Genome‐wide discovery of DNA polymorphisms via resequencing of chickpea cultivars with contrasting response to drought stress

2021 ◽  
Author(s):  
Mohan Singh Rajkumar ◽  
Rohini Garg ◽  
Mukesh Jain
Keyword(s):  
Drought Stress ◽  
Dna Polymorphisms ◽  
Genome Wide ◽  
Chickpea Cultivars

scholarly journals Genome wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Teame Gereziher MEHARI ◽  
Yanchao XU ◽  
Richard Odongo MAGWANGA ◽  
Muhammad Jawad UMER ◽  
Joy Nyangasi KIRUNGU ◽  
...  
Keyword(s):  
Drought Stress ◽  
Gossypium Hirsutum ◽  
Abiotic Stresses ◽  
Substitution Rate ◽  
Synonymous Substitution ◽  
Synonymous Substitution Rate ◽  
Drought Tolerant ◽  
Genome Wide ◽  
Identification And Characterization

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.

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

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

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

BMC Genomics ◽  
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.

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

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

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

2018 ◽  
Vol 69 (10) ◽  
pp. 1009 ◽  
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.

scholarly journals Genome-wide transcriptional and physiological responses to drought stress in leaves and roots of two willow genotypes

2015 ◽  
Vol 15 (1) ◽  
Author(s):  
Pascal Pucholt ◽  
Per Sjödin ◽  
Martin Weih ◽  
Ann Christin Rönnberg-Wästljung ◽  
Sofia Berlin
Keyword(s):  
Drought Stress ◽  
Physiological Responses ◽  
Genome Wide ◽  
Leaves And Roots

Genome-wide identification and expression analysis of calmodulin-binding transcription activator genes in banana under drought stress

2019 ◽  
Vol 244 ◽  
pp. 10-14 ◽  
Author(s):  
Laraib Meer ◽  
Sana Mumtaz ◽  
Abdullahi Muhammad Labbo ◽  
Muhammad Jawad Khan ◽  
Irfan Sadiq
Keyword(s):  
Drought Stress ◽  
Expression Analysis ◽  
Transcription Activator ◽  
Calmodulin Binding ◽  
Genome Wide
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