Computational characterization of structural and functional roles of DREB1A, DREB1B and DREB1C in enhancing cold tolerance in rice plant

Donde, Ravindra; Gupta, Manoj; Gouda, Gayatri; Kumar, Jitendra; Vadde, Ramakrishna; Sahoo, Khirod Kumar; Dash, Sushanta Kumar; Behera, Lambodar

doi:10.1007/s00726-019-02727-0

Cited by 35 publications

(20 citation statements)

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“…QTL association has been widely used for the identification and mapping of QTLs for various traits such as tolerance to biotic and abiotic stresses, quality and grain yield in different crops [4,6,13,42,49,73]. This study also targets findings new QTLs, alleles, and genes [74] and validate the previously reported QTLs.…”

Section: Discussionsupporting

confidence: 60%

“…A breakthrough in productivity barrier is necessitated because of increasing competition for natural resources viz., land, water and others given population explosion coupled with expanding industrialization, urbanization and diversion of agricultural land [1,4,5]. This is still aggravated with the abnormal change in weather and climate with significant influence on crop productivity and quality [6, 7].…”

Section: Introductionmentioning

confidence: 99%

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Identification of QTLs for high grain yield and component traits in New Plant Types of rice

Donde

Mohapatra

Baksh

et al. 2020

Preprint

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16A panel of 60 genotypes consisting of New Plant Types (NPTs) along with indica, tropical and 17 temperate japonica genotypes were phenotypically evaluated for four seasons in irrigated situation 18 for grain yield per se and component traits. Twenty NPT genotypes were found to be promising with 19 an average grain yield of 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to 20 identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were 21 found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A 22 moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 23 8% within genotypes, 68% among the genotypes within the population and 24% among the 24 populations were observed (AMOVA). The association analysis using GLM and MLM models led to 25 the identification of 30 and 10 SSR markers were associated with 70 and 16 QTLs, respectively. 26 Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely, 27 tiller number (qTL-6. 29 total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight 30 qTGW-8.1 ), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, 31 qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se 11.1). This information could be useful for identification of highly potential parents for development 33 of transgressive segregants. Moreover, super rice genotypes could be developed through pyramiding 34 of these QTLS for important yield traits for prospective increment in yield potentiality and breaking 35 yield ceiling. 36 Introduction 39Rice (Oryza sativa L.) is a staple crop for more than 3.5 billion people in the globe. In current 40 scenario, rice productivity is increasing rate at 1% per year which is less than the 2.4% per year rate 41 required to double the global production by 2050 [1]. Considering a glimpse of the history, a 42 quantum jump in productivity was achieved due to the green revolution in mid-sixties, which 43 drastically enhanced the rice production of the world. However, a ceiling of productivity potentiality 44 is reported by and large in semi-dwarf inbred indica genotypes since release of , in spite of 45 substantial improvement in yield stability, per day productivity and grain quality [3]. A 46 breakthrough in productivity barrier is necessitated because of increasing competition for natural 47 resources viz., land, water and others given population explosion coupled with expanding 48 industrialization, urbanization and diversion of agricultural land [1,4,5]. This is still aggravated with 49 the abnormal change in weather and climate with significant influence on crop productivity and 50 quality [6,7]. 51Rice scientists are facing many challenges for doubling rice production by 2050. Irrigated 52 rice has a share of 75% of total rice production in the world, although it has a share of about 55% of 53 the total rice area [2]. Therefore, improveme...

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Section: Discussionsupporting

confidence: 60%

Section: Introductionmentioning

confidence: 99%

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

Donde

Mohapatra

Baksh

et al. 2020

Preprint

Self Cite

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“…Heterologous overexpression of zoysia grass (Zoysia japonica) ZjDREB1.4 in Arabidopsis enhanced tolerance to high and freezing temperature stresses without obvious growth inhibition (Feng et al 2019). In rice (Oryza sativa), the interaction of OsDREB1A, OsDREB1B, and OsDREB1C with the GCC box enhanced the cold tolerance of the plants (Donde et al 2019). Thus, DREB1 TFs are mainly associated with cold stress regulation.…”

Section: Introductionmentioning

confidence: 99%

Peer Review #4 of "Identification and expression analysis of the DREB transcription factor family in pineapple (Ananas comosus (L.) Merr.) (v0.1)"

Faraji¹

2020

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Background: Dehydration responsive element-binding (DREB) transcription factors play a crucial role in plant growth, development, and stress responses. Although DREB genes have been characterized in many plant species, genome-wide identification of the DREB gene family has not yet been reported in pineapple (Ananas comosus (L.) Merr.). Results: Using comprehensive genome-wide screening, we identified 20 AcoDREB genes on 14 chromosomes. These were categorized into five subgroups. AcoDREBs within a group had similar gene structures and domain compositions. Using gene structure analysis, we showed that most AcoDREB genes (75%) lacked introns, and that the promoter regions of all 20 AcoDREB genes had at least one stress response-related cis-element. We identified four genes with high expression levels and six genes with low expression levels in all analyzed tissues. We detected expression changes under abiotic stress for eight selected AcoDREB genes. Conclusions: This report presents the first genome-wide analysis of the DREB transcription factor family in pineapple. Our results provide preliminary data for future functional analysis of AcoDREB genes in pineapple, and useful information for developing new pineapple varieties with key agronomic traits such as stress tolerance.

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“…As it is native to India, it has been widely cultivated since ancient times in South and South-East Asian countries (Patel et al 2017). However, the fast industrialization and mechanization that are associated with shortening agricultural lands have severely affected crops developments via enhancing both abiotic and biotic stresses on crops plant (Gupta et al, 2018;Gouda et al, 2019;Donde et al, 2019;Gupta et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

“…However, in response to these pathogen, plants induce multiple signalling pathways at transcriptional as well as translational level, including activation of cytosolic Ca2+, mitogen-activated protein kinases (MAPKs), reactive oxygen species (ROS), fortification of plant cell wall, various transcription factors and initiation of several pathogenesis-related (PR) gene products that in turn either inhibit the growth or penetration of pathogen into the plant (Gupta et al, 2018;Gouda et al, 2019;Donde et al, 2019;Gupta et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

De novo assembly and characterization of transcriptome towards understanding molecular mechanism associated with MYMIV-resistance in Vigna mungo - A computational study

Gupta

Donde

Gouda

et al. 2019

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The fast climate change affects yield in Vigna mungo via enhancing both biotic and abiotic stresses.Out of all factors, the yellow mosaic disease has the most damaging effect. However, due to lack of reference genome of Vigna mungo, the complete mechanism associated with MYMIV (Mungbean Yellow Mosaic Indian Virus) resistance in Vigna mungo remain elusive to date. Considering this, the authors made an attempt to release new transcriptome and its annotation by employing computational approaches. Quality assessment of the generated transcriptomes reveals that it successfully aligned with 99.03% of the raw reads and hence can be employed for future research. Functional annotation of the transcriptome reveals that 31% and ~14% of the total transcripts encode lncRNAs and protein-coding sequences, respectively. Further, analysis reveals that, out of total transcripts, only 4536 and 78808 are significantly down and up-regulated during MYMIV infection in Vigna mungo, respectively. These significant transcripts are mainly associated with ribosome, spliceosome, glycolysis /gluconeogenesis, RNA transport, oxidative phosphorylation, protein processing in the endoplasmic reticulum, MAPK signaling pathway -plant, methionine and cysteine metabolism, purine metabolism and RNA degradation. Unlike the previous study, this is for the first time, the present study identified these pathways may play key role in MYMIV resistance in Vigna mungo. Thus, information and transcriptomes data available in the present study make a significant contribution to understanding the genomic structure of Vigna mungo, enabling future analyses as well as downstream applications of gene expression, sequence evolution, and genome annotation.

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Computational characterization of structural and functional roles of DREB1A, DREB1B and DREB1C in enhancing cold tolerance in rice plant

Cited by 35 publications

References 55 publications

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

Identification of QTLs for high grain yield and component traits in New Plant Types of rice

Peer Review #4 of "Identification and expression analysis of the DREB transcription factor family in pineapple (Ananas comosus (L.) Merr.) (v0.1)"

De novo assembly and characterization of transcriptome towards understanding molecular mechanism associated with MYMIV-resistance in Vigna mungo - A computational study

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