Subtractive hybridization‐mediated analysis of genes and <i>in silico</i> prediction of associated microRNAs under waterlogged conditions in sugarcane (<i>Saccharum</i> spp.)

Khan, Mohammad Suhail; Khraiwesh, Basel; Pugalenthi, Ganesan; Gupta, R. S.; Singh, Jogendra; Duttamajumder, S. K.; Kapur, Raman

doi:10.1016/j.fob.2014.05.007

Cited by 22 publications

(16 citation statements)

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“…Subtractive suppression hybridization is a powerful technique that enables researchers to compare two populations of mRNA and obtain clones of genes that are expressed in one population but not in the other (Almeida et al 2013;Ding et al 2014;Khan et al 2014). In the present study, drought stress responsive subtractive cDNA library was constructed from 22 days old pearl millet seedlings [P. glaucum cv.…”

Section: Discussionmentioning

confidence: 99%

“…Among the various methods for differential transcriptome analysis, Suppression Subtractive Hybridization (SSH) proves to be an efficient approach to isolate and identify cDNAs of differentially expressed genes in the absence of sequence information (Mishra et al 2007;Almeida et al 2013;Ding et al 2014;Khan et al 2014). In this technique differentially expressed genes can be normalized and enriched over 1000-fold in a single round of hybridization (Diatchenko et al 1996).…”

Section: Introductionmentioning

confidence: 99%

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Transcriptional profiling in pearl millet (Pennisetum glaucum L.R. Br.) for identification of differentially expressed drought responsive genes

Choudhary

Jayanand

Padaria

2015

Physiol Mol Biol Plants

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Pearl millet (Pennisetum glaucum) is an important cereal of traditional farming systems that has the natural ability to withstand various abiotic stresses. The present study aims at the identification and validation of major differentially expressed genes in response to drought stress in P. glaucum by Suppression Subtractive Hybridization (SSH) analysis. Twenty-two days old seedlings of P. glaucum cultivar PPMI741 were subjected to drought stress by treatment of 30 % Polyethylene glycol for different time periods 30 min

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Transcriptional profiling in pearl millet (Pennisetum glaucum L.R. Br.) for identification of differentially expressed drought responsive genes

Choudhary

Jayanand

Padaria

2015

Physiol Mol Biol Plants

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“…The gene SUFT, which is involved in the Fe/S cluster assembly pathway, has been reported that it is necessary for effective symbiosis to enhance iron availability [42]. Heat shock cognate 70 kDa protein is a chaperone which assist the folding of other proteins in vivo, and it was found to have increased expression in sugarcane plant subjected to WL treatment [43]. SAR1 in plants plays roles in GTPase activity, cargo secretion, membrane constriction, etc.…”

Section: Discussionmentioning

confidence: 99%

iTRAQ-based Comparative Proteomic Analysis of Flag Leaves of Two Wheat (Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance at Anthesis

Wei

Xie

et al. 2020

Preprint

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Background: Waterlogging is one of the major abiotic stresses limiting wheat product. Plants can adapt to waterlogging with changes in morphology, anatomy, and metabolism. Many genes and proteins play critical roles in adaptation to waterlogging. Results: the iTRAQ-based proteomic strategy was applied to identify the waterlogging-responsive proteins in wheat. A total of 4,999 unique proteins were identified in two wheat varieties, XM55 (waterlogging-tolerant) and YM158 (waterlogging-sensitive), at anthesis under waterlogging or not. Sixteen proteins were differentially accumulated between XM55 and YM158 under waterlogging with cultivar specificity. Of these, 11 proteins were up-regulated and 5 proteins were down-regulated. The up-regulated proteins included Fe-S cluster assembly factor, heat shock cognate 70, GTP-binding protein SAR1A-like, and CBS domain-containing protein. The down-regulated proteins contained photosystem II reaction center protein H, carotenoid 9,10 (9',10')-cleavage dioxygenase-like, psbP-like protein 1, and mitochondrial ATPase inhibitor. In addition, 9 proteins were responsive to waterlogging with non-cultivar specificity. These proteins included 3-isopropylmalate dehydratase large subunit, solanesyl-diphosphate synthase 2, DEAD-box ATP-dependent RNA helicase 3, and 3 predicted or uncharacterized proteins. Conclusions: This study revealed that the proteins were differential accumulated between the two contrast waterlogging wheat varieties in response to waterlogging, which provide valuable insights into wheat response to waterlogging stress. These differentially accumulated proteins might be applied to develop waterlogging tolerant wheat in further breeding programs.

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“…The gene sufT, which is involved in the Fe/S cluster assembly pathway, has been shown necessary for effective symbiosis to enhance iron availability [29]. Heat shock cognate 70 kDa protein is a chaperone which assist the folding of other proteins in vivo, and it was found to have increased expression in sugarcane plant subjected to WL [30]. Sar1 in plants showing GTPase activity, cargo secretion, membrane constriction, etc.…”

Section: Comparison Of Protein Changes In Xm55 and Ym158 Under Wlmentioning

confidence: 99%

iTRAQ-based Comparative Proteomic Analysis of Flag Leaves of Two Wheat (Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance at Anthesis

Wei

Xie

et al. 2019

Preprint

View full text Add to dashboard Cite

Background Waterlogging is one of the major abiotic stresses limiting wheat product. Plants can adapt to waterlogging with changes in morphology, anatomy, and metabolism. A number of genes or proteins were responsive to waterlogging. Results in this sduty, the iTRAQ-based proteomic strategy was applied to identify waterlogging-responsive proteins in wheat. A total of 7710 proteins were identified in waterlogging tolerant and sensitive wheat varieties XM55 and YM158 at anthesis under waterlogging or not. Sixteen proteins were differentially accumulated between XM55 and YM158 under waterlogging with cultivar specificity. Among them, eleven proteins were up-regulated and five proteins were down-regulated. The up-regulated proteins included Fe-S cluster assembly factor, heat shock cognate 70, GTP-binding protein SAR1A-like, and CBS domain-containing protein. The down-regulated proteins contained photosystem II reaction center protein H, carotenoid 9,10 (9',10')-cleavage dioxygenase-like, psbP-like protein 1, and mitochondrial ATPase inhibitor. In addition, nine proteins were responsive to waterlogging with non-cultivar specificity. These proteins included 3-isopropylmalate dehydratase large subunit, solanesyl-diphosphate synthase 2, DEAD-box ATP-dependent RNA helicase 3, and three predicted or uncharacterized proteins. Sixteen out of the twenty-eight selected proteins showed consistent expression patterns between mRNA and protein levels by quantitative real-time PCR. Conclusions: Our study indicates the much proteins were differential accumulated between the two contrast waterlogging wheat varieties in response to waterlogging, which provide insight into wheat response to waterlogging stress. The identified differentially accumulated protein might be applied to develop waterlogging tolerant wheat.

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Subtractive hybridization‐mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.)

Cited by 22 publications

References 68 publications

Transcriptional profiling in pearl millet (Pennisetum glaucum L.R. Br.) for identification of differentially expressed drought responsive genes

Transcriptional profiling in pearl millet (Pennisetum glaucum L.R. Br.) for identification of differentially expressed drought responsive genes

iTRAQ-based Comparative Proteomic Analysis of Flag Leaves of Two Wheat (Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance at Anthesis

iTRAQ-based Comparative Proteomic Analysis of Flag Leaves of Two Wheat (Triticum aestivum L.) Genotypes Differing in Waterlogging Tolerance at Anthesis

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