scholarly journals IDENTIFYING PLANT GENES SHAPING MICROBIOTA COMPOSITION IN THE BARLEY RHIZOSPHERE

2021 ◽  
Author(s):  
Carmen Escudero-Martinez ◽  
Max Coulter ◽  
Rodrigo Alegria Terrazas ◽  
Alexandre Foito ◽  
Rumana Kapadia ◽  
...  
Keyword(s):  
Crop Production ◽  
Structural Variation ◽  
Crop Improvement ◽  
Major Effect ◽  
Microbiota Composition ◽  
Leucine Rich Repeat ◽  
Rna Seq ◽  
Genetic Determinants ◽  
Plant Genes ◽  
Host Genetic

A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here we used metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identified a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS locus, emerged as a major determinant of microbiota composition. We then subjected soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allowed us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide novel insights into the footprint of crop improvement on the plants capacity of shaping rhizosphere microbes.

scholarly journals Drought-Induced Root Pressure in Sorghum bicolor

2021 ◽  
Vol 12 ◽  
Author(s):  
Sarah Tepler Drobnitch ◽  
Louise H. Comas ◽  
Nora Flynn ◽  
Jorge Ibarra Caballero ◽  
Ryan W. Barton ◽  
...  
Keyword(s):  
Sorghum Bicolor ◽  
Biomass Production ◽  
Crop Production ◽  
Shoot Biomass ◽  
Cellular Transport ◽  
Rna Seq ◽  
Root Pressure ◽  
Coarse Root ◽  
Gene Transcripts

Root pressure, also manifested as profusive sap flowing from cut stems, is a phenomenon in some species that has perplexed biologists for much of the last century. It is associated with increased crop production under drought, but its function and regulation remain largely unknown. In this study, we investigated the initiation, mechanisms, and possible adaptive function of root pressure in six genotypes of Sorghum bicolor during a drought experiment in the greenhouse. We observed that root pressure was induced in plants exposed to drought followed by re-watering but possibly inhibited by 100% re-watering in some genotypes. We found that root pressure in drought stressed and re-watered plants was associated with greater ratio of fine: coarse root length and shoot biomass production, indicating a possible role of root allocation in creating root pressure and adaptive benefit of root pressure for shoot biomass production. Using RNA-Seq, we identified gene transcripts that were up- and down-regulated in plants with root pressure expression, focusing on genes for aquaporins, membrane transporters, and ATPases that could regulate inter- and intra-cellular transport of water and ions to generate positive xylem pressure in root tissue.

scholarly journals Dual RNA-seq reveals large-scale non-conserved genotype x genotype specific genetic reprograming and molecular crosstalk in the mycorrhizal symbiosis

2018 ◽  
Author(s):  
Ivan D. Mateus ◽  
Frédéric G. Masclaux ◽  
Consolée Aletti ◽  
Edward C. Rojas ◽  
Romain Savary ◽  
...  
Keyword(s):  
Mycorrhizal Fungi ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Arbuscular Mycorrhizal ◽  
Mycorrhizal Symbiosis ◽  
Rna Seq ◽  
Plant Host ◽  
Transcriptional Responses ◽  
Plant Genes ◽  
Fungal Genetic

AbstractArbuscular mycorrhizal fungi (AMF) impact plant growth and are a major driver of plant diversity and productivity. We quantified the contribution of intra-specific genetic variability in cassava (Manihot esculenta) and Rhizophagus irregularis to gene reprogramming in symbioses using dual RNA-sequencing. A large number of cassava genes exhibited altered transcriptional responses to the fungus but transcription of most of these plant genes (72%) responded in a different direction or magnitude depending on the plant genotype. Two AMF isolates displayed large differences in their transcription, but the direction and magnitude of the transcriptional responses for a large number of these genes was also strongly influenced by the genotype of the plant host. This indicates that unlike the highly conserved plant genes necessary for the symbiosis establishment, plant and fungal gene transcriptional responses are not conserved and are greatly influenced by plant and fungal genetic differences, even at the within-species level. The transcriptional variability detected allowed us to identify an extensive gene network showing the interplay in plant-fungal reprogramming in the symbiosis. Key genes illustrated that the two organisms jointly program their cytoskeleton organisation during growth of the fungus inside roots. Our study reveals that plant and fungal genetic variation plays a strong role in shaping the genetic reprograming in response to symbiosis, indicating considerable genotype x genotype interactions in the mycorrhizal symbiosis. Such variation needs to be considered in order to understand the molecular mechanisms between AMF and their plant hosts in natural communities.

scholarly journals Transcriptional Profile of Aedes aegypti Leucine-Rich Repeat Proteins in Response to Zika and Chikungunya Viruses

2019 ◽  
Vol 20 (3) ◽  
pp. 615 ◽  
Author(s):  
Liming Zhao ◽  
Barry Alto ◽  
Dongyoung Shin
Keyword(s):  
Aedes Aegypti ◽  
Zika Virus ◽  
Time Course ◽  
Developmental Stages ◽  
Analysis Data ◽  
Leucine Rich Repeat ◽  
Rna Seq ◽  
Gene Expressions ◽  
Transcription Profiles ◽  
Time Course Study

Aedes aegypti (L.) is the primary vector of chikungunya, dengue, yellow fever, and Zika viruses. The leucine-rich repeats (LRR)-containing domain is evolutionarily conserved in many proteins associated with innate immunity in invertebrates and vertebrates, as well as plants. We focused on the AaeLRIM1 and AaeAPL1 gene expressions in response to Zika virus (ZIKV) and chikungunya virus (CHIKV) infection using a time course study, as well as the developmental expressions in the eggs, larvae, pupae, and adults. RNA-seq analysis data provided 60 leucine-rich repeat related transcriptions in Ae. aegypti in response to Zika virus (Accession number: GSE118858, accessed on: August 22, 2018, GEO DataSets). RNA-seq analysis data showed that AaeLRIM1 (AAEL012086-RA) and AaeAPL1 (AAEL009520-RA) were significantly upregulated 2.5 and 3-fold during infection by ZIKV 7-days post infection (dpi) of an Ae. aegypti Key West strain compared to an Orlando strain. The qPCR data showed that LRR-containing proteins related genes, AaeLRIM1 and AaeAPL1, and five paralogues were expressed 100-fold lower than other nuclear genes, such as defensin, during all developmental stages examined. Together, these data provide insights into the transcription profiles of LRR proteins of Ae. aegypti during its development and in response to infection with emergent arboviruses.

scholarly journals Genetic determinants of gut microbiota composition and bile acid profiles in mice

PLoS Genetics ◽  
2019 ◽  
Vol 15 (8) ◽  
pp. e1008073 ◽  
Author(s):  
Julia H. Kemis ◽  
Vanessa Linke ◽  
Kelsey L. Barrett ◽  
Frederick J. Boehm ◽  
Lindsay L. Traeger ◽  
...  
Keyword(s):  
Bile Acid ◽  
Gut Microbiota ◽  
Microbiota Composition ◽  
Genetic Determinants ◽  
Bile Acid Profiles ◽  
Gut Microbiota Composition

scholarly journals Identification of Bna.IAA7.C05 as allelic gene for dwarf mutant generated from tissue culture in oilseed rape

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Hongtao Cheng ◽  
Fenwei Jin ◽  
Qamar U. Zaman ◽  
Bingli Ding ◽  
Mengyu Hao ◽  
...  
Keyword(s):  
Tissue Culture ◽  
Plant Height ◽  
High Throughput Sequencing ◽  
Agronomic Traits ◽  
Crop Improvement ◽  
Dwarf Mutant ◽  
Sequencing Analysis ◽  
Rna Seq ◽  
Dwarf Phenotype ◽  
Lodging Resistance

Abstract Background Plant height is one of the most important agronomic traits in many crops due to its influence on lodging resistance and yield performance. Although progress has been made in the use of dwarfing genes in crop improvement, identification of new dwarf germplasm is still of significant interest for breeding varieties with increased yield. Results Here we describe a dominant, dwarf mutant G7 of Brassica napus with down-curved leaves derived from tissue culture. To explore the genetic variation responsible for the dwarf phenotype, the mutant was crossed to a conventional line to develop a segregating F2 population. Bulks were formed from plants with either dwarf or conventional plant height and subjected to high throughput sequencing analysis via mutation mapping (MutMap). The dwarf mutation was mapped to a 0.6 Mb interval of B. napus chromosome C05. Candidate gene analysis revealed that one SNP causing an amino acid change in the domain II of Bna.IAA7.C05 may contribute to the dwarf phenotype. This is consistent with the phenotype of a gain-of-function indole-3-acetic acid (iaa) mutant in Bna.IAA7.C05 reported recently. GO and KEGG analysis of RNA-seq data revealed the down-regulation of auxin related genes, including many other IAA and small up regulated response (SAUR) genes, in the dwarf mutant. Conclusion Our studies characterize a new allele of Bna.IAA7.C05 responsible for the dwarf mutant generated from tissue culture. This may provide a valuable genetic resource for breeding for lodging resistance and compact plant stature in B. napus.

Water Use Efficiency as a Constraint and Target for Improving the Resilience and Productivity of C3and C4Crops

2019 ◽  
Vol 70 (1) ◽  
pp. 781-808 ◽  
Author(s):  
Andrew D.B. Leakey ◽  
John N. Ferguson ◽  
Charles P. Pignon ◽  
Alex Wu ◽  
Zhenong Jin ◽  
...  
Keyword(s):  
Water Use Efficiency ◽  
Water Use ◽  
Crop Production ◽  
Crop Improvement ◽  
Canopy Structure ◽  
Complex Trait ◽  
Carbon Gain ◽  
Crop Development ◽  
Component Traits ◽  
Use Efficiency

The ratio of plant carbon gain to water use, known as water use efficiency (WUE), has long been recognized as a key constraint on crop production and an important target for crop improvement. WUE is a physiologically and genetically complex trait that can be defined at a range of scales. Many component traits directly influence WUE, including photosynthesis, stomatal and mesophyll conductances, and canopy structure. Interactions of carbon and water relations with diverse aspects of the environment and crop development also modulate WUE. As a consequence, enhancing WUE by breeding or biotechnology has proven challenging but not impossible. This review aims to synthesize new knowledge of WUE arising from advances in phenotyping, modeling, physiology, genetics, and molecular biology in the context of classical theoretical principles. In addition, we discuss how rising atmospheric CO2concentration has created and will continue to create opportunities for enhancing WUE by modifying the trade-off between photosynthesis and transpiration.

701 HOST GENETIC DETERMINANTS IN HCV-RELATED MIXED CRYOGLOBULINEMIA

2010 ◽  
Vol 52 ◽  
pp. S272-S273
Author(s):  
A. Piluso ◽  
L. Gragnani ◽  
P. Caini ◽  
E. Fognani ◽  
C. Giannini ◽  
...  
Keyword(s):  
Mixed Cryoglobulinemia ◽  
Genetic Determinants ◽  
Host Genetic

scholarly journals The transcriptome variations of Panaxnotoginseng roots treated with different forms of nitrogen fertilizers

BMC Genomics ◽  
2019 ◽  
Vol 20 (S9) ◽  
Author(s):  
Xiaohong Ou ◽  
Shipeng Li ◽  
Peiran Liao ◽  
Xiuming Cui ◽  
Binglian Zheng ◽  
...  
Keyword(s):  
Crop Production ◽  
Tca Cycle ◽  
Panax Notoginseng ◽  
Ammonium Nitrogen ◽  
Nitrogen Fertilizers ◽  
Rna Seq ◽  
Root Yield ◽  
Qrt Pcr ◽  
The Tca Cycle ◽  
Nitrate Fertilizer

Abstract Background The sensitivity of plants to ammonia is a worldwide problem that limits crop production. Excessive use of ammonium as the sole nitrogen source results in morphological and physiological disorders, and retarded plant growth. Results In this study we found that the root growth of Panax notoginseng was inhibited when only adding ammonium nitrogen fertilizer, but the supplement of nitrate fertilizer recovered the integrity, activity and growth of root. Twelve RNA-seq profiles in four sample groups were produced and analyzed to identify deregulated genes in samples with different treatments. In comparisons to NH${~}_{4}^{+}$ 4 + treated samples, ACLA-3 gene is up-regulated in samples treated with NO${~}_{3}^{-}$ 3 − and with both NH$_{4}^{+}$ 4 + and NO${~}_{3}^{-}$ 3 − , which is further validated by qRT-PCR in another set of samples. Subsequently, we show that the some key metabolites in the TCA cycle are also significantly enhanced when introducing NO${~}_{3}^{-}$ 3 − . These potentially enhance the integrity and recover the growth of Panax notoginseng roots. Conclusion These results suggest that the activated TCA cycle, as demonstrated by up-regulation of ACLA-3 and several key metabolites in this cycle, contributes to the increased Panax notoginseng root yield when applying both ammonium and nitrate fertilizer.

Sign in / Sign up

Export Citation Format

Share Document