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Home > Next Generation Sequencing Based Identification and Characterization of Important Genes in Cotton.

Next Generation Sequencing Based Identification and Characterization of Important Genes in Cotton.

Thesis Info

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Author

Naqvi, Rubab Zahra

Program

PhD

Institute

Pakistan Institute of Engineering and Applied Sciences

City

Islamabad

Province

Islamabad.

Country

Pakistan

Thesis Completing Year

2018

Thesis Completion Status

Completed

Subject

Biotechnology

Language

English

Link

http://prr.hec.gov.pk/jspui/bitstream/123456789/10045/1/Rubab%20Zahra%20Naqvi_Biotechnology_2018_PIEAS_PRR.pdf

Added

2021-02-17 19:49:13

Modified

2024-03-24 20:25:49

ARI ID

1676726755191

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Cotton is an economically important crop that generates billions of dollars in annual revenue worldwide. Whitefly (Bemisia tabaci) and whitefly-transmitted cotton leaf curl disease (CLCuD) cause great damage to overall cotton production. Compared to widely cultivated cotton species Gossypium hirsutum, the diploid species G. arboreum is a natural source for resistance against CLCuD. However, the gene expression changes steered by whitefly and CLCuD infestation in G. arboreum and G. hirsutum and the interaction mechanisms of CLCuD to these cotton species remain to be elucidated. In the present study, RNA-Seq based transcriptomics have been subjected to elucidate the differential gene expression in G. arboreum and G. hirsutum under CLCuD infestation. G. arboreum plants were infested with CLCuD by graft and viruliferous whitefly-mediated inoculation. However, for G. hirsutum, CLCuD susceptible and resistant accession Mac7 were infested by whitefly-mediated CLCuD. RNA-Seq was done on plants from each experiment using Illumina HiSeq 2500 and data analysis identified differential gene expression in G. arboreum and G. hirsutum under CLCuD infestation. qRT-PCR, gene ontology enrichment, KEGG pathway analysis and homology searches were used for validation and functional annotation based characterization of identified genes in transcriptomic data in response to CLCuD. Several genes involved in disease resistance and pathogen defense were identified. Furthermore, coexpression network analysis on the RNA-Seq datasets, indicated the hub genes, showing their crucial role in defense or susceptibility of cotton in response to CLCuD. The important gene families identified in cotton under CLCuD stress include phytohormones, transcription factors, kinases, oxidative stress, membrane channel proteins, protein modifications, methylation and metabolism-related genes. Overall, it is concluded that the resulting datasets give inclusive insights into the cotton defense or susceptibility mechanisms under whiteflies and CLCuD infestation. This study reveals several candidate genes involved in a virus-host interaction that might be used for the control of whitefly, other sap-sucking insects and CLCuD in cotton
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مانا کہ زمانہ ستم ایجاد بہت ہے

مانا کہ زمانہ ستم ایجاد بہت ہے
مجھ کو شہہِ کونینؐ کی امداد بہت ہے

آیا تھا تصور میں بس اک پل کو مدینہ
دل ہے کہ اُسی لمحے سے آباد بہت ہے

بیکار ہے افکار کی دُنیا میں بھٹکنا
مجھ کو تو حضورؐ آپؐ کا ارشاد بہت ہے

کچھ اِس کے سنورنے کا بھی سامان ہو آقا ؐ
بستی جو زمیں پر ہے وُہ برباد بہت ہے

ایمان کی شمعیں ہوں فروزاں دل و جاں میں
اِس دورِ سیہ رنگ میں الحاد بہت ہے

ذبح سے پہلے عمل تدویخ اور معاصر فقہی تحقیقات

Stunning is the process of rendering animals immobile or unconscious, with or without killing the animal, when or immediately prior to slaughtering them for food. In modern slaughterhouses a variety of stunning methods are used on livestock. Methods include: Electrical stunning, Gas stunning, Percussive stunning. There are three opinions of Islamic scholars about stunning. Those scholars; who do not allow stunning at all; are of the view that the method of rendering animals unconscious before slaughter is against the shairah method and Sunnah, and it is Makrooh e Teḥreemi. Before slaughtering, if an animal died due to stunning, then that animal is carcass and is not allowed to be eaten. But, if before slaughter, ḥayat e Mustaqirrah is present in animal and it is slaughtered in that condition then it is permissible to eat it. Certain scholars allow stunning in certain situations with some terms and conditions. The decisions of Mjam e Faqhiyyah of modern age are also based on conditional permission. Moreover, Mufti Muḥammad Taqi Usmani, Dr. Wahabah  Zoḥaili and Abdul Aziz Bin Baaz agree with conditional permission, while some other scholars allow all types of stunning without any condition; Mufti Muḥammad Abduho and his pupil Allamah Rasheed Raza Miṣri agree with later opinion.

Crop Diversification Towards High Value Crops and its Determinants in Pakistan: An Empirical Analysis

VII Abstract Abstract Abstract Crop sector is an important sub-sector of the agricultural sector and is considered a vital part of Pakistan''s economy. This sub-sector contributed about 39.6 percent in the agricultural sector value added, during 2014-15. All major food crops, vegetables, oilseeds and fruits are produced in Pakistan due to its different ecological regions, climate change, soil types and sufficient water. Trends show a stagnant pattern of crop diversification in crop sector in terms of grains, cash crops, pulses, oilseeds, vegetables, fruits and other minor crops from 1980-81 to 2014-15. The Herfindahl Index (HI) was used to check the level of concentration and diversification in the structure of crops in Pakistan. The Herfindahl index values showed a high level of crop concentration in the country''s crop sector and required to be diversified towards high-value crops. The ARIMA (1,1,1) model of Time Series data was used to examine the impact of various factors on Transformed Herfindahl Index of diversity. To determine the impact of demand side factors on the Transformed Herfindahl Index. The regression coefficients of profitability of minor crops, per capita income and urbanization showed positive and significant relationship with diversification of crops. To check the influence of supply side factors; the length of roads was adopted in the model to check the impact of infrastructural development. The regression coefficient of roads showed a positive and significant relationship with the diversification of crops. The technology was determined with the help of fertilizers, the number of tubewells, production of tractors in numbers and Net Area Sown. The regression coefficients of fertilizers, number of tubewells and production of tractors in numbers showed positive and significant influence on the diversification of crops. The regression coefficient of Net Area Sown showed a negative relationship with the diversification of crops, but it was insignificant. The availability of water (MAF) for irrigation purposes showed a positive and significant relationship VIII with the diversification of crops. To determine the impact of climate, the average rainfall regression coefficient showed a negative and very significant impact with diversification of crops. In addition, results concluded that the average income per hectare of minor crops is higher than the average income per hectare of the major crops. This showed that farmers'' income increased through the diversification of crops towards high-value crops in Pakistan. To check the impact of various factors on the Index of High Value Crops, the credit availability, local production of oilseed crops, agricultural machinery, number of tubewells and urbanization regression coefficients showed positive and significant relationship with IHVC. The regression coefficient of import of oilseeds showed a negative and very significant impact on the Index of High Value crops in Pakistan. This showed that the huge import of oilseeds cost the public exchequer badly. The ADF unit root tests were used to check Stationarity of variables at levels. It showed that variables adopted in models were non-stationary at levels and turned out to be stationary with the first difference. LM test was used to check for a serial correlation in the errors of the regression model and found no serial correlation up to lag order 1 at the 95% confidence level. The residual of ΔResid01t were checked for the existence of a unit root to check the co-integration. The ADF test statistics showed that the series was stationary at the level and concluded that variables had long run relationship.