Biology subjects

Siddique, I.

Publications and source records attributed to Siddique, I..

4 recordsLinked to original sources

bioRxiv2026

Assessment of EMS-induced mutagenesis in Fagopyrum esculentum Moench (Buckwheat)

Global demand for pseudocereals, including buckwheat, has surged in recent years due to their higher nutritional and pharmaceutical value than cereals and also due to them being a climate-resilient, gluten-free, and potential crop for combating cancer, type ll diabetes, and overcoming micronutrients hidden hunger problems that lack in cereals. Major efforts are needed to make its cultivation more popular by improving its quantitative and qualitative traits through crop genetics by adopting modern genetic, molecular, and mutational approaches, which also necessitate the induction of genetic variation for better yielding and improved varieties. In this experimental study, the induced mutant populations of widely recommended VL-7 and PRB-1 varieties of buckwheat were generated using different concentrations treatments of ethyl methane sulfonate (EMS). Investigation on induced phenotypical and genotypical variations in individual plants of M1 population of different treatments resulted in morphological and cytological mutant types affecting plant germination, survival, height and morphology, leaf morphology, flower morphology, growth period, chlorophyll and pigments abnormalities in leaves, leaf growth pattern, plant fertility, yield, and cytological aberrations. This experiment showed that plant survival decreased with the concentration of the mutagen doses. The lower doses resulted in dwarf varieties suitable for cultivation as they increased yield by having higher breaking force and lower lodging index over the tall plants. Studies on various quantitative parameters revealed the general effectiveness of intermediate doses and stimulatory effectiveness of lower and higher concentrations in M1 generation.

plant biology↗

bioRxiv2025

The Agroforestry Species Switchboard, a global resource to explore information for 107,269 plant species

The Agroforestry Species Switchboard is a comprehensive vascular plant database that guides users to information for a particular taxon from a global but fragmented set of resources. Via standardized species names, a user can rapidly infer which among the 59 contributing databases contain information for a species of interest, and understand how this information can be accessed. By providing taxonomic identifiers to World Flora Online, it is straightforward to check for changes in taxonomy. Among the 59 databases referenced, ten covered over 10,000 species, 20 between 1,000 and 10,000 species, and 22 between 100 and 1,000 species. The ten species-richest plant families across covered databases were the Fabaceae (9,537 species), Asteraceae (6,041), Rubiaceae (4,812), Poaceae (3,947), Myrtaceae (3,544), Euphorbiaceae (2,689), Malvaceae (2,478), Rosaceae (2,374), Lauraceae (2,334) and Lamiaceae (2,107). Information included in the Switchboard distinguishes 54,812 tree-like species, covering most known tree species globally. Among its applications, the Switchboard can assist species selection for ecological restoration projects to synergize biodiversity and human well-being objectives.

ecology↗

bioRxiv2023

Development of a Next Generation SNP Genotyping Array for Wheat

High throughput genotyping arrays have provided a cost effective, reliable and interoperable system for genotyping hexaploid wheat and its related germplasm pool. Existing, highly cited arrays including our 35K Axiom Wheat Breeders genotyping array and the Illumina 90K iSelect array were designed based on a limited amount of varietal sequence diversity and with imperfect knowledge of SNP positions. Recent progress in sequencing wheat varieties and landraces has given us access to a vast pool of SNP diversity, whilst technological improvements in array design has allowed us to fit significantly more probes onto a 384-well format Axiom array than was previously possible. Here we describe a novel High Density Axiom genotyping array, the Triticum aestivum Next Generation array (TaNG), largely derived from whole genome skim sequencing of 204 elite wheat lines and 111 wheat landraces taken from the Watkins "Core Collection". We use a novel "minimal marker" optimisation approach to select up to six SNPs in each 1.5 MB region of the wheat genome with the highest combined varietal discrimination potential. A design iteration step allowed us to test and replace skim-sequence derived SNPs which failed to convert to reliable Axiom markers, resulting in a final design, designated TaNG1.1 with 43,372 SNPs derived from a haplotype-optimised combination of novel SNPs, DArTAG-derived and legacy wheat Axiom markers. We show that this design has an even distribution of SNPs across chromosomes and sub-genomes compared to previous arrays and can be used to generate genetic maps with a significantly higher number of distinct bins than our previous Axiom array. We also demonstrate the improved performance of TaNG1.1 for Genome Wide Association Studies (GWAS) and its utility for Copy Number Variation (CNV) analysis. The array is commercially available, and the marker annotations, initial genotyping results and software used to generate the optimised marker sets are freely available.

genomics↗

bioRxiv2021

Exophers are components of mammalian cell neurobiology in health and disease

Maintenance of cellular homeostasis is critically important for the survival of cells and organisms. Degradation and recycling of biomolecules and whole organelles is an essential mechanism for maintaining cellular homeostasis. The main systems responsible for these processes are the ubiquitin-proteasome system and autophagy-lysosome pathway. Another mechanism was reported in c. elegans--formation of large, membrane-enclosed projections called "exophers," into which cells direct debris and toxic protein aggregates1. Exophers were shown to act as large, temporary disposal compartments that disconnected from the cells within several hours. Here, we report the discovery of exophers in the mammalian brain, including the brains of humans and mice. Similar to those described in nematodes, the mammalian exophers appear to emanate from the cell body, initially connected by a nanotube, and eventually disconnect. Rare, innate exophers were found in healthy human brain and primary neurons from wild-type mice, presumably mediating transfer of large cargo between cells. The number of exophers increased as an adaptive response under proteostatic stress, e.g., in Alzheimers disease brain or in primary neurons from two tauopathy mouse models, where the exophers likely facilitated expulsion of proteotoxic material. Our findings suggest that exopherogenesis is a rare, innate house-keeping process that is elevated adaptively in response to proteostatic pressure and is a conserved mechanism from nematodes to humans.

cell biology↗