Biology subjects

Raza, Q.

Publications and source records attributed to Raza, Q..

8 recordsLinked to original sources

bioRxiv2025

Identification and Development of Functional Markers Associated with Triple Pistil Phenotype in Wheat

Triple pistil (TP) wheat is a historical genetic resource capable of producing up to three grains in a single floret and bolstering the current stagnant grain yield potential. TP phenotype is speculated to be the result of a spontaneous mutation; however, the exact underling genetic mechanism remains elusive, with lack of functional markers for early generation trait selection in hybrid wheat breeding programs. Here, scanning electron microscopy highlighted clear developmental differences between single and triple pistil plants started to arise during 1-2 cm long young spike stages. Using a forward genetics approach, we identified consistent TP-associated mutations in two genes (TraesCS2D02G490900 and TraesCS2D02G491600) exhibiting a nearly complete co-segregation with TP phenotype and developed functional markers for early generation trait selection. CRISPR-Cas9 mediated gene-editing of TraesCS2D02G490900 shifted grain set toward single-grain florets in one edited line in transgenic wheat plants. Furthermore, grain yield evaluation exhibited a significant increase in grains per spike, with no statistically significant reduction in grain weight per spike. Hybrids between common and TP wheat exhibited relatively higher yields, highlighting TP wheat as a significant donor to fortify grain yield potential. This study provides co-dominant functional markers for early generation TP trait selection and valuable targets for hybrid wheat breeding programs.

plant biology↗

bioRxiv2023

Genome-wide characterization of MLO family genes in bread wheat shed light on their role in powdery mildew, rusts, blight, abiotic stresses, and development

Powdery mildew (PM) is a notorious disease that causes up to 62% of yield losses in wheat. The 66 PM resistance quantitative trait loci (QTL)/genes (Pm1 - Pm66) break down when new pathogen races interact with plants. The knockout of three wheat Mildew resistance locus o (MLO) has conferred stable resistance against PM. However, only seven MLO genes are known in bread wheat, which has limited the development of PM-resistant cultivars. Taking advantage of IWGSC Ref-seq v2.1, we identified 47 MLO genes in wheat that were distributed on all 21 chromosomes in a non-random fashion. Phylogenetic analysis showed that MLOs are divided into four clades/subfamilies, while clades I, II, III, and IV harbored 6, 28, 6, and 7 MLO genes, respectively. The phylogenetic patterns were strongly supported by gene structure and motif distribution in different clades. Motif analysis found 16 conserved motifs in wheat MLOs. Comparative phylogenetic tree of wheat, Arabidopsis, and rice MLOs classified the genes into four clades. Evolution analysis showed that segmental duplications and purifying selection are prevalent in TaMLOs. Finally, nine MLOs showed in silico expression in different tissues during growth and development. Eight genes (TaMLO3/6-A2, TaMLO7-A1, TaMLO9-D1, TaMLO10-A2, TaMLO10-B1, TaMLO10-B2, TaMLO10-D1, and TaMLO10-D2) showed overlapping expression under cold, drought, heat stress, and phosphate starvation. Several MLOs showed differential in silico expression under PM (TaMLO10-A2, TaMLO3/6-A2, TaMLO7-A1, TaMLO10-D5), stripe rust (TaMLO9-D1), and head blight (TaMLO10-A2, TaMLO4-A1, TaMLO10-B1, TaMLO10-B2, TaMLO10-D1, TaMLO10-D2). The quantitative real-time polymerase chain reaction (qRT-PCR) showed that nine genes (TaMLO3/6-A2, TaMLO3/6-B2, TaMLO3/6-D2, TaMLO8-A1, TaMLO8-B1, TaMLO8-D1, TaMLO9-A1, TaMLO10-A1, and TaMLO10-D1) exhibited significant upregulation in PM-resistant line after 24, 48, and 72 hours of post-inoculation with the pathogen as compared with the susceptible cultivar. Whereas TaMLO9-D1 showed downregulation. Thus, these MLO genes have a potential role in wheat under these conditions. Therefore, we hope that the MLO genes identified in this study will be edited through CRISPR/Cas9 and/or will be overexpressed to develop PM and disease-resistant and abiotic stress-tolerant wheat.

bioinformatics↗

bioRxiv2023

GWAS and genomic selection for marker-assisted development of sucrose enriched soybean cultivars

Sucrose concentration in soy-derived foods is becoming a seminal trait for the production of food-grade soybeans. However, limited scientific knowledge is reported on this increasingly important breeding objective. In this study, 473 genetically diverse soybean germplasm accessions and 8,477 high-quality single nucleotide polymorphisms (SNPs) markers were utilized to pinpoint genomic regions associated with seed sucrose contents through a genome-wide association study (GWAS). A total of 75 significant SNPs (LOD [≥]6.0) were identified across GLM, FarmCPU and BLINK models, including four stable and novel SNPs (Gm03_45385087_ss715586641, Gm06_10919443_ss715592728, Gm09_45335932_ss715604570 and Gm14_10470463_ss715617454). Gene mining near 20 kb flanking genomic regions of four stable SNPs identified 23 candidate genes with the majority of them highly expressed in soybean seeds and pod shells. A sugar transporter encoding major facilitator superfamily gene (Glyma.06G132500) showing the highest expression in pod shells was also identified. Moreover, selection accuracy, efficiency and favorable alleles of 75 significantly associated SNPs were estimated for their utilization in soybean breeding programs. Furthermore, genomic predictions with three different scenarios revealed better feasibility of GWAS-derived SNPs for selection and improvement of seed sucrose concentration. These results could facilitate plant breeders in marker-assisted breeding and genomic selection of sucrose-enriched food-grade soybean cultivars for the global soy-food industry.

genomics↗

bioRxiv2020

MADS-box genes galore in wheat genome: phylogenomics, evolution and stress associated functions

MADS-box gene family members play multifarious roles in regulating the growth and development of crop plants and hold enormous promise for bolstering grain yield potential under changing global environments. Bread wheat (Triticum aestivum L.) is a key stable food crop around the globe. Until now, the available information concerning MADS-box genes in the wheat genome has been insufficient. However, a comprehensive genome-wide analysis identified 300 high confidence MADS-box genes from the latest publicly available reference genome of wheat. Comparative phylogenetic analyses with Arabidopsis and rice MADS-box genes classified the wheat genes into 16 distinct subfamilies, without a single FLOWERING LOCUS C homolog present in the wheat genome. Gene duplications were mainly identified in subfamilies containing unbalanced homeologs, pointing towards a potential mechanism for gene family expansion. Moreover, a more recent evolutionary origin was inferred for M-type genes, as compared with MIKC-type genes, indicating their significance in understanding the evolutionary history of the wheat genome. We speculate that subfamily-specific distal telomeric duplications in unbalanced homeologs facilitate the rapid adaptation of wheat to changing environments. Furthermore, our in-silico expression data strongly proposed MADS-box genes as active guardians of plants against pathogen insurgency and harsh environmental conditions. In conclusion, we provide an entire complement of MADS-box genes identified in the wheat genome that will accelerate functional genomics efforts and possibly facilitate bridging gaps between genotype-to-phenotype relationships through fine-tuning of agronomically important traits.

genomics↗

bioRxiv2020

Reproductive tissues-specific meta-QTLs and candidate genes for development of heat-tolerant rice cultivars

Rice holds the key to future food security. In rice-growing areas, temperature has already reached an optimum level for growth, hence, any further increase due to global climate change could significantly reduce rice yield. Several mapping studies have identified a plethora of reproductive tissue-specific and heat stress associated inconsistent quantitative trait loci (QTL), which could be exploited for improvement of heat tolerance. In this study, we performed a meta-analysis on previously reported QTLs and identified 35 most consistent meta-QTLs (MQTLs) across diverse genetic backgrounds and environments. Genetic and physical intervals of nearly 66% MQTLs were narrower than 5 cM and 2 Mb respectively, indicating hotspot genomic regions for heat tolerance. Comparative analyses of MQTLs underlying genes with microarray and RNA-seq based transcriptomic data sets revealed a core set of 45 heat-responsive genes, among which 24 were reproductive tissue-specific and have not been studied in detail before. Remarkably, all these genes corresponded to various stress associated functions, ranging from abiotic stress sensing to regulating plant stress responses, and included heat-shock genes (OsBiP2, OsMed37_1), transcription factors (OsNAS3, OsTEF1, OsWRKY10, OsWRKY21), transmembrane transporters (OsAAP7A, OsAMT2;1), sugar metabolizing (OsSUS4, -Gal III) and abiotic stress (OsRCI2-7, SRWD1) genes. Functional data evidences from Arabidopsis heat-shock genes also suggest that OsBIP2 may be associated with thermotolerance of pollen tubes under heat stress conditions. Furthermore, promoters of identified genes were enriched with heat, dehydration, pollen and sugar responsive cis-acting regulatory elements, proposing a common regulatory mechanism might exist in rice for mitigsating reproductive stage heat stress. These findings strongly support our results and provide new candidate genes for fast-track development of heat-tolerant rice cultivars. Key MessageBy integrating genetics and genomics data, reproductive tissues-specific and heat stress responsive 35 meta-QTLs and 45 candidate genes were identified, which could be exploited through marker-assisted breeding for fast-track development of heat-tolerant rice cultivars.

genomics↗

bioRxiv2020

Grain Fe and Zn Contents Linked SSR Markers Based Genetic Diversity Reveal Perspective for Marker Assisted Biofortification Breeding in Rice

Rice is critical for sustainable food and nutritional security; however, nominal micronutrient quantities in grains aggravate malnutrition in rice-eating poor populations. Here, we assessed genetic diversity in grain iron (Fe) and zinc (Zn) contents using trait-linked simple sequence repeat (SSR) markers in 56 fine and coarse grain rice accessions of different geographical origin. Aromatic fine gain accessions contained relatively higher Fe and Zn contents in brown rice (BR) than coarse grain accessions. Genotyping with 24 SSR markers identified 21 polymorphic markers, among which seventeen demonstrated higher gene diversity and polymorphism information content (PIC) values, strongly indicating that markers used in current research were moderate to highly informative for evaluating genetic diversity. Population structure, principal coordinate and phylogenetic analyses classified studied rice accessions into two fine grain specific and one fine and coarse grain admixture subpopulations. Single marker analysis recognized four ZnBR and single FeBR significant marker-trait associations (MTAs), contributing 15.41-39.72% in total observed phenotypic variance. Furthermore, high grain Fe and Zn contents linked marker alleles from significant MTAs were also identified. Collectively, these results indicate availability of wide genetic diversity in rice germplasm and perspective for marker-assisted biofortification breeding.

genetics↗

bioRxiv2019

Vinculin anchors contractile actin to the cardiomyocyte adherens junction

The adherens junction (AJ) couples the actin cytoskeletons of neighboring cells to allow mechanical integration and tissue organization. The physiological demands of intercellular adhesion require that the AJ be responsive to dynamic changes in force while maintaining mechanical load. These demands are tested in the heart, where cardiomyocyte AJs must withstand repeated cycles of actomyosin-mediated contractile force. Here we show that force-responsive cardiomyocyte AJs recruit actin-binding ligands to selectively couple actin networks and promote contact maturation. We employed a panel of N-cadherin-E-catenin fusion proteins to rebuild AJs with specific actin linkages in N-cadherin-null cardiomyocytes. In this system, vinculin recruitment was required to rescue myofibril integration and desmosome assembly at nascent contacts. In contrast, loss of vinculin disrupted junction morphology and blocked myofibril integration. Our results identify vinculin as a critical link to contractile actomyosin and offer insight to how actin integration at the AJ is regulated to provide mechanical stability and cellular organization.

cell biology↗

bioRxiv2018

Evolutionary rate covariation analysis of E-cadherin identifies Raskol as regulator of cell adhesion and actin dynamics in Drosophila

The adherens junction couples the actin cytoskeletons of neighboring cells to provide the foundation for multicellular organization. The core of the adherens junction is the cadherin-catenin complex that arose early in the evolution of multicellularity to link cortical actin to intercellular adhesions. Over time, evolutionary pressures have shaped the signaling and mechanical functions of the adherens junction to meet specific developmental and physiological demands. Evolutionary rate covariation (ERC) identifies genes with correlated fluctuations in evolutionary rate that can reflect shared selective pressures and functions. Here we use ERC to identify genes with evolutionary histories similar to shotgun (shg), which encodes the Drosophila E-cadherin (DE-Cad) ortholog. Core adherens junction components -catenin and p120-catenin displayed strong ERC correlations with shg, indicating that they evolved under similar selective pressures during evolution between Drosophila species. Further analysis of the shg ERC profile revealed a collection of genes not previously associated with shg function or cadherin-mediated adhesion. We then analyzed the function of a subset of ERC-identified candidate genes by RNAi during border cell (BC) migration and identified novel genes that function to regulate DE-Cad. Among these, we found that the gene CG42684, which encodes a putative GTPase activating protein (GAP), regulates BC migration and adhesion. We named CG42684 raskol (\"to split\" in Russian) and show that it regulates DE-Cad levels and actin protrusions in BCs. We propose that Raskol functions with DE-Cad to restrict Ras/Rho signaling and help guide BC migration. Our results demonstrate that a coordinated selective pressure has shaped the adherens junction and this can be leveraged to identify novel components of the complexes and signaling pathways that regulate cadherin-mediated adhesion.\n\nAuthor SummaryThe establishment of intercellular adhesions facilitated the genesis of multicellular organisms. The adherens junction, which links the actin cytoskeletons of neighboring cells, arose early in the evolution of multicellularity and selective pressures have shaped its function and molecular composition over time. In this study, we used evolutionary rate covariation (ERC) analysis to examine the evolutionary history of the adherens junction and to identify genes that coevolved with the adherens junction gene shotgun, which encodes the Drosophila E-cadherin (DE-Cad). ERC analysis of shotgun revealed a collection of genes with similar evolutionary histories. We then tested the role of these genes in border cell migration in the fly egg chamber, a process that requires the coordinated regulation of cell-cell adhesion and cell motility. Among these, we found that a previously uncharacterized gene CG42684, which encodes a putative GTPase activating protein (GAP), regulates the collective cell migration of border cells, stabilizes cell-cell adhesions and regulates the actin dynamics. Our results demonstrate that components of the adherens junction share an evolutionary history and that ERC analysis is a powerful method to identify novel components of cell adhesion complexes in Drosophila.

genetics↗