A KBase Case Study on Genome-wide Transcriptomics and Plant Primary Metabolism in response to Drought Stress in Sorghum.

Abstract Background Cotton is an important commercial crop for being a valuable source of natural fiber. Its production has undergone a sharp decline because of abiotic stresses, etc. Drought is one of the major abiotic stress causing significant yield losses in cotton. However, plants have evolved self-defense mechanisms to cope abiotic factors like drought, salt, cold, etc. The evolution of stress responsive transcription factors such as the trihelix, a nodule-inception-like protein (NLP), and the late embryogenesis abundant proteins have shown positive response in the resistance improvement to several abiotic stresses. Results Genome wide identification and characterization of the effects of Light-Harvesting Chloro a/b binding (LHC) genes were carried out in cotton under drought stress conditions. A hundred and nine proteins encoded by the LHC genes were found in the cotton genome, with 55, 27, and 27 genes found to be distributed in Gossypium hirsutum, G. arboreum, and G. raimondii, respectively. The proteins encoded by the genes were unevenly distributed on various chromosomes. The Ka/Ks (Non-synonymous substitution rate/Synonymous substitution rate) values were less than one, an indication of negative selection of the gene family. Differential expressions of genes showed that majority of the genes are being highly upregulated in the roots as compared with leaves and stem tissues. Most genes were found to be highly expressed in MR-85, a relative drought tolerant germplasm. Conclusion The results provide proofs of the possible role of the LHC genes in improving drought stress tolerance, and can be explored by cotton breeders in releasing a more drought tolerant cotton varieties.

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Genome-wide investigation on transcriptional responses to drought stress in wild and cultivated rice

Environmental and Experimental Botany ◽

10.1016/j.envexpbot.2021.104555 ◽

2021 ◽

pp. 104555

Author(s):

Mu-Fan Geng ◽

Xiu-Hua Wang ◽

Mei-Xia Wang ◽

Zhe Cai ◽

Qing-Lin Meng ◽

...

Keyword(s):

Drought Stress ◽

Cultivated Rice ◽

Transcriptional Responses ◽

Genome Wide

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Comprehensive analysis and identification of drought-responsive candidate NAC genes in three semi-arid tropics (SAT) legume crops

BMC Genomics ◽

10.1186/s12864-021-07602-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Sadhana Singh ◽

Himabindu Kudapa ◽

Vanika Garg ◽

Rajeev K. Varshney

Keyword(s):

Drought Stress ◽

Candidate Genes ◽

Developmental Stages ◽

Biological Activities ◽

Expression Patterns ◽

Genome Wide ◽

Legume Crops ◽

Root Tissues ◽

Semi Arid ◽

Comprehensive Study

Abstract Background Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem, ATAF - Arabidopsis transcription activation factor, and CUC - cup-shaped cotyledon) transcription factor family is known to be involved in majority of abiotic stresses, especially in the drought stress tolerance mechanism. Despite the knowledge available regarding NAC function, not much information is available on NAC genes in SAT legume crops. Results In this study, genome-wide NAC proteins – 72, 96, and 166 have been identified from the genomes of chickpea, pigeonpea, and groundnut, respectively, and later grouped into 10 clusters in chickpea and pigeonpea, while 12 clusters in groundnut. Phylogeny with well-known stress-responsive NACs in Arabidopsis thaliana, Oryza sativa (rice), Medicago truncatula, and Glycine max (soybean) enabled prediction of putative stress-responsive NACs in chickpea (22), pigeonpea (31), and groundnut (33). Transcriptome data revealed putative stress-responsive NACs at various developmental stages that showed differential expression patterns in the different tissues studied. Quantitative real-time PCR (qRT-PCR) was performed to validate the expression patterns of selected stress-responsive, Ca_NAC (Cicer arietinum - 14), Cc_NAC (Cajanus cajan - 15), and Ah_NAC (Arachis hypogaea - 14) genes using drought-stressed and well-watered root tissues from two contrasting drought-responsive genotypes of each of the three legumes. Based on expression analysis, Ca_06899, Ca_18090, Ca_22941, Ca_04337, Ca_04069, Ca_04233, Ca_12660, Ca_16379, Ca_16946, and Ca_21186; Cc_26125, Cc_43030, Cc_43785, Cc_43786, Cc_22429, and Cc_22430; Ah_ann1.G1V3KR.2, Ah_ann1.MI72XM.2, Ah_ann1.V0X4SV.1, Ah_ann1.FU1JML.2, and Ah_ann1.8AKD3R.1 were identified as potential drought stress-responsive candidate genes. Conclusion As NAC genes are known to play role in several physiological and biological activities, a more comprehensive study on genome-wide identification and expression analyses of the NAC proteins have been carried out in chickpea, pigeonpea and groundnut. We have identified a total of 21 potential drought-responsive NAC genes in these legumes. These genes displayed correlation between gene expression, transcriptional regulation, and better tolerance against drought. The identified candidate genes, after validation, may serve as a useful resource for molecular breeding for drought tolerance in the SAT legume crops.

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To Stretch the Boundary of Secondary Metabolite Production in Plant Cell-Based Bioprocessing: Anthocyanin as a Case Study

Journal of Biomedicine and Biotechnology ◽

10.1155/s1110724304404148 ◽

2004 ◽

Vol 2004 (5) ◽

pp. 264-271 ◽

Cited By ~ 18

Author(s):

Wei Zhang ◽

Chris Franco ◽

Chris Curtin ◽

Simon Conn

Keyword(s):

Secondary Metabolites ◽

Plant Cell ◽

Metabolic Pathways ◽

Anthocyanin Biosynthesis ◽

Rational Approach ◽

Great Promise ◽

Primary Metabolism ◽

Global Correlation ◽

Empirical Level

Plant cells and tissue cultures hold great promise for controlled production of a myriad of useful secondary metabolites on demand. The current yield and productivity cannot fulfill the commercial goal of a plant cell-based bioprocess for the production of most secondary metabolites. In order to stretch the boundary, recent advances, new directions and opportunities in plant cell-based bioprocessing, have been critically examined for the 10 years from 1992 to 2002. A review of the literature indicated that most of the R&D work was devoted predominantly to studies at an empirical level. A rational approach to molecular plant cell bioprocessing based on the fundamental understanding of metabolic pathways and their regulations is urgently required to stimulate further advances; however, the strategies and technical framework are still being developed. It is the aim of this review to take a step forward in framing workable strategies and technologies for molecular plant cell-based bioprocessing. Using anthocyanin biosynthesis as a case study, an integrated postgenomic approach has been proposed. This combines the functional analysis of metabolic pathways for biosynthesis of a particular metabolite from profiling of gene expression and protein expression to metabolic profiling. A global correlation not only can thus be established at the three molecular levels, but also places emphasis on the interactions between primary metabolism and secondary metabolism; between competing and/or complimentary pathways; and between biosynthetic and post-biosynthetic events.

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Advances in genome-wide RNAi cellular screens: a case study using the Drosophila JAK/STAT pathway

BMC Genomics ◽

10.1186/1471-2164-13-506 ◽

2012 ◽

Vol 13 (1) ◽

pp. 506 ◽

Cited By ~ 19

Author(s):

Katherine H Fisher ◽

Victoria M Wright ◽

Amy Taylor ◽

Martin P Zeidler ◽

Stephen Brown

Keyword(s):

Genome Wide ◽

Stat Pathway

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Genome-wide SNP discovery, linkage mapping, and analysis of QTL for morpho-physiological traits in rice during vegetative stage under drought stress

Physiology and Molecular Biology of Plants ◽

10.1007/s12298-021-01095-y ◽

2021 ◽

Author(s):

Rizky Dwi Satrio ◽

Miftahul Huda Fendiyanto ◽

Ence Darmo Jaya Supena ◽

Sony Suharsono ◽

Miftahudin Miftahudin

Keyword(s):

Drought Stress ◽

Linkage Mapping ◽

Physiological Traits ◽

Vegetative Stage ◽

Snp Discovery ◽

Genome Wide

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Genome-wide identification of AP2/ERF transcription factors in mungbean (Vigna radiata) and expression profiling of the VrDREB subfamily under drought stress

Crop and Pasture Science ◽

10.1071/cp18180 ◽

2018 ◽

Vol 69 (10) ◽

pp. 1009 ◽

Cited By ~ 3

Author(s):

Abdullahi Muhammad Labbo ◽

Maryam Mehmood ◽

Malik Nadeem Akhtar ◽

Muhammad Jawad Khan ◽

Aamira Tariq ◽

...

Keyword(s):

Transcription Factors ◽

Drought Stress ◽

Stress Tolerance ◽

Vigna Radiata ◽

Critical Role ◽

Drought Stress Tolerance ◽

Legume Crop ◽

Genome Wide ◽

Responsive Element ◽

Major Factors

Mungbean (Vigna radiata L.) is a valuable legume crop grown in tropical and subtropical areas of Asia. Drought is one of the major factors hindering its growth globally. APETALA2/ethylene-responsive element factor binding proteins (AP2/ERF) are an important family of plant-specific transcription factors (TFs) involved in drought-stress tolerance. We identified 71 AP2/ERF TFs in the mungbean genome by using bioinformatics tools and classified them into subfamilies: AP2 (16 members), ERF (22), RAV (2), DREB (30) and soloist (other proteins with no domain, 1). Members of DREB play a critical role in drought-stress tolerance. Ten-day-old mungbean plants cv. AZRI-06 were exposed to drought stress by complete withholding of water for 7 days. Root samples were collected from control and drought-stressed plants, and the expression pattern of 30 identified VrDREB genes was determined by qPCR. Most VrDREB genes exhibited differential expression in response to drought. Five genes (VrDREB5, VrDREB12, VrDREB13, VrDREB22, VrDREB30) were highly expressed under drought stress and might be considered excellent candidates for further functional analysis and for improvement of mungbean drought tolerance.

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Methylome and transcriptome analyses of soybean response to bean pyralid larvae

BMC Genomics ◽

10.1186/s12864-021-08140-w ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Wei-Ying Zeng ◽

Yu-Rong Tan ◽

Sheng-Feng Long ◽

Zu-Dong Sun ◽

Zhen-Guang Lai ◽

...

Keyword(s):

Dna Methylation ◽

Protein Biosynthesis ◽

Cell Structure ◽

Methylation Profile ◽

Primary Metabolism ◽

Global Methylation ◽

Genome Wide ◽

Differentially Methylated Genes ◽

Dna Methylation Profile ◽

Soybean Resistance

Abstract Background Bean pyralid is one of the major leaf-feeding insects that affect soybean crops. DNA methylation can control the networks of gene expressions, and it plays an important role in responses to biotic stress. However, at present the genome-wide DNA methylation profile of the soybean resistance to bean pyralid has not been reported so far. Results Using whole-genome bisulfite sequencing (WGBS) and RNA-sequencing (RNA-seq), we analyzed the highly resistant material (Gantai-2-2, HRK) and highly susceptible material (Wan82–178, HSK), under bean pyralid larvae feeding 0 h and 48 h, to clarify the molecular mechanism of the soybean resistance and explore its insect-resistant genes. We identified 2194, 6872, 39,704 and 40,018 differentially methylated regions (DMRs), as well as 497, 1594, 9596 and 9554 differentially methylated genes (DMGs) in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48 comparisons, respectively. Through the analysis of global methylation and transcription, 265 differentially expressed genes (DEGs) were negatively correlated with DMGs, there were 34, 49, 141 and 116 negatively correlated genes in the HRK0/HRK48, HSK0/HSK48, HSK0/HRK0 and HSK48/HRK48, respectively. The MapMan cluster analysis showed that 114 negatively correlated genes were clustered in 24 pathways, such as protein biosynthesis and modification; primary metabolism; secondary metabolism; cell cycle, cell structure and component; RNA biosynthesis and processing, and so on. Moreover, CRK40; CRK62; STK; MAPK9; L-type lectin-domain containing receptor kinase VIII.2; CesA; CSI1; fimbrin-1; KIN-14B; KIN-14 N; KIN-4A; cytochrome P450 81E8; BEE1; ERF; bHLH25; bHLH79; GATA26, were likely regulatory genes involved in the soybean responses to bean pyralid larvae. Finally, 5 DMRs were further validated that the genome-wide DNA data were reliable through PS-PCR and 5 DEGs were confirmed the relationship between DNA methylation and gene expression by qRT-PCR. The results showed an excellent agreement with deep sequencing. Conclusions Genome-wide DNA methylation profile of soybean response to bean pyralid was obtained for the first time. Several specific DMGs which participated in protein kinase, cell and organelle, flavonoid biosynthesis and transcription factor were further identified to be likely associated with soybean response to bean pyralid. Our data will provide better understanding of DNA methylation alteration and their potential role in soybean insect resistance.

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