scholarly journals Comparative Transcriptomics of Lowland Rice Varieties Uncovers Novel Candidate Genes for Adaptive Iron Excess Tolerance

2021 ◽  
Author(s):  
Saradia Kar ◽  
Hans-Jörg Mai ◽  
Hadeel Khalouf ◽  
Heithem Ben Abdallah ◽  
Samantha Flachbart ◽  
...  
Keyword(s):  
Leaf Growth ◽  
Expression Patterns ◽  
Reactive Oxygen Species Generation ◽  
Metal Homeostasis ◽  
Lowland Rice ◽  
Rice Varieties ◽  
Ontology Term ◽  
Fe Toxicity ◽  
Fe Excess ◽  
Excess Fe

Abstract Iron (Fe) toxicity is a major challenge for plant cultivation in acidic waterlogged soil environments, where lowland rice is a major staple food crop. Only few studies have addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance. Out of 16 lowland rice varieties, we identified a pair of contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. The two lines differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation and Fe and metal contents. These responses were likely due to genetic origin as they were mirrored by differential gene expression patterns, obtained through RNA sequencing, and corresponding gene ontology term enrichment in tolerant vs. susceptible lines. Thirty-five genes of the metal homeostasis category, mainly root expressed, showed differential transcriptomic profiles suggestive of an induced tolerance mechanism. Twenty-two out of these 35 metal homeostasis genes were present in selection sweep genomic regions, in breeding signatures, and/or differentiated during rice domestication. These findings suggest that Fe excess tolerance is an important trait in the domestication of lowland rice, and the identified genes may further serve to design the targeted Fe tolerance breeding of rice crops.

scholarly journals Transcriptomic expression patterns of two contrasting lowland rice varieties reveal high iron stress tolerance

2020 ◽  
Author(s):  
Saradia Kar ◽  
Hans-Jörg Mai ◽  
Hadeel Khalouf ◽  
Heithem Ben Abdallah ◽  
Samantha Flachbart ◽  
...  
Keyword(s):  
Leaf Growth ◽  
Expression Patterns ◽  
Reactive Oxygen Species Generation ◽  
Metal Homeostasis ◽  
Lowland Rice ◽  
Growth Responses ◽  
Rice Varieties ◽  
Fe Toxicity ◽  
Genomic Regions ◽  
Excess Fe

AbstractIron (Fe) toxicity is a major challenge for plant cultivation in acidic water-logged soil environments, where lowland rice is a major staple food crop. Only few studies addressed the molecular characterization of excess Fe tolerance in rice, and these highlight different mechanisms for Fe tolerance in the studied varieties.Here, we screened 16 lowland rice varieties for excess Fe stress growth responses to identify contrasting lines, Fe-tolerant Lachit and -susceptible Hacha. Hacha and Lachit differed in their physiological and morphological responses to excess Fe, including leaf growth, leaf rolling, reactive oxygen species generation, Fe and metal contents. These responses were mirrored by differential gene expression patterns, obtained through RNA-sequencing, and corresponding GO term enrichment in tolerant versus susceptible lines. From the comparative transcriptomic profiles between Lachit and Hacha in response to excess Fe stress, individual genes of the category metal homeostasis, mainly root-expressed, may contribute to the tolerance of Lachit. 22 out of these 35 metal homeostasis genes are present in selection sweep genomic regions, in breeding signatures and/or differentiated during rice domestication. These findings will serve to design targeted Fe tolerance breeding of rice crops.Summary statementLowland rice varieties Hacha and Lachit were selected for contrasting abilities to cope with iron excess stress. Morphological and physiological phenotypes were mirrored by molecular transcriptome changes, indicating altered metal homeostasis in the root as an adaptive tolerance mechanism in Lachit.

scholarly journals How Does Rice Defend Against Excess Iron?: Physiological and Molecular Mechanisms

2020 ◽  
Vol 11 ◽  
Author(s):  
May Sann Aung ◽  
Hiroshi Masuda
Keyword(s):  
Molecular Mechanisms ◽  
Low Ph ◽  
Ion Concentration ◽  
Growth And Yield ◽  
Association Analyses ◽  
Excess Iron ◽  
Fe Uptake ◽  
Fe Toxicity ◽  
Fe Excess ◽  
Excess Fe

Iron (Fe) is an essential nutrient for all living organisms but can lead to cytotoxicity when present in excess. Fe toxicity often occurs in rice grown in submerged paddy fields with low pH, leading dramatical increases in ferrous ion concentration, disrupting cell homeostasis and impairing growth and yield. However, the underlying molecular mechanisms of Fe toxicity response and tolerance in plants are not well characterized yet. Microarray and genome-wide association analyses have shown that rice employs four defense systems to regulate Fe homeostasis under Fe excess. In defense 1, Fe excess tolerance is implemented by Fe exclusion as a result of suppression of genes involved in Fe uptake and translocation such as OsIRT1, OsYSL2, OsTOM1, OsYSL15, OsNRAMP1, OsNAS1, OsNAS2, OsNAAT1, OsDMAS1, and OsIRO2. The Fe-binding ubiquitin ligase, HRZ, is a key regulator that represses Fe uptake genes in response to Fe excess in rice. In defense 2, rice retains Fe in the root system rather than transporting it to shoots. In defense 3, rice compartmentalizes Fe in the shoot. In defense 2 and 3, the vacuolar Fe transporter OsVIT2, Fe storage protein ferritin, and the nicotinamine synthase OsNAS3 mediate the isolation or detoxification of excess Fe. In defense 4, rice detoxifies the ROS produced within the plant body in response to excess Fe. Some OsWRKY transcription factors, S-nitrosoglutathione-reductase variants, p450-family proteins, and OsNAC4, 5, and 6 are implicated in defense 4. These knowledge will facilitate the breeding of tolerant crops with increased productivity in low-pH, Fe-excess soils.

scholarly journals Integrated Physiological and Transcriptomic Analyses Reveal a Regulatory Network of Anthocyanin Metabolism Contributing to the Ornamental Value in a Novel Hybrid Cultivar of Camellia japonica

Plants ◽  
2020 ◽  
Vol 9 (12) ◽  
pp. 1724
Author(s):  
Liqin Pan ◽  
Jiyuan Li ◽  
Hengfu Yin ◽  
Zhengqi Fan ◽  
Xinlei Li
Keyword(s):  
Regulatory Network ◽  
Leaf Growth ◽  
Expression Patterns ◽  
Differential Expression Analysis ◽  
Growth Stages ◽  
Potential Candidate ◽  
Leaf Color ◽  
Camellia Japonica ◽  
Leaf Phenotype ◽  
Hybrid Cultivar

Camellia japonica is a plant species with great ornamental and gardening values. A novel hybrid cultivar Chunjiang Hongxia (Camellia japonica cv. Chunjiang Hongxia, CH) possesses vivid red leaves from an early growth stage to a prolonged period and is, therefore, commercially valuable. The molecular mechanism underlying this red-leaf phenotype in C. japonica cv. CH is largely unknown. Here, we investigated the leaf coloration process, photosynthetic pigments contents, and different types of anthocyanin compounds in three growth stages of the hybrid cultivar CH and its parental cultivars. The gene co-expression network and differential expression analysis from the transcriptome data indicated that the changes of leaf color were strongly correlated to the anthocyanin metabolic processes in different leaf growth stages. Genes with expression patterns associated with leaf color changes were also discussed. Together, physiological and transcriptomic analyses uncovered the regulatory network of metabolism processes involved in the modulation of the ornamentally valuable red-leaf phenotype and provided the potential candidate genes for future molecular breeding of ornamental plants such as Camellia japonica.

scholarly journals Response of rain-fed lowland rice varieties to different sources of N fertilizer in Fogera Plain, Northwest Ethiopia

2019 ◽  
Vol 5 (1) ◽  
pp. 1707020
Author(s):  
Amare Aleminew ◽  
Getachew Alemayehu ◽  
Enyew Adgo ◽  
Tilahun Tadesse ◽  
Manuel Tejada Moral
Keyword(s):  
Northwest Ethiopia ◽  
N Fertilizer ◽  
Lowland Rice ◽  
Rice Varieties ◽  
Different Sources

scholarly journals Identification of candidate genes controlling chilling tolerance of rice in the cold region at the booting stage by BSA-Seq and RNA-Seq

2020 ◽  
Vol 7 (11) ◽  
pp. 201081
Author(s):  
Zhenhua Guo ◽  
Lijun Cai ◽  
Zhiqiang Chen ◽  
Ruiying Wang ◽  
Lanming Zhang ◽  
...  
Keyword(s):  
Candidate Genes ◽  
Bulked Segregant Analysis ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Chilling Tolerance ◽  
Pathway Enrichment Analysis ◽  
Potential Candidate ◽  
Rice Varieties ◽  
Booting Stage ◽  
F2 Population

Rice is sensitive to low temperatures, specifically at the booting stage. Chilling tolerance of rice is a quantitative trait loci that is governed by multiple genes, and thus, its precise identification through the conventional methods is an arduous task. In this study, we investigated the candidate genes related to chilling tolerance at the booting stage of rice. The F2 population was derived from Longjing25 (chilling-tolerant) and Longjing11 (chilling-sensitive) cross. Two bulked segregant analysis pools were constructed. A 0.82 Mb region containing 98 annotated genes on chromosomes 6 and 9 was recognized as the candidate region associated with chilling tolerance of rice at the booting stage. Transcriptomic analysis of Longjing25 and Longjing11 revealed 50 differentially expressed genes (DEGs) on the candidate intervals. KEGG pathway enrichment analysis of DEGs was performed. Nine pathways were found to be enriched, which contained 10 DEGs. A total of four genes had different expression patterns or levels between Longjing25 and Longjing11. Four out of the 10 DEGs were considered as potential candidate genes for chilling tolerance. This study will assist in the cloning of the candidate genes responsible for chilling tolerance and molecular breeding of rice for the development of chilling-tolerant rice varieties.

scholarly journals Mechanistic understanding of iron toxicity tolerance in contrasting rice varieties from Africa: 2. Root oxidation ability and oxidative stress control

2020 ◽  
Vol 47 (2) ◽  
pp. 145
Author(s):  
Dorothy A. Onyango ◽  
Fredrickson Entila ◽  
James Egdane ◽  
Myrish Pacleb ◽  
Meggy Lou Katimbang ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Sub Saharan Africa ◽  
Rice Varieties ◽  
Excess Iron ◽  
Improvement Programs ◽  
Sub Saharan ◽  
Breeding Efficiency ◽  
Biochemical Analyses ◽  
Fe Toxicity ◽  
And Control

To enhance breeding efficiency for iron (Fe) toxicity tolerance and boost lowland rice production in sub-Saharan Africa, we have characterised the morphological, physiological and biochemical responses of contrasting rice varieties to excess iron. Here, we report the capacity of four varieties (CK801 and Suakoko8 (tolerant), Supa and IR64 (sensitive)) to oxidise iron in the rhizosphere and control iron-induced oxidative stress. The experiments were conducted in hydroponic conditions using modified Magnavaca nutrient solution and 300 ppm of ferrous iron (Fe2+) supplied in the form of FeSO4. Severe oxidative stress was observed in sensitive varieties as revealed by their high levels of lipid peroxidation. Histochemical and biochemical analyses showed that tolerant varieties exhibited a better development of the aerenchyma and greater oxygen release than the sensitive varieties in response to excess Fe. Both suberin and lignin deposits were observed in the root, stem and leaf tissues but with varying intensities depending on the variety. Under iron toxic conditions, tolerant varieties displayed increased superoxide dismutase (SOD), glutathione reductase (GR), peroxidase (POX) and ascorbate peroxidase (APX) activities in both the roots and shoots, whereas sensitive varieties showed increased APX and catalase (CAT) activities in the roots. This study had revealed also that Suakoko8 mainly uses root oxidation to exclude Fe2+ from its rhizosphere, and CK801 possesses a strong reactive oxygen species scavenging system, in addition to root oxidation ability. Key traits associated with these tolerance mechanisms such as a well-developed aerenchyma, radial oxygen loss restricted to the root cap as well as strong activation of antioxidative enzymes (SOD, GR, POX and APX) could be useful selection criteria in rice varietal improvement programs for enhanced Fe toxicity tolerance.

INFLUENCES OF PHOSPHORUS DEFICIENCY ON THE UPTAKE OF NITROGEN, POTASSIUM, CALCIUM, MAGNESIUM, SULFUR, AND ZINC IN LOWLAND RICE VARIETIES

2001 ◽  
Vol 24 (10) ◽  
pp. 1621-1632 ◽  
Author(s):  
M. A. Saleque ◽  
M. J. Abedin ◽  
Z. U. Ahmed ◽  
M. Hasan ◽  
G. M. Panaullah
Keyword(s):  
Phosphorus Deficiency ◽  
Lowland Rice ◽  
Rice Varieties ◽  
Calcium Magnesium
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