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Home > Polymorphism Detection and Genotyping of Salt Tolerant Rice Genotypes Using Next Generation Sequencing

Polymorphism Detection and Genotyping of Salt Tolerant Rice Genotypes Using Next Generation Sequencing

Thesis Info

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Author

Tariq, Rida

Program

PhD

Institute

Pakistan Institute of Engineering and Applied Sciences

City

Islamabad

Province

Islamabad.

Country

Pakistan

Thesis Completing Year

2019

Thesis Completion Status

Completed

Subject

Biotechnology

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/11687/1/Rida%20Tariq_Biotech_2019_PIEAS.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676726963358

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Rice production is greatly limited by high level of soil salinity around the world. To overcome this major abiotic constraint, different strategies have been adopted for the development of salt tolerant rice varieties. In present study, tolerance potential of 63 rice genotypes was evaluated at seedling stage under different levels of salt stress. Among screened genotypes, six were found tolerant, 37 moderate tolerant and 20 were sensitive under tested levels of salt stress. Tolerant genotypes showed less reduction in root shoot length, fresh weight and dry weight, compared with FL478 (positive control). Sensitive genotypes showed ~ 90 % reduction in all growth parameters. Selected genotypes, were further assessed using 21 simple sequence repeat (SSR) markers, residing within SalTol QTL region on chromosome 1. Ninteen SSR markers were found polymorphic among salt tolerant and sensitive genotypes. Cluster analysis based on SSR markers, grouped genotypes into three clusters as sensitive, tolerant and moderate tolerant. However, population structure analysis combined tolerant and moderate tolerant genotypes in one set. To identify the genetic variation in stress-related genes in salt tolerant genotypes, we performed genotyping by sequencing (GBS) of seven rice lines with contrasting responses to salinity stress. Approximately 83 % reads were mapped to the rice reference genome (Nipponbare). We identified a total of 80,159 SNPs and 6,403 InDels among the seven rice genotypes. Of the SNPs 42 % were identified from the genic regions and out of these 27 % were observed in coding regions. Bioinformatics analysis was used to identify functional SNPs in the genes that changed the functions of proteins. We identified 116 abiotic stress related genes that contained 138 nsSNPs (between tolerant and sensitive) in coding regions, thus having effects on proteins. In other study, selected four BC1F5 populations derived by crossing a high yield recipient rice line (WTR-1) with four donors were used. These populations were sequenced by tGBS. Data analysis revealed presence of 99 non-synonymous deleterious SNPs in 62 loci. Of the 62 affected loci, 10 were predicted to be responsive towards salinity tolerance. Analysis indicated that these genes may contribute to salt stress phenotype in rice varieties, and the identified nonsynonymous deleterious SNPs are useful to distinguish tolerant and sensitive genotypes.
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حکیم محمد سعید

حکیم محمد سعید
حافظ حکیم محمد سعید کے وحشیانہ اور بے رحمانہ قتل پر کون ہے جو تڑپا اور بے قرار نہ ہوا ہوگا، وہ بین الاقوامی شخص، مملکتِ خداداد کے ہمدرد و مسیحا، پاکستان کے معمار، اس کا مقدر چمکانے اور بنانے کے لیے فکر مند، ہمدرد فاؤنڈیشن کے سربراہ اور مدینتہ الحکمت کے بانی، عالم، مصنف، مدبر، عالی دماغ، سچے اور پکے مسلمان، قوم و ملت کے بے لوث خادم، مخالف ہوا میں طب کا چراغ روشن کرنے، علم کو فروغ دینے، حکمت و محبت کا خزانہ لُٹانے والے، غریبوں اور مصیبت زدوں کے درد و غم میں شریک، پہلو میں درد مند دل رکھنے، پاکستان کے تشویش انگیز حالات سے بے چین اور پریشان رہنے والے کو چند دقیقوں میں جن لوگوں نے موت کے گھاٹ اُتارا وہ بڑے خوں خوار، درندہ صفت اور انسانوں کے بھیس میں وحوش سے بھی بدتر لوگ تھے۔ آخر اس فرشتہ صفت، پاک دل، پاک باز، رحم و مروت کے پیکر، مجسم شرافت اور اخلاقی خوبیوں سے منور انسان کا قصور کیا تھا، ذوق مرحوم کے شاگرد محمد مظفر خاں گرمؔ رامپوری کا وہ قطعۂ تاریخ وفات یاد آگیا جو نواب شمس الدین خاں مرحوم کو پھانسی دیے جانے پر کہا گیا تھا ؂
یہ دست درازیِ ستم کس سے بیاں ہو
بے جرم و گنہ مسند نواب کو الٹا
تاریخ معمے میں نئی طرز سے لکھ، گرمؔ!
کیا چرخ نے ’’نوابی سہراب‘‘ کو الٹا
جو مملکت اُس اسلام کے نام پر وجود میں آئی تھی جو سراپا امن و سلامتی ہے اور جس کے آئین میں خون خرابہ اور قتل و دہشت گردی کی کوئی گنجایش نہیں اور جس کے ماننے والے (مسلم) ساری دنیا کے لیے سراپا رحمت ہوئے ہیں، آج وہی مملکت جہنم کا نمونہ بنی ہوئی ہے، کراچی مقتل میں تبدیل ہوگیا ہے، پاکستان...

جماعت احمدیہ کے مولوی عبد اللطیف بہاولپوری کی چار قرآنی سورتوں کی تفاسیر کا تحقیقی و تنقیدی جائزہ

This informative article is a vital as well as analytical analyze of the several Sūrʼas translated as well as defined by Mūlvi Abdul Latīf around the facets of the guidelines connected with Translation as well as Tafsīr set by Mirza Ghulām Ahmad Qādyāni founder of Jamʽat-e-Āḥmadiya. Who offered a brand new principle connected with Tafsīr to verify the inappropriate beliefs as well as his views that are total contrary to the principles set by authentic former Muslim scholars. Many Qādyāni Mufasrīn implemented those principles within their books connected with Tafsīr. Most notable ended up being Mūlvi Abdul Latīf Bahāwalpūri who had written this Translation as well as Tafsīr of 5 Sūrʼas i. ESūrʼa Banī ʼisraeel, Sūrʼa Kahaf, Sūrʼa Yāseen, Sūrʼa Qiyāmah and Sūrʼa Dahar. He implemented the guidelines set by Mirza Ghulām Ahmad Qādyāni. Throughout his work he created a number of alterations not only with Translation but with Tafsīr too. This article is an eye bird review of the principles of the Translation as well as Tafsīr connected with Holy Qurʼan set by authentic former scholars.

Effect of Ion Beam Implantation Ofn Morphological, Electrical and Optical Properties of Polymer

In recent years, the demand of polymers is growing progressively in a wide variety of fields extending from everyday life to medical and high technological applications due to their unique inherent properties like lightweight, flexibility, weather and corrosion-resistance and low cost. Considering the bulk properties of polymer an effort has been made to modify the structural, morphological, electrical and optical properties of near-surface layer of polymer by ion implantation. Indeed, it is a useful technique to modify surface properties of polymers without altering their bulk properties. In particular, with an improvement in electrical conductivity the implanted polymer can be utilized as a promising candidate for its future utilization in the field of plastic electronics. In the present study, the effects of 400 keV C+, Cr+ and Ag+ ion implantation on Polymethylmethacrylate (PMMA) have been examined at different ion fluences ranging from 5x1013 to 5x1015 ions/cm2. The ion penetration depths have been estimated with the help of SRIM simulation. The chemical and structural modifications in implanted PMMA are examined by Fourier Transform Infrared and Raman Spectroscopy (FTIR), respectively. The surface topographical examination of the implanted polymer has been performed using Atomic Force Microscope (AFM). The effects of ion implantation on electrical and optical properties of PMMA have been investigated by four probe apparatus and UV–Visible spectroscopic analysis. The FTIR spectra confirmed the formation of C = C bonds in C+ and Cr+ implanted PMMA at a fluence of 5 × 1015 ions/cm2 while for Ag+ implanted PMMA the peak for C=C is developed at relatively lower fluence of 1 × 1015 ions/cm2. Moreover, the Raman spectra justified the growth of sp2 carbon clusterization and transformation of C+, Cr+ and Ag+ implanted layer of PMMA into quasi-continuous amorphous carbon at implantation fluence of about ≥5x1014 ions/cm2. The AFM images showed the topographical modification due to ion implantation on PMMA. However, the extent of modification depends on the type of ions and increase in ion fluence. The roughness analysis revealed the smoothness of the surface of C+ and Cr+ implanted PMMA with increasing ion fluence. On the other hand, the implantation of Ag+ ions showed dominant effects on the surface of PMMA rather than C+ and Cr+ implantation. As a result, the surface of Ag+ implanted PMMA became rougher due to the formation of nano-hillocks and nano sized grainy structures above the surface. Due to ion-induced structural modifications the electrical conductivity of PMMA is increased to semiconducting range with a rise in ion fluence. After C+ ion implantation the electrical conductivity of PMMA is increased from 2.14 × 10-10 S/cm (pristine) to 1.46 × 10-6 S/cm. Similarly, for Cr+ and Ag+ ion implantation the electrical conductivity has improved to 7.21 × 10-6 S/cm and 9.60 × 10-6 S/cm, respectively. The results of UV-Visible analysis also confirmed an increase in sp2 carbon clusters in implanted PMMA in the favor of other results. Due to creation of carbonaceous clusters the optical absorption spectra of PMMA exhibit a shift towards higher wavelength after C+, Cr+ and Ag+ implantation along with a significant reduction in the optical band gap energies. For C+ implanted PMMA the optical band gap is reduced from 3.13 (pristine) to 0.66 eV whereas, after Cr+ and Ag+ ion implantation it shrinks to 0.85 and 0.81 eV, respectively.