Dr Muhammad Waseem

About the Journal

Dr. Muhammad Waseem, Assistant Professor of Botany at the Department of Botany, University of Narowal, Pakistan. He got a doctoral degree (Ph.D., specialization in Plant Molecular Biology) from Prof. Zhengguo Li’s lab at the School of Life Sciences, Chongqing University, Chongqing, PR China. He then joined as a postdoctoral researcher at the College of Horticulture, South China Agricultural University Guangzhou, China in Prof. Xia Rui’s lab. Recently, he is appointed as Assistant Professor of Botany, Department of Botany, University of Narowal, Pakistan, and mainly engaged in teaching Botany with some other major courses in the field of Molecular Biology, Plant Biotechnology, Genetics, and Plant anatomy to undergraduate and postgraduate students.

His interests include transcriptional regulation of flowering time regulation, fruit ripening and development, and abiotic stresses such as salinity and drought. In addition, he has hands-on experience in next-generation sequencing data analysis, transcriptomics, and data visualization. In brief, he has published research in various high-impact factor journals including New Phytologist, International Journal of Macromolecules, Journal of Biotechnology, Planta, Scientific reports, Pakistan Journal of Botany, GM Crops & Food, International Journal of Molecular Biology, Genes, Plant Physiology, and Frontiers in Plant Science. He has also edited various book chapters in springer-nature, CRC press, and others. Moreover, currently, he is editing a few special issues as a leading guest editor in Frontiers in Plant Science, International Journal of Molecular Biology, and Functional Plant Biology.

Functional Characterization of SlbHLH22 gene in tomato

Tomato (Solanum lycopersicum) is an important economic and agricultural crop around the world, and the ideal model plant to study the fleshy fruit development and ripening. The basic Helix-Loop-Helix (bHLH) comprises the second largest superfamily of transcription factors in plants and is very diverse. Some progress has been made on the studies of bHLH TF but is limited in the model plant Arabidopsis. The bHLH TF are demonstrated to play essential roles in plant growth and development, ripening and stress response processes. In the present thesis, we use tomato as the model plant to study the functional roles of SlbHLH22 in tomato fruit ripening and stress response using molecular biology and physiology methods.

I evaluated the role of the bHLH transcription factor in tomato fruit ripening by overexpressing the corresponding SlbHLH22 gene. The overexpression of SlbHLH22 gene revealed that it is highly involved in controlling flowering time by activating SlSFT or SlLFY gene and promoting fruit ripening and subsequently produced fruits with enhanced pigmentation. Meanwhile, the carotenoid-related gene expression patterns (SlPYS1) was also upregulated in transgenic tomato fruits. In transgenic tomato fruit, we observed apparent changes in color from green to orange with enhanced expressions of SlbHLH22 gene, while SlbHLH22 was also upregulated under exogenous ACC, IAA, and ABA. Besides, overexpression of SlbHLH22 also promotes ethylene production. It was observed that plants overexpressing SlbHLH22 showed short height with small leaves and enhanced flavonoid accumulation. The transgenic plants overexpressing SlbHLH22 displayed enhanced vigour and more tolerant to drought and salinity than WT. Overexpression of SlbHLH22 significantly peaked the catalase (CAT), superoxide dismutase (SOD), and peroxidase (POD) activities under salinity and drought to minimize the impacts of reactive oxygen species such as H2O2, which was reduced significantly in transgenic plants along with Malondialdehyde (MDA). Additionally, the expression of ROS defense genes SlPOD, SlCAT, SlSOD, ABA biosynthesis genes, proline biosynthesis, and flavonoid synthesis were also activated under salinity and drought.

Deconstructing lncRNA architecture in litchi identifies a PHAS-loci in lncRNA instigate phasiR172 regulating flowering

Flowering is a complex, genetically controlled phenomenon pivotal for the reproductive success of plants. The floral transition has been extensively studied in various model plant species in plants, including tomato, Arabidopsis. This led to the identification of hundreds of regulatory components governing flowering. However, non-coding RNAs (ncRNAs) are among them. Litchi (Litchi chinensis Sonn.) is an evergreen fruit tree of subtropics in China, Africa, and Australia. The litchi flower buds are initiated and develop at the apex of mature current-season shoots. Recently, it was reported that miRNAs trigger phased small secondary RNAs (phasiRNAs) instigation through their target genes, the PHAS locus. Long non-coding RNAs (lncRNAs), particularly intergenic lncRNAs, could act as PHAS locus for generating 21-nucleotide phasiRNAs, indicating that litchi lncRNAs might play a role in regulating flowering. We identified that litchi miR482 could trigger the phasiRNAs origination by targeting PHAS locus, which was further verified in both sequencing data. Sequence analysis revealed that phasiRNA derived from this locus display homology with miR172, a repressor of APETALA2 (AP2).

Moreover, downstream target analysis of these phasiRNAs shown to target AP2 genes and these are different from those targeted by miR172. Hence, we named this locus as PHAS AP2 and generated phasiRNA as phasiR172. This led us to hypothesize that this miR482-PHAS_AP2-phasiR172-AP2 pathway may compete or hijack the miR172-AP2 flowering pathway in litchi. To better understand this pathway's regulatory role, we aimed to investigate the mechanism of action of phasiR172 and its direct or indirect in the flowering regulatory pathway. These results will be helpful to novel insight into the new regulatory mechanism involved in the induction of early flowering in litchi.

Investigating the genetic basis of extra-early maturing Brassica napus and molecular mechanism studying of important traits

Flowering is a complex genetically controlled phenomenon pivotal for the reproductive success of plants. In plants, the floral transition has been extensively studied in various model plant species including tomato, and Arabidopsis. This led to the identification of hundreds of regulatory genes governing the process of flowering, however, flowering time is one of the pivotal processes ensuring the maturation time of a crop. The flowering time involves an array of regulatory genes controlled by distinct internal and external environmental cues. Among those, photoperiod and vernalization are two key players of flower initiation. Brassica napus is a close relative to the model crucifer Arabidopsis. Most Arabidopsis flowering time genes are conserved in the species, indicating that flowering time regulation in oilseed rape is regulated in a similar way as in the model system. In China, the spring and winter B. napus varieties (more than 215 varieties) is mainly distributed in Northwest China. Due to the lack of suitable crop species to plant through winter, most cultivated land (rice paddy) lies idle without any cover in winter and early spring in southern China. This is because of the long maturation period of existing B. napus varieties between 210-180 days. To search for a suitable crop during this period, we developed a new B. napus ecotype with 90 days of maturation period making it an ideal crop of southern China barren rice paddy fields. This unusual behavior of B. napus ecotype maturation timer motivates us to explore the genetic difference of flowering time regulation network/genes in our newly developed ecotype than existing B. napus varieties. However, little is known about the complex regulatory mechanism of flowering in the winter B. napus responds to temperature and photoperiod. The present research proposal aims to advance our understanding of the underlying genetic network of the flowering period in Chinese B. napus varieties could provide a theoretical and practical basis for developing new cultivars adapted to different geographical environments. The expected results will also contribute to China’s development of sustainable agriculture aimed to ensure global food security.