Yazar "Rehman, Hafiz Mamoon" seçeneğine göre listele

Listeleniyor 1 - 6 / 6
  • Küçük Resim
    Öğe
    Characterization of cellulose synthase A (CESA) gene family in eudicots
    (Springer/Plenum Publishers, 2019) Nawaz, Muhammad Amjad; Lin, Xiao; Chan, Ting-Fung; Imtiaz, Muhammad; Rehman, Hafiz Mamoon; Baloch, Faheem Shehzad
    Cellulose synthase A (CESA) is a key enzyme involved in the complex process of plant cell wall biosynthesis, and it remains a productive subject for research. We employed systems biology approaches to explore structural diversity of eudicot CESAs by exon-intron organization, mode of duplication, synteny, and splice site analyses. Using a combined phylogenetics and comparative genomics approach coupled with co-expression networks we reconciled the evolution of cellulose synthase gene family in eudicots and found that the basic forms of CESA proteins are retained in angiosperms. Duplications have played an important role in expansion of CESA gene family members in eudicots. Co-expression networks showed that primary and secondary cell wall modules are duplicated in eudicots. We also identified 230 simple sequence repeat markers in 103 eudicot CESAs. The 13 identified conserved motifs in eudicots will provide a basis for gene identification and functional characterization in other plants. Furthermore, we characterized (in silico) eudicot CESAs against senescence and found that expression levels of CESAs decreased during leaf senescence.
  • Küçük Resim
    Öğe
    Development of a competent and trouble free dna isolation protocol for downstream genetic analyses in glycine species
    (2016) Nawaz, Muhammad Amjad; Baloch, Faheem Shehzad; Rehman, Hafiz Mamoon; Le, Bao; Akther, Fahima
    Extraction of deoxyribose nucleic acid (DNA) from plants is preliminary step in molecular biology. Fast and cost effective genomic DNA isolation from Glycine species for downstream application is a major bottleneck. Here we report a high throughput and trouble free method for genomic DNA extraction from leaf and seeds of Glycine species with high quality and quantity. Protocol reports the optimization by employing different concentrations of CTAB and PVP in extraction buffer. Efficiency of optimized protocol was compared with frequently used DNA extraction methods. Wide adoptability and utility of this protocol was confirmed by DNA extraction from leaves as well as seeds of G. max, G. soja, G. tomentella and G. latifolia. Extracted DNA was successfully subjected to PCR amplification of five microsatellite markers and four putative glycosyltransferase genes. DNA extraction protocol is reproducible, trouble free, rapid and can be adopted for plant molecular biology applications.
  • Küçük Resim Yok
    Öğe
    Development of a Competent and Trouble Free DNA Isolation Protocol for Downstream Genetic Analyses in Glycine Species
    (2016) Nawaz, Muhammad Amjad; Baloch, Faheem Shehzad; Rehman, Hafiz Mamoon; Le, Bao; Akther, Fahima; Yang, Seung Hwan; Chung, Gyuhwa
    Extraction of deoxyribose nucleic acid (DNA) from plants is preliminary step in molecular biology. Fast and cost effective genomic DNA isolation from Glycine species for downstream application is a major bottleneck. Here we report a high throughput and trouble free method for genomic DNA extraction from leaf and seeds of Glycine species with high quality and quantity. Protocol reports the optimization by employing different concentrations of CTAB and PVP in extraction buffer. Efficiency of optimized protocol was compared with frequently used DNA extraction methods. Wide adoptability and utility of this protocol was confirmed by DNA extraction from leaves as well as seeds of G. max, G. soja, G. tomentella and G. latifolia. Extracted DNA was successfully subjected to PCR amplification of five microsatellite markers and four putative glycosyltransferase genes. DNA extraction protocol is reproducible, trouble free, rapid and can be adopted for plant molecular biology applications.
  • Küçük Resim
    Öğe
    Genetic diversity and population structure of Korean wild soybean (Glycine soja Sieb. and Zucc.) inferred from microsatellite markers
    (Pergamon-Elsevier Science Ltd, 2017) Nawaz, Muhammad Amjad; Yang, Seung Hwan; Rehman, Hafiz Mamoon; Baloch, Faheem Shehzad; Lee, Jeong Dong
    Korea is considered one of the centers of genetic diversity for cultivated as well as wild soybeans. Natural habitats of wild soybeans are distributed across the Korean mainland and the islands surrounding the Korean peninsula. In this study, the genetic diversity of 100 mainland Korean wild soybean accessions was evaluated by using 42 simple sequence repeat markers covering 17 soybean chromosomes. All analyzed loci were polymorphic and a total of 114 alleles were found. The observed average genetic diversity was low (0.4). The results showed that the 100 selected accessions did not exactly follow the geographical distribution. These results were further confirmed by the phylogeny inferred from five morphological characteristics (i.e., leaf shape, leaf area, plant shape, seed area, and 100-seed weight). Together, the genetic and morphological evaluations suggested conclusively that the selected population did not follow the geographical distribution pattern. The present study could provide useful information for the ex situ conservation and exploitation of wild soybean accessions in soybean improvement stratagems, and will aid in further understanding about the phylogeography of the species in the Korean center of diversity. (C) 2017 Elsevier Ltd. All rights reserved.
  • Küçük Resim
    Öğe
    Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean
    (Elsevier GmbH, 2017) Nawaz, Muhammad Amjad; Rehman, Hafiz Mamoon; Baloch, Faheem Shehzad; Ijaz, Babar; Ali, Muhammad Amjad; Khan, Iqrar Ahmad; Lee, Jeong Dong
    The plant cellulose synthase gene superfamily belongs to the category of type-2 glycosyltransferases, and is involved in cellulose and hemicellulose biosynthesis. These enzymes are vital for maintaining cell-wall structural integrity throughout plant life. Here, we identified 78 putative cellulose synthases (CS) in the soybean genome. Phylogenetic analysis against 40 reference Arabidopsis CS genes clustered soybean CSs into seven major groups (CESA, CSL A, B, C, D, E and G), located on 19 chromosomes (except chromosome 18). Soybean CS expansion occurred in 66 duplication events. Additionally, we identified 95 simple sequence repeat makers related to 44 CSs. We next performed digital expression analysis using publically available datasets to understand potential CS functions in soybean. We found that CSs were highly expressed during soybean seed development, a pattern confirmed with an Affymatrix soybean IVT array and validated with RNA-seq profiles. Within CS groups, CESAs had higher relative expression than CSLs. Soybean CS models were designed based on maximum average RPKM values. Gene co-expression networks were developed to explore which CSs could work together in soybean. Finally, RT-PCR analysis confirmed the expression of 15 selected CSs during all four seed developmental stages. © 2017 Elsevier GmbH
  • Küçük Resim
    Öğe
    Systems identification and characterization of cell wall reassembly and degradation related genes in Glycine max (L.) Merill, a bioenergy legume
    (Nature Publishing Group, 2017) Nawaz, Muhammad Amjad; Rehman, Hafiz Mamoon; Imtiaz, Muhammad; Baloch, Faheem Shehzad; Lee, Jeong Dong
    Soybean is a promising biomass resource for generation of second-generation biofuels. Despite the utility of soybean cellulosic biomass and post-processing residues in biofuel generation, there is no comprehensive information available on cell wall loosening and degradation related gene families. In order to achieve enhanced lignocellulosic biomass with softened cell walls and reduced recalcitrance, it is important to identify genes involved in cell wall polymer loosening and degrading. Comprehensive genome-wide analysis of gene families involved in cell wall modifications is an efficient stratagem to find new candidate genes for soybean breeding for expanding biofuel industry. We report the identification of 505 genes distributed among 12 gene families related to cell wall loosening and degradation. 1262 tandem duplication events contributed towards expansion and diversification of studied gene families. We identified 687 Simple Sequence Repeat markers and 5 miRNA families distributed on 316 and 10 genes, respectively. Publically available microarray datasets were used to explore expression potential of identified genes in soybean plant developmental stages, 68 anatomical parts, abiotic and biotic stresses. Co-expression networks revealed transcriptional coordination of different gene families involved in cell wall loosening and degradation process.