentially expressed genes in quinoa genome that responded to plant development and floral transition: (i) 222 genes responsive to photoperiod in leaves, (ii) 1812 genes differentially expressed between accessions under long-day conditions in leaves, (iii) 57 genes responding to developmental changes under short-day conditions in leaves and (iv) 911 genes responding to floral transition within the shoot apical meristem. Interestingly, among numerous candidate genes, two putative FT orthologs together with other genes (e.g. SOC1, COL, AP1) were previously reported as key regulators of flowering time in other species. Additionally, we used coexpression networks to associate novel transcripts to a putative biological process based on the annotated genes within the same coexpression cluster. The candidate genes in this study would benefit quinoa breeding by identifying and integrating their beneficial haplotypes in crossing programs to develop adapted cultivars to diverse environmental conditions.

Effect of betanin synthesis on photosynthesis and tyrosine metabolism in transgenic carrot

BACKGROUND

Betalain is a natural pigment with important nutritional value and broad application prospects. Previously, we produced betanin biosynthesis transgenic carrots via expressing optimized genes CYP76AD1S, cDOPA5GTS and DODA1S. Betanin can accumulate throughout the whole transgenic carrots. But the effects of betanin accumulation on the metabolism of transgenic plants and whether it produces unexpected effects are still unclear.

RESULTS

The accumulation of betanin in leaves can significantly improve its antioxidant capacity and induce a decrease of chlorophyll content. Transcriptome and metabolomics analysis showed that 14.0% of genes and 33.1% of metabolites were significantly different, and metabolic pathways related to photosynthesis and tyrosine metabolism were markedly altered. Combined analysis showed that phenylpropane biosynthesis pathway significantly enriched the differentially expressed genes and significantly altered metabolites.

CONCLUSIONS

Results showed that the metabolic status was significantly altered between transgenic and non-transgenic carrots, especially the photosynthesis and tyrosine metabolism. The extra consumption of tyrosine and accumulation of betanin might be the leading causes.

An Agrobacterium-mediated transient expression method contributes to functional analysis of a transcription factor and potential application of gene editing in Chenopodium quinoa

An efficient Agrobacterium-mediated transient expression method was developed, which contributed to the functional characterization of the transcription factor CqPHR1, and demonstrates the potential application of gene editing in quinoa. Chenopodium quinoa is a crop expected to ensure global food security in future due to its high resistance to multiple abiotic stresses and nutritional value. We cloned one of the paralogous genes of the Arabidopsis homolog PHR1 (PHOSPHATE STARVATION RESPONSE 1) in quinoa-inbred lines by reverse genetic approach. Overexpression of CqPHR1 driven by the constitutive CaMV 35S promoter in Arabidopsis phr1 mutant can complement its phenotypes, including the induction of phosphate starvation-induced (PSI) genes and anthocyanin accumulation in leaves. By Agrobacterium-mediated gene transient expression, we found that CqPHR1 localized in the nucleus of quinoa cells, and overexpression of CqPHR1 in quinoa cells promoted PSI genes expression, which further revealed the function of CqPHR1 as a transcription factor. We have also shown that the transient expression system can be used to express Cas9 protein in various quinoa-inbred lines and perform effective gene editing in quinoa tissue. The method developed in this study will be useful for verifying the effectiveness of gene-editing systems in quinoa cells and has potential application in the generation of gene-edited quinoa with heritable traits.

Stalk cell polar ion transport provide for bladder-based salinity tolerance in Chenopodium quinoa

Chenopodium quinoa uses epidermal bladder cells (EBCs) to sequester excess salt. Each EBC complex consists of a leaf epidermal cell, a stalk cell, and the bladder. Under salt stress, sodium (Na⁺ ), chloride (Cl^- ), potassium (K⁺ ) and various metabolites are shuttled from the leaf lamina to the bladders. Stalk cells operate as both a selectivity filter and a flux controller. In line with the nature of a transfer cell, advanced transmission electron tomography, electrophysiology, and fluorescent tracer flux studies revealed the stalk cell's polar organization and bladder-directed solute flow. RNA sequencing and cluster analysis revealed the gene expression profiles of the stalk cells. Among the stalk cell enriched genes, ion channels and carriers as well as sugar transporters were most pronounced. Based on their electrophysiological fingerprint and thermodynamic considerations, a model for stalk cell transcellular transport was derived.

High-Density Mapping of Quantitative Trait Loci Controlling Agronomically Important Traits in Quinoa (Chenopodium quinoa Willd.)

Quinoa is a pseudocereal originating from the Andean regions. Despite quinoa's long cultivation history, genetic analysis of this crop is still in its infancy. We aimed to localize quantitative trait loci (QTL) contributing to the phenotypic variation of agronomically important traits. We crossed the Chilean accession PI-614889 and the Peruvian accession CHEN-109, which depicted significant differences in days to flowering, days to maturity, plant height, panicle length, and thousand kernel weight (TKW), saponin content, and mildew susceptibility. We observed sizeable phenotypic variation across F2 plants and F3 families grown in the greenhouse and the field, respectively. We used Skim-seq to genotype the F2 population and constructed a high-density genetic map with 133,923 single nucleotide polymorphism (SNPs). Fifteen QTL were found for ten traits. Two significant QTL, common in F2 and F3 generations, depicted pleiotropy for days to flowering, plant height, and TKW. The pleiotropic QTL harbored several putative candidate genes involved in photoperiod response and flowering time regulation. This study presents the first high-density genetic map of quinoa that incorporates QTL for several important agronomical traits. The pleiotropic loci can facilitate marker-assisted selection in quinoa breeding programs.

Recent Developments and Strategies for the Application of Agrobacterium-Mediated Transformation of Apple Malus × domestica Borkh

Genetic transformation has become an important tool in plant genome research over the last three decades. This applies not only to model plants such as Arabidopsis thaliana but also increasingly to cultivated plants, where the establishment of transformation methods could still pose many problems. One of such plants is the apple (Malus spp.), the most important fruit of the temperate climate zone. Although the genetic transformation of apple using Agrobacterium tumefaciens has been possible since 1989, only a few research groups worldwide have successfully applied this technology, and efficiency remains poor. Nevertheless, there have been some developments, especially in recent years, which allowed for the expansion of the toolbox of breeders and breeding researchers. This review article attempts to summarize recent developments in the Agrobacterium-mediated transformation strategies of apple. In addition to the use of different tissues and media for transformation, agroinfiltration, as well as pre-transformation with a Baby boom transcription factor are notable successes that have improved transformation efficiency in apple. Further, we highlight targeted gene silencing applications. Besides the classical strategies of RNAi-based silencing by stable transformation with hairpin gene constructs, optimized protocols for virus-induced gene silencing (VIGS) and artificial micro RNAs (amiRNAs) have emerged as powerful technologies for silencing genes of interest. Success has also been achieved in establishing methods for targeted genome editing (GE). For example, it was recently possible for the first time to generate a homohistont GE line into which a biallelic mutation was specifically inserted in a target gene. In addition to these methods, which are primarily aimed at increasing transformation efficiency, improving the precision of genetic modification and reducing the time required, methods are also discussed in which genetically modified plants are used for breeding purposes. In particular, the current state of the rapid crop cycle breeding system and its applications will be presented.