Differential Regulation of Protochlorophyllide Oxidoreductase Abundances by VIRESCENT 5A (OsV5A) and VIRESCENT 5B (OsV5B) in Rice Seedlings

Identification of Genetic Loci Affecting Flag Leaf Chlorophyll in Wheat Grown under Different Water Regimes

Chlorophyll content of the flag leaf is an important trait for drought resistance in wheat under drought stress. Understanding the regulatory mechanism of flag leaf chlorophyll content could accelerate breeding for drought resistance. In this study, we constructed a recombinant inbred line (RIL) population from a cross of drought-sensitive variety DH118 and drought-resistant variety Jinmai 919, and analyzed the chlorophyll contents of flag leaves in six experimental locations/years using the Wheat90K single-nucleotide polymorphism array. A total of 29 quantitative trait loci (QTLs) controlling flag leaf chlorophyll were detected with contributions to phenotypic variation ranging from 4.67 to 23.25%. Twelve QTLs were detected under irrigated conditions and 18 were detected under dryland (drought) conditions. Most of the QTLs detected under the different water regimes were different. Four major QTLs (Qchl.saw-3B.2, Qchl.saw-5A.2, Qchl.saw-5A.3, and Qchl.saw-5B.2) were detected in the RIL population. Qchl.saw-3B.2, possibly more suitable for marker-assisted selection of genotypes adapted to irrigated conditions, was validated by a tightly linked kompetitive allele specific PCR (KASP) marker in a doubled haploid population derived from a different cross. Qchl.saw-5A.3, a novel stably expressed QTL, was detected in the dryland environments and explained up to 23.25% of the phenotypic variation, and has potential for marker-assisted breeding of genotypes adapted to dryland conditions. The stable and major QTLs identified here add valuable information for understanding the genetic mechanism underlying chlorophyll content and provide a basis for molecular marker–assisted breeding.

Integrating physiology, genetics, and transcriptome to decipher a new thermo-sensitive and light-sensitive virescent leaf gene mutant in cucumber

Chloroplasts are the material basis of photosynthesis, and temperature and light severely affect chloroplast development and thus influence photosynthetic efficiency. This study identified a spontaneous virescent leaf mutant, SC311Y, whose cotyledons and true leaves were yellow and gradually turned green. However, temperature and light affected the process of turning green. In addition, this mutant (except at the seedling stage) had ruffled leaves with white stripes, sterile males, and poorly fertile female flowers. Genetic characteristics analysis revealed that the recessive gene controlled the virescent leaf. Two F₂ populations mapped v-3 to the interval of 33.54-35.66 Mb on chromosome 3. In this interval, BSA-Seq, RNA-Seq, and cDNA sequence analyses revealed only one nonsynonymous mutation in the Csa3G042730 gene, which encoded the RNA exosome supercomplex subunit resurrection1 (RST1). Csa3G042730 was predicted to be the candidate gene controlling the virescent leaf, and the candidate gene may regulate chloroplast development by regulating plastid division2 (PDV2). A transcriptome analysis showed that different factors caused the reduced chlorophyll and carotenoid content in the mutants. To our knowledge, this study is the first report of map-based cloning related to virescent leaf, male-sterile, and chloroplast RNA regulation in cucumber. The results could accelerate the study of the RNA exosome supercomplex for the dynamic regulation of chloroplast RNA.

Rice TSV2 encoding threonyl-tRNA synthetase is needed for early chloroplast development and seedling growth under cold stress

Threonyl-tRNA synthetase (ThrRS), one of the aminoacyl-tRNA synthetases (AARSs), plays a crucial role in protein synthesis. However, the AARS functions on rice chloroplast development and growth were not fully appraised. In this study, a thermo-sensitive virescent mutant tsv2, which showed albino phenotype and lethal after the 4-leaf stage at 20°C but recovered to normal when the temperatures rose, was identified and characterized. Map-based cloning and complementation tests showed that TSV2 encoded a chloroplast-located ThrRS protein in rice. The Lys-to-Arg mutation in the anticodon-binding domain hampered chloroplast development under cold stress, while the loss of function of the ThrRS core domain in TSV2 fatally led to seedling death regardless of growing temperatures. In addition, TSV2 had a specific expression in early leaves. Its disruption obviously resulted in the downregulation of certain genes associated with chlorophyll biosynthesis, photosynthesis, and chloroplast development at cold conditions. Our observations revealed that rice nuclear-encoded TSV2 plays an important role in chloroplast development at the early leaf stage under cold stress.

Transcriptomic and Metabolomic Analyses Reveals That Exogenous Methyl Jasmonate Regulates Galanthamine Biosynthesis in Lycoris longituba Seedlings

The Amaryllidaceae alkaloid galanthamine (Gal) in Lycoris longituba is a secondary metabolite that has been used to treat Alzheimer's disease. Plant secondary metabolism is affected by methyl jasmonate (MeJA) exposure, although the regulatory mechanisms of MeJA on L. longituba seedlings remains largely unknown. In the present study, 75, 150, and 300 μM MeJA were used as treatments on L. longituba seedlings for 7, 14, 21, and 28 days, while 0 μM MeJA was used as the control (MJ-0). The effect of exogenous MeJA on Gal synthesis in L. longituba was then investigated using transcriptomic sequencing and metabolite profiling via GC-MS and LC-MS analysis. Galanthamine (Gal), lycorine (Lyc), and lycoramine (Lycm) abundances were 2. 71-, 2. 01-, and 2.85-fold higher in 75 μM MeJA (MJ-75) treatment plants compared to MJ-0 treatment plants after 7 days of cultivation. Transcriptomic analysis further showed that MJ-75 treatment significantly induced the expression of norbelladine synthase (NBS) and norbelladine 4'-O-methyltransferase (OMT), which are involved in the Gal biosynthesis pathway. In addition, increased expression was observed in MJ-75 treatment plants for genes in the JA synthesis and JA signaling pathways including those of allene oxide cyclase (AOC), 12-oxo-phytodienoic acid reductase (OPR), jasmonic acid amino acid synthase (JAR), and transcription factor MYC. The L. longituba tyrosine decarboxylase (LlTYDC) enzyme was identified and proposed to be involved in the Gal biosynthetic pathway. Metabolomics results demonstrated that the accumulation of Amaryllidaceae alkaloids, and especially alkaloids in the Gal biosynthesis pathway, could be induced by MJ-75 treatment. Interestingly, metabolites in the JA synthesis pathway were also affected by MeJA treatment. Overall, this multi-omics study suggests that both the JA synthesis/JA signaling and Gal biosynthesis pathways were affected by exogenous MeJA treatment. This comprehensive study of gene expression and metabolite contents can help us better understand the molecular mechanisms underlying MeJA-mediated Gal biosynthesis in L. longituba.

Transcriptome Analysis of Different Tissues Reveals Key Genes Associated With Galanthamine Biosynthesis in Lycoris longituba

L ycoris longituba is a traditional medicinal plant containing the bioactive compound galanthamine (Gal), a type of Amaryllidaceae alkaloid and can be used to treat Alzheimer's disease. However, research on its genome or transcriptome and associated genes in the biosynthetic pathway is incomplete. In this study, we estimated the nuclear genome size of this species to be 29.33 Gb by flow cytometry. Then, RNA sequencing of the leaves, roots, and bulbs of L. longituba was carried out. After de novo assembly, 474,589 all-transcripts and 333,440 all-unigenes were finally generated. In addition, the differentially expressed genes (DEGs) were identified, and genes involved in the galanthamine metabolic pathway encoding tyrosine decarboxylase (TYDC), phenylalanine ammonia-lyase (PAL), cinnamate 4-hydroxylase (C4H), p-coumarate 3-hydroxylase (C3H), norbelladine synthase (NBS), norbelladine 4'-O-methyltransferase (OMT), and noroxomaritidine synthase (CYP96T1) were detected and validated by real-time quantitative PCR analysis. One candidate gene, Lycoris longituba O-Methyltransferase (LlOMT), was identified in the proposed galanthamine biosynthetic pathway. Sequence analysis showed that LlOMT is a class I OMT. LlOMT is localized in the cytoplasm, and biochemical analysis indicated that the recombinant LlOMT catalyzes norbelladine to generate 4'-O-methylnorbelladine. The protoplast transformation result showed that the overexpression of LlOMT could increase the Gal content. Our results indicate that LlOMT may play a role in galanthamine biosynthesis in L. longituba. This work provides a useful resource for the metabolic engineering of Amaryllidaceae alkaloids.

Fine mapping and molecular characterization of the virescent gene vsp in Upland cotton (Gossypium hirsutum)

The vsp gene was fine mapped to a 353.7-kb region, and a 201-bp deletion that affected chloroplast development and chlorophyll biosynthesis was found in the candidate gene GhPUR4. Virescent mutations can be used as marker traits in heterosis breeding and can also be used to research chloroplast development, chlorophyll biosynthesis and photosynthesis mechanisms. Here, we obtained a light-sensitive virescent mutant, vsp, that has reduced chlorophyll (Chl) content and abnormal chloroplast development. Then, the virescent space (vsp) gene in the vsp mutant was preliminarily mapped to a 38.32-Mb region of chromosome D04 using a high-density SNP genetic map with a total length of 5384.33 cM and 4472 bin markers. Furthermore, the vsp gene was narrowed down to a 353.7-kb region that contains 15 candidate genes using 484 virescent individuals from an F₂ population. Sequence analysis of genes in this region showed that a 201-bp deletion was present in the Gh_D04G1108 (GhPUR4) gene in the vsp mutant. The 201-bp deletion of Gh_D04G1108 caused the deletion of 67 AAs in the GhPUR4 protein. Virus-induced gene silencing (VIGS) of GhPUR4 in normal plants caused reduced GhPUR4 gene expression levels, reduced Chl content, abnormal chloroplast development and virescent true leaves. This study could help us unravel the function of GhPUR4 in chloroplast development and Chl biosynthesis at the early developmental stages of the true leaves in cotton, which could promote the research and application of virescent mutations in cotton heterosis breeding.

GRA78 encoding a putative S-sulfocysteine synthase is involved in chloroplast development at the early seedling stage of rice

Cysteine functions not only as an amino acid in proteins but also as a precursor for a large number of essential biomolecules. Cysteine is synthesized via the incorporation of sulfide to O-acetylserine under the catalysis of O-acetylserine(thiol)lyase (OASTL). In dicotyledonous Arabidopsis, nine OASTL genes have been reported. However, in their null mutants, only the mutant of CS26 encoding S-sulfocysteine synthase showed the visible phenotypic changes, displaying significantly small plants and pale-green leaves under long-day condition but not short-day condition. Up to now, no OASTL gene or mutant has been identified in monocotyledon. In this study, we isolated a green-revertible albino mutant gra78 in rice (Oryza sativa). Its albino phenotype at the early seedling stage was sensitive to temperature but independent of photoperiod. Map-based cloning revealed that candidate gene LOC_Os01g59920 of GRA78 encodes a putative S-sulfocysteine synthase showing significant similarity with Arabidopsis CS26. Complementation experiment confirmed that mutation in LOC_Os01g59920 accounted for the mutant phenotype of gra78. GRA78 is constitutively expressed in all tissues and its encoded protein is targeted to the chloroplast. In addition, qRT-PCR suggested that expression levels of four OASTL homolog genes and five photosynthetic genes were remarkably down-regulated.

A Suppressor Mutation Partially Reverts the xantha Trait via Lowered Methylation in the Promoter of Genomes Uncoupled 4 in Rice

The xantha trait of a yellow leaf rice mutant (HYB), controlled epigenetically by elevated CHG methylation of the genomes uncoupled 4 (OsGUN4) promoter, has reduced chlorophyll content, altered tetrapyrrole biosynthesis, and deregulated transcription of photosynthesis-associated nuclear genes (PhANGs) compared to its wild-type progenitor Longtefu B (LTB). In the present study, we identified a suppressor mutant (CYB) of HYB and characterized its genetic, molecular, and physiological basis of the mutant phenotype. We found that the light-green phenotype of CYB was caused by a suppressor mutation in an unknown gene other than OsGUN4. Compared to HYB, the CHG methylation in the OsGUN4 promoter was reduced, while OsGUN4 transcript and protein abundance levels were increased in CYB. The contents of total chlorophyll and its intermediate metabolites (except protoporphyrin IX) in CYB plants were intermediate between HYB and LTB. The expression levels of 30 genes involved in tetrapyrrole biosynthesis in CYB were all partially reverted to those of LTB, so were the PhANGs. In summary, a suppressor mutation caused the reversion of the xantha trait via reducing CHG methylation in OsGUN4 promoter.

A Single Nucleotide Mutation of the IspE Gene Participating in the MEP Pathway for Isoprenoid Biosynthesis Causes a Green-Revertible Yellow Leaf Phenotype in Rice

Plant isoprenoids are dependent on two independent pathways, the cytosolic mevalonate (MVA) pathway and the plastidic methylerythritol phosphate (MEP) pathway. IspE is one of seven known enzymes in the MEP pathway. Currently, no IspE gene has been identified in rice. In addition, no virescent mutants have been reported to result from a gene mutation affecting the MEP pathway. In this study, we isolated a green-revertible yellow leaf mutant gry340 in rice. The mutant exhibited a reduced level of photosynthetic pigments, and an arrested development of chloroplasts and mitochondria in its yellow leaves. Map-based cloning revealed a missense mutation in OsIspE (LOC_Os01g58790) in gry340 mutant plants. OsIspE is constitutively expressed in all tissues, and its encoded protein is targeted to the chloroplast. Further, the mutant phenotype of gry340 was rescued by introduction of the wild-type gene. Therefore, we have successfully identified an IspE gene in monocotyledons via map-based cloning, and confirmed that the green-revertible yellow leaf phenotype of gry340 does result from a single nucleotide mutation in the IspE gene. In addition, the ispE ispF double mutant displayed an etiolation lethal phenotype, indicating that the isoprenoid precursors from the cytosol cannot efficiently compensate for the deficiency of the MEP pathway in rice chloroplasts. Furthermore, real-time quantitative reverse transcription-PCR suggested that this functional defect in OsIspE affected the expression of not only other MEP pathway genes but also that of MVA pathway genes, photosynthetic genes and mitochondrial genes.

The xantha Marker Trait Is Associated with Altered Tetrapyrrole Biosynthesis and Deregulated Transcription of PhANGs in Rice

The xantha marker trait, which is controlled by a down-regulating epi-mutation of OsGUN4, has been applied to the production of hybrid rice. However, the molecular basis for the ability of xantha mutants to attain high photosynthetic capacity even with decreased chlorophyll contents has not been characterized. In the present study, we observed that the total chlorophyll content of the xantha mutant was only 27.2% of that of the wild-type (WT) plants. However, the xantha mutant still accumulated 59.9% of the WT δ-aminolevulinic acid content, 72.8% of the WT Mg-protoporphyrin IX content, and 63.0% of the WT protochlorophyllide a content. Additionally, the protoporphyrin IX and heme contents in the mutant increased to 155.0 and 160.0%, respectively, of the WT levels. A search for homologs resulted in the identification of 124 rice genes involved in tetrapyrrole biosynthesis and photosynthesis. With the exception of OsGUN4, OsHO-1, and OsHO-2, the expression levels of the genes involved in tetrapyrrole biosynthesis were significantly higher in the xantha mutant than in the WT plants, as were all 72 photosynthesis-associated nuclear genes. In contrast, there were no differences between the xantha mutant and WT plants regarding the expression of all 22 photosynthesis-associated chloroplast genes. Furthermore, the abundance of ¹O₂ and the expression levels of ¹O₂-related genes were lower in the xantha mutant than in the WT plants, indicating ¹O₂-mediated retrograde signaling was repressed in the mutant plants. These results suggested that the abundance of protoporphyrin IX used for chlorophyll synthesis decreased in the mutant, which ultimately decreased the amount of chlorophyll in the xantha mutant. Additionally, the up-regulated expression of photosynthesis-associated nuclear genes enabled the mutant to attain a high photosynthetic capacity. Our findings confirm that OsGUN4 plays an important role in tetrapyrrole biosynthesis and photosynthesis in rice. GUN4, chlorophyll synthesis pathways, and photosynthetic activities are highly conserved in plants and hence, novel traits (e.g., xantha marker trait) may be generated in other cereal crops by modifying the GUN4 gene.