Variety‐specific transcript accumulation during reproductive stage in drought‐ stressed rice

Abstrak Cekaman kekeringan merupakan faktor pembatas penting bagi pertumbuhan dan produktivitas tanaman termasuk padi. Penelitian ini bertujuan menganalisis respon padi IR64 terhadap cekaman kekeringan dengan pemberian polietilen glikol (PEG) pada fase reproduktif. Penelitian juga bertujuan menganalisis ekspresi gen aquaporin akibat cekaman kekeringan. Bibit padi ditanam dalam pot dan perlakuan PEG dengan konsentrasi 108g/L (-0.25MPa) dan 178g/L (-0.52 MPa) diberikan saat munculnya panikula. Perlakuan diberikan selama 2 minggu, kemudian tanaman disiram kembali. Ekspresi gen diamati pada akhir perlakuan dengan semi kuantitatif real time PCR. Ekstraksi RNA menggunakan RNeasy plant mini kit, sedangkan sintesis cDNA menggunakan Transcriptor First Strand cDNA Kit. Hasil penelitian menunjukkan bahwa jumlah malai dan berat total malai berkurang akibat cekaman kekeringan. Persentase gabah kosong mencapai 84,6% pada perlakuan PEG-0,52 MPa, sedangkan pada perlakuan PEG -0,25 MPa persentase gabah kosong sebesar 67,8%. Pada kontrol persentase gabah kosong adalah 10,3%. Ekspresi gen OsPIP2;7 sedikit menurun pada perlakuan PEG -0,52 MPa.Kata kunci: ekspresi gen, IR64, kekeringan, padi, PEG Abstract Drought stress is one of the limiting factors of plant growth and productivity including rice. The aim of this study was to analyze responses of IR64 rice to polyethylene glycol (PEG)-induced-drought stress at the reproductive stage. This study also aimed to analyze the expression of aquaporin under drought stress. Rice seedlings were grown in pot system and PEG treatment at concentration of -0.25MPa (108g/L) and -0.52 MPa (178g/L) were given when the panicles arose. Treatments were conducted for 2 weeks, after that the plants were rewatered. Gene expression was evaluated at the end of PEG treatment using semi quantitative real time PCR. RNA was extracted using RNeasy plant mini kit, while cDNA synthesis was done using Transcriptor First Strand cDNA Kit. The results showed that the number and weight of rice ear were less in plant treated with PEG than in control. The percentage of empty rice grain reached 84.6% at PEG -0.52 MPa, while at PEG -0.25 MPa the percentage of empty grain was 67.8%. In control plant, the percentage of empty grain was 10.3%. Drought stress did not alter the expression of OsPIP2;7. Keywords: drought, gene expression, IR64, PEG, rice

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Evaluation of salinity tolerance indices in North African barley accessions at reproductive stage

Czech Journal of Genetics and Plant Breeding ◽

10.17221/50/2017-cjgpb ◽

2019 ◽

Vol 55 (No. 2) ◽

pp. 61-69 ◽

Cited By ~ 3

Author(s):

Dorsaf Allel ◽

Anis BenAmar ◽

Mounawer Badri ◽

Chedly Abdelly

Keyword(s):

Salt Tolerance ◽

Grain Yield ◽

Salinity Tolerance ◽

Selection Criteria ◽

Reproductive Stage ◽

Shoot Biomass ◽

Salt Tolerant ◽

North African ◽

Grain Number ◽

Selection Indices

Soil salinity is one of the main factors limiting cereal productivity in worldwide agriculture. Exploitation of natural variation in local barley germplasm is an effective approach to overcome yield losses. Three gene pools of North African Hordeum vulgare L. grown in Tunisia, Algeria and Egypt were evaluated at the reproductive stage under control and saline conditions. Assessment of stress tolerance was monitored using morphological, yield-related traits and phenological parameters of reproductive organs showing significant genetic variation. High heritability and positive relationships were found suggesting that some traits associated with salt tolerance could be used as selection criteria. The phenotypic correlations revealed that vegetative traits including shoot biomass, tiller number and leaf number along with yield-related traits such as spike number, one spike dry weight, grain number/plant and grain number/spike were highly positively correlated with grain yield under saline conditions. Hence, these traits can be used as reliable selection criteria to improve barley grain yield. Keeping a higher shoot biomass and longer heading and maturity periods as well as privileged filling ability might contribute to higher grain production in barley and thus could be potential target traits in barley crop breeding toward improvement of salinity tolerance. Multiple selection indices revealed that salt tolerance trait index provided a better discrimination of barley landraces allowing selection of highly salt-tolerant and highly productive genotypes under severe salinity level. Effective evaluation of salt tolerance requires an integration of selection indices to successfully identify and characterize salt tolerant lines required for valuable exploitation in the management of salt-affected areas.

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Dendritic Cell-Specific Transcript: Dendritic Cell Marker and Regulator of TLR-Induced Cytokine Production

The Journal of Immunology ◽

10.4049/jimmunol.1103709 ◽

2012 ◽

Vol 189 (1) ◽

pp. 138-145 ◽

Cited By ~ 17

Author(s):

Saartje Hontelez ◽

Marleen Ansems ◽

Nina Karthaus ◽

Malou Zuidscherwoude ◽

Maaike W. Looman ◽

...

Keyword(s):

Dendritic Cell ◽

Cytokine Production ◽

Cell Marker ◽

Specific Transcript

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High-density linkage mapping for agronomic and physiological traits of rice (Oryza sativa L.) under reproductive-stage salt stress

Journal of Genetics ◽

10.1007/s12041-021-01301-6 ◽

2021 ◽

Vol 100 (2) ◽

Author(s):

Mostafa Ahmadizadeh ◽

Nadali Babaeian-Jelodar ◽

Ghasem Mohammadi-Nejad ◽

Nadali Bagheri ◽

Rakesh Kumar Singh

Keyword(s):

Oryza Sativa ◽

Salt Stress ◽

Linkage Mapping ◽

Oryza Sativa L ◽

High Density ◽

Reproductive Stage ◽

Physiological Traits

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CRISPRi enables isoform-specific loss-of-function screens and identification of gastric cancer-specific isoform dependencies

Genome Biology ◽

10.1186/s13059-021-02266-6 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Rebecca Davies ◽

Ling Liu ◽

Sheng Taotao ◽

Natasha Tuano ◽

Richa Chaturvedi ◽

...

Keyword(s):

Gastric Cancer ◽

Functional Dependencies ◽

Loss Of Function ◽

Genetic Screens ◽

Transcript Isoforms ◽

Specific Loss ◽

Current Loss ◽

Specific Transcript ◽

Multiple Promoters ◽

Poor Patient

Abstract Introduction Genes contain multiple promoters that can drive the expression of various transcript isoforms. Although transcript isoforms from the same gene could have diverse and non-overlapping functions, current loss-of-function methodologies are not able to differentiate between isoform-specific phenotypes. Results Here, we show that CRISPR interference (CRISPRi) can be adopted for targeting specific promoters within a gene, enabling isoform-specific loss-of-function genetic screens. We use this strategy to test functional dependencies of 820 transcript isoforms that are gained in gastric cancer (GC). We identify a subset of GC-gained transcript isoform dependencies, and of these, we validate CIT kinase as a novel GC dependency. We further show that some genes express isoforms with opposite functions. Specifically, we find that the tumour suppressor ZFHX3 expresses an isoform that has a paradoxical oncogenic role that correlates with poor patient outcome. Conclusions Our work finds isoform-specific phenotypes that would not be identified using current loss-of-function approaches that are not designed to target specific transcript isoforms.

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Genotypic variation in nitrogen utilization efficiency in oilseed rape is related to the coordination of leaf senescence and root N uptake during reproductive stage

Plant and Soil ◽

10.1007/s11104-021-04838-8 ◽

2021 ◽

Author(s):

Huiying He ◽

Yuyu Xie ◽

Anyu Zhao ◽

Wencong Hu ◽

Xiao Guo ◽

...

Keyword(s):

Oilseed Rape ◽

Leaf Senescence ◽

N Uptake ◽

Genotypic Variation ◽

Nitrogen Utilization ◽

Reproductive Stage ◽

Utilization Efficiency ◽

Nitrogen Utilization Efficiency

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Mutator-Suppressible Alleles of rough sheath1 and liguleless3 in Maize Reveal Multiple Mechanisms for Suppression

Genetics ◽

10.1093/genetics/154.1.437 ◽

2000 ◽

Vol 154 (1) ◽

pp. 437-446 ◽

Cited By ~ 1

Author(s):

Lisa Girard ◽

Michael Freeling

Keyword(s):

Untranslated Region ◽

Mutant Allele ◽

Negative Regulation ◽

Wild Type ◽

Knox Gene ◽

Transcript Accumulation ◽

Mu Suppression ◽

Different Types ◽

Rna Blot Analysis

Abstract Insertions of Mutator transposons into maize genes can generate suppressible alleles. Mu suppression is when, in the absence of Mu activity, the phenotype of a mutant allele reverts to that of its progenitor. Here we present the characterization of five dominant Mu-suppressible alleles of the knox (knotted1-like homeobox) genes liguleless3 and rough sheath1, which exhibit neomorphic phenotypes in the leaves. RNA blot analysis suggests that Mu suppression affects only the neomorphic aspect of the allele, not the wild-type aspect. Additionally, Mu suppression appears to be exerting its effects at the level of transcription or transcript accumulation. We show that truncated transcripts are produced by three alleles, implying a mechanism for Mu suppression of 5′ untranslated region insertion alleles distinct from that which has been described previously. Additionally, it is found that Mu suppression can be caused by at least three different types of Mutator elements. Evidence presented here suggests that whether an allele is suppressible or not may depend upon the site of insertion. We cite previous work on the knox gene kn1, and discuss our results in the context of interactions between Mu-encoded products and the inherently negative regulation of neomorphic liguleless3 and rough sheath1 transcription.

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Drought Tolerant near Isogenic Lines (NILs) of Pusa 44 Developed through Marker Assisted Introgression of qDTY2.1 and qDTY3.1 Enhances Yield under Reproductive Stage Drought Stress

Agriculture ◽

10.3390/agriculture11010064 ◽

2021 ◽

Vol 11 (1) ◽

pp. 64

Author(s):

Priyanka Dwivedi ◽

Naleeni Ramawat ◽

Gaurav Dhawan ◽

Subbaiyan Gopala Krishnan ◽

Kunnummal Kurungara Vinod ◽

...

Keyword(s):

Drought Stress ◽

Drought Tolerance ◽

Grain Quality ◽

Reproductive Stage ◽

Recurrent Parent ◽

Near Isogenic Lines ◽

Improvement Project ◽

Isogenic Lines ◽

Drought Tolerant ◽

Rice Improvement

Reproductive stage drought stress (RSDS) is detrimental for rice, which affects its productivity as well as grain quality. In the present study, we introgressed two major quantitative trait loci (QTLs), namely, qDTY2.1 and qDTY3.1, governing RSDS tolerance in a popular high yielding non-aromatic rice cultivar, Pusa 44, through marker-assisted backcross breeding (MABB). Pusa 44 is highly sensitive to RSDS, which restricts its cultivation across drought-prone environments. Foreground selection was carried out using markers, RM520 for qDTY3.1 and RM 521 for qDTY2.1. Background selection was achieved with 97 polymorphic SSR markers in tandem with phenotypic selection to achieve faster recurrent parent genome (RPG) recovery. Three successive backcrosses followed by three selfings aided RPG recoveries of 98.6% to 99.4% among 31 near isogenic lines (NILs). Fourteen NILs were found to be significantly superior in yield and grain quality under RSDS with higher drought tolerance efficiency (DTE) than Pusa 44. Among these, the evaluation of two promising NILs in the multilocational trial during Kharif 2019 showed that they were significantly superior to Pusa 44 under reproductive stage drought stress, while performing on par with Pusa 44 under normal irrigated conditions. These di-QTL pyramided drought-tolerant NILs are in the final stages of testing the All India Coordinated Rice Improvement Project varietal trials for cultivar release. Alternately, the elite drought-tolerant Pusa 44 NILs will serve as an invaluable source of drought tolerance in rice improvement.

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