Genome-Wide Consistent Molecular Markers Associated with Phenology, Plant Production and Root Traits in Diverse Rice (Oryza sativa L.) Accessions under Drought in Rainfed Target Populations of the Environment

2018 ◽  
Vol 114 (02) ◽  
pp. 329 ◽  
Author(s):  
Vivek Deshmukh ◽  
Sumeet Prabakar Mankar ◽  
C. Muthukumar ◽  
P. Divahar ◽  
A. Bharathi ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Molecular Markers ◽  
Root Traits ◽  
Plant Production ◽  
Target Populations ◽  
Genome Wide

Evaluation of rice (Oryza sativa L.) near iso-genic lines with root QTLs for plant production and root traits in rainfed target populations of environment

2012 ◽  
Vol 137 ◽  
pp. 89-96 ◽  
Author(s):  
K.K. Suji ◽  
K. Silvas Jebakumar Prince ◽  
P. Sumeet Mankhar ◽  
P. Kanagaraj ◽  
R. Poornima ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Oryza Sativa L ◽  
Root Traits ◽  
Plant Production ◽  
Target Populations

Genome-wide Identification of Molecular Markers Based on Genomic Re-sequencing of Foxtail Millet Elite Cultivar Jingu 21

2018 ◽  
Vol 44 (5) ◽  
pp. 686 ◽  
Author(s):  
Qing-Ying ZHAO ◽  
Rui-Juan ZHANG ◽  
Rui-Liang WANG ◽  
Jian-Hua GAO ◽  
Yuan-Huai HAN ◽  
...  
Keyword(s):  
Molecular Markers ◽  
Foxtail Millet ◽  
Genome Wide ◽  
Elite Cultivar

scholarly journals Shoot and Root Traits Underlying Genotypic Variation in Early Vigor and Nutrient Accumulation in Spring Wheat Grown in High-Latitude Light Conditions

Plants ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 174
Author(s):  
Hui Liu ◽  
Fabio Fiorani ◽  
Ortrud Jäck ◽  
Tino Colombi ◽  
Kerstin A. Nagel ◽  
...  
Keyword(s):  
Root System ◽  
Leaf Area ◽  
Spring Wheat ◽  
High Latitude ◽  
Root Length ◽  
Nutrient Use Efficiency ◽  
Root Traits ◽  
Plant Production ◽  
Nutrient Accumulation ◽  
Early Vigor

Plants with improved nutrient use efficiency are needed to maintain and enhance future crop plant production. The aim of this study was to explore candidate traits for pre-breeding to improve nutrient accumulation and early vigor of spring wheat grown at high latitudes. We quantified shoot and root traits together with nutrient accumulation in nine contrasting spring wheat genotypes grown in rhizoboxes for 20 days in a greenhouse. Whole-plant relative growth rate was here correlated with leaf area productivity and plant nitrogen productivity, but not leaf area ratio. Furthermore, the total leaf area was correlated with the accumulation of six macronutrients, and could be suggested as a candidate trait for the pre-breeding towards improved nutrient accumulation and early vigor in wheat to be grown in high-latitude environments. Depending on the nutrient of interest, different root system traits were identified as relevant for their accumulation. Accumulation of nitrogen, potassium, sulfur and calcium was correlated with lateral root length, whilst accumulation of phosphorus and magnesium was correlated with main root length. Therefore, special attention needs to be paid to specific root system traits in the breeding of wheat towards improved nutrient accumulation to counteract the suboptimal uptake of some nutrient elements.

scholarly journals Genome-wide characterization of MATE gene family and expression profiles in response to abiotic stresses in rice (Oryza sativa)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Zhixuan Du ◽  
Qitao Su ◽  
Zheng Wu ◽  
Zhou Huang ◽  
Jianzhong Bao ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Gene Family ◽  
Tandem Repeats ◽  
Expression Profiles ◽  
Functional Divergence ◽  
Expression Patterns ◽  
Regulatory Elements ◽  
Genome Wide ◽  
Comprehensive Information ◽  
Family Gene

AbstractMultidrug and toxic compound extrusion (MATE) proteins are involved in many physiological functions of plant growth and development. Although an increasing number of MATE proteins have been identified, the understanding of MATE proteins is still very limited in rice. In this study, 46 MATE proteins were identified from the rice (Oryza sativa) genome by homology searches and domain prediction. The rice MATE family was divided into four subfamilies based on the phylogenetic tree. Tandem repeats and fragment replication contribute to the expansion of the rice MATE gene family. Gene structure and cis-regulatory elements reveal the potential functions of MATE genes. Analysis of gene expression showed that most of MATE genes were constitutively expressed and the expression patterns of genes in different tissues were analyzed using RNA-seq. Furthermore, qRT-PCR-based analysis showed differential expression patterns in response to salt and drought stress. The analysis results of this study provide comprehensive information on the MATE gene family in rice and will aid in understanding the functional divergence of MATE genes.

scholarly journals Genome-wide association study and transcriptome analysis discover new genes for bacterial leaf blight resistance in rice (Oryza sativa L.)

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Xinyue Shu ◽  
Aijun Wang ◽  
Bo Jiang ◽  
Yuqi Jiang ◽  
Xing Xiang ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Association Study ◽  
Transcriptome Analysis ◽  
Genome Wide Association Study ◽  
Leaf Blight ◽  
Genome Wide Association ◽  
Bacterial Leaf Blight ◽  
Significant Differential Expression ◽  
Genome Wide ◽  
A Genome

Abstract Background Rice (Oryza sativa) bacterial leaf blight (BLB), caused by the hemibiotrophic Xanthomonas oryzae pv. oryzae (Xoo), is one of the most devastating diseases affecting the production of rice worldwide. The development and use of resistant rice varieties or genes is currently the most effective strategy to control BLB. Results Here, we used 259 rice accessions, which are genotyped with 2 888 332 high-confidence single nucleotide polymorphisms (SNPs). Combining resistance variation data of 259 rice lines for two Xoo races observed in 2 years, we conducted a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) conferring plant resistance against BLB. The expression levels of genes, which contains in GWAS results were also identified between the resistant and susceptible rice lines by transcriptome analysis at four time points after pathogen inoculation. From that 109 candidate resistance genes showing significant differential expression between resistant and susceptible rice lines were uncovered. Furthermore, the haplotype block structure analysis predicted 58 candidate genes for BLB resistance based on Chr. 7_707158 with a minimum P-value (–log 10 P = 9.72). Among them, two NLR protein-encoding genes, LOC_Os07g02560 and LOC_Os07g02570, exhibited significantly high expression in the resistant line, but had low expression in the susceptible line of rice. Conclusions Together, our results reveal novel BLB resistance gene resources, and provide important genetic basis for BLB resistance breeding of rice crops.

scholarly journals Genome-wide H3K9 Acetylation Level Increases with Age-Dependent Senescence of Flag Leaf in Rice (Oryza sativa)

2021 ◽  
Author(s):  
Yu Zhang ◽  
Yanyun Li ◽  
Yuanyuan Zhang ◽  
Zeyu Zhang ◽  
Deyu Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Oryza Sativa ◽  
Leaf Senescence ◽  
Epigenetic Modification ◽  
Flag Leaf ◽  
Regulation Of Gene Expression ◽  
Leaf Aging ◽  
Genome Wide ◽  
Age Dependent ◽  
H3k9 Acetylation

Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and epigenetic modification, but the precise mechanism is as of yet unclear. Here, we analyzed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq) and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac and gene expression and transcript elongation. A set of 1,249 up-regulated, differentially expressed genes (DEGs) and 996 down-regulated DEGs showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac was observed during rice flag leaf aging. We produced a landscape of H3K9 acetylation- modified gene expression targets that includes known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis- related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac and also elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.

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