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  1. Book ; Online ; E-Book: Cotton precision breeding

    Zhang, Tianzhen / Zafar, Yusuf / Mehboob-ur-Rahman

    2021  

    Abstract: Cotton, the most important natural fiber crop, has been improved by conventional breeding—largely through planned hybridization of different cotton genotypes, since the discovery of Mendelian genetics. All these efforts resulted in the development of ... ...

    Author's details Mehboob Ur Rahman, Yusuf Zafar and Tianzhen Zhang (editors)
    Abstract Cotton, the most important natural fiber crop, has been improved by conventional breeding—largely through planned hybridization of different cotton genotypes, since the discovery of Mendelian genetics. All these efforts resulted in the development of resilient high yielding cotton varieties. However, the progress through conventional breeding procedures is slow because of long lag periods for developing a variety, little control over the new genetic combinations, unwanted traits and lack of foolproof performance testing system. Genomic assays discovered over the last two decades have made it possible to understand the “language” of the genome by associating the genes with specific traits. Together with the more recently established gene-editing tools like CRISPR-Cas9, the cotton genome can be tailored much more precisely than ever before. In this regard, genetic information has been harnessed, through (i) sequencing of the progenitor and cultivated cotton species, (ii) ongoing mega pan-genome sequencing projects, (iii) genetic and physical mapping, and (iv) introgression of genes from alien sources, that resulted in the development of resilient cotton cultivars. These technologies have been deployed or are attempting to overcome the challenges of water shortage, excessive heat in most cotton growing regions, infectious diseases and infestation of insect pests, as well as rising production cost, for sustainable cotton production beyond 2030. In this book, new knowledge generated by the cotton research community and its application for developing resilient cotton are comprehensively summarized. This book contributed by well-known cotton researchers is a timely collection of the challenges and successes of precision cotton breeding in a changing environment.
    Keywords Cotton/Genetics ; Cotton/Breeding ; Cotó ; Conreu del cotoner
    Subject code 633.51
    Language English
    Size 1 online resource (XII, 459 p. 43 illus., 37 illus. in color.)
    Edition 1st ed. 2021.
    Publisher Springer
    Publishing place Cham, Switzerland
    Document type Book ; Online ; E-Book
    Remark Zugriff für angemeldete ZB MED-Nutzerinnen und -Nutzer
    ISBN 3-030-64504-5 ; 3-030-64503-7 ; 978-3-030-64504-5 ; 978-3-030-64503-8
    DOI 10.1007/978-3-030-64504-5
    Database ZB MED Catalogue: Medicine, Health, Nutrition, Environment, Agriculture

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  2. Article ; Online: Genome Editing in Brassica juncea Using CRISPR/Cas9 Technology.

    Ahmad, Niaz / Fatima, Samia / Hundleby, Penny / Mehboob-Ur-Rahman

    Methods in molecular biology (Clifton, N.J.)

    2024  Volume 2788, Page(s) 337–354

    Abstract: Modern genome editing tools particularly CRISPR/Cas9 have revolutionized plant genome manipulation for engineering resilience against changing climatic conditions, disease infestation, as well as functional genomic studies. CRISPR-mediated genome editing ...

    Abstract Modern genome editing tools particularly CRISPR/Cas9 have revolutionized plant genome manipulation for engineering resilience against changing climatic conditions, disease infestation, as well as functional genomic studies. CRISPR-mediated genome editing allows for editing at a single as well as multiple locations in the genome simultaneously, making it an effective tool for polyploid species too. However, still, its applications are limited to the model crops only. Extending it to crop plants will help improve field crops against the changing climates more rapidly and precisely. Here we describe the protocol for editing the genome of a field crop Brassica juncea (mustard), an allotetraploid and important oilseed crop of the Indo-Pak Subcontinent region. This protocol is based on the Agrobacterium-mediated transformation for the delivery of CRISPR components into the plant genome using cotyledon as explants. We elaborate on steps for recovering genome-edited knockouts, for validation of the edits, as well as recovering the transgene-free edited plants through a commonly used segregating approach.
    MeSH term(s) CRISPR-Cas Systems ; Gene Editing/methods ; Mustard Plant/genetics ; Genome, Plant ; Plants, Genetically Modified/genetics ; Agrobacterium/genetics ; Transformation, Genetic
    Language English
    Publishing date 2024-04-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3782-1_20
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Precision Genome Editing with CRISPR-Cas9.

    Rahman, Shahroz / Ikram, Abdul Rehman / Azeem, Farrukh / Tahir Ul Qamar, Muhammad / Shaheen, Tayyaba / Mehboob-Ur-Rahman

    Methods in molecular biology (Clifton, N.J.)

    2024  Volume 2788, Page(s) 355–372

    Abstract: The CRISPR/Cas9 system is a revolutionary technology for genome editing that allows for precise and efficient modifications of DNA sequences. The system is composed of two main components, the Cas9 enzyme and a guide RNA (gRNA). The gRNA is designed to ... ...

    Abstract The CRISPR/Cas9 system is a revolutionary technology for genome editing that allows for precise and efficient modifications of DNA sequences. The system is composed of two main components, the Cas9 enzyme and a guide RNA (gRNA). The gRNA is designed to specifically target a desired DNA sequence, while the Cas9 enzyme acts as molecular scissors to cut the DNA at that specific location. The cell then repairs the digested DNA, either through nonhomologous end joining (NHEJ) or homology-directed repair (HDR), resulting in either indels or precise modifications of DNA sequences with broad implications in biotechnology, agriculture, and medicine. This chapter provides a practical approach for utilizing CRISPR/Cas9 in precise genome editing, including identifying the target gene sequence, designing gRNA and protein (Cas9), and delivering the CRISPR components to target cells.
    MeSH term(s) CRISPR-Cas Systems ; Gene Editing/methods ; RNA, Guide, CRISPR-Cas Systems/genetics ; Humans ; DNA End-Joining Repair ; CRISPR-Associated Protein 9/metabolism ; CRISPR-Associated Protein 9/genetics
    Chemical Substances RNA, Guide, CRISPR-Cas Systems ; CRISPR-Associated Protein 9 (EC 3.1.-)
    Language English
    Publishing date 2024-04-24
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1940-6029
    ISSN (online) 1940-6029
    DOI 10.1007/978-1-0716-3782-1_21
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Genome-wide survey of HMA gene family and its characterization in wheat (

    Zahra, Sadaf / Shaheen, Tayyaba / Qasim, Muhammad / Mahmood-Ur-Rahman / Hussain, Momina / Zulfiqar, Sana / Shaukat, Kanval / Mehboob-Ur-Rahman

    PeerJ

    2023  Volume 11, Page(s) e14920

    Abstract: Background: Abiotic stresses, particularly drought and heavy metal toxicity, have presented a significant risk to long-term agricultural output around the world. Although the heavy-metal-associated domain (HMA) gene family has been widely explored in ... ...

    Abstract Background: Abiotic stresses, particularly drought and heavy metal toxicity, have presented a significant risk to long-term agricultural output around the world. Although the heavy-metal-associated domain (HMA) gene family has been widely explored in Arabidopsis and other plants, it has not been thoroughly studied in wheat (
    Methods: To analyze the phylogenetic relationships, gene structure, gene ontology, and conserved motifs, a comparative study of wheat HMA genes with the Arabidopsis genome was performed.
    Results: A total of 27
    Conclusion: As a result, the current work offered important information regarding HMA family genes in the
    MeSH term(s) Triticum/genetics ; Genome, Plant/genetics ; Phylogeny ; Arabidopsis/genetics ; Metals, Heavy/metabolism
    Chemical Substances Metals, Heavy
    Language English
    Publishing date 2023-03-03
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2703241-3
    ISSN 2167-8359 ; 2167-8359
    ISSN (online) 2167-8359
    ISSN 2167-8359
    DOI 10.7717/peerj.14920
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Book ; Online: Past, Present and Future Trends in Cotton Breeding

    Mehboob-Ur-Rahman / Yusuf Zafar

    2018  

    Abstract: Cotton, a source of natural fiber for textile industry, has a long breeding history aiming at increasing cotton fiber yield and its quality. Newly developed cotton varieties poorly respond in low-input environments. Secondly, the impact of changing ... ...

    Abstract Cotton, a source of natural fiber for textile industry, has a long breeding history aiming at increasing cotton fiber yield and its quality. Newly developed cotton varieties poorly respond in low-input environments. Secondly, the impact of changing climate may threaten the cotton production in the future. To address these challenges, efforts toward the development of resilient cotton varieties have been initiated using genetic and modern genomic approaches. In this book, research updates on cotton fiber types and properties, DNA markers for selecting desirable cotton plants, and cotton fiber genomics were compiled. Also, the modern breeding trends including development of transgenic cotton and the biosafety studies and possibilities of improving cotton genome using modern genome editing tools were also compressively discussed.
    Keywords Life Sciences ; Agricultural and Biological Sciences ; Agronomy ; Plant Genetics
    Language English
    Publisher IntechOpen
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  6. Article ; Online: Genome-wide survey of HMA gene family and its characterization in wheat (Triticum aestivum)

    Sadaf Zahra / Tayyaba Shaheen / Muhammad Qasim / Mahmood-ur-Rahman / Momina Hussain / Sana Zulfiqar / Kanval Shaukat / Mehboob-ur-Rahman

    PeerJ, Vol 11, p e

    2023  Volume 14920

    Abstract: Background Abiotic stresses, particularly drought and heavy metal toxicity, have presented a significant risk to long-term agricultural output around the world. Although the heavy-metal-associated domain (HMA) gene family has been widely explored in ... ...

    Abstract Background Abiotic stresses, particularly drought and heavy metal toxicity, have presented a significant risk to long-term agricultural output around the world. Although the heavy-metal-associated domain (HMA) gene family has been widely explored in Arabidopsis and other plants, it has not been thoroughly studied in wheat (Triticum aestivum). This study was proposed to investigate the HMA gene family in wheat. Methods To analyze the phylogenetic relationships, gene structure, gene ontology, and conserved motifs, a comparative study of wheat HMA genes with the Arabidopsis genome was performed. Results A total of 27 T. aestivum proteins belonging to the HMA gene family were identified in this study, with amino acid counts ranging from 262 to 1,071. HMA proteins were found to be grouped into three subgroups in a phylogenetic tree, and closely related proteins in the tree showed the same expression patterns as motifs found in distinct subgroups. Gene structural study elucidated that intron and exon arrangement differed by family. Conclusion As a result, the current work offered important information regarding HMA family genes in the T. aestivum genome, which will be valuable in understanding their putative functions in other wheat species.
    Keywords Bioinformatics ; Genome-wide analysis ; Heavy metal toxicity ; HMA gene family ; Phylogenetic analysis ; Medicine ; R ; Biology (General) ; QH301-705.5
    Subject code 572
    Language English
    Publishing date 2023-03-01T00:00:00Z
    Publisher PeerJ Inc.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article: Mitigation of water scarcity with sustained growth of Rice by plant growth promoting bacteria.

    Mahreen, Naima / Yasmin, Sumera / Asif, Muhammad / Yahya, Mahreen / Ejaz, Khansa / Mehboob-Ur-Rahman / Yousaf, Sumaira / Amin, Imran / Zulfiqar, Sana / Imran, Asma / Khaliq, Shazia / Arif, Muhammad

    Frontiers in plant science

    2023  Volume 14, Page(s) 1081537

    Abstract: Climate change augments the risk to food security by inducing drought stress and a drastic decline in global rice production. Plant growth-promoting bacteria (PGPB) have been known to improve plant growth under drought stress. Here in the present study, ... ...

    Abstract Climate change augments the risk to food security by inducing drought stress and a drastic decline in global rice production. Plant growth-promoting bacteria (PGPB) have been known to improve plant growth under drought stress. Here in the present study, we isolated, identified, and well-characterized eight drought-tolerant bacteria from the rice rhizosphere that are tolerant to 20% PEG-8000. These strains exhibited multiple plant growth-promoting traits, i.e., 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase activity, exopolysaccharide production, phosphate (P)-solubilizing activity (51-356 µg ml
    Language English
    Publishing date 2023-01-23
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2023.1081537
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Characterization of Gamma-Rays-Induced Spring Wheat Mutants for Morphological and Quality Traits through Multivariate and GT Bi-Plot Analysis

    Sana Zulfiqar / Shumila Ishfaq / Muhammad Ikram / Muhammad Amjad Nawaz / Mehboob-ur- Rahman

    Agronomy, Vol 11, Iss 2288, p

    2021  Volume 2288

    Abstract: Exploiting new genetic resources is an effective way to achieve sustainable wheat production. To this end, we exposed wheat seeds of the “Punjab-11” cultivar to gamma rays. A total of 32 stable mutants (M 7 ) were developed, followed by characterization ... ...

    Abstract Exploiting new genetic resources is an effective way to achieve sustainable wheat production. To this end, we exposed wheat seeds of the “Punjab-11” cultivar to gamma rays. A total of 32 stable mutants (M 7 ) were developed, followed by characterization by conducting multilocation trials over two seasons. Principal component analysis (PCA) showed that the first six components accounted for 90.28% of the total variation among the plant height, tillers per plant, 1000-kernel weight, grain yield, and quality traits. All mutants were grouped into three clusters based on high yield index values. The genotype by trait (GT) bi-plot revealed significant associations between yield and its components among the mutants. Positive correlations were estimated for tillers per plant, plant height, 1000-kernel weight, and grain yield; however, yield components showed negative associations with protein, moisture, and gluten contents. The mutant lines Pb-M-59 waxy, Pb-M-1272 waxy, Pb-M-2260, Pb-M-1027 waxy, Pb-M-1323 waxy, and Pb-M-1854 exhibited maximum grain yield, 1000-grain weight, and tillers per plant values. Likewise, Pb-M-2725, Pb-M-2550, and Pb-M-2728 were found to be the best mutant lines in terms of grain quality; thus, the use of gamma radiation is effective in improving the desirable traits, including yield and grain quality. It is suggested that these traits can be improved beyond the performance of corresponding traits in their parent genotypes. The newly produced mutants can also be used to explore the genetic mechanisms of complex traits in the future.
    Keywords Triticum aestivum L ; physical mutagen ; phenotypic diversity ; grain yield ; quality traits ; principal component analysis ; Agriculture ; S
    Subject code 580
    Language English
    Publishing date 2021-11-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  9. Article ; Online: Identification of induced mutations in hexaploid wheat genome using exome capture assay.

    Momina Hussain / Muhammad Atif Iqbal / Bradley J Till / Mehboob-Ur- Rahman

    PLoS ONE, Vol 13, Iss 8, p e

    2018  Volume 0201918

    Abstract: Wheat is a staple food crop of many countries. Improving resilience to biotic and abiotic stresses remain key breeding targets. Among these, rust diseases are the most detrimental in terms of depressing wheat production. In the present study, chemical ... ...

    Abstract Wheat is a staple food crop of many countries. Improving resilience to biotic and abiotic stresses remain key breeding targets. Among these, rust diseases are the most detrimental in terms of depressing wheat production. In the present study, chemical mutagenesis was used to induce mutations in the wheat variety NN-Gandum-1. This cultivar is moderately resistant to leaf and yellow rust. The aim of mutagenesis was to improve resistance to the disease as well as to study function of genes conferring resistance to the disease. In the present investigation, a 0.8% EMS dose was found optimum for supporting 45-55% germination of NN-Gandum-1. A total of 3,634 M2 fertile plants were produced from each of the M1 plant. Out of these, 33 (0.91%) and 20 plants (0.55%) showed absolute resistance to leaf and yellow rust, respectively. While 126 (3.46%) and 127 plants (3.49%) exhibited high susceptibility to the leaf and yellow rust, respectively. In the M4 generation, a total of 11 M4 lines (nine absolute resistant and two highly susceptible) and one wild type were selected for NGS-based exome capture assay. A total of 104,779 SNPs were identified that were randomly distributed throughout the wheat sub genomes (A, B and D). Induced mutations in intronic sequences predominated. The highest total number of SNPs detected in this assay were mapped to chr.2B (14,273 SNPs), which contains the highest number of targeted base pairs in the assay. The average mutation density across all regions interrogated was estimated to be one mutation per 20.91 Mb. The highest mutation frequency was found in chr.2D (1/11.7 kb) and the lowest in chr.7D (1/353.4 kb). Out of the detected mutations, 101 SNPs were filtered using analysis criteria aimed to enrich for mutations that may affect gene function. Out of these, one putative SNP detected in Lr21 were selected for further analysis. The SNP identified in chimeric allele (Lr21) of a resistant mutant (N1-252) was located in a NBS domain of chr.1BS at 3.4 Mb position. Through computational analysis, ...
    Keywords Medicine ; R ; Science ; Q
    Subject code 580
    Language English
    Publishing date 2018-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article: Prospects of Developing Novel Genetic Resources by Chemical and Physical Mutagenesis to Enlarge the Genetic Window in Bread Wheat Varieties

    Hussain, Momina / Gul, Maryyam / Kamal, Roop / Iqbal, Muhammad Atif / Zulfiqar, Sana / Abbas, Ammad / Röder, Marion S. / Muqaddasi, Quddoos H. / Mehboob-ur-Rahman

    Agriculture (Basel). 2021 July 01, v. 11, no. 7

    2021  

    Abstract: Sustainable production and improved genetic gains can be achieved by broadening the genetic window of elite wheat germplasm. Here, we induced mutations in two spring wheat varieties, viz., NN-Gandum-1 (NN-1) and Punjab-11 (Pb-11), by exposing their seeds ...

    Abstract Sustainable production and improved genetic gains can be achieved by broadening the genetic window of elite wheat germplasm. Here, we induced mutations in two spring wheat varieties, viz., NN-Gandum-1 (NN-1) and Punjab-11 (Pb-11), by exposing their seeds to ethyl methane sulfonate (EMS) and γ-rays, respectively. We characterized >3500 lines of each NN-1 and Pb-11 derived population in three consecutive generations, viz., M₅, M₆, and M₇, for important traits, e.g., plant height, heading date, spike morphology and rust resistance. We observed significant genetic variation and correlations in both populations for all investigated traits. We observed differences in terms of number of mutants between NN-1 (22.76%) and Pb-11 (26.18%) which could be ascribed to the genotype-by-mutagen interaction. High broad-sense heritability (H²) estimates, that are vital for higher genetic gains, were observed for all of the investigated traits in both populations (H² = 0.69–0.91 in NN-1 and 0.84–0.98 in Pb-11). Particularly, to breed for rust resistance, we selected a subset (n = 239) of M₇ lines that also showed phenotypic variation for other traits. Our studies (1) show the relevance to artificial mutagenesis to create genetic variation in elite germplasm for their immediate use in current breeding programs, and (2) provide material for downstream identification of genes associated with traits of high agronomic importance.
    Keywords agriculture ; ethyl methanesulfonate ; genetic variation ; germplasm ; heritability ; mutagenesis ; phenotypic variation ; plant height ; spring wheat
    Language English
    Dates of publication 2021-0701
    Publishing place Multidisciplinary Digital Publishing Institute
    Document type Article
    ZDB-ID 2651678-0
    ISSN 2077-0472
    ISSN 2077-0472
    DOI 10.3390/agriculture11070621
    Database NAL-Catalogue (AGRICOLA)

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