Biology subjects

Kabir, A. H.

Publications and source records attributed to Kabir, A. H..

3 recordsLinked to original sources

bioRxiv2020

Genome Wide Association Studies on 7 Yield-relatedTraits of 183 Rice Varieties in Bangladesh

MotivationRice genetic diversity is regulated by multiple genes and is largely dependent on various environmental factors. Uncovering the genetic variations associated with the diversity in rice populations is the key to breed stable and high yielding rice varieties. ResultsWe performed Genome Wide Association Studies (GWAS) on 7 rice yielding traits (grain length, grain width, grain weight, panicle length, leaf length, leaf width and leaf angle) based on a population of 183 rice landraces of Bangladesh. Our GWA studies reveal various chromosomal regions and candidate genes that are associated with different traits in Bangladeshi rice varieties. Noteworthy was the recurrent implication of chromosome 10 in all three grain shape related traits (grain length, grain width, and grain weight), indicating its pivotal role in shaping rice grain morphology. Our study also underscores the involvement of transposon gene families across these three traits. For leaf related traits, chromosome 10 was found to harbor regions that are significantly associated with leaf length and leaf width. The results of these association studies support previous findings as well as provide additional insights into the genetic diversity of rice. ConclusionsThis is the first known GWAS study on various yield-related traits in the varieties of Oryza sativa available in Bangladesh - the fourth largest rice-producing country. We believe this study will accelerate rice genetics research and breeding stable high-yielding rice in Bangladesh.

bioinformatics↗

bioRxiv2020

In silico characterization of MTP1 gene associated with Zn homeostasis across different dicot plant species

Zinc (Zn) is tightly regulated in plants. The MTP1/ZAT (metal tolerance protein) plays a critical role in adjusting Zn homeostasis upon Zn fluctuation in plants. This study characterizes MTP1 homologs with particular emphasis on AtMT1 in various dicot plants. The protein BLAST search was used to identify a total of 21 MTP1 proteins. Generally, all these MTP1 proteins showed around 400 residues long, six transmembrane helices, stable instability index along with cation transmembrane transporter activity (GO:0008324). These physio-chemical features of MTP1 can be utilized as a benchmark in the prediction of Zn uptake and tolerance in plants. These MTP1 homologs were located on chromosomes 2, 7, and 14 with one exon. Motif analysis showed conserved sequences of 41-50 residues belonging to the family of cation efflux, which may be helpful for binding sites targeting and transcription factor analysis. Phylogenetic studies revealed close similarities of AtZAT with Glycine max and Medicago trunculata that may infer a functional relationship in Zn tolerance or uptake across different plant species. Further, interactome analysis suggests that AtZAT is closely linked cadmium/zinc-transporting ATPase and ZIP metal ion transporter, which could provide essential background for functional genomics studies in plants. The network of AtZAT is predominantly connected to cadmium/zinc-transporting ATPase (HMA2, HMA3, HMA4), cation efflux protein (MTP11), and metal tolerance protein C3 (AT4G58060). The Genevestigator platform further predicts the high expression potential of AtMTP1 in root tissue at the germination and grain filling stage. The structural analysis of MTP1 proteins suggests the conserved N-glyco motifs as well as similar hydrophobicity, net charge and nonpolar residues, alpha-helix in all MTP1 proteins. Altogether, these in silico characterization features of MTP1 and its orthologs will provide an essential theoretical background to perform wet-lab experiments and to better understand Zn homeostasis aiming to develop genetically engineered plants.

plant biology↗

bioRxiv2020

In silico characterization and expression profiles of zinc transporter-like (LOC100037509) gene of tomato

Zinc (Zn) is an essential microelement for plants. ZIP transporters play a critical role in Zn homeostasis in plants. This in silico study characterizes different characteristics of putative Zn transporter of tomato (Solyc07g065380) and its homologs. A total of 10 ZIP protein homologs were identified across nine plant species by protein BLAST. All these ZIP protein homologs located at chromosome 7 showed 305-350 amino acid residues, 7-8 transmembrane helices, and stable instability index. Further, these ZIP protein homologs are localized in the plasma membrane at the subcellular level corresponding to the ZIP zinc transporter (PF02535) domain. Gene organization analysis reveals the presence of 3 exon along with the position of the promoter, TATA-box, transcriptional start site, and splice sites in these ZIP transporter homologs, in which tomato ZIP transporter (NM_001247420.1) contains a promoter, TATA-box, transcriptional start site at 500, 911 and 946 bp, respectively along with several splice sites, which may be useful for targeting binding sites and transcription factor analysis. Further, the cutting sites and restriction enzymes of each ZIP gene homologs might be helpful for future transgenic studies underlying Zn homeostasis. MEMO displayed five conserved motifs associated with the ZIP zinc transporter, N-glycosylation site, and phosphorylation site. Phylogenetic studies reveal a closet relationship of Solyc07g065380 with Solanum pennellii homolog, while ZIP transporter of Nicotiana sylvestris and Nicotiana tabacum predicted to be in close connection. The Solyc07g065380 transporter is predominantly linked to several uncharacterized zinc metal ion transporters and expressed in diverse anatomical part, developmental stage, and subjected to pathogen and heat stress. The secondary structural prediction reveals unique signal peptide in the ZIP protein homologs of S. lycopersicum and S. pennellii along with extended alpha-helix. These bioinformatics analyses might provide essential background to perform wet-lab experiments and to understand Zn homeostasis for the development of Zn-biofortified crops. Key message{diamondsuit} ZIP protein homologs are localized in the plasma membrane and are linked to ZIP zinc transporter (PF02535) domain at chromosome 7. {diamondsuit}ZIP protein motifs are associated with the ZIP zinc transporter, N-glycosylation site, and phosphorylation site. {diamondsuit}Phylogenetic studies reveal a closet relationship of Solyc07g065380 with Solanum pennellii homolog. {diamondsuit}ZIP protein homologs of S. lycopersicum and S. pennellii show unique signal peptide along with extended alpha-helix.

physiology↗