Biology subjects

Shakoor, N.

Publications and source records attributed to Shakoor, N..

6 recordsLinked to original sources

bioRxiv2025

Pangenome of U.S. ex-PVP and Wild Sorghum Reveals Structural Variants and Selective Sweeps Shaping Adaptation and Trait Improvement

Sorghum is a cereal crop grown for food, feed, and biofuel, yet the genomic diversity of elite commercial lines remains underexplored. Here, we assembled a sorghum pangenome from long-read sequences of 46 U.S. ex-Plant Variety Protection Act (ex-PVP) cultivars and a haplotype-resolved assembly of one wild accession. The pangenome revealed largely conserved genomic architecture across elite lines but identified presence-absence variations (PAVs) in 28% of gene families, including genes involved in stress responses and starch metabolism, such as STARCH BRANCHING ENZYME I (SBE1). Selective sweep analyses detected strong signals at key flowering-time loci (Ma1/SbPRR37, Ma2, Ma6) and circadian/light regulators (PHOT1, DET1, XAP5), with PHYA showing copy number variations (CNVs). Analysis of 24 wild accessions, beyond the core pangenome panel, detected CNVs in MULTIDRUG AND TOXIC COMPOUND EXTRUSION (MATE) transporters, potentially reflecting selection or breeding for enhanced herbicide detoxification. These results highlight breeding-shaped regions and position the pangenome as a resource for sorghum improvement.

genomics↗

bioRxiv2024

Soil depth determines the microbial communities in Sorghum bicolor fields

Sorghum bicolor, an important global crop, adapted to thrive in hotter and drier conditions than maize or rice, has deep roots that interact with a unique and stratified soil microbiome that plays a crucial role in plant health, growth, and carbon storage. Microbiome studies on agricultural soils, particularly fields growing S. bicolor, have been mostly limited to surface soils (<30 cm). Here we investigated the abiotic factors of soil properties, field location, depth, and the biotic factors of sorghum type across 38 genotypes on the soil microbiome. Utilizing 16S rRNA gene amplicon sequencing, our analysis reveals significant changes in microbial composition and decreasing diversity at increasing soil depths within S. bicolor regardless of genotype or fields. Notably, specific microbial families, such as Thermogemmatisporaceae and an unclassified family within the ABS-6 order, were enriched in deeper soil layers beyond 30 cm. Additionally, microbial richness and diversity declined with depth, reaching a minimum at the 60 - 90 cm layer, with layers beyond 90 cm increasing in alpha diversity. These findings highlight the importance of soil depth in agricultural soil microbiome studies.

microbiology↗

bioRxiv2022

Responses of Agricultural plants to Lithium pollution: Trends, Meta-Analysis, and Perspectives

Lithium (Li) is gaining attention due to rapid rise of modern industries but their ultimate fingerprints on plants are not well established. Herein, we executed a meta-analysis of the existing recent literature investigating the impact of Li sources and levels on plant species under different growth conditions to understand the existing state of knowledge. Toxic effects of Li exposure in plants varies as a function of medium and interestingly, more negative responses are reported in hydroponic media as compared to soil and foliar application. Additionally, toxic effects of Li vary with Li source materials and LiCl more negatively affected plant development parameters such as plant germination (n=48) and root biomass (n=57) and recorded highly uptake in plants (n=78), while LiNO3 has more negative effects on shoot biomass. The Li at <50 mg L-1 concentrations significantly influenced the plant physiological indicators including plant germination and root biomass, while 50-500 mg L-1 Li concentration influence the biochemical parameters. The uptake potential of Li is dose dependent and their translocation/bioaccumulation remains unknown. Future work should include complete lifespan studies of the crop to elucidate the bioaccumulation of Li in edible tissues and to investigate possible trophic transfer of Li. Environmental significanceAccumulation of Li sources is increasing in ecosystem compartments, and this might be vulnerable to plants.

plant biology↗

bioRxiv2022

Micro and Nanoplastics Interactions with Plant Species Trends, Meta-Analysis, and Perspectives

The ubiquitous presence of nano plastics (NPx) and micro plastics (MPx) in the environment has been demonstrated, and as such, the exposure scenarios, mechanisms of plant response, and ultimate risk must be determined. However, the current literature reports ambiguous outcomes and provides limited mechanistic insight into critical governing processes. Here, we performed a meta-analysis of the most recent literature investigating the effect of MPx/NPx on plant species under laboratory and field conditions so as to evaluate the current state of knowledge. Toxic effects of MPx/NPx exposure in plants varies as a function of plant species and interestingly, generally non-significant responses are reported in staple crops. NPx (<100 nm) more negatively affected plant development parameters (n=341) (n is total number of observations), photosynthetic pigments (n=80), and biochemical indicators (n=91) than did MPx (>100 nm). Surprisingly, NPx exposure yielded negligible effects on germination rate (n=17), although root morphology (n=45) was negatively affected. Alternatively, MPx negatively affected on germination (n= 27) and generally non-significant affect with regard to root morphology (n=64). The effect of MPx/NPx on plant health decreases with increasing exposure time. No specific trends were evident for the production of biochemical enzymes as related to MPx/NPx concentration or size. Future work should include crop full life cycle studies to highlight the accumulation of MPx/NPx in edible tissues and also to investigate potential trophic transfer of MPx/NPx. Furthermore, we provide a framework for additional investigative work to address these and other knowledge gaps and to enable accurate assessment of the fate and risk of these materials to environmental and human health. Environmental significanceAccumulation of plastic (MPx and NPx) particles is increasing in environmental compartments, and this might be threatened to agricultural plants. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/480069v1_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@c71fd2org.highwire.dtl.DTLVardef@fa1facorg.highwire.dtl.DTLVardef@1358c12org.highwire.dtl.DTLVardef@7f1851_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2019

Comparative evolutionary analysis and prediction of deleterious mutation patterns between sorghum and maize

Sorghum and maize share a close evolutionary history that can be explored through comparative genomics. To perform a large-scale comparison of the genomic variation between these two species, we analyzed 13 million variants identified from whole genome resequencing of 468 sorghum lines together with 25 million variants previously identified in 1,218 maize lines. Deleterious mutations in both species were prevalent in pericentromeric regions, enriched in non-syntenic genes, and present at low allele frequencies. A comparison of deleterious burden between sorghum and maize revealed that sorghum, in contrast to maize, departed from the \"domestication cost\" hypothesis that predicts a higher deleterious burden among domesticates compared to wild lines. Additionally, sorghum and maize population genetic summary statistics were used to predict a gene deleterious index with an accuracy higher than 0.5. This research represents a key step towards understanding the evolutionary dynamics of deleterious variants in sorghum and provides a comparative genomics framework to start prioritizing them for removal through genome editing and breeding.

genomics↗

bioRxiv2019

Genomewide association study reveals transient loci underlying the genetic architecture of biomass accumulation under cold stress in Sorghum.

Sorghum bicolor is a promising cellulosic feedstock crop for bioenergy because of its potential for high biomass yields. However, in its early growth phases, sorghum is sensitive to cold stress, preventing early planting in temperate environments. Cold temperature adaptability is vital for the successful cultivation of both bioenergy and grain sorghum at higher latitudes and elevations, and for early season planting or to extend the growing season. Identification of genes and alleles that enhance biomass accumulation of sorghum grown under early cold stress would enable the development of improved bioenergy sorghum through breeding or genetic engineering. We conducted image-based phenotyping on 369 accessions from the sorghum Bioenergy Association Panel (BAP) in a controlled environment with early cold treatment. The BAP is a collection of densely genotyped and racially, geographically, and phenotypically diverse accessions. The plants were weighed, watered, and imaged daily to measure growth dynamics and water use efficiency (WUE). Daily, non-destructive imaging allowed for a temporal analysis of growth-related traits in response to cold stress. We performed a genome-wide association study (GWAS) to identify candidate genomic intervals and genes controlling response to early cold stress. GWAS identified transient quantitative trait loci (QTL) strongly associated with each growth-related trait, permitting an investigation into the genetic basis of cold stress response at different stages of development. The analysis identified a priori and novel candidate genes associated with growth-related traits and the temporal response to cold stress.\n\nSIGNIFICANCE STATEMENTGenome-wide association study of bioenergy sorghum accessions phenotyped under early season cold stress revealed transient QTLs for highly heritable biomass and growth-related traits that appeared as the temperature increased and plants developed. Sorghum accessions clustered into multiple groups for each heritable trait with distinct growth profiles. GWAS identified candidate genes associated with growth traits and cold stress responses. The top-performing accessions with the highest growth-related trait values over time and temperature shifts will be useful for further genetic analysis and breeding or engineering efforts directed at biomass yield enhancements.

plant biology↗