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The importance of increasing photosynthetic efficiency for sustainable crop yield increases to feed the growing world population is well recognized. The natural genetic variation in leaf photosynthesis in crop plants is largely unexploited for increasing yield potential. The genus Oryza, including cultivated rice and wild relatives, offers tremendous genetic variability to explore photosynthetic differences and underlying biochemical, photochemical, and developmental traits. We quantified leaf photosynthesis and related physiological parameters for six cultivated and three wild rice genotypes, and identified photosynthetically efficient wild rice accessions. Fitting A/Ci curves and biochemical analyses showed that leaf photosynthesis in cultivated rice varieties IR 64 and Nipponbare was limited due to leaf nitrogen content, Rubisco activity, and electron transport rate compared with photosynthetically efficient wild rice accessions Oryza australiensis and Oryza latifolia. The selected wild rice accessions with high leaf photosynthesis per unit area had anatomical features such as larger mesophyll cells with more chloroplasts, fewer mesophyll cells between two adjacent veins, and higher mesophyll cell and chloroplast surface area exposed to intercellular space. Our results show the existence of desirable variations in Rubisco activity, electron transport rate, and leaf anatomical features that could be targeted for increasing the photosynthetic efficiency of cultivated rice varieties.

Ascochyta blight (AB) caused by a filamentous fungus Ascochyta rabiei is a major threat to global chickpea production. The mechanisms underlying chickpea response to A. rabiei remain elusive. Here, we investigated the comparative transcriptional dynamics of AB-resistant and susceptible chickpea genotypes upon A. rabiei infection to understand the early host defence response. Our findings revealed that AB-resistant plants underwent rapid and extensive transcriptional reprogramming compared to susceptible host. At early stage (24-hpi), mainly cell wall remodeling and secondary metabolite pathways were highly activated, while DEGs related with signaling components viz. protein kinases, transcription factors, and hormonal pathways show remarkable upsurge at 72-hpi, especially in resistant genotype. Notably, our data suggests imperative role of JA, ET, and ABA signaling in providing immunity against A. rabiei. Furthermore, gene co-expression networks and modules corroborated the importance of cell wall remodeling, signal transduction and phytohormone pathways. The hub genes such as MYB14, PRE6 and MADS-SOC1 discovered in these modules might be the master regulators governing chickpea immunity. Overall, we not only provide novel insights for comprehensive understanding of immune signaling components mediating AB resistance/susceptibility at early Cicer-Ascochyta interactions, but also offer a valuable resource for developing AB-resistant chickpea.HighlightsComparative transcriptomic and co-expression analysis of AB-resistant and susceptible chickpea genotypes reveals high-amplitude transcriptional dynamics in resistant plants, and also identifies TFs, PKs and phytohormone-crosstalk as core regulators for AB-resistance.

The SWEET (SUGARS WILL EVENTUALLY BE EXPORTED TRANSPORTERS) family of transporters in plants is identified as a novel class of sugar carriers capable of transporting sugars, sugar alcohols, and hormones. Functioning in intercellular sugar transport, SWEETs influence a wide range of physiologically important processes. SWEETs regulate the development of sink organs by providing nutritional support from source leaves, responses to abiotic stresses by maintaining intracellular sugar concentrations, and host-pathogen interactions through the modulation of apoplastic sugar levels. Many bacterial and fungal pathogens activate the expression of SWEET genes in species such as rice and Arabidopsis to gain access to the nutrients that support virulence. The genetic manipulation of SWEETs has led to the generation of Bacterial Blight (BB) resistant rice varieties. Similarly, while the overexpression of the SWEETs involved in sucrose export from leaves and pathogenesis led to growth retardation and yield penalties, plants overexpressing SWEETs show improved disease resistance. Such findings demonstrate the complex functions of SWEETs in growth and stress tolerance. Here, we review the importance of SWEETs in plant-pathogen and source-sink interactions and abiotic stress resistance. We highlight the possible applications of SWEETs in crop improvement programs aimed at improving sink and source strengths important for enhancing the sustainability of yield. We discuss how the adverse effects of the overexpression of SWEETs on plant growth may be overcome.

High ambient temperature suppresses Arabidopsis rosette leaf area, in contrast to elongation of stem and petiole. While the mechanism underlying temperature-induced elongation response is extensively studied, the genetic basis of temperature-regulation of leaf size is largely unknown. Here we show that warm temperature inhibits cell proliferation in the Arabidopsis leaves resulting in fewer cells compared to the control condition. Cellular phenotyping, genetic, and biochemical analyses established the key roles of PIF4 and TCP4 transcription factors in the suppression of Arabidopsis leaf area under high temperature by a reduction in cell number. We show that temperature-mediated suppression of cell proliferation requires PHYTOCHROME INTERACTING FACTOR 4 (PIF4). PIF4 interacts with TEOSINTE BRANCHED1/CYCLOIDEA/PCF4 (TCP4) and regulates the expression of cell cycle inhibitor, KIP-RELATED PROTEIN 1 (KRP1), to control the leaf size under high temperature. Warm temperature induces binding of both PIF4 and TCP4 to the KRP1 promoter. PIF4 binding to KRP1 under high temperature is TCP4 dependent as TCP4 regulates PIF4 levels under high temperature. We propose a model where a warm temperature-mediated accumulation of PIF4 in the leaf cells promotes its binding to the KRP1 promoter in a TCP4-dependent way to regulate cell production and leaf size. Our finding of high temperature-mediated transcriptional upregulation of KRP1 integrates a developmental signal with an environmental signal that converges on a basal cell regulatory process.One sentence summaryHigh ambient temperature suppresses Arabidopsis leaf area by reducing cell proliferation via PIF4- and TCP4-dependent transcription control of KRP1.

This work presents an extensive review of hierarchical control strategies that provide effective and robust control for a DC microgrid. DC microgrid is an efficient, scalable and reliable solution for electrification in remote areas and needs a reliable control scheme such as hierarchical control. The hierarchical control strategy is divided into three layers namely primary, secondary and tertiary based on their functionality. In this study, different methods of primary control for current and voltage regulation, secondary control for error-correction in voltage and current, power sharing in a microgrid and microgrid clusters and tertiary control for power and energy management with a primary focus on minimal power loss and operational cost in a DC microgrid system are reviewed in-depth. Along with this, the advantages and limitations of various control structures like centralised, decentralised, distributed are discussed in this study. After a comparative study of all control strategies, the optimum control schemes from the author's point of view are also presented.

Cellular and genetic understanding of the rice leaf size regulation is limited, despite rice being the staple food of more than half of the global population. We investigated the mechanism controlling the rice leaf length using cultivated and wild rice accessions that remarkably differed for leaf size. Comparative transcriptomics, gibberellic acid (GA) quantification and leaf kinematics of the contrasting accessions suggested the involvement of GA, cell cycle and growth-regulating factors (GRFs) in the rice leaf size regulation. Zone-specific expression analysis and VIGS established the functions of specific GRFs in the process. The leaf length of the selected accessions was strongly correlated with GA levels. Higher GA content in wild rice accessions with longer leaves and GA-induced increase in the leaf length via an increase in cell division confirmed a GA-mediated regulation of division zone in rice. Downstream to GA, OsGRF7 and OsGRF8 function for controlling cell division to determine the rice leaf length. Spatial control of cell division to determine the division zone size mediated by GA and downstream OsGRF7 and OsGRF8 explains the leaf length differences between the cultivated and wild rice. This mechanism to control the rice leaf length might have contributed to optimizing leaf size during domestication.

Oryza punctata Kotschy ex Steud. (BB, 2n = 24) is a wild species of rice that has many useful agronomic traits. An interspecific hybrid (AB, 2n = 24) was produced by crossing O. punctata and Oryza sativa variety Punjab Rice 122 (PR122, AA, 2n = 24) to broaden the narrow genetic base of cultivated rice. Cytological analysis of the pollen mother cells (PMCs) of the interspecific hybrids confirmed that they have 24 chromosomes. The F1hybrids showed the presence of 19–20 univalents and 1–3 bivalents. The interspecific hybrid was treated with colchicine to produce a synthetic amphiploid (AABB, 2n = 48). Pollen fertility of the synthetic amphiploid was found to be greater than 50% and partial seed set was observed. Chromosome numbers in the PMCs of the synthetic amphiploid were 24II, showing normal pairing. Flow cytometric analysis also confirmed doubled genomic content in the synthetic amphiploid. Leaf morphological and anatomical studies of the synthetic amphiploid showed higher chlorophyll content and enlarged bundle sheath cells as compared with both of its parents. The synthetic amphiploid was backcrossed with PR122 to develop a series of addition and substitution lines for the transfer of useful genes from O. punctata with least linkage drag.

Leaf size is a major determinant of crop performance by influencing leaf physiological processes, such as light capture, transpiration, and gas exchange. Therefore, understanding the genetic basis of leaf size regulation is imperative for crop improvement. Natural variation in leaf size for a crop plant is a valuable genetic resource for a detailed understanding of leaf size regulation. We investigated the mechanism controlling the rice leaf length using cultivated and wild rice accessions that showed remarkable differences for the leaf features. Comparative transcriptomic profiling of the contrasting accessions suggested the involvement of Gibberellic Acid (GA), Growth Regulating Factor (GRF) transcription factors, and cell cycle in the rice leaf size regulation. Leaf kinematics studies showed that the increased domain of cell division activity along with a faster cell production rate drove the longer leaves in the wild rice Oryza australiensis compared to the cultivated varieties. Higher GA levels in the leaves of Oryza australiensis, and GA-induced increase in the rice leaf length via an increase in cell division zone emphasized the key role of GA in rice leaf length regulation. Zone-specific expression and silencing of the GA biosynthesis and signaling genes confirmed that OsGRF7 and OsGRF8 function downstream to GA for controlling cell cycle to determine the rice leaf length. The GA-GRF-cell cycle module for rice leaf length regulation might have contributed to optimizing leaf features during the domestication and could also be a way for plants to achieve leaf plasticity in response to the environment. Summary High Gibberellic Acid level promotes cell division and cell production rate in rice leaves to increase the leaf length.

The Arabidopsis COP1/SPA complex is a key repressor of photomorphogenesis that suppresses light signaling in the dark. Both COP1 and SPA proteins are essential components of this complex. Although COP1 also exists in humans, SPA genes are specific to the green lineage. To elucidate the evolution of SPA genes we analyzed SPA functions in the moss Physcomitrella patens by characterizing knockout mutants in the two Physcomitrella SPA genes PpSPAa and PpSPAb. Light-grown PpspaAB double mutants exhibit smaller gametophores than the wild-type. In the dark, PpspaAB mutant gametophores show enhanced continuation of growth but etiolate normally. Gravitropism in the dark is reduced in PpspaAB mutant protonemata. The expression of light-regulated genes is mostly not constitutive in PpspaAB mutants. PpSPA and PpCOP1 interact; PpCOP1 also interacts with the transcription factor PpHY5 and, indeed, PpHY5 is destabilized in dark-grown Physcomitrella. Degradation of PpHY5 in darkness, however, does not require PpSPAa and PpSPAb. The data suggest that COP1/SPA-mediated light signaling is only partially conserved between Arabidopsis and Physcomitrella. Whereas COP1/SPA interaction and HY5 degradation in darkness is conserved, the role of SPA proteins appears to have diverged. PpSPA genes, unlike their Arabidopsis counterparts, are only required to suppress a subset of light responses in darkness.

In this paper, closed-loop control of isolated bidirectional dual-active bridge (DAB) DC-DC converter is proposed for dual-phase-shift (DPS) scheme using fixed frequency pulse-width-modulation (PWM) plus transmitted command power. DPS is a well-known control scheme to reduce backflow power, current stress, and losses, it also provides better power transfer flexibility under high frequency. However, the conventional DPS scheme has limited performance in light load conditions. The discussed control technique overcomes the instant variation of inner phase shift ratio (D 1 ) w.r.t outer phase shift ratio (D 2 ) during light load conditions. The theoretical concepts of the transmitted power in different modes of operation are presented in this paper along with a detailed analysis of MATLAB simulation results in dynamic conditions and both directions of power flow. The implemented control scheme leverages most of the improved features of the DPS scheme to transfer power from one end to another end.

The source-sink relationship is key to overall crop performance. Detailed understanding of the factors that determine source-sink dynamics is imperative for the balance of biomass and grain yield in crop plants. We investigated the differences in the source-sink relationship between a cultivated rice Oryza sativa cv. Nipponbare and a wild rice Oryza australiensis that show striking differences in biomass and grain yield. Oryza australiensis, accumulating higher biomass, not only showed higher photosynthesis per unit leaf area but also exported more sucrose from leaves than Nipponbare. However, grain features and sugar levels suggested limited sucrose mobilization to the grains in the wild rice due to vasculature and sucrose transporter functions. Low cell wall invertase activity and high sucrose synthase cleavage activity followed by higher expression of cellulose synthase genes in Oryza australiensis stem utilized photosynthates preferentially for the synthesis of structural carbohydrates, resulting in high biomass. In contrast, the source-sink relationship favored high grain yield in Nipponbare via accumulation of transitory starch in the stem, due to higher expression of starch biosynthetic genes, which is mobilized to panicles at the grain filling stage. Thus, vascular features, sucrose transport, and functions of sugar metabolic enzymes explained the differences in the source-sink relationship between Nipponbare and Oryza australiensis.HighlightVascular features, sucrose transport, and sugar metabolic enzyme activity contribute to the differential source-sink relationship between the selected cultivated and wild rice that differ in biomass and grain yield.

Abiotic stresses, including drought and salinity, negatively affect plant development and physiology at molecular and metabolic levels. Sucrose transport, mediating distribution of photosynthates in plant, is a key physiological process impacted by drought and salinity stresses, as sucrose is a prime energy and signaling molecule as well as an osmolyte. Therefore, understanding the effects of abiotic stresses on sucrose transport and transporters, and underlying genetic and molecular mechanisms, is imperative to maintain sugar homeostasis in plants under stress. Here, we investigated the effects of drought and salinity stresses on sucrose transport and distribution, and on expression levels of genes encoding Sugars Will Eventually be Exported Transporters (SWEETs), along with a potential transcription factor regulating SWEET expression in rice. We observed that drought and salinity stresses increased the sucrose content in leaf and root tissues and in phloem sap of rice indica varieties. Expression analyses of SWEET genes and histochemical analysis of β-glucuronidase-reporter transgenic plants suggested that OsSWEET13 and OsSWEET15 are major SWEET transporters regulating the sucrose transport and levels in response to the abiotic stresses. Transactivation analyses showed that an abscisic acid (ABA)-responsive transcription factor OsbZIP72 directly binds to the promoters of OsSWEET13 and OsSWEET15 and activates their expression. Taken together, the results showed that the higher expressions of OsSWEET13 and OsSWEET15 genes, induced by binding of an ABA-responsive transcription factor OsbZIP72 to the promoters, potentially modulate sucrose transport and distribution in response to the abiotic stresses. The mechanism could possibly be targeted for maintaining sugar homeostasis in rice under drought and salinity stresses.

Genes encoding subunits of the mitochondrial ribosomal protein complex are distributed between the mitochondrial and nuclear genomes. In Arabidopsis thaliana only seven out of the nearly 70 genes coding for mitochondrial ribosomal subunit proteins are present in the mitochondrial genome. Nevertheless, these genes are co-ordinately expressed. Here, we present the first report of characterization of promoter of a plant mitochondrial ribosomal protein gene AtRps19 (At5g47320), a single copy nuclear gene in A. thaliana. Analysis of transgenic A. thaliana plants carrying seven different AtRps19 upstream fragments linked to the uidA reporter gene revealed that the 879 bp fragment containing the 5′ UTR and the intergenic region is capable of driving gene expression in most of the vegetative tissues. However, inclusion of 447 bp of the upstream gene sequences was essential for obtaining full expression in all tissues including anthers and pollen. Thus, we provide the first experimental proof of overlapping genes in plants. qRT-PCR analysis showed that uidA and native AtRps19 transcript levels were comparable in plants carrying the D4 (−676/+650) construct, indicating that the 1326 bp D4 fragment represents the native promoter of the AtRps19 gene. Comparison of AtRps19 promoter with the widely used CaMV35S promoter showed that AtRps19 promoter is capable of driving gene expression in all tissues including anthers and pollen but was less efficient than the CaMV35S promoter.

The importance of increasing photosynthetic efficiency for sustainable crop yield increases to feed the growing world population is well recognized. The natural genetic variation for leaf photosynthesis in crop plants is largely unexploited for increasing genetic yield potential. The genus Oryza, including cultivated rice and wild relatives, offers tremendous genetic variability to explore photosynthetic differences, and underlying biochemical, photochemical, and developmental bases. We quantified leaf photosynthesis and related physiological parameters for six cultivated and three wild rice genotypes, and identified photosynthetically efficient wild rice accessions. Fitting A/Ci curves and biochemical analyses showed that the leaf photosynthesis in cultivated rice varieties, IR64 and Nipponbare, was limited due to leaf nitrogen content, Rubisco activity, and electron transport rate compared to photosynthetically efficient accessions of wild rice Oryza australiensis and Oryza latifolia. The selected wild rice accessions with high leaf photosynthesis per unit area had striking anatomical features, such as larger mesophyll cells with more chloroplasts, fewer mesophyll cells between two consecutive veins, and higher mesophyll cell and chloroplast surface area exposed to intercellular space. Our results show the existence of desirable variations in Rubisco activity, electron transport rate, and leaf anatomical features in the rice system itself that could be targeted for increasing the photosynthetic efficiency of cultivated rice varieties.HighlightDistinct leaf biochemical, photochemical, and developmental features contribute to efficient photosynthesis in the selected wild rice accessions that could potentially be exploited to increase rice leaf photosynthesis.

The Arabidopsis COP1/SPA complex is a key repressor of photomorphogenesis that suppresses light signaling in the dark. Both COP1 and SPA proteins are essential components of this complex. Although COP1 also exists in humans, SPA genes are specific to the green lineage. To elucidate the evolution of SPA genes we analyzed SPA functions in the moss Physcomitrella patens by characterizing knockout mutants in the two Physcomitrella SPA genes PpSPAa and PpSPAb. Light-grown PpspaAB double mutants exhibit smaller gametophores than the wild-type. In the dark, PpspaAB mutant gametophores show enhanced continuation of growth but etiolate normally. Gravitropism in the dark is reduced in PpspaAB mutant protonemata. The expression of light-regulated genes is mostly not constitutive in PpspaAB mutants. PpSPA and PpCOP1 interact; PpCOP1 also interacts with the transcription factor PpHY5 and, indeed, PpHY5 is destabilized in dark-grown Physcomitrella. Degradation of PpHY5 in darkness, however, does not require PpSPAa and PpSPAb. The data suggest that COP1/SPA-mediated light signaling is only partially conserved between Arabidopsis and Physcomitrella. Whereas COP1/SPA interaction and HY5 degradation in darkness is conserved, the role of SPA proteins appears to have diverged. PpSPA genes, unlike their Arabidopsis counterparts, are only required to suppress a subset of light responses in darkness.

Quantitative Trait Locus (QTL) mapping is a powerful technique for dissecting the genetic basis of traits and species differences. Established tomato mapping populations between domesticated tomato (Solanum lycopersicum) and its more distant interfertile relatives typically follow a near isogenic line (NIL) design, such as theSolanum pennelliiIntrogression Line (IL) population, with a single wild introgression per line in an otherwise domesticated genetic background. Here we report on a new advanced backcross QTL mapping resource for tomato, derived from a cross between the M82 tomato cultivar andS. pennelli. This so-called Backcrossed Inbred Line (BIL) population is comprised of a mix ofBC2andBC3lines, with domesticated tomato as the recurrent parent. The BIL population is complementary to the existingS. pennelliiIL population, with which it shares parents. Using the BILs we mapped traits for leaf complexity, leaflet shape, and flowering time. We demonstrate the utility of the BILs for fine-mapping QTL, particularly QTL initially mapped in the ILs, by fine-mapping several QTL to single or few candidate genes. Moreover, we confirm the value of a backcrossed population with multiple introgressions per line, such as the BILs, for epistatic QTL mapping. Our work was further enabled by the development of our own statistical inference and visualization tools, namely a heterogeneous Hidden Markov Model for genotyping the lines, and by using state of the art sparse regression techniques for QTL mapping.

Heteroblasty, the temporal development of the meristem, can produce diverse leaf shapes within a plant. Gevuina avellana, a tree from the South American temperate rainforest shows strong heteroblasty affecting leaf shape, transitioning from juvenile simple leaves to highly pinnate adult leaves. Light availability within the forest canopy also modulates its leaf size and complexity. Here we studied how the interaction between the light environment and the heteroblastic progression of leaves is coordinated in this species. We used RNA-seq on the Illumina platform to compare the range of transcriptional responses in leaf primordia of G. avellana at different heteroblastic stages and growing under different light environments. We found a steady up-regulation of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL), NAC, YUCCA and AGAMOUS-LIKE genes associated with increases in age, leaf complexity, and light availability. In contrast, expression of TCP, TPR and KNOTTED1 homeobox genes showed a sustained down-regulation. Additionally, genes involved in auxin synthesis/transport and jasmonate activity were differentially expressed, indicating an active regulation of processes controlled by these hormones. Our large-scale transcriptional analysis of the leaf primordia of G. avellana sheds light on the integration of internal and external cues during heteroblastic development in this species.

Cassava germplasm collection is important for the preservation of genetic variability, allowing the development of improved cultivars with desirable traits such as drought and disease tolerance, better starch quality and yield. Therefore, the assessment of diversity in cassava germplasm maintained by farmers is important for maintaining biodiversity and crop improvement. Herein, we report genetic diversity relationships of 52 farmer-preferred cassava landraces from the eastern zone of Tanzania based on morphological descriptors and single nucleotide polymorphisms (SNPs). Cluster analysis was performed for both morphological traits (genetic distance 1.18–0.15) and SNPs (genetic distance 0.078–0.002). The analysis revealed that there were a total of 17,393 variant positions, and that several of the SNPs were distributed across all the chromosomes. The abundance of SNP varied remarkably among the 18 cassava chromosomes, with chromosome 2 having the highest number of SNPs (1335) and chromosome 18 having the lowest number of SNPs (734). The power of SNPs in distinguishing morphologically similar landraces was shown. Both analyses did not group landraces according to geographical locations, suggesting that farmers were moving cassava germplasm to different areas. Their diversity was mainly due to adaptation and preferential selection by farmers. This further implied that within a geographical location, the cultivars were more diverse and there was no misnaming of cassava cultivars by farmers. The collection revealed a wide range of genetic diversity, and represented a valuable resource for trait improvement, allowing the capture of farmer-preferred traits in future cassava breeding programmes.

Light and temperature are two of the most important environmental stimuli regulating plant growth and development. While majority of the studies so far investigated light and temperature signaling in isolation, an understanding of the interaction of the two pathways is essential to generate a holistic view of plant responses to environmental cues. Recent studies have demonstrated significant overlap between the two signaling pathways at the molecular level to optimize plant growth as evident by involvement of phytochromes and downstream transcription factors in both the pathways. Plants respond to limited light availability and high ambient temperature via similar phenotypic response, such as stem elongation. Moreover, the existence of shared signaling components, such as common plant hormones and transcription factors, for the two pathways has also been deciphered. Together, the studies showing a significant overlap between light and temperature signaling cascades at the molecular level that involves an array of transcription factors and phytohormone-related genes suggest a complex cross talk between the two signaling pathways, which is fundamental to plant growth in natural environments.

Stomatal development is tightly regulated through internal and external factors that are integrated by a complex signalling network. Light represents an external factor that strongly promotes stomata formation. Here, we show that auxin-resistant aux/iaa mutants, e.g. axr3-1, exhibit a de-repression of stomata differentiation in dark-grown seedlings. The higher stomatal index in dark-grown axr3-1 mutants when compared with the wild type is due to increased cell division in the stomatal lineage. Excessive stomata in dark-grown seedlings were also observed in mutants defective in auxin biosynthesis or auxin perception and in seedlings treated with the polar auxin transport inhibitor NPA. Consistent with these findings, exogenous auxin repressed stomata formation in light-grown seedlings. Taken together, these results indicate that auxin is a negative regulator of stomatal development in dark-grown seedlings. Epistasis analysis revealed that axr3-1 acts genetically upstream of the bHLH transcription factors SPCH, MUTE and FAMA, as well as the YDA MAP kinase cascade, but in parallel with the repressor of photomorphogenesis COP1 and the receptor-like protein TMM. The effect of exogenous auxin required the ER family of leucine-rich repeat receptor-like kinases, suggesting that auxin acts at least in part through the ER family. Expression of axr3-1 in the stomatal lineage was insufficient to alter the stomatal index, implying that cell-cell communication is necessary to mediate the effect of auxin. In summary, our results show that auxin signalling contributes to the suppression of stomatal differentiation observed in dark-grown seedlings.

Parasitic flowering plants are one of the most destructive agricultural pests and have major impact on crop yields throughout the world. Being dependent on finding a host plant for growth, parasitic plants penetrate their host using specialized organs called haustoria. Haustoria establish vascular connections with the host, which enable the parasite to steal nutrients and water. The underlying molecular and developmental basis of parasitism by plants is largely unknown. In order to investigate the process of parasitism, RNAs from different stages (i.e. seed, seedling, vegetative strand, prehaustoria, haustoria, and flower) were used to de novo assemble and annotate the transcriptome of the obligate plant stem parasite dodder (Cuscuta pentagona). The assembled transcriptome was used to dissect transcriptional dynamics during dodder development and parasitism and identified key gene categories involved in the process of plant parasitism. Host plant infection is accompanied by increased expression of parasite genes underlying transport and transporter categories, response to stress and stimuli, as well as genes encoding enzymes involved in cell wall modifications. By contrast, expression of photosynthetic genes is decreased in the dodder infective stages compared with normal stem. In addition, genes relating to biosynthesis, transport, and response of phytohormones, such as auxin, gibberellins, and strigolactone, were differentially expressed in the dodder infective stages compared with stems and seedlings. This analysis sheds light on the transcriptional changes that accompany plant parasitism and will aid in identifying potential gene targets for use in controlling the infestation of crops by parasitic weeds.

Terroir, the unique interaction between genotype, environment, and culture, is highly refined in domesticated grape (Vitis vinifera). Toward cultivating terroir, the science of ampelography tried to distinguish thousands of grape cultivars without the aid of genetics. This led to sophisticated phenotypic analyses of natural variation in grape leaves, which within a palmate-lobed framework exhibit diverse patterns of blade outgrowth, hirsuteness, and venation patterning. Here, we provide a morphometric analysis of more than 1,200 grape accessions. Elliptical Fourier descriptors provide a global analysis of leaf outlines and lobe positioning, while a Procrustes analysis quantitatively describes venation patterning. Correlation with previous ampelography suggests an important genetic component, which we confirm with estimates of heritability. We further use RNA-Seq of mutant varieties and perform a genome-wide association study to explore the genetic basis of leaf shape. Meta-analysis reveals a relationship between leaf morphology and hirsuteness, traits known to correlate with climate in the fossil record and extant species. Together, our data demonstrate a genetic basis for the intricate diversity present in grape leaves. We discuss the possibility of using grape leaves as a breeding target to preserve terroir in the face of anticipated climate change, a major problem facing viticulture.

A number of plant features and traits, such as overall plant architecture, leaf structure and morphological features, vascular architecture and flowering time are important determinants of photosynthetic efficiency and hence the overall performance of crop plants. The optimization of such developmental traits thus has great potential to increase biomass and crop yield. Here, we provide a comprehensive review of these developmental traits in crop plants, summarizing their genetic regulation and highlighting the potential of manipulating these traits for crop improvement. We also briefly review the effects of domestication on the developmental features of crop plants. Finally, we discuss the potential of functional genomics-based approaches to optimize plant developmental traits to increase yield.

Variation in gene expression, in addition to sequence polymorphisms, is known to influence developmental, physiological and metabolic traits in plants. Genetic mapping populations have facilitated identification of expression Quantitative Trait Loci (eQTL), the genetic determinants of variation in gene expression patterns. We used an introgression population developed from the wild desert-adaptedSolanum pennelliiand domesticated tomatoSolanum lycopersicumto identify the genetic basis of transcript level variation. We established the effect of each introgression on the transcriptome, and identified ~7,200 eQTL regulating the steady state transcript levels of 5,300 genes. Barnes-Hutt-distributed stochastic neighbor embedding clustering identified 42 modules revealing novel associations between transcript level patterns and biological processes. The results showed a complex genetic architecture of global transcript abundance pattern in tomato. Several genetic hotspots regulating a large number of transcript level patterns relating to diverse biological processes such as plant defense and photosynthesis were identified. Important eQTL regulating transcript level patterns were related to leaf number and complexity, and hypocotyl length. Genes associated with leaf development showed an inverse correlation with photosynthetic gene expression but eQTL regulating genes associated with leaf development and photosynthesis were dispersed across the genome. This comprehensive expression QTL analysis details the influence of these loci on plant phenotypes, and will be a valuable community resource for investigations on the genetic effects of eQTL on phenotypic traits in tomato.

For the realization of face recognition systems in the static as well as in the real time frame, algorithms such as principal component analysis, independent component analysis, linear discriminate analysis, neural networks and genetic algorithms are used for decades. This paper discusses an approach which is a wavelet decomposition based principal component analysis for face recognition. Principal component analysis is chosen over other algorithms due to its relative simplicity, efficiency, and robustness features. The term face recognition stands for identifying a person from his facial gestures and having resemblance with factor analysis in some sense, i.e. extraction of the principal component of an image. Principal component analysis is subjected to some drawbacks, mainly the poor discriminatory power and the large computational load in finding eigenvectors, in particular. These drawbacks can be greatly reduced by combining both wavelet transform decomposition for feature extraction and principal component analysis for pattern representation and classification together, by analyzing the facial gestures into space and time domain, where, frequency and time are used interchangeably. From the experimental results, it is envisaged that this face recognition method has made a significant percentage improvement in recognition rate as well as having a better computational efficiency.

In a majority of species, leaf development is thought to proceed in a bilaterally symmetric fashion without systematic asymmetries. This is despite the left and right sides of an initiating primordium occupying niches that differ in their distance from sinks and sources of auxin. Here, we revisit an existing model of auxin transport sufficient to recreate spiral phyllotactic patterns and find previously overlooked asymmetries between auxin distribution and the centers of leaf primordia. We show that it is the direction of the phyllotactic spiral that determines the side of the leaf these asymmetries fall on. We empirically confirm the presence of an asymmetric auxin response using a DR5 reporter and observe morphological asymmetries in young leaf primordia. Notably, these morphological asymmetries persist in mature leaves, and we observe left-right asymmetries in the superficially bilaterally symmetric leaves of tomato (Solanum lycopersicum) and Arabidopsis thaliana that are consistent with modeled predictions. We further demonstrate that auxin application to a single side of a leaf primordium is sufficient to recapitulate the asymmetries we observe. Our results provide a framework to study a previously overlooked developmental axis and provide insights into the developmental constraints imposed upon leaf morphology by auxin-dependent phyllotactic patterning.

Light is an essential resource for photosynthesis. Limitation of light by shade from plant neighbors can induce a light competition program known as the shade avoidance response (SAR), thereby altering plant growth and development for the sake of survival. Natural genetic variation in SAR is found in plants adapted to distinct environments, including domesticated tomato Solanum lycopersicum and its wild relative Solanum pennellii. QTL mapping was used to examine variation of the SAR between these two species. We found organ specific responses in the elongation of the stem and petiole, including developmental acceleration of growth. Through RNAseq analysis we identified a number of ILs with reduced expression of auxin-related genes in shade treatment. These same ILs display a shade tolerant phenotype in stem growth and overall height. We also identified ILs with altered SAR expression of cell wall expansion genes, although these genotypes had no accompanying alteration in phenotype. Examination of weighted gene co-expression connectivity networks in sun- and shade-treated plants revealed connectivity changes in auxin and light signaling genes; this result was supported by the identification of motifs within the promoters of a subset of shade-responsive genes that were enriched in light signaling, developmental pathways, and auxin responsive transcriptional domains. The identification of both systemic and organ-specific shade tolerance in the ILs, as well as associated changes in the transcriptome, has the potential to inform future studies for breeding plants able to be grown closely (while neighbor-shaded), yet still maintaining high yield.

Plants sense the foliar shade of competitors and alter their developmental programs through the shade-avoidance response. Internode and petiole elongation, and changes in overall leaf area and leaf mass per area, are the stereotypical architectural responses to foliar shade in the shoot. However, changes in leaf shape and complexity in response to shade remain incompletely, and qualitatively, described. Using a meta-analysis of more than 18,000 previously published leaflet outlines, we demonstrate that shade avoidance alters leaf shape in domesticated tomato (Solanum lycopersicum) and wild relatives. The effects of shade avoidance on leaf shape are subtle with respect to individual traits but are combinatorially strong. We then seek to describe the developmental origins of shade-induced changes in leaf shape by swapping plants between light treatments. Leaf size is light responsive late into development, but patterning events, such as stomatal index, are irrevocably specified earlier. Observing that shade induces increases in shoot apical meristem size, we then describe gene expression changes in early leaf primordia and the meristem using laser microdissection. We find that in leaf primordia, shade avoidance is not mediated through canonical pathways described in mature organs but rather through the expression of KNOTTED1-LIKE HOMEOBOX and other indeterminacy genes, altering known developmental pathways responsible for patterning leaf shape. We also demonstrate that shade-induced changes in leaf primordium gene expression largely do not overlap with those found in successively initiated leaf primordia, providing evidence against classic hypotheses that shaded leaf morphology results from the prolonged production of juvenile leaf types.

Heteroblasty, the temporal development of the meristem, can produce diverse leaf shapes within a plant. Gevuina avellana, a tree from the South American temperate rainforest shows strong heteroblasty affecting leaf shape, transitioning from juvenile simple leaves to highly pinnate adult leaves. Light availability within the forest canopy also modulates its leaf size and complexity. Here we studied how the interaction between the light environment and the heteroblastic progression of leaves is coordinated in this species. We used RNA-seq on the Illumina platform to compare the range of transcriptional responses in leaf primordia of G. avellana at different heteroblastic stages and growing under different light environments. We found a steady up-regulation of SQUAMOSA PROMOTER BINDING PROTEIN LIKE (SPL), NAC, YUCCA and AGAMOUS-LIKE genes associated with increases in age, leaf complexity, and light availability. In contrast, expression of TCP, TPR and KNOTTED1 homeobox genes showed a sustained down-regulation. Additionally, genes involved in auxin synthesis/transport and jasmonate activity were differentially expressed, indicating an active regulation of processes controlled by these hormones. Our large-scale transcriptional analysis of the leaf primordia of G. avellana sheds light on the integration of internal and external cues during heteroblastic development in this species.

Convergent morphologies have arisen in plants multiple times. In non-vascular and vascular land plants, convergent morphology in the form of roots, stems, and leaves arose. The morphology of some green algae includes an anchoring holdfast, stipe, and leaf-like fronds. Such morphology occurs in the absence of multicellularity in the siphonous algae, which are single cells. Morphogenesis is separate from cellular division in the land plants, which although are multicellular, have been argued to exhibit properties similar to single celled organisms. Within the single, macroscopic cell of a siphonous alga, how are transcripts partitioned, and what can this tell us about the development of similar convergent structures in land plants? Here, we present a de novo assembled, intracellular transcriptomic atlas for the giant coenocyte Caulerpa taxifolia. Transcripts show a global, basal-apical pattern of distribution from the holdfast to the frond apex in which transcript identities roughly follow the flow of genetic information in the cell, transcription-to-translation. The analysis of the intersection of transcriptomic atlases of a land plant and Caulerpa suggests the recurrent recruitment of transcript accumulation patterns to organs over large evolutionary distances. Our results not only provide an intracellular atlas of transcript localization, but also demonstrate the contribution of transcript partitioning to morphology, independent from multicellularity, in plants., Author Summary Plants include both the green algae and land plants. Multiple times, root, stem, and leaf-like structures arose independently in plant lineages. In some instances, such as the siphonous algae, these structures arose in the absence of multicellularity. It has been argued by some that the morphology of multicellular land plant organs similarly arises independently of cell division patterns. Here, we explore the partitioning of gene transcripts within what is debatably the largest single-celled organism in the world, the siphonous alga Caulerpa taxifolia. We find that within this giant cell specific transcripts localize within pseudo-organs (morphological structures that are not comprised of cells or tissue). The overall pattern of transcript accumulation follows an apical-basal pattern within the cell. Moreover, transcripts related to different cellular processes, such as transcription and translation, localize to specific regions. Analyzing the signatures of transcript accumulation in land plant organs and the pseudo-organs of Caulerpa, we find that groups of transcripts accumulate together in morphological structures across evolution at rates higher than expected by chance. Together, our results demonstrate a relationship between transcript partitioning and organism morphology, independent from multicellularity, throughout diverse plant lineages.

Flexible Manufacturing Cell (FMC) has been adopted as means to curb cycle time, increase productivity and improve product quality. One of the most crucial decisions that severely affect the design of FMC is selection of machines. In resolving the machine selection issues, a decision‐maker has to consider number of attributes such as type of machines, its costs, size of floor surface area, productivity etc. This article aims to develop a fuzzy based MADM approach to assist a decision maker in solving machine selection problem for a given FMC in a most pragmatic way. Adoption of an appropriate rating methodology empowers the decision‐maker to assign different importance to the various attributes. The proposed approach is exemplified by a case study reported in literature.

Sustainability in livestock production system is mostly affected by climate change. Climate change affects various factors associated with production, reproduction, heath and adaptability of the animals. Dairy sector is more susceptible to climate change. The temperature humidity index (THI) is the widely used as index to measurement of thermal stress in animals. Environmental stress has adverse effects on health status of dairy animals and decreases the milk production and reproductive performance of dairy cows resulting in huge economic losses. Global climate change is expected to alter temperature, humidity, rainfall, atmospheric carbon dioxide. The dairy sector is a more susceptible to climate change and global warming where it is mostly affected by the temperature and humidity such as temperature humidity index (THI). Combined effect of high ambient temperature and high humidity results adverse effect on reproductive performance of farm animals. The management strategies viz., microclimatic modification, nutritional management, feeding strategies and artificial insemination protocol are to be strictly followed to ameliorate the adverse effects of heat stress in dairy animals.

Leaf shape is mutable, changing in ways modulated by both development and environment within genotypes. A complete model of leaf phenotype would incorporate the changes in leaf shape during juvenile-to-adult phase transitions and the ontogeny of each leaf. Here, we provide a morphometric description of >33,000 leaflets from a set of tomato (Solanum spp) introgression lines grown under controlled environment conditions. We first compare the shape of these leaves, arising during vegetative development, with >11,000 previously published leaflets from a field setting and >11,000 leaflets from wild tomato relatives. We then quantify the changes in shape, across ontogeny, for successive leaves in the heteroblastic series. Using principal component analysis, we then separate genetic effects modulating (1) the overall shape of all leaves versus (2) the shape of specific leaves in the series, finding the former more heritable than the latter and comparing quantitative trait loci regulating each. Our results demonstrate that phenotype is highly contextual and that unbiased assessments of phenotype, for quantitative genetic or other purposes, would ideally sample the many developmental and environmental factors that modulate it.

Background: Plants have evolved light sensing mechanisms to optimally adapt their growth and development to the ambient light environment. The COP1/SPA complex is a key negative regulator of light signaling in the well-studied dicot Arabidopsis thaliana. COP1 and members of the four SPA proteins are part of an E3 ubiquitin ligase that acts in darkness to ubiquitinate several transcription factors involved in light responses, thereby targeting them for degradation by the proteasome. While COP1 is also found in humans, SPA proteins appear specific to plants. Here, we have functionally addressed evolutionary conservation of COP1 and SPA orthologs from the moss Physcomitrella, the monocot rice and the dicot Arabidopsis. Results: To this end, we analyzed the activities of COP1- and SPA-like proteins from Physcomitrella patens and rice when expressed in Arabidopsis. Expression of r ice COP1 and Physcomitrella COP1 protein sequences predominantly complemented all phenotypic aspects of the viable, hypomorphic cop1-4 mutant and the null, seedling-lethal cop1-5 mutant of Arabidopsis: rice COP1 fully rescued the constitutive-photomorphogenesis phenotype in darkness and the leaf expansion defect of cop1 mutants, while it partially restored normal photoperiodic flowering in cop1. Physcomitrella COP1 partially restored normal seedling growth and flowering time, while it fully restored normal leaf expansion in the cop1 mutants. In contrast, expression of a SPA ortholog from Physcomitrella (PpSPAb) in Arabidopsis spa mutants did not rescue any facet of the spa mutant phenotype, suggesting that the PpSPAb protein is not functionally conserved or that the Arabidopsis function evolved after the split of mosses and seed plants. The SPA1 ortholog from rice (OsSPA1) rescued the spa mutant phenotype in dark-grown seedlings, but did not complement any spa mutant phenotype in light-grown seedlings or in adult plants. Conclusion: Our results show that COP1 protein sequences from Physcomitrella, rice and Arabidopsis have been functionally conserved during evolution, while the SPA proteins showed considerable functional divergence. This may -a t least in part -r eflect the fact thatCOP1 is a single copy gene in seed plants, while SPA proteins are encoded by a small gene family of two to four members with possibly sub- or neofunctionalized tasks.