Yinglong Chen

Transcriptome Profiling of Radish (Raphanus sativus L.) Root and Identification of Genes Involved in Response to Lead (Pb) Stress with Next Generation Sequencing

Lead (Pb), one of the most toxic heavy metals, can be absorbed and accumulated by plant roots and then enter the food chain resulting in potential health risks for human beings. The radish (Raphanus sativus L.) is an important root vegetable crop with fleshy taproots as the edible parts. Little is known about the mechanism by which radishes respond to Pb stress at the molecular level. In this study, Next Generation Sequencing (NGS)–based RNA-seq technology was employed to characterize the de novo transcriptome of radish roots and identify differentially expressed genes (DEGs) during Pb stress. A total of 68,940 assembled unique transcripts including 33,337 unigenes were obtained from radish root cDNA samples. Based on the assembled de novo transcriptome, 4,614 DEGs were detected between the two libraries of untreated (CK) and Pb-treated (Pb1000) roots. Gene Ontology (GO) and pathway enrichment analysis revealed that upregulated DEGs under Pb stress are predominately involved in defense responses in cell walls and glutathione metabolism-related processes, while downregulated DEGs were mainly involved in carbohydrate metabolism-related pathways. The expression patterns of 22 selected genes were validated by quantitative real-time PCR, and the results were highly accordant with the Solexa analysis. Furthermore, many candidate genes, which were involved in defense and detoxification mechanisms including signaling protein kinases, transcription factors, metal transporters and chelate compound biosynthesis related enzymes, were successfully identified in response to heavy metal Pb. Identification of potential DEGs involved in responses to Pb stress significantly reflected alterations in major biological processes and metabolic pathways. The molecular basis of the response to Pb stress in radishes was comprehensively characterized. Useful information and new insights were provided for investigating the molecular regulation mechanism of heavy metal Pb accumulation and tolerance in root vegetable crops.

Phenotypic variability and modelling of root structure of wild Lupinus angustifolius genotypes

Background and aimsRoot plasticity in response to the edaphic environment represents a challenge in the quantification of phenotypic variation in crop germplasm. The aim of this study was to use various growth systems to assess phenotypic variation among wild genotypes of Lupinus angustifolius.MethodsTen wild genotypes of L. angustifolius selected from an earlier phenotyping study were grown in three different growth systems: semi-hydroponics, potting-mix filled pots, and river-sand filled pots.ResultsMajor root-trait data collected in the present study in the semi-hydroponic growth system were strongly correlated with those from the earlier large phenotyping trial. Plants grown in the two solid media had some of the measured parameters significantly correlated. Principal component analysis captured the major variability in three (semi-hydroponics) or four (solid media) principal components. The genotypes were grouped into five clusters for each growth media, but cluster composition varied among the media. We found genetic variation and phenotypic plasticity in some root traits among tested genotypes. Using input parameters derived from the semihydroponic phenotyping system, simulation models (ROOTMAP and SimRoot) closely reproduced the root systems of a diverse range of lupin genotypes.ConclusionsWild L. angustifolius genotypes displayed genetic variation and phenotypic plasticity when exposed to various growth conditions. The consistent ranking of genotypes in the semihydroponic phenotyping system and the two solid media confirmed the capacity of the semihydroponic phenotyping system of providing simple and relevant growing conditions. The results demonstrated the utility of this system in gathering the data for parameterising the simulation models of root architecture.

Dual colonization of Eucalyptus urophylla S.T. Blake by arbuscular and ectomycorrhizal fungi affects levels of insect herbivore attack

Abstract  1 Eucalypts are an important part of plantation forestry in Asia but, in south China, productivity is very low. This is due to infertile soils and lack of indigenous symbiotic mycorrhizal fungi. The genus Eucalyptus is unusual because it forms both arbuscular (AM) and ectomycorrhizal (ECM) associations.

Moderate Drought Stress Affected Root Growth and Grain Yield in Old, Modern and Newly Released Cultivars of Winter Wheat

To determine root growth and grain yield of winter wheat (Triticum aestivum L) under moderate drought stress, a nursery experiment and a field trial were conducted with or without water stress using three representative cultivars released in different years: CW134 (old landrace), CH58 (modern cultivar) and CH1 (new release). In the nursery experiment, plants were grown in soil-filled rhizoboxes under moderate drought (MD, 55% of field capacity) or well-watered (WW, 85% of field capacity) conditions. In the field trial, plots were either rainfed (moderate drought stress) or irrigated with 30 mm of water at each of stem elongation, booting and anthesis stages (irrigated). Compared to drought stress, grain yields increased under sufficient water supply in all cultivars, particular the newly released cultivar CH1 with 70% increase in the nursery and 23% in the field. When well-watered (nursery) or irrigated (field), CH1 had the highest grain yields compared to the other two cultivars, but produced similar yield to the modern cultivar (CH58) under water-stressed (nursery) or rainfed (field) conditions. When exposed to drought stress, CW134 had the highest topsoil root dry mass in topsoil but lowest in subsoil among the cultivars at stem elongation, anthesis, and maturity, respectively; while CH1 had the lowest topsoil and highest subsoil root dry mass at respective sampling times. Topsoil root mass and root length density were negatively correlated with grain yield for the two water treatments in nursery experiment. When water was limited, subsoil root mass was positively correlated with thousand kernel weight (TKW). In the field trial, CH1 and CH58 used less water during vegetative growth than CW134, but after anthesis stage, CH1 used more water than the other two cultivars, especially in the soil profile below 100 cm, which was associated with the increased TKW. This study demonstrated that greater root mass and root length density in subsoil layers, with enhanced access to subsoil water after anthesis, contribute to high grain yield when soil water is scarce.

Ultrastructural and physiological responses of potato (Solanum tuberosum L.) plantlets to gradient saline stress

Salinity is one of the major abiotic stresses that impacts plant growth and reduces the productivity of field crops. Compared to field plants, test tube plantlets offer a direct and fast approach to investigate the mechanism of salt tolerance. Here we examined the ultrastructural and physiological responses of potato (Solanum tuberosum L. c.v. “Longshu No. 3”) plantlets to gradient saline stress (0, 25, 50, 100, and 200 mM NaCl) with two consequent observations (2 and 6 weeks, respectively). The results showed that, with the increase of external NaCl concentration and the duration of treatments, (1) the number of chloroplasts and cell intercellular spaces markedly decreased, (2) cell walls were thickened and even ruptured, (3) mesophyll cells and chloroplasts were gradually damaged to a complete disorganization containing more starch, (4) leaf Na and Cl contents increased while leaf K content decreased, (5) leaf proline content and the activities of catalase (CAT) and superoxide dismutase (SOD) increased significantly, and (6) leaf malondialdehyde (MDA) content increased significantly and stomatal area and chlorophyll content decline were also detected. Severe salt stress (200 mM NaCl) inhibited plantlet growth. These results indicated that potato plantlets adapt to salt stress to some extent through accumulating osmoprotectants, such as proline, increasing the activities of antioxidant enzymes, such as CAT and SOD. The outcomes of this study provide ultrastructural and physiological insights into characterizing potential damages induced by salt stress for selecting salt-tolerant potato cultivars.

Transcriptome-wide analysis of chromium-stress responsive microRNAs to explore miRNA-mediated regulatory networks in radish (Raphanus sativus L.)

MicroRNAs (miRNAs) are small noncoding RNAs that play pivotal roles in plant growth, development and stress response. Chromium (Cr) is one of common environmental contaminants possessing potential health hazards to living organisms. To date, little is known about the regulatory roles of miRNAs in response to Cr stress in radish. To systematically identify Cr-responsive miRNAs and their targets in radish, two sRNA libraries derived from Cr-free (CK) and Cr-treated (Cr200) roots were constructed. With Solexa sequencing, 81 known and 72 novel miRNAs were identified, from which 54 known and 16 novel miRNAs were significantly differentially expressed under Cr stress. Several target genes for Cr-responsive miRNAs encode different transcription factor (TF) families, including SPLs, MYBs, ERFs and bZIPs, might regulate corresponding HM-related transcriptional processes in plants. Notably, a few key responsive enzymes or proteins, including HMA, YSL1 and ABC transporter protein were involved in Cr uptake and homeostasis process. Furthermore, the expression patterns of some Cr-responsive miRNAs and their targets were validated by RT-qPCR. This study represents the first characterization of Cr-responsive miRNAs and their targets in radish. The outcomes of this study could provide novel insights into miRNA-mediated regulatory mechanisms underlying plant response to Cr stress in root vegetable crops.

Effects of Arbuscular Mycorrhizal Fungi Communities on Soil Quality and the Growth of Cucumber Seedlings in a Greenhouse Soil of Continuously Planting Cucumber

A pot experiment was performed to determine the effects of arbuscular mycorrhizal fungi (AMF) communities on soil properties and the growth of cucumber seedlings in a degraded soil that had been used for continuous cucumber monoculture in a greenhouse for 15 years. In the experiment, AMF communities (created by combining various AMF species that were found to be dominant in natural farm soil) were inoculated into the degraded soil, and then the soil was planted with cucumber. Inoculation with AMF communities did not affect soil pH but increased soil aggregate stability and decreased the concentrations of salt ions and electrical conductivity (EC) in the soil. Inoculation with AMF communities increased the numbers of culturable bacteria and actinomycetes but reduced the number of fungi. AMF communities increased plant growth, soluble sugar content, chlorophyll content, and root activity compared to non-mycorrhizal or a single AMF species treatments. Improvements of soil quality and plant growth were greatest with the following two communities: Glomus etunicatum + G. mosseae + Gigaspora margarita + Acaulospora lacunosa and G. aggregatum + G. etunicatum + G. mosseae + G. versiforme + G. margarita + A. lacunosa. The results suggested that certain AMF communities could substantially improve the quality of degraded soil.

The diversity of arbuscular mycorrhizas of selected Australian Fabaceae

Abstract Members of the Australian native perennial Fabaceae have been little explored with regard to their root biology and the role played by arbuscular mycorrhizal (AM) fungi in their establishment, nutrition and long-term health. The ultimate goal of our research is to determine the dependency of native perennial legumes on their co-evolved AM fungi and conversely, the impact of AM fungal species in agricultural fields on the productivity of sown native perennial legume pastures. In this paper we investigate the colonisation morphology in roots and the AMF, identified by spores extracted from rhizosphere soil, from three replicate plots of each of the native legumes, Cullen australasicum, C. tenax and Lotus australis and the exotic legumes L. pedunculatus and Medicago sativa. The plants were grown in an agricultural field. The level and density of colonisation by AM fungi, and the frequency of intraradical and extraradical hyphae, arbuscules, intraradical spores and hyphal coils all differed between host plants and did not consistently differ between native and exotic species. However, there were strong similarities between species in the same genus. The three dominant species of AM fungi in rhizosphere soil also differed with host plant, but one fungus (Glomus mosseae) was always the most dominant. Sub-dominant AM species were the same between species in the same genus. No consistent differences in dominant spores were observed between the exotic and native Fabaceae species. Our results suggest that plant host influences the mycorrhizal community in the rhizosphere soil and that structural and functional differences in the symbiosis may occur at the plant genus level, not the species level or due to provenance.

Characterising root trait variability in chickpea (Cicer arietinum L.) germplasm

Highlight Large variation in root system architecture in chickpea germplasm was identified across 270 genotypes, providing information that can be used in developing genotypes with root traits for improved adaptation to specific environments.

Diversity and distribution of arbuscular mycorrhizal fungi along altitudinal gradients in Mount Taibai of the Qinling Mountains

Elevational patterns of plant and animal diversity have been studied for centuries; however, the effects of land elevation on arbuscular mycorrhizal (AM) fungal diversity remains unclear. We examined AM fungal diversity and distribution along 19 elevation belts in Mount Taibai of the Qinling Mountains, with the aim to assess the altitudinal diversity patterns. In total, 63 AM fungal taxa belonging to 12 genera were discovered. Mycorrhizal colonization rates on roots; AM fungal spore density; and fungal species richness, evenness, and diversity had different patterns in terms of the changes of elevation. Root colonization followed a cubical parabolic pattern, with a peak and a foot at an elevation of about 2000 and 3000 m above sea level, respectively. Species richness decreased monotonically from the lowest to the highest elevations. Spore density and α-diversity exhibited a unimodal pattern and peaked at an elevation of 2107 and 1350 m, respectively. Species evenness increased monotonically at an elevation of between 1050 and 2250 m. β-Diversity also presented a basically incremental pattern along altitudinal gradients. Our findings suggest that elevation changes were the main factor governing the patterns of AM fungal diversity.