Expression profiling of reciprocal maize hybrids divergent for cold germination and desiccation tolerance

Changes in Medicago truncatula seed proteome along the rehydration-dehydration cycle highlight new players in the genotoxic stress response

Introduction

Several molecular aspects underlying the seed response to priming and the resulting vigor profile are still poorly understood. Mechanisms involved in genome maintenance deserve attention since the balance between stimulation of germination and DNA damage accumulation versus active repair is a key determinant for designing successful seed priming protocols.

Methods

Changes in the Medicago truncatula seed proteome were investigated in this study, using discovery mass spectrometry and label-free quantification, along the rehydration-dehydration cycle of a standard vigorization treatment (hydropriming plus dry-back), and during post-priming imbibition.

Resuts and discussion

From 2056 to 2190 proteins were detected in each pairwise comparison, among which six were differentially accumulated and 36 were detected only in one condition. The following proteins were selected for further investigation: MtDRP2B (DYNAMIN-RELATED PROTEIN), MtTRXm4 (THIOREDOXIN m4), and MtASPG1 (ASPARTIC PROTEASE IN GUARD CELL 1) showing changes in seeds under dehydration stress; MtITPA (INOSINE TRIPHOSPHATE PYROPHOSPHORYLASE), MtABA2 (ABSCISIC ACID DEFICIENT 2), MtRS2Z32 (SERINE/ARGININE-RICH SPLICING FACTOR RS2Z32), and MtAQR (RNA HELICASE AQUARIUS) that were differentially regulated during post-priming imbibition. Changes in the corresponding transcript levels were assessed by qRT-PCR. In animal cells, ITPA hydrolyses 2'-deoxyinosine triphosphate and other inosine nucleotides, preventing genotoxic damage. A proof of concept was performed by imbibing primed and control M. truncatula seeds in presence/absence of 20 mM 2'-deoxyinosine (dI). Results from comet assay highlighted the ability of primed seeds to cope with dI-induced genotoxic damage. The seed repair response was assessed by monitoring the expression profiles of MtAAG (ALKYL-ADENINE DNA GLYCOSILASE) and MtEndoV (ENDONUCLEASE V) genes that participate in the repair of the mismatched I:T pair in BER (base excision repair) and AER (alternative excision repair) pathways, respectively.

Physiological aspects of sex differences and Haldane's rule in Rumex hastatulus

Haldane's rule (HR, impairment of fertility and/or viability of interracial hybrids) seems to be one of few generalizations in evolutionary biology. The validity of HR has been confirmed in animals, and more recently in some dioecious plants (Silene and Rumex). Dioecious Rumex hastatulus has two races differing in the sex chromosome system: Texas (T) and North Carolina (NC), and T × NC males showed both reduced pollen fertility and rarity-two classical symptoms of Haldane's rule (HR). The reduced fertility of these plants has a simple mechanistic explanation, but the reason for their rarity was not elucidated. Here, we measured selected physiological parameters related to the antioxidant defense system in parental races and reciprocal hybrids of R. hastatulus. We showed that the X-autosome configurations, as well as asymmetries associated with Y chromosomes and cytoplasm, could modulate this system in hybrids. The levels and quantitative patterns of the measured parameters distinguish the T × NC hybrid from the other analyzed forms. Our observations suggest that the rarity of T × NC males is caused postzygotically and most likely related to the higher level of oxidative stress induced by the chromosomal incompatibilities. It is the first report on the physiological aspects of HR in plants.

Methylglyoxal induces stress signaling and promotes the germination of maize at low temperature

Maize is sensitive to cold injury, especially during germination. Since cold causes oxidative stress, compounds that promote the accumulation of free radical forms, such as the reactive aldehyde (RA) methylglyoxal (MG), may be suitable to trigger a systemic defense response. In this study, maize seeds were soaked in MG solution for one night at room temperature, before germination test at 13°C. The exogenous MG enhanced the germination and photosynthetic performance of maize at low temperature. Transcriptome analysis, hormonal, and flavonoid profiling indicated MG-induced changes in photosystem antenna proteins, pigments, late embryogenesis abundant proteins, abscisic acid (ABA) derivatives, chaperons, and certain dihydroflavonols, members of the phenylpropanoid pathway. MG-response of the two maize cultivars (A654 and Cm174) were somewhat different, but we recorded higher endogenous hydrogen peroxide (H₂ O₂ ) and lower nitric oxide (NO) level in at least one of the treated genotypes. These secondary signal molecules may provoke some of the changes in the hormonal, metabolic and gene expression profile. Decreased auxin transport, but increased ABA degradation and cytokinin and jasmonic acid (JA) synthesis, as well as an altered carbohydrate metabolism and transport (amylases, invertases, and SWEET transporters) could have promoted germination of MG-pretreated seeds. While LEA accumulation could have protected against osmotic stress and catalase expression and production of many antioxidants, like para-hydroxybenzoic acid (p-HBA) and anthocyanins may have balanced the oxidative environment for maize germination. Our results showed that MG-pretreatment could be an effective way to promote cold germination and its effect was more pronounced in the originally cold-sensitive maize genotype.

Gene expression and genetic control to cold tolerance during maize seed germination

BACKGROUND

The study of cold tolerance in maize seeds and seedlings through physiological quality assessments, as well as the genetic control associated with this trait, allows an early characterization of genotypes. Here we studied the genetic control for cold tolerance during the germination process in maize seeds and genes influenced by this stress.

RESULTS

Six maize lines were used, three classified as tolerant and three as susceptible to low germination temperature. A field was developed to produce the hybrid seeds, in a partial diallel scheme including the reciprocal crosses. For the expression analysis, seeds from two contrasting lines were used, as well as their hybrid combination and their reciprocal crosses, on dried and moistened seeds at 10 °C for 4 and 7 days. It was evaluated the catalase (CAT) and esterase (EST) enzymes, heat-resistant proteins and the genes Putative stearoyl-ACP desaturase (SAD), Ascorbate Peroxidase (APX), Superoxide Dismutase (SOD) and Mitogen Activated Protein Kinase (ZmMPK5). The estimated values ​​for heterosis, general and specific combining abilities and reciprocal maternal and non-maternal effects were carried out and it showed that there is heterosis for germination at low temperatures, also the non-additive genes were more important and there was a reciprocal effect.

CONCLUSIONS

There is a greater expression of the CAT and EST enzymes in moistened seeds at seven days and there is less expression of heat-resistant proteins and the SAD gene at seven days of moistening. Also, there are variations in the expression of the APX, SOD and ZmMPK5 genes in dried and moistened seeds, as well as among the genotypes studied.

Transcriptomic diversity in seedling roots of European flint maize in response to cold

BACKGROUND

Low temperatures decrease the capacity for biomass production and lead to growth retardation up to irreversible cellular damage in modern maize cultivars. European flint landraces are an untapped genetic resource for genes and alleles conferring cold tolerance which they acquired during their adaptation to the agroecological conditions in Europe.

RESULTS

Based on a phenotyping experiment of 276 doubled haploid lines derived from the European flint landrace "Petkuser Ferdinand Rot" diverging for cold tolerance, we selected 21 of these lines for an RNA-seq experiment. The different genotypes showed highly variable transcriptomic responses to cold. We identified 148, 3254 and 563 genes differentially expressed with respect to cold treatment, cold tolerance and growth rate at cold, respectively. Gene ontology (GO) term enrichment demonstrated that the detoxification of reactive oxygen species is associated with cold tolerance, whereas amino acids might play a crucial role as antioxidant precursors and signaling molecules.

CONCLUSION

Doubled haploids representing a European maize flint landrace display genotype-specific transcriptome patterns associated with cold response, cold tolerance and seedling growth rate at cold. Identification of cold regulated genes in European flint germplasm, could be a starting point for introgressing such alleles in modern breeding material for maize improvement.

Heat Shock Proteins: Dynamic Biomolecules to Counter Plant Biotic and Abiotic Stresses

Due to the present scenario of climate change, plants have to evolve strategies to survive and perform under a plethora of biotic and abiotic stresses, which restrict plant productivity. Maintenance of plant protein functional conformation and preventing non-native proteins from aggregation, which leads to metabolic disruption, are of prime importance. Plant heat shock proteins (HSPs), as chaperones, play a pivotal role in conferring biotic and abiotic stress tolerance. Moreover, HSP also enhances membrane stability and detoxifies the reactive oxygen species (ROS) by positively regulating the antioxidant enzymes system. Additionally, it uses ROS as a signal to molecules to induce HSP production. HSP also enhances plant immunity by the accumulation and stability of pathogenesis-related (PR) proteins under various biotic stresses. Thus, to unravel the entire plant defense system, the role of HSPs are discussed with a special focus on plant response to biotic and abiotic stresses, which will be helpful in the development of stress tolerance in plant crops.

Evaluation of Switchgrass Genotypes for Cold-Tolerant Seed Germination from Native Populations in the Northeast USA

The focus of this research was to evaluate genotypes for cold-tolerant germination from wild switchgrass (Panicum virgatum L.) populations collected in the Northeast USA. Switchgrass nurseries were established in 2008 and 2009 with seed collected from native stands of switchgrass in the Northeast USA between 1991 and 2008. Switchgrass seed harvested from individual genotypes was evaluated for cold-tolerant germination in a series of laboratory experiments. Germination assays of seed of 13 switchgrass genotypes harvested in the fall of 2016 are the primary focus of this reported research. The selected genotypes were evaluated for cold-tolerant seed germination in three experiments, during the spring of 2017, fall of 2017 and spring of 2018, (with and without stratification) using a 10/15 °C regime with a 12 h photoperiod. Germination tests showed that several genotypes had significantly higher percentage germination as well as faster germination rates expressed as T50 (number of days required to reach 50% maximum germination) when compared to Cave-in-Rock, a moderately sensitive cold-tolerant commercial cultivar established in the original switchgrass nursery as a control. A final germination test was conducted to compare seed from the original population (no selection cycle 0), with one of the top performing cold-tolerant germination genotypes, and a commercial cultivar, 'Espresso', developed for low seed dormancy and low temperature germination. In this test, the selected genotype had significantly higher percentage germination in the stratified treatment and was not significantly different than Espresso in the non-stratified test. These data indicate successful selection for cold-tolerant germination in switchgrass genotypes from native germplasm collected in the Northeast USA.

Enhanced arsenic tolerance and secondary metabolism by modulation of gene expression and proteome profile in Artemisia annua L. after application of exogenous salicylic acid

This study was designed to investigate the effect of exogenous application of salicylic acid (SA) on proteins pattern and secondary metabolites in arsenic (As) stressed Artemisia annua. A. annua was treated by As 100 μM, SA 100 μM and combined treatment of SA 100 μM + As 100 μM upto 3 days. Significant accumulation of As was observed in roots than shoots at As 100 μM treatment. Under As treatment, oxidative stress was induced as indicated by increased TBARS content. Biomass, carotenoid, flavonoids were enhanced whereas total chlorophyll pigment was reduced under As treatment. Combined treatment of SA 100 μM + As 100 μM was more effective for increment of biomass, total chlorophyll content, and flavonoids as compared to As 100 μM treatment. Protein profiling revealed 20 differentially abundant proteins by 2-DE PAGE and MALDI-TOF-MS analysis. Identified proteins were related to photosynthesis, energy metabolism, transcriptional regulators, secondary metabolism, lipid metabolism, transport proteins and unknown/hypothetical proteins. All identified proteins were significantly increased in abundance under combined treatments of SA 100 μM + As 100 μM. The expression analysis of key genes involved in biosynthesis of lipid metabolism, signal molecule, transcriptional regulators, artemisinin biosynthetic genes, isoprenoids pathway, terpenes and flavonoids pathway were significantly upregulated under combined treatments of SA 100 μM + As 100 μM, suggesting a fine linkage in regulation of primary and secondary metabolism to modulate tolerance capacity and to improve phytoremediation property of A. annua against arsenic toxicity.

Differential gene expression profiling through transcriptome approach of Saccharum spontaneum L. under low temperature stress reveals genes potentially involved in cold acclimation

Sugarcane (Saccharum sp.) is predominantly grown in both tropics and subtropics in India, and the subtropics alone contribute more than half of sugarcane production. Sugarcane active growth period in subtropics is restricted to 8-9 months mainly due to winter's low temperature stress prevailing during November to February every year. Being a commercial crop, tolerance to low temperature is important in sugarcane improvement programs. Development of cold tolerant sugarcane varieties require a deep knowledge on molecular mechanism naturally adapted by cold tolerant genotypes during low temperature stress. To understand gene regulation under low temperature stress, control and stressed (10 °C, 24 h) leaf samples of cold tolerant S. spontaneum IND 00-1037 collected from high altitude region in Arunachal Pradesh were used for transcriptome analysis using the Illumina NextSeq 500 platform with paired-end sequencing method. Raw reads of 5.1 GB (control) and 5.3 GB (stressed) obtained were assembled using trinity and annotated with UNIPROT, KEGG, GO, COG and SUCEST databases, and transcriptome was validated using qRT-PCR. The differential gene expression (DGE) analysis showed that 2583 genes were upregulated and 3302 genes were down-regulated upon low temperature stress. A total of 170 cold responsive transcriptional factors belonging to 30 families were differentially regulated. CBF6 (C-binding factor), a DNA binding transcriptional activation protein associated with cold acclimation and freezing tolerance was differentially upregulated. Many low temperature responsive genes involved in various metabolic pathways, viz. cold sensing through membrane fluidity, calcium and lipid signaling genes, MAP kinases, phytohormone signaling and biosynthetic genes, antioxidative enzymes, membrane and cellular stabilizing genes, genes involved in biosynthesis of polyunsaturated fatty acids, chaperones, LEA proteins, soluble sugars, osmoprotectants, lignin and pectin biosynthetic genes were also differentially upregulated. Potential cold responsive genes and transcriptional factors involved in cold tolerance mechanism in cold tolerant S. spontaneum IND 00-1037 were identified. Together, this study provides insights into the cold tolerance to low temperature stress in S. spontaneum, thus opening applications in the genetic improvement of cold stress tolerance in sugarcane.

Bayesian Diallel Analysis Reveals Mx1-Dependent and Mx1-Independent Effects on Response to Influenza A Virus in Mice

Influenza A virus (IAV) is a respiratory pathogen that causes substantial morbidity and mortality during both seasonal and pandemic outbreaks. Infection outcomes in unexposed populations are affected by host genetics, but the host genetic architecture is not well understood. Here, we obtain a broad view of how heritable factors affect a mouse model of response to IAV infection using an 8 × 8 diallel of the eight inbred founder strains of the Collaborative Cross (CC). Expanding on a prior statistical framework for modeling treatment response in diallels, we explore how a range of heritable effects modify acute host response to IAV through 4 d postinfection. Heritable effects in aggregate explained ∼57% of the variance in IAV-induced weight loss. Much of this was attributable to a pattern of additive effects that became more prominent through day 4 postinfection and was consistent with previous reports of antiinfluenza myxovirus resistance 1 (Mx1) polymorphisms segregating between these strains; these additive effects largely recapitulated haplotype effects observed at the Mx1 locus in a previous study of the incipient CC, and are also replicated here in a CC recombinant intercross population. Genetic dominance of protective Mx1 haplotypes was observed to differ by subspecies of origin: relative to the domesticus null Mx1 allele, musculus acts dominantly whereas castaneus acts additively. After controlling for Mx1, heritable effects, though less distinct, accounted for ∼34% of the phenotypic variance. Implications for future mapping studies are discussed.

Spatial Mapping and Profiling of Metabolite Distributions during Germination

Germination is a highly complex process by which seeds begin to develop and establish themselves as viable organisms. In this study, we utilize a combination of gas chromatography-mass spectrometry, liquid chromatography-fluorescence, and mass spectrometry imaging approaches to profile and visualize the metabolic distributions of germinating seeds from two different inbreds of maize (Zea mays) seeds, B73 and Mo17. Gas chromatography and liquid chromatography analyses demonstrate that the two inbreds are highly differentiated in their metabolite profiles throughout the course of germination, especially with regard to amino acids, sugar alcohols, and small organic acids. Crude dissection of the seed followed by gas chromatography-mass spectrometry analysis of polar metabolites also revealed that many compounds were highly sequestered among the various seed tissue types. To further localize compounds, matrix-assisted laser desorption/ionization mass spectrometry imaging was utilized to visualize compounds in fine detail in their native environments over the course of germination. Most notably, the fatty acyl chain-dependent differential localization of phospholipids and triacylglycerols was observed within the embryo and radicle, showing correlation with the heterogeneous distribution of fatty acids. Other interesting observations include unusual localization of ceramides on the endosperm/scutellum boundary and subcellular localization of ferulate in the aleurone.

Photosynthetic responses mediate the adaptation of two Lotus japonicus ecotypes to low temperature

Lotus species are important forage legumes due to their high nutritional value and adaptability to marginal conditions. However, the dry matter production and regrowth rate of cultivable Lotus spp. is drastically reduced during colder seasons. In this work, we evaluated the chilling response of Lotus japonicus ecotypes MG-1 and MG-20. No significant increases were observed in reactive oxygen species and nitric oxide production or in lipid peroxidation, although a chilling-induced redox imbalance was suggested through NADPH/NADP(+) ratio alterations. Antioxidant enzyme catalase, ascorbate peroxidase, and superoxide dismutase activities were also measured. Superoxide dismutase, in particular the chloroplastic isoform, showed different activity for different ecotypes and treatments. Stress-induced photoinhibition also differentially influenced both ecotypes, with MG-1 more affected than MG-20. Data showed that the D2 PSII subunit was more affected than D1 after 1 d of low temperature exposure, although its protein levels recovered over the course of the experiment. Interestingly, D2 recovery was accompanied by improvements in photosynthetic parameters (Asat and Fv/Fm) and the NADPH/NADP(+) ratio. Our results suggest that the D2 protein is involved in the acclimation response of L. japonicus to low temperature. This may provide a deeper insight into the chilling tolerance mechanisms of the Lotus genus.

Heterosis and differential gene expression in hybrids and parents in Bombyx mori by digital gene expression profiling

Heterosis is a concern to all breeders, but the mechanism of heterosis remains unknown. In F1 organisms, genetic material is inherited from the two parents and theoretically, heterosis might be caused by differences in gene expression or modification. Differential gene expression was analyzed in hybrids and parents in Bombyx mori. The results showed that there were significant changes in gene expression in the fat body involving biological regulation, cellular and metabolic processes. Consistent trends in expression patterns covering different hybrid combinations were seen in 74 genes. Moreover, these differential gene expression patterns included overdominance, dominance, and additive effects. By correlating these patterns with economic traits, a potential relationship was found. Differential gene expression was seen in different cross combinations and in different sexes. In addition, a regulatory mechanism involving metabolism and ErbB signaling pathways was also found, suggesting that such a network might also be related to heterosis in Bombyx mori. Together, our data provide a comprehensive overview and useful resource for transcriptional analysis of heterosis of Bombyx mori.

Comparative study of the protein profiles of Sunki mandarin and Rangpur lime plants in response to water deficit

BACKGROUND

Rootstocks play a major role in the tolerance of citrus plants to water deficit by controlling and adjusting the water supply to meet the transpiration demand of the shoots. Alterations in protein abundance in citrus roots are crucial for plant adaptation to water deficit. We performed two-dimensional electrophoresis (2-DE) separation followed by LC/MS/MS to assess the proteome responses of the roots of two citrus rootstocks, Rangpur lime (Citrus limonia Osbeck) and 'Sunki Maravilha' (Citrus sunki) mandarin, which show contrasting tolerances to water deficits at the physiological and molecular levels.

RESULTS

Changes in the abundance of 36 and 38 proteins in Rangpur lime and 'Sunki Maravilha' mandarin, respectively, were observed via LC/MS/MS in response to water deficit. Multivariate principal component analysis (PCA) of the data revealed major changes in the protein profile of 'Sunki Maravilha' in response to water deficit. Additionally, proteomics and systems biology analyses allowed for the general elucidation of the major mechanisms associated with the differential responses to water deficit of both varieties. The defense mechanisms of Rangpur lime included changes in the metabolism of carbohydrates and amino acids as well as in the activation of reactive oxygen species (ROS) detoxification and in the levels of proteins involved in water stress defense. In contrast, the adaptation of 'Sunki Maravilha' to stress was aided by the activation of DNA repair and processing proteins.

CONCLUSIONS

Our study reveals that the levels of a number of proteins involved in various cellular pathways are affected during water deficit in the roots of citrus plants. The results show that acclimatization to water deficit involves specific responses in Rangpur lime and 'Sunki Maravilha' mandarin. This study provides insights into the effects of drought on the abundance of proteins in the roots of two varieties of citrus rootstocks. In addition, this work allows for a better understanding of the molecular basis of the response to water deficit in citrus. Further analysis is needed to elucidate the behaviors of the key target proteins involved in this response.

Abiotic stress responses in plant roots: a proteomics perspective

Abiotic stress conditions adversely affect plant growth, resulting in significant decline in crop productivity. To mitigate and recover from the damaging effects of such adverse environmental conditions, plants have evolved various adaptive strategies at cellular and metabolic levels. Most of these strategies involve dynamic changes in protein abundance that can be best explored through proteomics. This review summarizes comparative proteomic studies conducted with roots of various plant species subjected to different abiotic stresses especially drought, salinity, flood, and cold. The main purpose of this article is to highlight and classify the protein level changes in abiotic stress response pathways specifically in plant roots. Shared as well as stressor-specific proteome signatures and adaptive mechanism(s) are simultaneously described. Such a comprehensive account will facilitate the design of genetic engineering strategies that enable the development of broad-spectrum abiotic stress-tolerant crops.

Divergent selection in a maize population for germination at low temperature in controlled environment: study of the direct response, of the trait inheritance and of correlated responses in the field

Improving cold tolerance in maize (Zea mays L.) is an important breeding objective, allowing early sowings which result in many agronomic advantages. Using as source the F(2) population of B73 × IABO78 single cross, we previously conducted four cycles of divergent recurrent selection for high (H) and low (L) cold tolerance level, evaluated as the difference (DG) between germination at 9.5 °C and at 25 °C in the germinator. Then, we pursued the divergent selection in inbreeding from S(1) to S(4). This research was conducted to study (1) the direct response to selection (by testing ten S(4) L and ten S(4) H lines), (2) the trait inheritance (in a complete diallel scheme involving four L and four H lines), (3) the associated responses for cold tolerance in the field (at early and delayed sowings) and (4) the responses for other traits, by testing the ten L and the ten H lines at usual sowing. Selection was effective, leading to appreciable and symmetric responses for DG. Variation among crosses was mainly due to additive effects and the ability to predict hybrid DG based on parental lines DG was appreciable. Associated responses for cold tolerance traits in the field were noticeable, though the relationship between DG and these traits was not outstanding. High tolerance was also associated with early flowering, short plants, less leaves, low kernel moisture, red and thin cob, and flint kernels. These divergently selected lines can represent valuable materials for undertaking basic studies and breeding works concerning cold tolerance.

Heterosis: emerging ideas about hybrid vigour

Perceived by Charles Darwin in many vegetable plants and rediscovered by George H Shull and Edward M East in maize, heterosis or hybrid vigour is one of the most widely utilized phenomena, not only in agriculture but also in animal breeding. Although, numerous studies have been carried out to understand its genetic and/or molecular basis in the past 100 years, our knowledge of the underlying molecular processes that results in hybrid vigour can best be defined as superficial. Even after century long deliberations, there is no consensus on the relative/individual contribution of the genetic/epigenetic factors in the manifestation of heterosis. However, with the recent advancements in functional genomics, transcriptomics, proteomics, and metabolomics-related technologies, the riddle of heterosis is being reinvestigated by adopting systems-level approaches to understand the underlying molecular mechanisms. A number of intriguing hypotheses are converging towards the idea of a cumulative positive effect of the differential expression of a variety of genes, on one or several yield-affecting metabolic pathways or overall energy-use efficiency, as the underlying mechanism for the manifestation of heterosis. Presented here is a brief account of clues gathered from various investigative approaches targeted towards better scientific understanding of this process.

Can we improve heterosis for root growth of maize by selecting parental inbred lines with different temperature behaviour?

Tolerance to high and low temperature is an important breeding aim for Central and Northern Europe, where temperature fluctuations are predicted to increase. However, the extent to which genotypes differ in their response to the whole range of possible temperatures is not well understood. We tested the hypothesis that the combination of maize (Zea mays L.) inbred lines with differing temperature optima for root growth would lead to superior hybrids. This hypothesis is based on the concept of 'marginal overdominance' in which the hybrid expresses higher relative fitness than its parents, summed over all situations. The elongation rates of axile and lateral roots of the reciprocal cross between two flint and two dent inbred lines were assessed at temperatures between 15°C and 40°C. Indeed, the cross between UH005 and UH250 with lateral root growth temperature optima at 34°C and 28°C, respectively, resulted in intermediate hybrids. At temperatures below and above 31°C, the hybrids' root growth was comparable to the better parent, respectively, thereby increasing temperature tolerance of the hybrid compared with its parents. The implications of and reasons for this heterosis effect are discussed in the context of breeding for abiotic stress tolerance and of putatively underlying molecular mechanisms. This finding paves the way for more detailed investigations of this phenomenon in future studies.

The differential proteome of endosperm and embryo from mature seed of Jatropha curcas

Jatrpha curcas L., a non-model woody plant belonging to Euphorbiaceae family, is a promising economic plant due to the high oil content in seed and high tolerance to drought and salt stress. The embryo and endosperm of J. curcas seed differ in morphology, function and ploidy. To characterize the protein profiles of these two tissues, we have performed proteomic analysis with the dry mature J. curcas seeds. The data showed that the 2-DE profiles of endosperm and embryo were similar to each other. There are 66 differential proteins between the two seed tissues, in which 28 proteins distributed in 9 distinct functional classes, have been identified successfully in endosperm or embryo. The major groups of differential proteins are associated with metabolism (25%) and disease/defence (18%). Our results demonstrated that in the dry mature J. curcas seeds, the proteins involved in oil mobilization, signal transduction, transcription, protein synthesis, and cell cycle which are essential for the seed germination have occurred in endosperm and embryo, reflecting the fact that proteins required for germination are already present in the dry mature seed.

A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding

Hybrids between genetically diverse varieties display enhanced growth, and increased total biomass, stress resistance and grain yield. Gene expression and metabolic studies in maize, rice and other species suggest that protein metabolism plays a role in the growth differences between hybrids and inbreds. Single trait heterosis can be explained by the existing theories of dominance, overdominance and epistasis. General multigenic heterosis is observed in a wide variety of different species and is likely to share a common underlying biological mechanism. This review presents a model to explain differences in growth and yield caused by general multigenic heterosis. The model describes multigenic heterosis in terms of energy-use efficiency and faster cell cycle progression where hybrids have more efficient growth than inbreds because of differences in protein metabolism. The proposed model is consistent with the observed variation of gene expression in different pairs of inbred lines and hybrid offspring as well as growth differences in polyploids and aneuploids. It also suggests an approach to enhance yield gains in both hybrid and inbred crops via the creation of an appropriate computational analysis pipeline coupled to an efficient molecular breeding program.

Systemic properties of metabolic networks lead to an epistasis-based model for heterosis

The genetic and molecular approaches to heterosis usually do not rely on any model of the genotype-phenotype relationship. From the generalization of Kacser and Burns' biochemical model for dominance and epistasis to networks with several variable enzymes, we hypothesized that metabolic heterosis could be observed because the response of the flux towards enzyme activities and/or concentrations follows a multi-dimensional hyperbolic-like relationship. To corroborate this, we used the values of systemic parameters accounting for the kinetic behaviour of four enzymes of the upstream part of glycolysis, and simulated genetic variability by varying in silico enzyme concentrations. Then we "crossed" virtual parents to get 1,000 hybrids, and showed that best-parent heterosis was frequently observed. The decomposition of the flux value into genetic effects, with the help of a novel multilocus epistasis index, revealed that antagonistic additive-by-additive epistasis effects play the major role in this framework of the genotype-phenotype relationship. This result is consistent with various observations in quantitative and evolutionary genetics, and provides a model unifying the genetic effects underlying heterosis.

A comparative analysis of embryo and endosperm proteome from seeds of Jatropha curcas

Jatropha curcas is an important economic plant for biodiesel, which is extracted mainly from the endosperm of its mature seeds. Despite the morphological and functional differences between the embryo and endosperm, proteomic characteristics of the two tissues are not yet known. Similar proteomic profiles were observed in the two-dimensional gel electrophoresis maps from the two tissues. There were 380 and 533 major protein spots in the embryo and endosperm, respectively. Fourteen identical spots, showing a notable change, were selected and identified by tandem mass spectrometry. Among these proteins, dihydrolipoamide acetyltransferase (spot 27) participates in tricarboxylic acid cycle, which is an amphibolic pathway. The two parts both included proteins related to stress (spots 8, 115, 118, 125, 130) and signal transduction (spots 7, 100, 108). According to the volume percentage of proteins in embryo and endosperm, the proteins in endosperm (spots 54, 61, 73) were catabolism-related enzymes and reserves to provide the nutrition for seed germination; the proteins in embryo (spots 27, 62, 122) were inclined to anabolism and utilized the nutrition from the endosperm to generate a new life.

Advances in maize genomics and their value for enhancing genetic gains from breeding

Maize is an important crop for food, feed, forage, and fuel across tropical and temperate areas of the world. Diversity studies at genetic, molecular, and functional levels have revealed that, tropical maize germplasm, landraces, and wild relatives harbor a significantly wider range of genetic variation. Among all types of markers, SNP markers are increasingly the marker-of-choice for all genomics applications in maize breeding. Genetic mapping has been developed through conventional linkage mapping and more recently through linkage disequilibrium-based association analyses. Maize genome sequencing, initially focused on gene-rich regions, now aims for the availability of complete genome sequence. Conventional insertion mutation-based cloning has been complemented recently by EST- and map-based cloning. Transgenics and nutritional genomics are rapidly advancing fields targeting important agronomic traits including pest resistance and grain quality. Substantial advances have been made in methodologies for genomics-assisted breeding, enhancing progress in yield as well as abiotic and biotic stress resistances. Various genomic databases and informatics tools have been developed, among which MaizeGDB is the most developed and widely used by the maize research community. In the future, more emphasis should be given to the development of tools and strategic germplasm resources for more effective molecular breeding of tropical maize products.

Chilling stress-induced proteomic changes in rice roots

Roots are highly sensitive organs in plants. To gain a better knowledge of the chilling stress responses of plants, it is imperative to analyze the tissue-specific proteome patterns under chilling stress. In the present study, two-dimensional gel electrophoresis (2-DE) coupled with mass spectrometry, has been adopted to investigate the protein expression patterns of rice roots in response to chilling stress. Rice seedlings were subjected to 10 degrees C and samples were collected 24 and 72h after treatment. To identify the low-abundant proteins in root tissues, samples were fractionated by 15% polyethylene glycol (PEG), separated by 2-DE, and visualized by silver or CBB staining. A total of 27 up-regulated proteins were identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry or electrospray ionization-tandem mass spectrometry (ESI-MS/MS) analysis. Together with the previously identified cold-stress-responsive proteins, a group of novel proteins were identified including acetyl transferase, phosphogluconate dehydrogenase, NADP-specific isocitrate dehydrogenase, fructokinase, PrMC3, putative alpha-soluble N-ethylmaleimide-sensitive factor (NSF) attachment protein, and glyoxalase 1. These proteins are involved in several cellular processes, including energy production and metabolism, vesicular trafficking, and detoxification. Gene expression at the mRNA level of some selected proteins revealed that transcription levels are not always concomitant to the translational level. Thus, investigation of root proteome expression and identification of some novel proteins could be useful in better understanding the molecular basis of chilling stress responses in plants.

Towards the molecular basis of heterosis

Heterosis describes the superior performance of heterozygous hybrid plants over their homozygous parental inbred lines. Despite the rediscovery of this phenomenon a century ago and its paramount agronomic importance, the genetic and molecular basis of heterosis remains enigmatic. Recently, various pioneer studies described differences in genome organization and gene expression of hybrids and their parental inbred lines. At the genomic level, a significant loss of colinearity at many loci between different inbred lines of maize was observed. At the level of gene expression, complex transcriptional networks specific for different developmental stages and tissues were monitored in maize (Zea mays), rice (Oryza sativa) and Arabidopsis (Arabidopsis thaliana). Integration of this complex expression data might contribute to improve our understanding of the molecular basis of heterosis.

Inherited maternal effects on the drought tolerance of a natural hybrid aquatic plant, Potamogeton anguillanus

We tested whether maternal effects have led to the adaptive divergence of strains of the natural hybrid Potamogeton anguillanus, whose putative parents show contrastingly divergent ecologies. To examine the correlation between phenotypic characters and maternal types, we conducted drought experiments and DNA typing using nuclear and chloroplast genes. In the field, we investigated the distribution of the maternal type along the depth and the inshore-offshore gradient. Hybrids of P. malaianus mothers (M-hybrids) and those of P. perfoliatus mothers (P-hybrids) could not be distinguished morphologically under submerged conditions, but differed in drought tolerance. M-hybrids and P. malaianus formed more terrestrial shoots and exhibited higher survival than P-hybrids and P. perfoliatus in drought experiments. The distribution survey clarified that M-hybrids were dominant in shallow and inshore areas, whereas they were almost absent in deeper and offshore areas. These results indicate that the natural hybrid P. anguillanus differs in adaptive values depending on the maternal type. Bidirectional hybridization and heritable maternal effects may have played important roles in its phenotypic adaptation to local environmental conditions.

Mapping reciprocal effects and interactions with plant density stress in Zea mays L

Reciprocal effects are due to genetic effects of the parents (i.e. maternal and paternal effects), cytoplasmic effects and parent-of-origin effects. However, in Zea mays L. the extent to which reciprocal effects exist, or can be attributed to specific underlying components, remains an area of interest and study. Reciprocal effects have been reported by several investigators for various agronomic characters in different types of maize materials for grain and silage usage. Maize geneticists and breeders have recognized reciprocal effects as one source of genetic variability, but the lack of consistency in the observation of these effects, particularly due to stress conditions, has prevented a systematic exploitation of these effects in practical breeding programs. There is mounting molecular evidence for underlying mechanisms in maize, which could be responsible for both the existence, and the instability of reciprocal effects. In this study, we developed population of reciprocal backcrosses based on an initial set of recombinant inbred lines. This population was used for dissecting reciprocal effects into the underlying components (maternal, cytoplasmic and parent-of-origin) effects. We also developed statistical framework to identify and map contributions of specific nuclear chromosomal regions to reciprocal effects. We showed that differences in maternal parents, endosperm DNA and maternally transmitted factors collectively influence reciprocal effects early during the season, and that their influence diluted at later stages. We also found evidence that parent-of-origin effects in the sporophyte DNA existed at all stages and played an important role in establishing differences between reciprocal backcrosses at later developmental stages.

Plant proteome analysis: A 2004–2006 update

Since the appearance of the review entitled "Plant Proteome Analysis" in Proteomics in February 2004 (Cánovas, F. M., Dumas-Gaudot, E., Recorbert, G., Jorrín, J. et al., Proteomics 2004, 4, 285-298), about 200 original articles focusing on plant proteomics have been published. Although this represents less than 1% of the global proteomics output during this period, it nevertheless reflects an increase in activity over the period 1999-2004. These papers concern the proteome of at least 35 plant species but have concentrated mainly on thale cress (Arabidopsis thaliana) and rice (Oryza sativa). The scientific objectives have ranged from a proteomic analysis of organs, tissues, cell suspensions, or subcellular fractions to the study of plant development and response to various stresses. A number of contributions have covered PTMs and protein interactions. The dominant analytical platform has been 2-DE coupled to MS, but "second generation" techniques such as DIGE, multidimensional protein identification technology, isotope-coded affinity tags, and stable isotope labeling by amino acids in cell culture have begun to make an impact. This review aims to provide an update of the contribution of proteomics to plant biology during the period 2004-2006, and is divided into six sections: introduction, subcellular proteomes, plant development, responses to biotic and abiotic stresses, PTMs, and protein interactions. The conclusions summarize a view of the major pitfalls and challenges of plant proteomics.

A ginseng-specific abundant protein (GSAP) located on the cell wall is involved in abiotic stress tolerance

Ginseng ESTs allowed us to identify an unknown transcript which is highly abundant in rhizomes and seeds. We called the cDNA ginseng-specific abundant protein (GSAP), and identified three homologues, GSAP1, GSAP2, and GSAP3. GSAP cDNAs encode a small polypeptide consisting of 121 or 117 amino acids, and GSAP3 shows 87.6% amino acid sequence homology with GSAP1. GSAP transcripts were detected in most plant tissues, but GSAP3 is highly expressed in seeds, and is up-regulated under stressed conditions, water deficit. GSAP3-GFP fusion protein is located in the cell wall when expressed in onion epidermis cells. The transgenic Arabidopsis seedlings which over-expressed GSAP3 grew faster than those of the wild-type plant on the medium containing 300 mM mannitol and 100 mM NaCl. GSAP3 may play a role in altering the characteristics of the cell wall to allow for more tolerance of water deficit stress under abiotic stress conditions.

Genome-wide transcript analysis of maize hybrids: allelic additive gene expression and yield heterosis

Heterosis, or hybrid vigor, has been widely exploited in plant breeding for many decades, but the molecular mechanisms underlying the phenomenon remain unknown. In this study, we applied genome-wide transcript profiling to gain a global picture of the ways in which a large proportion of genes are expressed in the immature ear tissues of a series of 16 maize hybrids that vary in their degree of heterosis. Key observations include: (1) the proportion of allelic additively expressed genes is positively associated with hybrid yield and heterosis; (2) the proportion of genes that exhibit a bias towards the expression level of the paternal parent is negatively correlated with hybrid yield and heterosis; and (3) there is no correlation between the over- or under-expression of specific genes in maize hybrids with either yield or heterosis. The relationship of the expression patterns with hybrid performance is substantiated by analysis of a genetically improved modern hybrid (Pioneer hybrid 3394) versus a less improved older hybrid (Pioneer hybrid 3306) grown at different levels of plant density stress. The proportion of allelic additively expressed genes is positively associated with the modern high yielding hybrid, heterosis and high yielding environments, whereas the converse is true for the paternally biased gene expression. The dynamic changes of gene expression in hybrids responding to genotype and environment may result from differential regulation of the two parental alleles. Our findings suggest that differential allele regulation may play an important role in hybrid yield or heterosis, and provide a new insight to the molecular understanding of the underlying mechanisms of heterosis.

Manifestation of heterosis during early maize (Zea mays L.) root development

Heterosis is typically detected in adult hybrid plants as increased yield or vigor compared to their parental inbred lines. Only little is known about the manifestation of heterosis during early postembryonic development. Objective of this study was to identify heterotic traits during early maize root development. Four German inbred lines of the flint (UH002 and UH005) and dent (UH250 and UH301) pool and the 12 reciprocal hybrids generated from these inbred lines were subjected to a morphological and histological analysis during early root development. Primary root length and width were measured daily in a time course between 3 and 7 days after germination (DAG) and displayed average midparent heterosis (MPH) of 17-25% and 1-7%, respectively. Longitudinal size of cortical cells in primary roots was determined 5 DAG and displayed on average 24% MPH thus demonstrating that enlarged primary roots of hybrids can mainly be attributed to elongated cortical cells. The number of seminal roots determined 14 DAG showed on average 18% MPH. Lateral root density of all tested hybrids was determined 5 DAG. This root trait showed the highest degree of heterosis with an average MPH value of 51%. This study demonstrated that heterosis is already manifesting during the very early stages of root development a few days after germination. The young root system is therefore a suitable model for subsequent molecular studies of the early stages of heterosis manifestation during seedling development.

Genetic analysis of variation in gene expression in Arabidopsis thaliana

In Arabidopsis thaliana, significant efforts to determine the extent of genomic variation between phenotypically divergent accessions are under way, but virtually nothing is known about variation at the transcription level. We used microarrays to examine variation in transcript abundance among three inbred lines and two pairs of reciprocal F1 hybrids of the highly self-fertilizing species Arabidopsis. Composite additive genetic effects for gene expression were estimated from pairwise comparisons of the three accessions Columbia (Col), Landsberg erecta (Ler), and Cape Verde Islands (Cvi). For the pair Col and Ler, 27.0% of the 4876 genes exhibited additive genetic effects in their expression (alpha = 0.001) vs. 32.2 and 37.5% for Cvi with Ler and Col, respectively. Significant differential expression ranged from 32.45 down to 1.10 in fold change and typically differed by a factor of 1.56. Maternal or paternal transmission affected only a few genes, suggesting that the reciprocal effects observed in the two crosses analyzed were minimal. Dominance effects were estimated from the comparisons of hybrids with the corresponding midparent value. The percentage of genes showing dominance at the expression level in the F1 hybrids ranged from 6.4 to 21.1% (alpha = 0.001). Breakdown of these numbers of genes according to the magnitude of the dominance ratio revealed heterosis for expression for on average 9% of the genes. Further advances in the genetic analysis of gene expression variation may contribute to a better understanding of its role in affecting quantitative trait variation at the phenotypic level.

Optimal allocation in designs for assessing heterosis from cDNA gene expression data

Heterosis is defined as the superiority of a hybrid cross over its two parents. Plant and animals breeders have long been exploiting heterosis, but the causes of this phenomenon are as yet only partly understood. Recently, chip technology has opened up the opportunity to study heterosis at the gene expression level. This article considers the cDNA chip technology, which allows assaying two genotypes simultaneously on the same chip. Heterosis involves the response of at least three genotypes (two parents and their hybrid), so a chip or microarray constitutes an incomplete block, which raises a design problem specific to heterosis studies. The question to be answered is how genotype pairs should be allocated to chips. We address this design problem for two types of heterosis: midparent heterosis and better-parent heterosis. The general picture emerging from our results is that most of the resources should be allocated to parent-hybrid pairs, while chips with parent-parent pairs or hybrid-reciprocal pairs should be used sparingly or not at all.

Designing a microarray experiment to estimate dominance in maize (Zea mays L.)

Experiments using cDNA microarrays for the identification of genes with certain expression patterns require a thoughtfully planned design. This study was conducted to determine an optimal design for a microarray experiment to estimate differential gene expression between hybrids and their parental inbred lines in maize (i.e. dominance). It has two features: the contrasts of interest contain more than two genotypes and the procedure may be customised to other microarray experiments where different effects may influence hybridisation signals. A mixed model was used to include all important effects. Impacts during growth of the plant material were taken into consideration as well as those occurring during hybridisation. The results of a preliminary experiment were used to determine which effects were to be included in the model, and data from another microarray experiment were used to estimate variance components. In order to select good designs, an optimality criterion adapted to the problem of differential gene expression between hybrids and their parental inbred lines was defined. Two approaches were used to determine an optimal design: the first one simplifies the problem by dividing it into several subproblems, whereas the second is more sophisticated and uses a simulated annealing (SA) algorithm. We found that the first approach constitutes a useful means for designing microarray experiments to study this problem. Using the more sophisticated SA approach the design can be further improved.

A transcriptomics resource for wheat functional genomics

Grain development, germination and plant development under abiotic stresses are areas of biology that are of considerable interest to the cereal community. Within the Investigating Gene Function programme we have produced the resources required to investigate alterations in the transcriptome of hexaploid wheat during these developmental processes. We have single pass sequenced the cDNAs of between 700 and 1300 randomly picked clones from each of 35 cDNA libraries representing highly specific stages of grain and plant development. Annotated sequencing results have been stored in a publicly accessible, online database at http://www.cerealsdb.uk.net. Each of the tissue stages used has also been photographed in detail, resulting in a collection of high-quality micrograph images detailing wheat grain development. These images have been collated and annotated in order to produce a web site focused on wheat development (http://www.wheatbp.net/). We have also produced high-density microarrays of a publicly available wheat unigene set based on the 35 cDNA libraries and have completed a number of microarray experiments which validate their quality.

Freezing tolerance of plants: current understanding and selected emerging concepts

The formation of ice on and inside plant tissues represents a major challenge to survival. The resulting phase transition and spatial redistribution of liquid water from inside the cell to extracellular ice results in physical changes to cells and enormous physical stresses and strains. The ability of higher plants to acclimate and tolerate freezing stress is a complex quantitative trait and the product of the activities of not one, but a sizable suite of genes. Many of the known cold-regulated genes are under the control of a primary master regulator, CBF/DREB1, but it is not likely to be the sole master regulator. In considering the origin of freezing tolerance in higher plants, it has been suggested that freezing tolerance likely arose by adopting drought tolerance mechanisms. This may explain why many genes responsive to cold stress are also responsive to drought and (or) other osmotic stresses.Key words: abiotic, dehydration, gene expression, physiology, signal transduction, transcriptome.

Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm

We have taken a genomic approach to examine global gene expression in the maize endosperm in relation to dosage and parental effects. Endosperm of eight hybrids generated by reciprocal crosses and their seven inbred parents were sampled at three developmental stages: 10, 14, and 21 days after pollination (DAP). These samples were subjected to GeneCalling, an open-ended mRNA-profiling technology, which simultaneously analyzes thousands of genes. Results indicated that the overall level of gene expression in the maize endosperm was dosage-dependent, that is, the gene expression was proportional to the parental genome contribution of 2n maternal : 1n paternal. However, approximately 8% of the genes deviated from such allelic additive expression and exhibited differential expression in hybrids of reciprocal crosses, resembling either maternally or paternally expressed genes. There were more genes with maternal-like expression (MLE) than those with paternal-like expression (PLE). Allele-specific expression analysis of four selected genes using the WAVE denaturing HPLC (dHPLC) system revealed several mechanisms responsible for the deviation from the allelic additive expression in the hybrid endosperm: heterochronic allelic variation, allelic variation in the level of expression, and genomic imprinting. We discovered a novel imprinted gene no-apical-meristem (NAM) related protein1 (nrp1) that was expressed only in the endosperm and regulated by gene-specific imprinting. The nrp1 gene, a putative transcriptional factor, may play an important role in endosperm development.