scholarly journals Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice (Oryza sativa L.)

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 716
Author(s):  
Nurhanis Selamat ◽  
Kalaivani K. Nadarajah
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Qtl Analysis ◽  
Oryza Sativa L ◽  
Genetic Maps ◽  
Chromosome 1 ◽  
Chromosome 2 ◽  
Consensus Map ◽  
Breeding Programs ◽  
Stable Qtls

Rice is an important grain that is the staple food for most of the world’s population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Therefore, to ensure success in breeding programs for drought tolerant rice, QTLs (quantitative trait loci) of interest must be stable in a variety of plant genotypes and environments. This study identified stable QTLs in rice chromosomes in a variety of backgrounds and environments and conducted a meta-QTL analysis of stable QTLs that have been reported by previous research for use in breeding programs. A total of 653 QTLs for drought tolerance in rice from 27 genetic maps were recorded for analysis. The QTLs recorded were related to 13 traits in rice that respond to drought. Through the use of BioMercartor V4.2, a consensus map containing QTLs and molecular markers were generated using 27 genetic maps that were extracted from the previous 20 studies and meta-QTL analysis was conducted on the consensus map. A total of 70 MQTLs were identified and a total of 453 QTLs were mapped into the meta-QTL areas. Five meta-QTLs from chromosome 1 (MQTL 1.5 and MQTL 1.6), chromosome 2 (MQTL2.1 and MQTL 2.2) and chromosome 3 (MQTL 3.1) were selected for functional annotation as these regions have high number of QTLs and include many traits in rice that respond to drought. A number of genes in MQTL1.5 (268 genes), MQTL1.6 (640 genes), MQTL 2.1 (319 genes), MQTL 2.2 (19 genes) and MQTL 3.1 (787 genes) were annotated through Blast2GO. Few major proteins that respond to drought stress were identified in the meta-QTL areas which are Abscisic Acid-Insensitive Protein 5 (ABI5), the G-box binding factor 4 (GBF4), protein kinase PINOID (PID), histidine kinase 2 (AHK2), protein related to autophagy 18A (ATG18A), mitochondrial transcription termination factor (MTERF), aquaporin PIP 1-2, protein detoxification 48 (DTX48) and inositol-tetrakisphosphate 1-kinase 2 (ITPK2). These proteins are regulatory proteins involved in the regulation of signal transduction and gene expression that respond to drought stress. The meta-QTLs derived from this study and the genes that have been identified can be used effectively in molecular breeding and in genetic engineering for drought resistance/tolerance in rice.

scholarly journals Discrimination of drought tolerance in a worldwide collection of safflower (Carthamus tinctorius L.) genotypes based on selection indices

2021 ◽  
Vol 117 (1) ◽  
pp. 1
Author(s):  
Pooran GOLKAR ◽  
Esmaeil HAMZEH ◽  
Seyed Ali Mohammad MIRMOHAMMADY MAIBODY
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Geometric Mean ◽  
Resistance Index ◽  
Stability Index ◽  
Carthamus Tinctorius ◽  
Tolerance Index ◽  
Breeding Programs ◽  
Drought Tolerance Indices ◽  
Tolerance Indices

<p>Improvement of elite safflower genotypes for drought-tolerance is hampered by a deficiency of effective selection criteria. The present study evaluated 100 genotypes of safflower in terms of their drought tolerance over a period of three years (2016–2018) under both non-stress and drought-stress conditions. The eight drought-tolerance indices of tolerance index (TOL), mean productivity (MP), geometric mean productivity (GMP), stress susceptibility index (SSI), stress tolerance index (STI), yield stability index (YSI), drought resistance index (DI), and harmonic mean (HARM) were calculated based on seed yield under drought (Y<sub>s</sub>) and non-drought (Y<sub>p</sub>) conditions. A high genetic variation was found in drought tolerance among the genotypes studied. The MP, GMP, and STI indices were able to discriminate between tolerant and drought-sensitive genotypes. Plots of the first and second principal components identified drought-tolerant genotypes averaged over the three study years. Cluster analysis divided the genotypes into three distinct groups using the drought tolerance indices. Ultimately, eight genotypes (namely, G<sub>3</sub>, G<sub>11</sub>, G<sub>13</sub>, G<sub>24</sub>, G<sub>33</sub>, G<sub>47</sub>, G<sub>58</sub>, and G<sub>61</sub>) from different origins were detected as more tolerant to drought stress suitable for use in safflower breeding programs in drought-affected areas. The most tolerant and susceptible genotypes could be exploited to produce mapping populations for drought tolerance breeding programs in safflower.</p>

scholarly journals In Vitro Assessment of Kurdish Rice Genotypes in Response to PEG-Induced Drought Stress

2020 ◽  
Vol 10 (13) ◽  
pp. 4471
Author(s):  
Didar Rahim ◽  
Petr Kalousek ◽  
Nawroz Tahir ◽  
Tomáš Vyhnánek ◽  
Petr Tarkowski ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Growth Parameters ◽  
Oryza Sativa L ◽  
Polymorphic Information Content ◽  
Callus Growth ◽  
Antioxidant Systems ◽  
In Vitro Tests ◽  
Rice Genotypes

Rice (Oryza sativa L.) is productively affected by different environmental factors, including biotic and abiotic stress. The objectives of this research were to evaluate the genetic distinction among Kurdish rice genotypes using the simple sequence repeats (SSRs) molecular markers and to perform in vitro tests to characterize the drought tolerance of six local rice genotypes. The polymorphic information content (PIC) varied from 0.38 to 0.84 with an average of 0.56. The genetic distance ranged from 0.33 to 0.88. Drought stress had a significant impact (p ≤ 0.05) on callus growth parameters. Enzymatic antioxidant systems were predicted and exhibited a significant variation. The findings revealed that proline levels increase in proportion to polyethylene glycol (PEG) concentrations. Kalar and Gwll Swr genotypes showed the worst performances in phenotypic and biochemical traits, while Choman and Shawre exhibited the best phenotypic and biochemical performances. A positive and substantial relationship between callus fresh weight (CFW) and callus dry weight (CDW) was found under stressful and optimized conditions. Callus induction (CI) was positively and significantly associated with the catalase activity (CAT) in all stressed treatments. Based on the results for callus growth and the biochemical parameters under stress conditions, a remarkable genotype distinction, based on the tolerance reaction, was noted as follows: PEG resistant > susceptible, Choman > Shawre > White Bazyan > Red Bazyan > Gwll Swr > Kalar. The CI and CAT characteristics were considered as reliable predictors of drought tolerance in rice genotypes.

scholarly journals Evaluation of Rice (Oryza sativa L.) Genotypes for Drought Tolerance at Germination and Early Seedling Stage

2018 ◽  
Vol 16 (1) ◽  
pp. 44-54 ◽  
Author(s):  
M M Islam ◽  
E Kayesh ◽  
E Zaman ◽  
T A Urmi ◽  
M M Haque
Keyword(s):  
Oryza Sativa ◽  
Water Stress ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Evaluation System ◽  
Oryza Sativa L ◽  
Dry Weight ◽  
Seedling Height ◽  
Early Seedling ◽  
Rice Genotypes

Drought stress is a major constraint to the production and yield stability of crops. Rice (Oryza sativa L.) is considered as a drought-sensitive crop species. Within this species, there are considerable varietal differences in sensitivity to this environmental stress. An experiment was conducted at the laboratory of the Department of Agronomy, Bangabandhu Sheikh Mujibur Rahman Agricultural University (BSMRAU), Bangladesh during April to September 2016 to evaluate 100 rice genotypes for drought tolerance during germination and early seedling growth stage. The genotypes were tested against five levels of drought stress imposed by Polyethylene glycol 6000 (PEG-6000) @ 0, 5, 10, 15 and 20%. The experiment was laid out in a complete randomized design with four replications. The results showed that with increasing water stress, germination in all the genotypes decreased from 95.8% in control to 6.6 % in highest stress (20% PEG) level. Seedling height and dry weight also decreased in all rice genotypes with the increase in water stress level. Based on Standard Evaluation System (SES),18 genotypes were selected primarily. Among the 18 genotypes, Ratoil and Chinisakkar showed higher germination index, relative seedling height and relative seedling dry weight than the check drought tolerant BRRI dhan43 at 20% PEG. Beside these, performance of Kumridhan, Pusur and Somondori was also well at this level compared to BRRI dhan43. The genotypes Ratoil, Chinisakkar, Kumridhan, Pusur and Somondori showed the best performance under drought condition. The Agriculturists 2018; 16(1) 44-54

scholarly journals Microbial Diversity of Upland Rice Roots and Their Influence on Rice Growth and Drought Tolerance

2020 ◽  
Vol 8 (9) ◽  
pp. 1329
Author(s):  
Zhiqiang Pang ◽  
Ying Zhao ◽  
Peng Xu ◽  
Diqiu Yu
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Plant Growth ◽  
Upland Rice ◽  
Oryza Sativa L ◽  
Soluble Sugar ◽  
Stress Conditions ◽  
Rice Roots ◽  
Microbial Resources

Among abiotic stresses, drought is one of the most important factors limiting plant growth. To increase their drought tolerance and survival, most plants interact directly with a variety of microbes. Upland rice (Oryza sativa L.) is a rice ecotype that differs from irrigated ecotype rice; it is adapted to both drought-stress and aerobic conditions. However, its root microbial resources have not been explored. We isolated bacteria and fungi from roots of upland rice in Xishuangbanna, China. Four hundred sixty-two endophytic and rhizospheric isolates (337 bacteria and 125 fungi) were distributed. They were distributed among 43 genera on the basis of 16S rRNA and internal transcribed spacer (ITS) gene sequence analysis. Notably, these root microbes differed from irrigated rice root microbes in irrigated environments; for example, members of the Firmicutes phylum were enriched (by 28.54%) in the roots of the upland plants. The plant growth-promoting (PGP) potential of 217 isolates was investigated in vitro. The PGP ability of 17 endophytic and 10 rhizospheric isolates from upland rice roots was evaluated under well-irrigated and drought-stress conditions, and 9 fungal strains increased rice seedling shoot length, shoot and root fresh weight (FW), antioxidant capability, and proline (Pro) and soluble sugar contents. Our work suggests that fungi from upland rice roots can increase plant growth under irrigated and drought-stress conditions and can serve as effective microbial resources for sustainable agricultural production in arid regions.

scholarly journals Molecular-genetic maps for group 1 chromosomes of Triticeae species and their relation to chromosomes in rice and oat

Genome ◽  
1995 ◽  
Vol 38 (1) ◽  
pp. 45-59 ◽  
Author(s):  
A. E. Van Deynze ◽  
J. Dubcovsky ◽  
K. S. Gill ◽  
J. C. Nelson ◽  
M. E. Sorrells ◽  
...  
Keyword(s):  
Dna Markers ◽  
Molecular Genetic ◽  
Genetic Maps ◽  
Chromosome 1 ◽  
Linkage Maps ◽  
Consensus Map ◽  
Triticeae Species ◽  
Group 1 Chromosomes ◽  
Homoeologous Chromosomes ◽  
Group 1

Group 1 chromosomes of the Triticeae tribe have been studied extensively because many important genes have been assigned to them. In this paper, chromosome 1 linkage maps of Triticum aestivum, T. tauschii, and T. monococcum are compared with existing barley and rye maps to develop a consensus map for Triticeae species and thus facilitate the mapping of agronomic genes in this tribe. The consensus map that was developed consists of 14 agronomically important genes, 17 DNA markers that were derived from known-function clones, and 76 DNA markers derived from anonymous clones. There are 12 inconsistencies in the order of markers among seven wheat, four barley, and two rye maps. A comparison of the Triticeae group 1 chromosome consensus map with linkage maps of homoeologous chromosomes in rice indicates that the linkage maps for the long arm and the proximal portion of the short arm of group 1 chromosomes are conserved among these species. Similarly, gene order is conserved between Triticeae chromosome 1 and its homoeologous chromosome in oat. The location of the centromere in rice and oat chromosomes is estimated from its position in homoeologous group 1 chromosomes of Triticeae.Key words: Triticeae, RFLP, consensus, comparative.

scholarly journals Genotype by environment analysis of rice (Oryza sativa L.) populations under drought stressed and well-watered environments

2020 ◽  
pp. 259-262
Author(s):  
Lourine Chebet Bii ◽  
Kahiu Ngugi ◽  
John M. Kimani ◽  
George N. Chemining’ wa
Keyword(s):  
Oryza Sativa ◽  
Drought Stress ◽  
Drought Tolerance ◽  
Grain Yield ◽  
Oryza Sativa L ◽  
Phenotypic Traits ◽  
Yield Data ◽  
Physiological Maturity ◽  
Lattice Design ◽  
Gge Biplots

In Kenya, the key abiotic stress affecting rice production is drought stress which is experienced mainly during reproductive phase of the crop. This study evaluated the performance of Kenyan rice populations including 19 generation of crosses, 6 parental and 5 checks under well-watered and drought stressed environment with the aim of identifying the phenotypic traits that confer drought tolerance in rice. The 19 generation of crosses were in F3 when they were evaluated in the short rains season and later advanced to F4 in the long rains season. Nineteen generation of crosses rice (Oryza sativa L.) lines, six parental and five check lines were evaluated for response to drought under drought stressed and well-watered environment. The study was conducted over two seasons in the year 2016/2017 at Kenya Agricultural Livestock Research Organization (KALRO) -Mwea Centre. The experiment was set up in an alpha lattice design with three replications. Drought stress was imposed at panicle initiation by withholding irrigation till physiological maturity meanwhile the well-watered environment continued to enjoy the recommended irrigation regime from planting to physiological maturity. Yield data were scored for drought tolerance. AMMI analysis of variance for grain yield showed that genotypes from crosses of crosses of SARO5XNERICA11, NERICA2XSARO5 and NERICA15XSARO5 expressed high grain yield. AMMI stability Variance (ASV) showed genotypes NERICA15, Duorado Precoce and progenies from crosses of NERICA11XNERICA2, SARO5XKomboka and NERICA2XNERICA11 expressed high stability in both well-watered and drought-stressed environment. GGE analysis showed that Principal Components (PC1) and PC2 accounted for 96.46% and 3.54%, respectively. GGE biplots showed that genotypes from crosses SARO5XNERICA11 and NERICA15XSARO5 were the most stable and high yielding. GGE biplots ranked the rice lines as follows: those above average in performance, the stable ones, unstable and those below average in performance. SARO5XNERICA11 is worth of selection due to its high mean yield value and is stable across the mega-environments.

QTL analysis of floral traits of rice (Oryza Sativa L.) under well-watered and drought stress conditions

2009 ◽  
Vol 31 (2) ◽  
pp. 173-181 ◽  
Author(s):  
Hu Songping ◽  
Zhou Ying ◽  
Zhang Lin ◽  
Zhu Xudong ◽  
Wang Zhenggong ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Drought Stress ◽  
Qtl Analysis ◽  
Oryza Sativa L ◽  
Stress Conditions ◽  
Floral Traits

scholarly journals Drought-Tolerance Gene Identification Using Genome Comparison and Co-Expression Network Analysis of Chromosome Substitution Lines in Rice

Genes ◽  
2020 ◽  
Vol 11 (10) ◽  
pp. 1197
Author(s):  
Chutarat Punchkhon ◽  
Kitiporn Plaimas ◽  
Teerapong Buaboocha ◽  
Jonaliza L. Siangliw ◽  
Theerayut Toojinda ◽  
...  
Keyword(s):  
Drought Stress ◽  
Network Analysis ◽  
Drought Tolerance ◽  
Rice Variety ◽  
Rice Genome ◽  
Net Photosynthesis ◽  
Chromosome 1 ◽  
Genome Comparison ◽  
Substitution Lines ◽  
Chromosome Segment Substitution Lines

Drought stress limits plant growth and productivity. It triggers many responses by inducing changes in plant morphology and physiology. KDML105 rice is a key rice variety in Thailand and is normally grown in the northeastern part of the country. The chromosome segment substitution lines (CSSLs) were developed by transferring putative drought tolerance loci (QTLs) on chromosome 1, 3, 4, 8, or 9 into the KDML105 rice genome. CSSL104 is a drought-tolerant line with higher net photosynthesis and leaf water potential than KDML105 rice. The analysis of CSSL104 gene regulation identified the loci associated with these traits via gene co-expression network analysis. Most of the predicted genes are involved in the photosynthesis process. These genes are also conserved in Arabidopsis thaliana. Seven genes encoding chloroplast proteins were selected for further analysis through characterization of Arabidopsis tagged mutants. The response of these mutants to drought stress was analyzed daily for seven days after treatment by scoring green tissue areas via the PlantScreen™ XYZ system. Mutation of these genes affected green areas of the plant and stability index under drought stress, suggesting their involvement in drought tolerance.

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