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Muhammad Waqas,Muhammad Tehseen Azhar,Iqrar Ahmad Rana,Farrukh Azeem,Muhammad Amjad Ali,Muhammad Amjad Nawaz,정규화,Rana Muhammad Atif 한국유전학회 2019 Genes & Genomics Vol.41 No.4
Background WRKY proteins play a vital role in the regulation of several imperative plant metabolic processes and pathways, especially under biotic and abiotic stresses. Although WRKY genes have been characterized in various major crop plants, their identification and characterization in pulse legumes is still in its infancy. Chickpea (Cicer arietinum L.) is the most important pulse legume grown in arid and semi-arid tropics. Objective In silico identification and characterization of WRKY transcription factor-encoding genes in chickpea genome. Methods For this purpose, a systematic genome-wide analysis was carried out to identify the non-redundant WRKY transcription factors in the chickpea genome. Results We have computationally identified 70 WRKY-encoding non-redundant genes which were randomly distributed on all the chickpea chromosomes except chromosome 8. The evolutionary phylogenetic analysis classified the WRKY proteins into three major groups (I, II and III) and seven sub-groups (IN, IC, IIa, IIb, IIc, IId and IIe). The gene structure analysis revealed the presence of 2–7 introns among the family members. Along with the presence of absolutely conserved signatory WRKY domain, 19 different domains were also found to be conserved in a group-specific manner. Insights of gene duplication analysis revealed the predominant role of segmental duplications for the expansion of WRKY genes in chickpea. Purifying selection seems to be operated during the evolution and expansion of paralogous WRKY genes. The transcriptome data-based in silico expression analysis revealed the differential expression of CarWRKY genes in root and shoot tissues under salt, drought, and cold stress conditions. Moreover, some of these genes showed identical expression pattern under these stresses, revealing the possibility of involvement of these genes in conserved abiotic stress–response pathways. Conclusion This genome-wide computational analysis will serve as a base to accelerate the functional characterization of WRKY TFs especially under biotic and abiotic stresses.
Nawaz, Muhammad Amjad,Yang, Seung Hwan,Rehman, Hafiz Mamoon,Baloch, Faheem Shehzad,Lee, Jeong Dong,Park, Jong Hyun,Chung, Gyuhwa Elsevier 2017 Biochemical systematics and ecology Vol.71 No.-
<P><B>Abstract</B></P> <P>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 <I>ex situ</I> 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.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Microsatellite analysis and morphological characterization of Korean wild soybean was done. </LI> <LI> Korean mainland wild soybeans have low genetic diversity. </LI> <LI> Selected populations do not follow geographical distribution pattern. </LI> </UL> </P>
Genome and transcriptome-wide analyses of cellulose synthase gene superfamily in soybean
Nawaz, Muhammad Amjad,Rehman, Hafiz Mamoon,Baloch, Faheem Shehzad,Ijaz, Babar,Ali, Muhammad Amjad,Khan, Iqrar Ahmad,Lee, Jeong Dong,Chung, Gyuhwa,Yang, Seung Hwan G. Fischer 2017 Journal of plant physiology Vol. No.
<P><B>Abstract</B></P> <P>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 <I>Arabidopsis</I> 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.</P>
Thermal stress effects on microtubules based on orthotropic model: Vibrational analysis
Taj, Muhammad,Khadimallah, Mohamed A.,Hussain, Muzamal,Fareed, Khurram,Safeer, Muhammad,Khedher, Khaled Mohamed,Ahmad, Manzoor,Naeem, M. Nawaz,Qazaq, Amjad,Qahtani, Abdelaziz Al,Mahmoud, S.R.,Alwabli, Techno-Press 2021 Advances in concrete construction Vol.11 No.3
Vibration of protein microtubules is investigated based upon Orthotropic Elastic Shell Model, considering the effect of thermal stresses. The complete analytical formulas of thermal vibration for microtubules are obtained. It is observed that the effects of thermal stresses on the vibrational frequency mode are more significant when the longitudinal and circumferential wave vectors are large enough. But when the length of wave vector reduces to 5 nm, these effects have no significant effects. The present results well agree with the lattice vibrations of microtubules. Moreover, the results show that the effects of thermal stresses due to small change in temperature are not so significant but with the increase in temperature its effects are obvious.
Isoflavone profile diversity in Korean wild soybeans ( Glycine soja Sieb. & Zucc.)
TSUKAMOTO, Chigen,NAWAZ, Muhammad Amjad,KUROSAKA, Ayaka,LE, Bao,LEE, Jeong Dong,SON, Eunho,YANG, Seung Hwan,KURT, Cemal,BALOCH, Faheem Shehzad,CHUNG, Gyuhwa Scientific and Technological Research Council of T 2018 Turkish journal of agriculture & forestry Vol.42 No.4
정규화,Bao Le,Muhammad Amjad Nawaz,Hafiz Mamoon Rehman,Thu Le,양승환,Kirill S. Golokhvast,손은호 한국유전학회 2016 Genes & Genomics Vol.38 No.12
Auxin response factors (ARFs) encode one of the most abundant groups of auxin-mediated response transcription factors in higher plants and play a major role in various biological processes. The success of whole genome sequencing allows for comprehensive phylogenetic analysis of ARF genes in plants. Here, we identified 80 ARF genes belonging to five different groups in legume species, soybean (Glycine max, 55) and common bean (Phaseolus vulgaris, 25), based on phylogenetic analysis and supported by motif analysis. There is no member ARF of common bean in group V which contained two members from soybean, GmARF12 and GmARF55. The duplication events among two species were also observed by using Ks values. A majority of the ARF genes (96.1 %; 38 GmARFs and 56.0 %, 14 PvARFs) were segmentally duplicated while only two and one of ARF G. max and P. vulgaris genes were tandemly duplicated, respectively. In addition, expression profiling indicated that ARF genes in soybean and common bean perform various functions in plant growth and development, excluding flowering development. Furthermore, diversity of cis-elements in promoter regions also revealed differential expression of ARF proteins.