Sid: a Mendelian locus controlling thylakoid membrane disassembly in senescing leaves of Festuca pratensis

Homolog of Pea SGR Controls Stay-Green in Faba Bean (Vicia faba L.)

Faba bean is an important legume crop consumed as a vegetable or snack food, and its green cotyledons could present an attractive color for consumers. A mutation in SGR causes stay-green in plants. In this study, vfsgr was identified from a green-cotyledon-mutant faba bean, SNB7, by homologous blast between the SGR of pea and the transcriptome of faba bean. Sequence analysis revealed that a SNP at position 513 of the CDS of VfSGR caused a pre-stop codon, resulting in a shorter protein in the green-cotyledon faba bean SNB7. A dCaps marker was developed according to the SNP that caused the pre-stop, and this marker was completely associated with the color of the cotyledon of faba bean. SNB7 stayed green during dark treatment, while the expression level of VfSGR increased during dark-induced senescence in the yellow-cotyledon faba bean HST. Transient expression of VfSGR in Nicotiana. benthamiana leaves resulted in chlorophyll degradation. These results indicate that vfsgr is the gene responsible for the stay-green of faba bean, and the dCaps marker developed in this study provides a molecular tool for the breeding of green-cotyledon faba beans.

Meiosis in Polyploids and Implications for Genetic Mapping: A Review

Plant cytogenetic studies have provided essential knowledge on chromosome behavior during meiosis, contributing to our understanding of this complex process. In this review, we describe in detail the meiotic process in auto- and allopolyploids from the onset of prophase I through pairing, recombination, and bivalent formation, highlighting recent findings on the genetic control and mode of action of specific proteins that lead to diploid-like meiosis behavior in polyploid species. During the meiosis of newly formed polyploids, related chromosomes (homologous in autopolyploids; homologous and homoeologous in allopolyploids) can combine in complex structures called multivalents. These structures occur when multiple chromosomes simultaneously pair, synapse, and recombine. We discuss the effectiveness of crossover frequency in preventing multivalent formation and favoring regular meiosis. Homoeologous recombination in particular can generate new gene (locus) combinations and phenotypes, but it may destabilize the karyotype and lead to aberrant meiotic behavior, reducing fertility. In crop species, understanding the factors that control pairing and recombination has the potential to provide plant breeders with resources to make fuller use of available chromosome variations in number and structure. We focused on wheat and oilseed rape, since there is an abundance of elucidating studies on this subject, including the molecular characterization of the Ph1 (wheat) and PrBn (oilseed rape) loci, which are known to play a crucial role in regulating meiosis. Finally, we exploited the consequences of chromosome pairing and recombination for genetic map construction in polyploids, highlighting two case studies of complex genomes: (i) modern sugarcane, which has a man-made genome harboring two subgenomes with some recombinant chromosomes; and (ii) hexaploid sweet potato, a naturally occurring polyploid. The recent inclusion of allelic dosage information has improved linkage estimation in polyploids, allowing multilocus genetic maps to be constructed.

The Senescence (Stay-Green)—An Important Trait to Exploit Crop Residuals for Bioenergy

In this review, we present a comprehensive revisit of past research and advances developed on the stay-green (SG) paradigm. The study aims to provide an application-focused review of the SG phenotypes as crop residuals for bioenergy. Little is known about the SG trait as a germplasm enhancer resource for energy storage as a system for alternative energy. Initially described as a single locus recessive trait, SG was shortly after reported as a quantitative trait governed by complex physiological and metabolic networks including chlorophyll efficiency, nitrogen contents, nutrient remobilization and source-sink balance. Together with the fact that phenotyping efforts have improved rapidly in the last decade, new approaches based on sensing technologies have had an impact in SG identification. Since SG is linked to delayed senescence, we present a review of the term senescence applied to crop residuals and bioenergy. Firstly, we discuss the idiosyncrasy of senescence. Secondly, we present biological processes that determine the fate of senescence. Thirdly, we present the genetics underlying SG for crop-trait improvement in different crops. Further, this review explores the potential uses of senescence for bioenergy crops. Finally, we discuss how high-throughput phenotyping methods assist new technologies such as genomic selection in a cost-efficient manner.

The H3K27me3 demethylase REF6 promotes leaf senescence through directly activating major senescence regulatory and functional genes in Arabidopsis

The roles of histone demethylation in the regulation of plant flowering, disease resistance, rhythmical response, and seed germination have been elucidated recently; however, how histone demethylation affects leaf senescence remains largely unclear. In this study, we exploited yeast one-hybrid (Y1H) to screen for the upstream regulators of NONYELLOWING1 (NYE1), and identified RELATIVE OF EARLY FLOWERING6 (REF6), a histone H3 lysine 27 tri-methylation (H3K27me3) demethylase, as a putative binding protein of NYE1 promoter. By in vivo and in vitro analyses, we demonstrated that REF6 directly binds to the motif CTCGYTY in NYE1/2 promoters through its zinc finger domain and positively regulates their expression. Loss-of-function of REF6 delayed chlorophyll (Chl) degradation, whereas overexpression of REF6 accelerated Chl degradation. Subsequently, we revealed that REF6 positively regulates the general senescence process by directly up-regulating ETHYLENE INSENSITIVE 2 (EIN2), ORESARA1 (ORE1), NAC-LIKE, ACTIVATED BY AP3/PI (NAP), PYRUVATE ORTHOPHOSPHATE DIKINASE (PPDK), PHYTOALEXIN DEFICIENT 4 (PAD4), LIPOXYGENASE 1 (LOX1), NAC DOMAIN CONTAINING PROTEIN 3 (AtNAC3), and NAC TRANSCRIPTION FACTOR-LIKE 9 (NTL9), the key regulatory and functional genes predominantly involved in the regulation of developmental leaf senescence. Importantly, loss-of-function of REF6 increased H3K27me3 levels at all the target Senescence associated genes (SAGs). We therefore conclusively demonstrate that H3K27me3 methylation represents an epigenetic mechanism prohibiting the premature transcriptional activation of key developmentally up-regulated senescence regulatory as well as functional genes in Arabidopsis.

Leaves of higher plants start yellowing and subsequently die (senescence) at particular developmental stages as a result of both internal and external regulations. Leaf senescence is evolved to facilitate nutrient remobilization to young/important organs to meet their rapid development, and a large number of genes (Senescence associated genes, SAGs) are activated to regulate/facilitate the process. It has been intriguing how these genes are kept transcriptionally inactive to ensure an effective photosynthesis before the initiation of leaf senescence. Here, we reveal an epigenetic mechanism responsible for the prohibition of their premature transcription. We found that an H3K27me3 demethylase, RELATIVE OF EARLY FLOWERING 6 (REF6), directly promotes the expression of its ten target senescence regulatory and functional genes (EIN2, ORE1, NAP, AtNAC3, NTL9, NYE1/2, LOX1, PAD4, and PPDK), which are involved in major phytohormones’ signaling, biosynthesis, and chlorophyll degradation. Crucially, REF6 is substantially involved in promoting the H3K27me3 demethylation of both their promoter and/or coding regions during the aging process of leaves. We therefore provide conclusive evidence that H3K27me3 methylation is an epigenetic mechanism hindering the premature transcriptional activation of key SAGs, which helps to explain the “aging effect” of senescence initiation.

Metabolic Reprogramming in Chloroplasts under Heat Stress in Plants

Increases in ambient temperatures have been a severe threat to crop production in many countries around the world under climate change. Chloroplasts serve as metabolic centers and play a key role in physiological adaptive processes to heat stress. In addition to expressing heat shock proteins that protect proteins from heat-induced damage, metabolic reprogramming occurs during adaptive physiological processes in chloroplasts. Heat stress leads to inhibition of plant photosynthetic activity by damaging key components functioning in a variety of metabolic processes, with concomitant reductions in biomass production and crop yield. In this review article, we will focus on events through extensive and transient metabolic reprogramming in response to heat stress, which included chlorophyll breakdown, generation of reactive oxygen species (ROS), antioxidant defense, protein turnover, and metabolic alterations with carbon assimilation. Such diverse metabolic reprogramming in chloroplasts is required for systemic acquired acclimation to heat stress in plants.

Identification and fine mapping of a stay-green gene (Brnye1) in pakchoi (Brassica campestris L. ssp. chinensis)

Using bulked segregant analysis combined with next-generation sequencing, we delimited the Brnye1 gene responsible for the stay-green trait of nye in pakchoi. Sequence analysis identified Bra019346 as the candidate gene. "Stay-green" refers to a plant trait whereby leaves remain green during senescence. This trait is useful in the cultivation of pakchoi (Brassica campestris L. ssp. chinensis), which is marketed as a green leaf product. This study aimed to identify the gene responsible for the stay-green trait in pakchoi. We identified a stay-green mutant in pakchoi, which we termed "nye". Genetic analysis revealed that the stay-green trait is controlled by a single recessive gene, Brnye1. Using the BSA-seq method, a 3.0-Mb candidate region was mapped on chromosome A03, which helped us localize Brnye1 to an 81.01-kb interval between SSR markers SSRWN27 and SSRWN30 via linkage analysis in an F₂ population. We identified 12 genes in this region, 11 of which were annotated based on the Brassica rapa annotation database, and one was a functionally unknown gene. An orthologous gene of the Arabidopsis gene AtNYE1, Bra019346, was identified as the potential candidate for Brnye1. Sequence analysis revealed a 40-bp insertion in the second exon of Bra019346 in nye, which generated the TAA stop codon. A candidate gene-specific Indel marker in 1561 F₂ individuals showed perfect cosegregation with Brnye1 in the nye mutant. These results provide a foundation for uncovering the molecular mechanism of the stay-green trait in pakchoi.

Toward Systems Understanding of Leaf Senescence: An Integrated Multi-Omics Perspective on Leaf Senescence Research

Leaf senescence is a complex but tightly regulated developmental process involving a coordinated sequence of multiple molecular events, which ultimately leads to death of the leaf. Efforts to understand the mechanistic principles underlying leaf senescence have been largely made by transcriptomic, proteomic, and metabolomic studies over the past decade. This review focuses on recent milestones in leaf senescence research obtained using multi-omics technologies, as well as future endeavors toward systems understanding of leaf senescence processes. In particular, we discuss recent advances in understanding molecular events during leaf senescence through genome-wide transcriptome analyses in Arabidopsis. We also describe comparative transcriptome analyses used to unveil the commonality and diversity of regulatory mechanisms governing leaf senescence in the plant kingdom. Finally, we provide current illustrations of epigenomic, proteomic, and metabolomic landscapes of leaf senescence. We envisage that integration of multi-omics leaf senescence data will enable us to address unresolved questions regarding leaf senescence, including determining the molecular principles that coordinate concurrent and ordered changes in biological events during leaf senescence.

Gene expression profiling of the green seed problem in Soybean

BACKGROUND

Due to the climate change of the past few decades, some agricultural areas in the world are now experiencing new climatic extremes. For soybean, high temperatures and drought stress can potentially lead to the "green seed problem", which is characterized by chlorophyll retention in mature seeds and is associated with lower oil and seed quality, thus negatively impacting the production of soybean seeds.

RESULTS

Here we show that heat and drought stress result in a "mild" stay-green phenotype and impaired expression of the STAY-GREEN 1 and STAY-GREEN 2 (D1, D2), PHEOPHORBIDASE 2 (PPH2) and NON-YELLOW COLORING 1 (NYC1_1) genes in soybean seeds of a susceptible soybean cultivar. We suggest that the higher expression of these genes in fully mature seeds of a tolerant cultivar allows these seeds to cope with stressful conditions and complete chlorophyll degradation.

CONCLUSIONS

The gene expression results obtained in this study represent a significant advance in understanding chlorophyll retention in mature soybean seeds produced under stressful conditions. This will open new research possibilities towards finding molecular markers for breeding programs to produce cultivars which are less susceptible to chlorophyll retention under the hot and dry climate conditions which are increasingly common in the largest soybean production areas of the world.

Concerted evolution of D1 and D2 to regulate chlorophyll degradation in soybean

Polyploidy is a common phenomenon, particularly in plants. The soybean (Glycine max [L.] Merr.) genome has undergone two whole genome duplication (WGD) events. The conservation and divergence of duplicated gene pairs are major contributors to genome evolution. D1 and D2 are two unlinked, paralogous nuclear genes, whose double-recessive mutant (d1d1d2d2) results in chlorophyll retention, called 'stay-green'. Through molecular cloning and functional analyses, we demonstrated that D1 and D2 are homologs of the STAY-GREEN (SGR) genes from other plant species and were duplicated as a result of the most recent WGD in soybean. Transcriptional analysis showed that both D1 and D2 were more highly expressed in older tissues, and chlorophyll degradation and programmed cell death-related genes were suppressed in a d1d2 double mutant, this situation indicated that these genes are probably involved in the early stages of tissue senescence. Investigation of genes that flank D1 and D2 revealed that evolution within collinear duplicated blocks may affect the conservation of individual gene pairs within the blocks. Moreover, we found that a long terminal repeat retrotransposon, GmD2IN, resulted in the d2 mutation. Further analysis of this retrotransposon family showed that insertion in or near the coding regions can affect gene expression or splicing patterns, and may be an important force to promote the divergence of duplicated gene pairs.

Nitric oxide deficiency accelerates chlorophyll breakdown and stability loss of thylakoid membranes during dark-induced leaf senescence in Arabidopsis

Nitric oxide (NO) has been known to preserve the level of chlorophyll (Chl) during leaf senescence. However, the mechanism by which NO regulates Chl breakdown remains unknown. Here we report that NO negatively regulates the activities of Chl catabolic enzymes during dark-induced leaf senescence. The transcriptional levels of the major enzyme genes involving Chl breakdown pathway except for RED CHL CATABOLITE REDUCTASE (RCCR) were dramatically up-regulated during dark-induced Chl degradation in the leaves of Arabidopsis NO-deficient mutant nos1/noa1 that exhibited an early-senescence phenotype. The activity of pheide a oxygenase (PAO) was higher in the dark-induced senescent leaves of nos1/noa1 compared with wild type. Furthermore, the knockout of PAO in nos1/noa1 background led to pheide a accumulation in the double mutant pao1 nos1/noa1, which retained the level of Chl during dark-induced leaf senescence. The accumulated pheide a in darkened leaves of pao1 nos1/noa1 was likely to inhibit the senescence-activated transcriptional levels of Chl catabolic genes as a feed-back inhibitory effect. We also found that NO deficiency led to decrease in the stability of photosynthetic complexes in thylakoid membranes. Importantly, the accumulation of pheide a caused by PAO mutations in combination with NO deficiency had a synergistic effect on the stability loss of thylakoid membrane complexes in the double mutant pao1 nos1/noa1 during dark-induced leaf senescence. Taken together, our findings have demonstrated that NO is a novel negative regulator of Chl catabolic pathway and positively functions in maintaining the stability of thylakoid membranes during leaf senescence.

From model to crop: functional analysis of a STAY-GREEN gene in the model legume Medicago truncatula and effective use of the gene for alfalfa improvement

Medicago truncatula has been developed into a model legume. Its close relative alfalfa (Medicago sativa) is the most widely grown forage legume crop in the United States. By screening a large population of M. truncatula mutants tagged with the transposable element of tobacco (Nicotiana tabacum) cell type1 (Tnt1), we identified a mutant line (NF2089) that maintained green leaves and showed green anthers, central carpels, mature pods, and seeds during senescence. Genetic and molecular analyses revealed that the mutation was caused by Tnt1 insertion in a STAY-GREEN (MtSGR) gene. Transcript profiling analysis of the mutant showed that loss of the MtSGR function affected the expression of a large number of genes involved in different biological processes. Further analyses revealed that SGR is implicated in nodule development and senescence. MtSGR expression was detected across all nodule developmental zones and was higher in the senescence zone. The number of young nodules on the mutant roots was higher than in the wild type. Expression levels of several nodule senescence markers were reduced in the sgr mutant. Based on the MtSGR sequence, an alfalfa SGR gene (MsSGR) was cloned, and transgenic alfalfa lines were produced by RNA interference. Silencing of MsSGR led to the production of stay-green transgenic alfalfa. This beneficial trait offers the opportunity to produce premium alfalfa hay with a more greenish appearance. In addition, most of the transgenic alfalfa lines retained more than 50% of chlorophylls during senescence and had increased crude protein content. This study illustrates the effective use of knowledge gained from a model system for the genetic improvement of an important commercial crop.

Pheophytin pheophorbide hydrolase (pheophytinase) is involved in chlorophyll breakdown during leaf senescence in Arabidopsis

During leaf senescence, chlorophyll is removed from thylakoid membranes and converted in a multistep pathway to colorless breakdown products that are stored in vacuoles. Dephytylation, an early step of this pathway, increases water solubility of the breakdown products. It is widely accepted that chlorophyll is converted into pheophorbide via chlorophyllide. However, chlorophyllase, which converts chlorophyll to chlorophyllide, was found not to be essential for dephytylation in Arabidopsis thaliana. Here, we identify pheophytinase (PPH), a chloroplast-located and senescence-induced hydrolase widely distributed in algae and land plants. In vitro, Arabidopsis PPH specifically dephytylates the Mg-free chlorophyll pigment, pheophytin (phein), yielding pheophorbide. An Arabidopsis mutant deficient in PPH (pph-1) is unable to degrade chlorophyll during senescence and therefore exhibits a stay-green phenotype. Furthermore, pph-1 accumulates phein during senescence. Therefore, PPH is an important component of the chlorophyll breakdown machinery of senescent leaves, and we propose that the sequence of early chlorophyll catabolic reactions be revised. Removal of Mg most likely precedes dephytylation, resulting in the following order of early breakdown intermediates: chlorophyll --> pheophytin --> pheophorbide. Chlorophyllide, the last precursor of chlorophyll biosynthesis, is most likely not an intermediate of breakdown. Thus, chlorophyll anabolic and catabolic reactions are metabolically separated.

The control of chlorophyll catabolism and the status of yellowing as a biomarker of leaf senescence

The pathway of chlorophyll catabolism during leaf senescence is known in a fair amount of biochemical and cell biological detail. In the last few years, genes encoding a number of the catabolic enzymes have been characterized, including the key ring-opening activities, phaeophorbide a oxygenase (PaO) and red chlorophyll catabolite reductase (RCCR). Recently, a gene that modulates disassembly of chlorophyll-protein complexes and activation of pigment ring-opening has been isolated by comparative mapping in monocot species, positional cloning exploiting rice genomics resources and functional testing in Arabidopsis. The corresponding gene in pea has been identified as Mendel's I locus (green/yellow cotyledons). Mutations in this and other chlorophyll catabolic genes have significant consequences, both for the course of leaf senescence and senescence-like stress responses, notably hypersensitivity to pathogen challenge. Loss of chlorophyll can occur via routes other than the PaO/RCCR pathway, resulting in changes that superficially resemble senescence. Such 'pseudosenescence' responses tend to be pathological rather than physiological and may differ from senescence in fundamental aspects of biochemistry and regulation.

An evaluation of the basis and consequences of a stay-green mutation in the navel negra citrus mutant using transcriptomic and proteomic profiling and metabolite analysis

A Citrus sinensis spontaneous mutant, navel negra (nan), produces fruit with an abnormal brown-colored flavedo during ripening. Analysis of pigment composition in the wild-type and nan flavedo suggested that typical ripening-related chlorophyll (Chl) degradation, but not carotenoid biosynthesis, was impaired in the mutant, identifying nan as a type C stay-green mutant. nan exhibited normal expression of Chl biosynthetic and catabolic genes and chlorophyllase activity but no accumulation of dephytylated Chl compounds during ripening, suggesting that the mutation is not related to a lesion in any of the principal enzymatic steps in Chl catabolism. Transcript profiling using a citrus microarray indicated that a citrus ortholog of a number of SGR (for STAY-GREEN) genes was expressed at substantially lower levels in nan, both prior to and during ripening. However, the pattern of catabolite accumulation and SGR sequence analysis suggested that the nan mutation is distinct from those in previously described stay-green mutants and is associated with an upstream regulatory step, rather than directly influencing a specific component of Chl catabolism. Transcriptomic and comparative proteomic profiling further indicated that the nan mutation resulted in the suppressed expression of numerous photosynthesis-related genes and in the induction of genes that are associated with oxidative stress. These data, along with metabolite analyses, suggest that nan fruit employ a number of molecular mechanisms to compensate for the elevated Chl levels and associated photooxidative stress.

Stay-green protein, defective in Mendel's green cotyledon mutant, acts independent and upstream of pheophorbide a oxygenase in the chlorophyll catabolic pathway

Type C stay-green mutants are defined as being defective in the pathway of chlorophyll breakdown, which involves pheophorbide a oxygenase (PAO), required for loss of green color. By analyzing senescence parameters, such as protein degradation, expression of senescence-associated genes and loss of photosynthetic capacity, we demonstrate that JI2775, the green cotyledon (i) pea line used by Gregor Mendel to establish the law of genetics, is a true type C stay-green mutant. STAY-GREEN (SGR) had earlier been shown to map to the I locus. The defect in JI2775 is due to both reduced expression of SGR and loss of SGR protein function. Regulation of PAO through SGR had been proposed. By determining PAO protein abundance and activity, we show that PAO is unaffected in JI2775. Furthermore we show that pheophorbide a accumulation in the mutant is independent of PAO. When silencing SGR expression in Arabidopsis pao1 mutant, both pheophorbide a accumulation and cell death phenotype, typical features of pao1, are lost. These results confirm that SGR function within the chlorophyll catabolic pathway is independent and upstream of PAO.

Molecular cloning and function analysis of the stay green gene in rice

Chloroplasts undergo drastic morphological and physiological changes during senescence with a visible symptom of chlorophyll (Chl) degradation. A stay green mutant was identified and then isolated from the japonica rice (Oryza sativa) cv. Huazhiwu by gamma-ray irradiation. The stay green mutant was characterized by Chl retention, stable Chl-protein complexes, and stable thylakoid membrane structures, but lost its photosynthetic competence during senescence. The gene, designated Stay Green Rice (SGR), was cloned by a positional cloning strategy encoding an ancient protein containing a putative chloroplast transit peptide. SGR protein was found in both soluble and thylakoid membranes in rice. SGR, like the gene for pheophorbide a oxygenase (PaO), was constitutively expressed, but was upregulated by dark-induced senescence in rice leaves. Senescence-induced expression of SGR and PaO was enhanced by ABA, but inhibited by cytokinin. Overexpression of SGR reduced the number of lamellae in the grana thylakoids and reduced the Chl content of normally growing leaves. This indicates that upregulation of SGR increases Chl breakdown during senescence in rice. A small quantity of chlorophyllide a accumulated in sgr leaves, but this also accumulated in wild-type rice leaves during senescence. Some pheophorbide a was detected in sgr leaves in the dark. According to these observations, we propose that SGR may be involved in regulating or taking part in the activity of PaO, and then may influence Chl breakdown and degradation of pigment-protein complex.

Identification of a novel chloroplast protein AtNYE1 regulating chlorophyll degradation during leaf senescence in Arabidopsis

A dramatic increase of chlorophyll (Chl) degradation occurs during senescence of vegetative plant organs and fruit ripening. Although the biochemical pathway of Chl degradation has long been proposed, little is known about its regulatory mechanism. Identification of Chl degradation-disturbed mutants and subsequently isolation of responsible genes would greatly facilitate the elucidation of the regulation of Chl degradation. Here, we describe a nonyellowing mutant of Arabidopsis (Arabidopsis thaliana), nye1-1, in which 50% Chl was retained, compared to less than 10% in the wild type (Columbia-0), at the end of a 6-d dark incubation. Nevertheless, neither photosynthesis- nor senescence-associated process was significantly affected in nye1-1. Characteristically, a significant reduction in pheophorbide a oxygenase activity was detected in nye1-1. However, no detectable accumulation of either chlorophyllide a or pheophorbide a was observed. Reciprocal crossings revealed that the mutant phenotype was caused by a monogenic semidominant nuclear mutation. We have identified AtNYE1 by positional cloning. Dozens of its putative orthologs, predominantly appearing in higher plant species, were identified, some of which have been associated with Chl degradation in a few crop species. Quantitative polymerase chain reaction analysis showed that AtNYE1 was drastically induced by senescence signals. Constitutive overexpression of AtNYE1 could result in either pale-yellow true leaves or even albino seedlings. These results collectively indicate that NYE1 plays an important regulatory role in Chl degradation during senescence by modulating pheophorbide a oxygenase activity.

Introgression mapping in the grasses

The unique properties of Lolium/Festuca hybrids and their derivatives provide an ideal system for intergeneric introgression. At IGER a focus on the Lolium perenne/Festuca pratensis system is being exploited to elucidate genome organization in the grasses, determination of the genetic control of target traits and the isolation of markers for marker-assisted selection in breeding programmes.

Nitrogen management and senescence in two maize hybrids differing in the persistence of leaf greenness: agronomic, physiological and molecular aspects

Here, nitrogen management within the plant was compared in an early-senescing maize hybrid and in a late-senescing maize hybrid, both grown under field conditions with a high fertilisation input involving large quantities of fertiliser. We monitored, in representative leaf stages, the changes in metabolite content, enzyme activities and steady-state levels of transcripts for marker genes of N primary assimilation, N recycling and leaf senescence. The hybrids differed in terms of persistence of leaf greenness, the expression of marker genes and the concentration of enzymes used to describe the transition from N assimilation to N recycling. The transcription of leaf-senescence marker genes did not differ. Agronomic studies confirmed the ability of the late-senescing hybrid to absorb and store more N in shoots. Despite the differences in the mode of N management adopted by the two hybrids, we conclude that leaf senescence occurs independently of the source-to-sink transition at the high level of fertilisation used involving large quantities of fertiliser. The possibility of improving N metabolic efficiency in the latest maize hybrids is discussed.

Molecular tagging of a senescence gene by introgression mapping of a stay-green mutation from Festuca pratensis

* Intergeneric hybrids between Lolium multiflorum and Festuca pratensis (Lm/Fp) and their derivatives exhibit a unique combination of genetic and cytogenetic characteristics: chromosomes undergo a high frequency of homoeologous recombination at meiosis; the chromosomes of the two species can easily be discriminated by genomic in situ hybridization (GISH); recombination occurs along the entire length of homoeologous bivalents; a high frequency of marker polymorphism is observed between the two species. * This combination of characters has been used to transfer and isolate a F. pratensis chromosome segment carrying a mutant 'stay-green' gene conferring a disrupted leaf senescence phenotype into L. multiflorum. * The genetic location within the introgressed F. pratensis segment of the senescence gene has been mapped using amplified fragment length polymorphisms (AFLPs), and F. pratensis-specific AFLP markers closely flanking the green gene have been cloned. * The use of these cloned sequences as markers for the stay-green locus in marker-assisted selection programmes has been tested. The potential application of Lm/Fp introgressions as a tool for the map-based cloning of introgressed Fp genes is discussed.

The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines derived from an indica by japonica cross

Delayed leaf-senescence, or stay-green, has been regarded as a desired characteristic for the production of a number of crops including rice. In this study, we analyzed the genetic basis of stay-green using a population of 190 doubled haploid lines from the cross between an indica parent Zhenshan 97 and a stay-green japonica parent Wuyujing 2. The population was tested in replicated field trials in 2 consecutive years, and six traits were defined to evaluate the stay-green characteristics. A genetic linkage map with 179 SSR (simple sequence repeat) marker loci was constructed. The software QTLMapper, based on a mixed linear model approach, was applied to detect QTLs, epistatic effects and their environmental interactions for these traits. A total of 46 main-effect QTLs was detected for the six traits that can be localized to 25 chromosomal regions. The individual effects of all the QTLs were small. Fifty digenic interactions were resolved that involved 66 loci distributed on all 12 chromosomes. Environmental interactions were detected for 18 of the main-effect QTLs and 14 of the epistatic interactions. Collectively, the epistatic effects and QTL by year interactions accounted for large proportions of the phenotypic variations. The results also showed that most of the stay-green traits were negatively correlated with yield and its component traits. The implications of the results in crop improvement were discussed.

Increased stability of LHCII by aggregate formation during dark-induced leaf senescence in the Arabidopsis mutant, ore10

Leaf senescence in a stay-green mutant of Arabidopsis thaliana, ore10, was investigated during dark-incubation of its detached leaves. During this dark-induced senescence (DIS), Chl loss was delayed in ore10 mutants, as compared with wild type, but the rate of decline in the photochemical efficiency of PSII was not delayed in mutant leaves. After 2 d of DIS, native green gel electrophoresis of ore 10 leaf proteins resulted in a significant amount of pigment remaining as aggregates on top of the stacking gel. In addition, the accumulation of aggregates coincided with the emergence of a new band near 700 nm (F(699)) in the 77 K fluorescence emission spectrum of the aggregates. At 4 d, F(699) became a major band, both in the isolated aggregates and in intact leaves. Prolonged treatment with detergents revealed that light-harvesting complex II (LHCII) remaining after 2 d was highly stable, and the accumulation of aggregates coincided with the appearance of truncated LHCII in senescing ore10 leaves. These results suggest that increased LHCII stability is due to the formation of aggregates of trimmed LHCII. Thus, the LHCII protein degradation step that follows proteolysis of its terminal peptides is a possible lesion site of the ore10 mutant.

The molecular analysis of leaf senescence--a genomics approach

Senescence in green plants is a complex and highly regulated process that occurs as part of plant development or can be prematurely induced by stress. In the last decade, the main focus of research has been on the identification of senescence mutants, as well as on genes that show enhanced expression during senescence. Analysis of these is beginning to expand our understanding of the processes by which senescence functions. Recent rapid advances in genomics resources, especially for the model plant species Arabidopsis, are providing scientists with a dazzling array of tools for the identification and functional analysis of the genes and pathways involved in senescence. In this review, we present the current understanding of the mechanisms by which plants control senescence and the processes that are involved.

Differences in growth and nitrogen productivity between a stay-green genotype and a wild-type of Lolium perenne under limiting relative addition rates of nitrate supply

The stay-green mutation of the nuclear gene sid inhibits chlorophyll degradation during leaf senescence in grasses. Decreased productivity is expected under conditions of limited external N availability, due to the higher retention of N in senescent tissues. However, this has not been reported when plants are grown at limiting low external concentrations of N. In the present study a different approach was taken, based on the relative addition rate method for defining limiting N supply. Wild-type and stay-green genotypes of Lolium perenne L. were grown for 30 days in flowing solution culture and then supplied with NO3- on an hourly basis over 35 days at relative addition rates (RARs) of 0.03, 0.06, 0.09 and 0.12 day-1, ranging from severe N limitation to optimal supply. Plants were steady-state labelled with 15NO3- prior to RAR treatments, then switched to 14NO3- to allow measurement of the re-distribution of N absorbed prior to RAR control. Following acclimation, relative growth rates (RGRs) approached the corresponding RAR, but were significantly lower for stay-green than wild-type at RARs of 0.03 and 0.06 day-1. Tiller numbers were lower in stay-green plants after 35 days at all RARs except 0.12 day-1. Concentrations of total N in senescent laminae of stay-green plants exceeded those in wild-type plants by a similar margin (4.8-6.8 mg g-1 DW) irrespective of RAR. Maximum nitrogen productivity (Pn) was 3.9 g DW g-1 N day-1 (Nmin = 7.1 mg g-1 DW) in wild-type plants, and 5.1 g DW g-1 N day-1 (Nmin = 10.7 mg g-1 DW) in stay-green plants. The higher N productivity of stay-green plants indicated these plants used a smaller pool of metabolically available N more efficiently in biosynthesis compared with wild-type plants. The retention of N, absorbed prior to RAR treatments, in senescent laminae was significantly higher in stay-green plants at RAR of 0.03 day-1 after day 21 (i.e. 20% versus 15% of the total N recovered). However, in terms of the whole N economy of the plant the margin represented only 1.7% of the total N content on day 35.

Extended leaf longevity in the ore4-1 mutant of Arabidopsis with a reduced expression of a plastid ribosomal protein gene

The longevity of plant leaf organs is genetically determined. However, the molecular mechanisms underlying the control of longevity are still largely unknown. Here, we describe a T-DNA-insertional mutation of Arabidopsis thaliana that confers extended leaf longevity. The mutation, termed ore4-1, delays a broad spectrum of age-dependent leaf senescence, but has little effect on leaf senescence artificially induced by darkness, abscisic acid (ABA), methyl jasmonate (MeJA), or ethylene. The T-DNA was inserted within the promoter region of the plastid ribosomal small subunit protein 17 (PRPS17) gene, and this insertion dramatically reduced PRPS17 mRNA expression. In the ore4-1 mutant, the leaf growth rate is decreased, while the maturation timing is similar to that of wild-type. In addition, the activity of the photosystem I (PSI) is significantly reduced in the ore4-1 mutant, as compared to wild-type. Thus, the ore4-1 mutation results in a deficiency in various chloroplast functions, including photosynthesis, which may decrease leaf growth. Our results suggest a possible link between reduced metabolism and extended longevity of the leaf organs in the ore4-1 mutation.

What stay-green mutants tell us about nitrogen remobilization in leaf senescence

Leaf senescence has an important role in the plant's nitrogen economy. Chlorophyll catabolism is a visible symptom of protein mobilization. Genetic and environmental factors that interfere with yellowing tend to modify protein degradation as well. The chlorophyll-protein relationship is much closer for membrane proteins than it is for soluble or total leaf proteins. In stay-greens, genotypes with a specific defect in the chlorophyll catabolism pathway, soluble protein degradation during senescence may be close to normal, but light-harvesting and reaction centre thylakoid membrane proteins are much more stable. Genes for the chlorophyll catabolism pathway and its control are important in the regulation of protein mobilization. Genes for three steps in the pathway are reported to have been isolated. The gene responsible for the stay-green phenotype in grasses and legumes has not yet been cloned but a fair amount is known about it. Pigment metabolism in senescing leaves of the Festuca-Lolium stay-green mutant is clearly disturbed and is consistent with a blockage at the ring-opening (PaO) step in chlorophyll breakdown. PaO is de novo synthesized in senescence and thought to be the key enzyme in the chlorophyll a catabolic pathway. The stay-green mutation is likely to be located in the PaO gene, or a specific regulator of it. These genes may well be in the various senescence-enhanced cDNA collections that have been generated, but functional handles on them are currently lacking. When the stay-green locus from Festuca pratensis was introgressed into Lolium temulentum, a gene encoding F. pratensis UDPG-pyrophosphorylase was shown to have been transferred on the same chromosome segment. A strategy is described for cloning the stay-green gene, based on subtractive PCR-based analyses of intergeneric introgressions and map-based cloning.

Five ways to stay green

The relationship between carbon income and expenditure over the life of a leaf is described and related to the productivity benefits of altering the timing of senescence initiation. In genetic variants with delayed leaf senescence ('stay-greens') deconstruction of the photosynthetic apparatus during leaf senescence is partially or completely prevented. Although the staygreen phenotype is superficially similar in all species and genotypes, the genetic and physiological routes to the trait are diverse. In one type of stay-green, chlorophyll catabolism is disabled. Legumes and monocots with pigment breakdown lesions are discussed. Sorghum is presented as an example of another kind of stay-green in which perennial tendencies have been bred into a monocarpic annual crop species. Transgenic approaches are briefly discussed (enhanced endogenous cytokinins, reduced ethylene production or perception). An alternative route towards making a stay-green phenotype is through quantitative trait mapping and marker-assisted selection. Loci for greenness in pearl millet have been identified, some of which are associated with drought responses or flowering time. Finally the question of the limits on stay-green as a productivity-enhancing character is addressed.

CHLOROPHYLL DEGRADATION

Although the loss of green color in senescent leaves and ripening fruits is a spectacular natural phenomenon, research on chlorophyll breakdown has been largely neglected until recently. This review summarizes knowledge about the fate of chlorophyll in degreening tissues that has been gained during the past few years. Structures of end- and intermediary products of degradation as well as the biochemistry of the porphyrin-cleaving reaction have been elucidated. The intracellular localization of the catabolic pathway is particularly important in the regulation of chlorophyll breakdown. None of the genes encoding the related catabolic enzymes has so far been isolated, which makes chlorophyll degradation an area of opportunity for future research.

A stay-green mutation of Lolium perenne affects NO3 - uptake and translocation of N during prolonged N starvation

Apparent K_m and V_max for net NO_S″ uptake and short-term translocation patterns of recently absorbed N were compared in a stay-green mutant and wild-type selection line of Lolium perenne L. by means of a series of depletion studies using ¹⁸ NO₃ , performed over 12 d under conditions of progressively increasing N deprivation. In view of the greater retention of N in senescent leaves of the stay-green phenotype, it was predicted that NO_S″ uptake would be up-regulated relative to the normal line, and that a proportionally higher fraction of recently absorbed N would be allocated to young leaves. It was shown that the stay-green trait had significant phenotypic consequences for plant N relations, with higher 'sink strength' of shoots for recently absorbed N, and higher V_max for NO₃ uptake compared with those of normal plants. The stay-green mutation had no effect on the K_m of the nitrate uptake system. Although the N-use efficiency might he expected to be lower in stay-green than in normal plants, there were no differences in rates of dry matter production.

Identification of parental and recombined chromosomes in hybrid derivatives of Lolium multiflorum × Festuca pratensis by genomic in situ hybridization

Genomic in situ hybridization (GISH) was used to identify Festuca chromatin in mitotic chromosomes of Lolium multiflorum (Lm) × Festuca pratensis (Fp) hybrids and hybrid derivatives. In two inverse autoallotriploids LmLmFp and LmFpFp, in situ hybridization was able to discriminate between the Lolium and Festuca chromosomes. In a third triploid hybrid produced by crossing an amphiploid of L. multiflorum × F. pratensis (2n=4x=28) with L. multiflorum (2n=2x=14), the technique identified chromosomes with interspecific recombination. Also, in an introgressed line of L. multiflorum which was homozygous for the recessive sid (senescence induced degradation) allele from F. pratensis, a pair of chromosome segments carrying the sid gene could be identified, indicating the suitability of GISH in showing the presence and location of introgressed genes. By screening backcross progeny for the presence of critical alien segments and the absence of other segments the reconstitution of the genome of the recipient species can be accelerated.

Leaf development in Lolium temulentum L.: characterization of a slow-to-green mutant

A nuclear-gene mutation of the C3 grass Lolium temulentum L., which arose following cell suspension culture and plant regeneration, is manifested as delayed and incomplete greening, which occurs from the leaf tip downwards. Many plastids in the mutant exhibit abnormal morphology when examined by transmission electron microscopy; the plastid outer envelope lacks integrity and thylakoids, while still stacked, are spread over a wide area surrounded by diffuse stromal contents. These aberrant plastids can coexist with apparently normal chloroplasts in the same cell of mutant plants. Levels of chlorophyll a and b, and carotenoids, are all lower in the mutants than in normal Lolium temulentum. Leaf length, absolute growth rate, and number of cells per unit length at the leaf base, are greatly reduced (20-30% the normal values) in slow-to-green plants, but relative growth rate, duration of leaf growth, length of cell division zone and proportion of cells dividing are little affected. This novel mutant is a potentially valuable resource for studying interrelationships between photosynthetic function and leaf extension growth in grasses.

Immunochemical quantification of cytochrome f in leaves of a non-yellowing senescence mutant of Festuca pratensis

A non-competitive enzyme-linked immunosorbent assay (ELISA) which enables detection of as little as 0.1 ng cytochrome f in leaf extracts has been developed. No evidence for specific or non-specific interference by proteins other than cytochrome f was found. The assay was applied to a comparative study of age-related changes in the cytochrome f content of leaves of Festuca pratensis Huds. cv. Rossa, and a non-yellowing mutant genotype (Bf993) having a lesion in the mechanism responsible for thylakoid membrane disassembly. Cytochrome f in senescent leaves of the latter genotype was found to be present at significantly higher levels than in the wild-type, implying an inability on the part of the mutant to degrade this protein. The results obtained by ELISA were confirmed by antibody probing of Western blots.

Leaf senescence in a non-yellowing mutant of Festuca pratensis: Proteins of photosystem II

The senescence of leaves is characterized by yellowing as chlorophyll pigments are degraded. Proteins of the chloroplasts also decline during this phase of development. There exists a non-yellowing mutant genotype of Festuca pratensis Huds. which does not suffer a loss of chlorophyll during senescence. The fate of chloroplast membrane proteins was studied in mutant and wild-type plants by immune blotting and immuno-electron microscopy. Intrinsic proteins of photosystem II, exemplified by the light-harvesting chlorophyll a/b-binding protein (LHCP-2) and D1, were shown to be unusually stable in the mutant during senescence, whereas the extrinsic 33-kilodalton protein of the oxygen-evolving complex was equally lable in both genotypes. An ultrastructural study revealed that while the intrinsic proteins remained in the internal membranes of the chloroplasts, they ceased to display the heterogenous lateral distribution within the lamellae which was characteristic of nonsenescent chloroplasts. These observations are discussed in the light of possible mechanisms of protein turnover in chloroplasts.

Kinetic implications of structural modification in protein turnover

It is thought that an important function of protein turnover is to purge the cell of damaged, displaced or unwanted polypeptide molecules. A model combining kinetic equations for synthesis, degradation and alteration is employed to evaluate this proposed role for protein turnover. It is demonstrated that the degradative system need not be aimed exclusively at altered protein molecules for turnover to be capable of controlling the size both of the total population and of the altered subpopulation. These conclusions are relevant to the part played by turnover in metabolic homeostasis, adaptation and catastrophe, and for the notion of control of protein turnover through specific "tagging" of molecules destined for breakdown.