Plant Agronomic Traits Research Articles

Diversification of plant agronomic traits by genome editing of brassinosteroid signaling family genes in rice.

Brassinosteroids (BRs) regulate various agronomic traits such as plant height, leaf angle, and grain size in rice (Oryza sativa L.); thus, BR signaling components are promising targets for molecular rational design. However, genetic materials for BR-signaling genes or family members remain limited in rice. Here, by genome editing using clustered regularly interspaced short palindromic repeats (CRSPR)/Cas9tools, we generated a panel of single, double, triple, or quadruple mutants within three BR signaling gene families, including GSK3/SHAGGY-LIKE KINASE1 (GSK1)-GSK4, BRASSINAZOLE-RESISTANT1 (OsBZR1)-OsBZR4, and protein phosphatases with kelch-like (PPKL)1-PPKL3, under the same background (Zhonghua11, japonica). The high-order mutants were produced by either simultaneously targeting multiple sites on different genes of one family (GSKs and PPKLs) or targeting the overlapping sequences of family members (OsBZRs). The mutants exhibited a diversity of plant height, leaf angle, and grain morphology. Comparison analysis of the phenotypes together with BR sensitivity tests suggested the existence of functional redundancy, differentiation, or dominancy among the members within each family. In addition, we generated a set of transgenic plants overexpressing GSK2, OsBZR1/2, and PPKL2, respectively, in wild-type or activated forms with fusion of different tags, and also verified the protein response to BR application. Collectively, these plants greatly enriched the diversity of important agronomic traits in rice. We propose that editing of BR-related family genes could be a feasible approach for screening of desired plants to meet different requirements. Release of these materials as well as the related information also provides valuable resources for further BR research and utilization.

Specific-Locus Amplified Fragment Sequencing (SLAF-Seq) as High-Throughput SNP Genotyping Methods.

Most plant agronomic traits are quantitatively inherited. Identification of quantitative trait loci (QTL) is a challenging target for most scientists and crop breeders as large-scale genotyping is difficult. Molecular marker technology has continuously evolved from hybridization-based technology to PCR-based technology, and finally, sequencing-based high-throughput single-nucleotide polymorphisms (SNPs). High-throughput sequencing technologies can provide strategies for sequence-based SNP genotyping. Here we describe the SLAF-seq that can be applied as the SNP genotyping approach. The high-throughput SNP genotyping methods will prove useful for the construction of high-density genetic maps and identification of QTLs for their deployment in plant breeding and facilitate genome-wide selection (GWS) and genome-wide association studies (GWAS).

Capsicum annuum (hot pepper): An ancient Latin-American crop with outstanding bioactive compounds and nutraceutical potential. A review.

Hot pepper (Capsicum annuum) fruits, usually termed as chili, have been used since ancient times as food vegetables, flavoring ingredients, natural colorants, and in traditional medicines. Nowadays, a wide variation of sweet and pungent peppers are consumed worldwide in a large variety of forms. Interestingly, the most important hot pepper at the global level in commercial terms is C. annuum with a high number of varieties. This review compares C. annuum to other Capsicum species for plant agronomic traits, biochemical composition, the content of capsaicin and capsaicinoids and their nutraceutical and medical potentialities, and the effects of processing on quality and key components of the fruit, among other aspects. Chili contains important levels of pigments (i.e., chlorophyll, anthocyanin, and lutein) with potential health benefits; it also contains additional outstanding health-promoting chemical compounds, such as vitamins, minerals, flavonoids, carotenoids, and capsaicinoids, in general. And capsaicin, the major active compound responsible for the pungent taste of these species has been proven to have a positive role in health. We report here on how dietary chili and capsaicinoids consumption, especially capsaicin, are involved in body weight reduction and their potential antiobesity effects, in urinary disorders, as well as antioxidants, antimicrobial, anticancer, and analgesic capacity. Selected characteristics of processing for the fruit preservation on its quality and content of these compounds are described as well. However, additional clinical research on the mechanism of action and efficacy of frequent capsaicinoid consumption on human health is needed.

Application of Reverse Genetics in Functional Genomics of Potyvirus.

Numerous potyvirus studies, including virus biology, transmission, viral protein function, as well as virus–host interaction, have greatly benefited from the utilization of reverse genetic techniques. Reverse genetics of RNA viruses refers to the manipulation of viral genomes, transfection of the modified cDNAs into cells, and the production of live infectious progenies, either wild-type or mutated. Reverse genetic technology provides an opportunity of developing potyviruses into vectors for improving agronomic traits in plants, as a reporter system for tracking virus infection in hosts or a production system for target proteins. Therefore, this review provides an overview on the breakthroughs achieved in potyvirus research through the implementation of reverse genetic systems.

Accumulation potential and tolerance response of Typha latifolia L. under citric acid assisted phytoextraction of lead and mercury

Chelate-assisted phytoextraction by high biomass producing macrophyte plant Typha latifolia L. commonly known as cattail, is gaining much attention worldwide. The present study investigated the effects of Lead (Pb) and Mercury (Hg) on physiology and biochemistry of plant, Pb and Hg uptake in T. latifolia with and without citric acid (CA) amendment. The uniform seedlings of T. latifolia were treated with various concentrations in the hydroponics as: Pb and Hg (1, 2.5, 5 mM) each alone and/or with CA (5 mM). After four weeks of treatments, the results revealed that Pb and Hg significantly reduced the plant agronomic traits as compare to non-treated plants. The addition of CA improved the plant physiology and enhanced the antioxidant enzymes activities to overcome Pb and Hg induced oxidative damage and electrolyte leakage. Our results depicted that Pb and Hg uptake and accumulation by T. latifolia was dose depend whereas, the addition of CA further increased the concentration and accumulation of Pb and Hg by up to 22 & 35% Pb and 72 & 40% Hg in roots, 25 & 26% Pb and 85 & 60% Hg in stems and 22 & 15 Pb and 100 & 58% Hg in leaves respectively compared to Pb and Hg treated only plants. On other hand, the root-shoot translocation factor was ≥1 and bioconcentration factor was also ≥2 for both Pb & Hg. The results also revealed that T. latifolia showed greater tolerance towards Hg and accumulated higher Hg in all parts compared with Pb.

Decoding Plant-Environment Interactions That Influence Crop Agronomic Traits.

To ensure food security in the face of increasing global demand due to population growth and progressive urbanization, it will be crucial to integrate emerging technologies in multiple disciplines to accelerate overall throughput of gene discovery and crop breeding. Plant agronomic traits often appear during the plants’ later growth stages due to the cumulative effects of their lifetime interactions with the environment. Therefore, decoding plant–environment interactions by elucidating plants’ temporal physiological responses to environmental changes throughout their lifespans will facilitate the identification of genetic and environmental factors, timing and pathways that influence complex end-point agronomic traits, such as yield. Here, we discuss the expected role of the life-course approach to monitoring plant and crop health status in improving crop productivity by enhancing the understanding of plant–environment interactions. We review recent advances in analytical technologies for monitoring health status in plants based on multi-omics analyses and strategies for integrating heterogeneous datasets from multiple omics areas to identify informative factors associated with traits of interest. In addition, we showcase emerging phenomics techniques that enable the noninvasive and continuous monitoring of plant growth by various means, including three-dimensional phenotyping, plant root phenotyping, implantable/injectable sensors and affordable phenotyping devices. Finally, we present an integrated review of analytical technologies and applications for monitoring plant growth, developed across disciplines, such as plant science, data science and sensors and Internet-of-things technologies, to improve plant productivity.

Citric acid enhanced phytoextraction of nickel (Ni) and alleviate Mentha piperita (L.) from Ni-induced physiological and biochemical damages.

Phytoremediation is considered one of the well-established and sustainable techniques for the removal of heavy metals and metalloids from contaminated sites. The metal extraction ability of the plants can be enhanced by using suitable organic materials in combination with metal-tolerant plants. This experiment was carried out to investigate the phytoextraction potential of Mentha piperita L. for nickel (Ni) with and without citric acid (CA) amendment in hydroponic experiment. The experiment was performed in controlled glass containers with continuous aeration in complete randomized design (CRD). Juvenile M. piperita plants were treated with different concentrations of Ni (100, 250, and 500μM) alone and/or combined with CA (5mM). After harvesting the plants, the morpho-physiological and biochemical attributes as well as Ni concentrations in different tissues of M. piperita plants were measured. Results revealed that Ni stress significantly decreased the plant agronomic traits, photosynthesis in comparison to control. Nickel stress enhanced the antioxidant enzymes activities and caused the production of reactive oxygen species (ROS) in M. piperita. The CA treatment under Ni stress significantly improved the plant morpho-physiological and biochemical characteristics when compared with Ni treatments alone. The results demonstrated that CA enhanced the Ni concentrations in roots, stems, and leaves up to 138.2%, 54.2%, and 38%, respectively, compared to Ni-only-treated plants. The improvement in plant growth with CA under Ni stress indicated that CA is beneficial for Ni phytoextraction by using tolerant plant species. Graphical abstract.

Differential Effects of Day/Night Cues and the Circadian Clock on the Barley Transcriptome

The circadian clock is a complex transcriptional network that regulates gene expression in anticipation of the day/night cycle and controls agronomic traits in plants. However, in crops, how the internal clock and day/night cues affect the transcriptome remains poorly understood. We analyzed the diel and circadian leaf transcriptomes in the barley (Hordeum vulgare) cultivar 'Bowman' and derived introgression lines harboring mutations in EARLY FLOWERING3 (ELF3), LUX ARRHYTHMO1 (LUX1), and EARLY MATURITY7 (EAM7). The elf3 and lux1 mutants exhibited abolished circadian transcriptome oscillations under constant conditions, whereas eam7 maintained oscillations of ≈30% of the circadian transcriptome. However, day/night cues fully restored transcript oscillations in all three mutants and thus compensated for a disrupted oscillator in the arrhythmic barley clock mutants elf3 and lux1 Nevertheless, elf3, but not lux1, affected the phase of the diel oscillating transcriptome and thus the integration of external cues into the clock. Using dynamical modeling, we predicted a structure of the barley circadian oscillator and interactions of its individual components with day/night cues. Our findings provide a valuable resource for exploring the function and output targets of the circadian clock and for further investigations into the diel and circadian control of the barley transcriptome.

Efficacy of Alternanthera bettzickiana to Remediate Copper and Cobalt Contaminated Soil Physiological and Biochemical Alterations

Increasing world population triggers intensive agricultural practices responsible for higher heavy metal contamination of soil and water. The present study was conducted to evaluate the morpho-physiological and biochemical response along with phytoextraction potential of Alternanthera bettzickiana for cobalt (Co) and copper (Cu) contaminated soil. Healthy and uniform plants of A. bettzickiana were collected and placed in pots each filled with 5 kg of sandy loam soil. Plants were treated with different concentrations of Cu and Co (2.5, 5, 7.5, and 10 mM). After 8 weeks of treatments, plant agronomic traits such as plant growth, biomass, chlorophyll content, and activities of antioxidant enzymes were measured and results revealed no visual signs of toxicity whereas all characteristics were enhanced as compared to control plants except 10 mM where it significantly decreased the plant’s morpho-physiological and biochemical characteristics. Further, Cu and Co concentration and accumulation in all parts of plants significantly increased with increasing concentration of applied heavy metal. The plants significantly accumulate 2.1 and 2.0 times more Cu in shoots and 1.5 and 1.2 times more Co in roots as compared to controls. The results concluded that A. bettzickiana is a potential hyperaccumulator and halophyte of Co and Cu therefore it can be a potential candidate for the remediation of Cu and Co contaminated sites.

Light Stress Responses and Prospects for Engineering Light Stress Tolerance in Crop Plants

Light constitutes one of the most important environmental factors for plant growth and development. It determines the photosynthetic rate and accumulate-assimilation besides its regulatory roles in plant growth and productivity. However, plants are frequently exposed to excess or inadequate light intensities and these fluctuations, collectively known as light stress, affect the agronomic traits in plants via inhibiting their physiological metabolic processes including photosynthesis, antioxidant machinery, and their abilities to fix atmospheric carbon and nitrogen. Within the photosynthetic machinery, photosystem II (PSII) and its reaction centers are particularly sensitive to these perturbations and have therefore been characterized as primary targets of light stress at physiological, biochemical, and molecular levels including microRNA (miRNA)-mediated post-transcriptional modifications. Through this review, we are presenting herein the current knowledge and recent updates on light stress and its significance for plant growth and crop yields, plant responses, and multilevel adaptation strategies to cope up with light stress including excess and low light. The review highlights and assesses the utilization of biotechnological tools for engineering light stress tolerance in major crops and model plants including omics and transgenic approaches and exploration of molecular markers and quantitative trait loci. The roles of miRNAs in regulation of light stress responses and adaptive mechanisms in plants have been discussed besides emphasizing on possible exploration of light-regulated miRNAs as potential targets for engineering light stress tolerance in crop plants.

Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.)

BackgroundRamie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known.ResultsA genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P < 0.01. The favorable SNP Marker20170–64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F1 hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170–64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie.ConclusionsThe identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.

N6-Methyladenine DNA Methylation in Japonica and Indica Rice Genomes and Its Association with Gene Expression, Plant Development, and Stress Responses

N6-Methyladenine (6mA) DNA methylation has recently been implicated as a potential new epigenetic marker in eukaryotes, including the dicot model Arabidopsis thaliana. However, the conservation and divergence of 6mA distribution patterns and functions in plants remain elusive. Here we report high-quality 6mA methylomes at single-nucleotide resolution in rice based on substantially improved genome sequences of two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica). Analysis of 6mA genomic distribution and its association with transcription suggest that 6mA distribution and function is rather conserved between rice and Arabidopsis. We found that 6mA levels are positively correlated with the expression of key stress-related genes, which may be responsible for the difference in stress tolerance between Nip and 93-11. Moreover, we showed that mutations in DDM1 cause defects in plant growth and decreased 6mA level. Our results reveal that 6mA is a conserved DNA modification that is positively associated with gene expression and contributes to key agronomic traits in plants.

Simple Sequence Repeat (SSR) Genetic Linkage Map of D Genome Diploid Cotton Derived from an Interspecific Cross between Gossypium davidsonii and Gossypium klotzschianum.

The challenge in tetraploid cotton cultivars is the narrow genetic base and therefore, the bottleneck is how to obtain interspecific hybrids and introduce the germplasm directly from wild cotton to elite cultivars. Construction of genetic maps has provided insight into understanding the genome structure, interrelationships between organisms in relation to evolution, and discovery of genes that carry important agronomic traits in plants. In this study, we generated an interspecific hybrid between two wild diploid cottons, Gossypium davidsonii and Gossypium klotzschianum, and genotyped 188 F2:3 populations in order to develop a genetic map. We screened 12,560 SWU Simple Sequence Repeat (SSR) primers and obtained 1000 polymorphic markers which accounted for only 8%. A total of 928 polymorphic primers were successfully scored and only 728 were effectively linked across the 13 chromosomes, but with an asymmetrical distribution. The map length was 1480.23 cM, with an average length of 2.182 cM between adjacent markers. A high percentage of the markers on the map developed, and for the physical map of G. raimondii, exhibited highly significant collinearity, with two types of duplication. High level of segregation distortion was observed. A total of 27 key genes were identified with diverse roles in plant hormone signaling, development, and defense reactions. The achievement of developing the F2:3 population and its genetic map constructions may be a landmark in establishing a new tool for the genetic improvement of cultivars from wild plants in cotton. Our map had an increased recombination length compared to other maps developed from other D genome cotton species.

Construction and application of functional gene modules to regulatory pathways in rice

Signal transduction and transcriptional regulation pathways are key elements in the control of diverse physiological responses and agronomic traits in plants. The regulatory roles of more than 1,000 known genes have been functionally characterized in rice, a model crop plant, and many of them are associated with transcriptional regulation and signal transduction pathways. In this study, we collected and analyzed 417 known genes associated with regulatory pathways, about 40% of the known genes, using the regulation overview installed in the MapMan toolkit. Connecting novel genes to current knowledge about regulatory pathways can elucidate their molecular functions and inspire ideas for further applications. We have summarized the functions of known regulatory genes in the areas of transcriptional regulation, epigenetic regulation, protein modification, protein degradation, signaling and hormone metabolism, also we have emphasized the unique features of several gene families in these classes, including MADS box families, which are strongly associated with the regulation of floral organ identity and flowering time. In addition, our construction of functional modules in four agronomic categories, morphological, physiological, biotic stress and abiotic stress, suggests a basic framework for expanding current knowledge about regulatory pathways to enhance agronomic traits in rice. We also provide a quick illustration of the positive and negative regulatory relationships of the target gene to manipulate agronomic trait by using genome-wide transcriptome data of knockout or overexpression mutations of genes of interest in each functional module.

Development of “Purple Endosperm Rice” by Engineering Anthocyanin Biosynthesis in the Endosperm with a High-Efficiency Transgene Stacking System

Anthocyanins have high antioxidant activities, and engineering of anthocyanin biosynthesis in staple crops, such as rice (Oryza sativa L.), could provide health-promoting foods for improving human health. However, engineering metabolic pathways for biofortification remains difficult, and previous attempts to engineer anthocyanin production in rice endosperm failed because of the sophisticated genetic regulatory network of its biosynthetic pathway. In this study, we developed a high-efficiency vector system for transgene stacking and used it to engineer anthocyanin biosynthesis in rice endosperm. We made a construct containing eight anthocyanin-related genes (two regulatory genes from maize and six structural genes from Coleus) driven by the endosperm-specific promoters,plus a selectable marker and a gene for marker excision. Transformation of rice with this construct generated a novel biofortified germplasm “Purple Endosperm Rice” (called “Zijingmi” in Chinese), which has high anthocyanin contents and antioxidant activity in the endosperm. This anthocyanin production results from expression of the transgenes and the resulting activation (or enhancement) of expression of 13 endogenous anthocyanin biosynthesis genes that are silenced or expressed at low levels in wild-type rice endosperm. This study provides an efficient, versatile toolkit for transgene stacking and demonstrates its use for successful engineering of a sophisticated biological pathway, suggesting the potential utility of this toolkit for synthetic biology and improvement of agronomic traits in plants.

Identification of QTLs for 14 Agronomically Important Traits in Setaria italica Based on SNPs Generated from High-Throughput Sequencing.

Foxtail millet (Setaria italica) is an important crop possessing C4 photosynthesis capability. The S. italica genome was de novo sequenced in 2012, but the sequence lacked high-density genetic maps with agronomic and yield trait linkages. In the present study, we resequenced a foxtail millet population of 439 recombinant inbred lines (RILs) and developed high-resolution bin map and high-density SNP markers, which could provide an effective approach for gene identification. A total of 59 QTL for 14 agronomic traits in plants grown under long- and short-day photoperiods were identified. The phenotypic variation explained ranged from 4.9 to 43.94%. In addition, we suggested that there may be segregation distortion on chromosome 6 that is significantly distorted toward Zhang gu. The newly identified QTL will provide a platform for sequence-based research on the S. italica genome, and for molecular marker-assisted breeding.

Evaluation of in vitro and in vivo nematicidal potential of a multifunctional streptomycete, Streptomyces hydrogenans strain DH16 against Meloidogyne incognita

The present work demonstrated the nematicidal potential of Streptomyces hydrogenans strain DH16 (a strain with strong antagonism against fungal phytopathogens and insect pest) against Meloidogyne incognita. The culture supernatant and solvent extract significantly inhibited egg hatching (almost 100%) along with J2 mortality of more than 95% after 96h. The nematicidal activity of 10-(2,2-dimethyl-cyclohexyl)-6,9-dihydroxy-4,9-dimethyl-dec-2-enoic acid methyl ester (SH2; a new antifungal compound) purified from this streptomycete was also evaluated using different concentrations. The juvenile mortality of the nematode increased with increasing concentration and exposure time and reached the maximum (95%) after 96h at concentration of 100μg/ml. After 160h of incubation, egg hatch of 16% was observed at concentration of 100μg/ml as compared to control where 100% egg hatching was achieved. However, at the highest concentration of the compound (200μg/ml), 100% J2 mortality and 0% egg hatching were observed after 72 and 160h of incubation, respectively. In vivo pot experiments further revealed the nematicidal potential of S. hydrogenans where soil drenching with its culture supernatant and cells effectively controlled root galls, egg masses in nematode infested tomato plants and at the same time promoted the growth of tomato plants. Additionally, in the absence of nematodes, soil drenching with culture supernatant and cells significantly enhanced the various agronomic traits of plants as compared to control plants. Thus, the outcomes of the current study endorse the potential of S. hydrogenans strain DH16 and its metabolites to be developed as safe nematicidal and plant growth promoting agents.

Chloroplast genomes: diversity, evolution, and applications in genetic engineering.

Chloroplasts play a crucial role in sustaining life on earth. The availability of over 800 sequenced chloroplast genomes from a variety of land plants has enhanced our understanding of chloroplast biology, intracellular gene transfer, conservation, diversity, and the genetic basis by which chloroplast transgenes can be engineered to enhance plant agronomic traits or to produce high-value agricultural or biomedical products. In this review, we discuss the impact of chloroplast genome sequences on understanding the origins of economically important cultivated species and changes that have taken place during domestication. We also discuss the potential biotechnological applications of chloroplast genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1004-2) contains supplementary material, which is available to authorized users.

Transcription factors SOD7/NGAL2 and DPA4/NGAL3 act redundantly to regulate seed size by directly repressing KLU expression in Arabidopsis thaliana.

Although seed size is one of the most important agronomic traits in plants, the genetic and molecular mechanisms that set the final size of seeds are largely unknown. We previously identified the ubiquitin receptor DA1 as a negative regulator of seed size, and the Arabidopsis thaliana da1-1 mutant produces larger seeds than the wild type. Here, we describe a B3 domain transcriptional repressor NGATHA-like protein (NGAL2), encoded by the suppressor of da1-1 (SOD7), which acts maternally to regulate seed size by restricting cell proliferation in the integuments of ovules and developing seeds. Overexpression of SOD7 significantly decreases seed size of wild-type plants, while the simultaneous disruption of SOD7 and its closest homolog DEVELOPMENT-RELATED PcG TARGET IN THE APEX4 (DPA4/NGAL3) increases seed size. Genetic analyses indicate that SOD7 and DPA4 act in a common pathway with the seed size regulator KLU to regulate seed growth, but do so independently of DA1. Further results show that SOD7 directly binds to the promoter of KLUH (KLU) in vitro and in vivo and represses the expression of KLU. Therefore, our findings reveal the genetic and molecular mechanisms of SOD7, DPA4, and KLU in seed size regulation and suggest that they are promising targets for seed size improvement in crops.

Analysis of Genetic Relationships between Seed Nutrient Traits and Plant Agronomic Traits in Indica Rice (Oryza Sativa L.)

Analysis of Genetic Relationships between Seed Nutrient Traits and Plant Agronomic Traits in Indica Rice (Oryza Sativa L.) Grain nutrient traits in rice and agronomic traits in plants are controlled by the genetic effects from different genetic systems, since rice grains growing on the plant are the progenies of its maternal plant. An analysis was conducted on the genetic relationships between seed nutrient traits and plant agronomic traits of indica rice (Oryza sativa L.).