Biology subjects

Razzaque, S.

Publications and source records attributed to Razzaque, S..

7 recordsLinked to original sources

bioRxiv2026

Inherited proliferation states organize plant transcriptomes

A central question in plant biology is whether natural transcriptome variation primarily reflects environmental adaptation or intrinsic genetic programs. Using transcriptomes from 665 natural Arabidopsis thaliana accessions, we show that inherited population structure, not environmental gradients, is the primary organizer of global transcriptome architecture. Genomic population structure uniquely explains 30.0% of transcriptome-wide variation, while environmental variables account for only 2.5%. This architecture is dominated by a single co-expression program (proliferation Module Eigengene: prolifME), enriched for cell cycle regulation and ribosome biogenesis, regulated by a bipartite transcription factor architecture, and genetically encoded at discrete loci with broad trans-regulatory effects. This proliferation program is associated with reduced plant size, biomass, growth rate and water-use efficiency, and these relationships persist under common-garden conditions. Gene contributions to this proliferation program are non-randomly conserved in rice and maize across 150-200 million years of divergence. These findings identify an intrinsic transcriptional proliferation program as a primary state of plant population transcriptomes, conserved across plant species.

plant biology↗

bioRxiv2024

Balancing Growth: GROOT Genes Link Plant Biomass and Temperature Adaptation in Arabidopsis

Root systems take up water and nutrients from the soil and thereby underpin all essential plant functions. The size of the root system affects the ability of roots to capture these resources and determine the amount of carbon that roots transfer into the soil. Understanding the genetic basis of root biomass is therefore very important for enhancing crop resilience and productivity, especially in the face of climate change, as for soil carbon sequestration efforts. In our study, we catalogued root biomass of a diverse set of Arabidopsis accessions mainly derived from Sweden and Spain and utilized GWAS to identify loci associated with root biomass in Arabidopsis thaliana. We found that genetic variants associated with high biomass are enriched in accessions originating from distinct biogeographic regions in Spain. Among the most significant SNPs, one SNP on chromosome 3, was closely linked to three genes for which loss of function mutations caused significant increases in root, shoot and seed biomass and that we named GROOT genes. These genes act as general growth limiters. Additionally, our analysis revealed that the GROOT genes are in strong linkage disequilibrium, implying a potential coordinated function in regulating growth. Furthermore, accessions carrying the non-reference allele at this SNP showed markedly higher biomass under elevated temperatures, suggesting that these genes may also play a role in temperature adaptation. The discovery that the GROOT genes can enhance biomass without negative trade-offs across multiple traits opens new avenues for further research aimed at understanding genetically determined growth limitations, and for improving crop resilience and adaptability, as well as carbon sequestration.

plant biology↗

bioRxiv2023

Exploring the Interactive Effects of Seed and Site Limitation on Recruitment Dynamics in Panicum hallii

Seedling recruitment is a critical life history stage that is likely driven by the interplay of seed and microsite limitation and their interaction with seed traits. Here, we performed a factorial experiment involving seed addition and surface soil disturbance to explore the combined effects of seed and site availability using genotypes characterized by varying seed mass and dormancy traits. Additionally, we included hybrids that exhibited recombined seed trait relationships compared to natural genotypes, allowing us to assess the impact of specific seed traits on establishment across different sites. We detected a significant three-way interaction between seed addition, site conditions, and soil surface disturbance, influencing both seedling and adult recruitment in Panicum hallii, a perennial grass found in coastal mesic (lowland) and inland xeric (upland) habitats. This recruitment pattern suggests that lowland and upland establishment at foreign site is constrained by the interplay of seed and site limitations. Notably, soil surface disturbance facilitated recruitment of the upland genotype while constraining recruitment of the lowland genotype across all sites. Our results highlight the importance of seed size and dormancy as key factors impacting recruitment, suggesting a potential interactive relationship between these traits.

evolutionary biology↗

bioRxiv2022

Natural variation identifies new effectors of water use efficiency in Arabidopsis.

Water use efficiency (WUE) is the ratio of biomass gained per unit of water consumed; thus, it can be altered by genetic factors that affect either side of the ratio. In the present study, we exploited natural variation for WUE as an unbiased approach to discover loci affecting either biomass accumulation or water use as factors affecting WUE. Genome-wide association (GWAS) analysis using integrated WUE measured through carbon isotope discrimination ({delta}13C) of Arabidopsis thaliana accessions identified genomic regions associated with WUE. Reverse genetic analysis of 70 candidate genes selected based on the GWAS results and transcriptome data identified 25 genes affecting WUE as measured by gravimetric and {delta}13C analyses. Mutants of four genes had higher WUE than wild type, while mutants of the other 21 genes had lower WUE. The differences in WUE were caused by either altered biomass or water consumption (or both). Stomatal density was not a primary cause of altered WUE in these mutants. Leaf surface temperatures indicated that transpiration differed for mutants of 16 genes, but generally biomass accumulation had greater effect on WUE. The genes we identified are involved in diverse cellular processes including hormone and calcium signaling, meristematic activity, photosynthesis, flowering time, leaf/vasculature development, and cell wall composition; however, none of them had been previously linked to WUE or traits related to plant water relations. Thus, our study successfully identified new effectors of WUE that can be used to understand the genetic basis of WUE and improve crop productivity.

plant biology↗

bioRxiv2022

A pleiotropic flowering time QTL exhibits gene-by-environmental interaction for fitness in a perennial grass

Flowering time is crucial for wild plant populations to adapt to their local environments. Although the genetic basis of flowering variation has been studied in many plant species, its mechanisms in non-model organisms and its adaptive value in the field are still poorly understood. Here, we report new insights into the genetic basis of flowering time and its effect on fitness in Panicum hallii, a native perennial grass. We conducted genetic mapping in populations derived from representative inland and coastal ecotypes to identify flowering time QTL and loci exhibited extensive QTL-by-environment interactions. Patterns of segregation within recombinant hybrids provide strong support for directional selection driving ecotypic divergence in flowering time. A major QTL on chromosome 5 (q-FT5) was detected in all experiments and is a key locus controlling flowering variation. Fine-mapping and expression studies identified a FLOWERING LOCUS T orthologue, FT-like 9 (PhFTL9), as the candidate underlying q-FT5. We used reciprocal transplant experiment to test for global local adaptation and the specific impact of q-FT5 on performance. We did not observe local adaptation in terms of fitness tradeoffs when contrasting ecotypes in home versus away habitats. However, we observed that the coastal allele of q-FT5 conferred a fitness advantage only in its local habitat but not at the inland site. Sequence analysis of the PhFTL9 promoter identified ecotypic specific cis-element variation associated with environmental responsiveness. Together, our findings demonstrate the genetic basis of flowering variation in a perennial grass and provide evidence for conditional neutrality underlying flowering divergence.

evolutionary biology↗

bioRxiv2021

The ecology and quantitative genetics of seed and seedling traits in upland and lowland ecotypes of a perennial grass

Plants have evolved diverse reproductive allocation strategies and seed traits to aid in dispersal, persistence in the seed bank, and establishment. In particular, seed size, dormancy, and early seedling vigor are thought to be key functional traits with important recruitment and fitness consequences across abiotic stress gradients. Selection for favored seed-trait combinations, or against maladaptive combinations, is likely an important driver shaping recruitment strategies. Here, we test for seed-trait plasticity and local adaptation in contrasting upland and lowland ecotypes of Panicum hallii with field experiments in native versus foreign habitats. Furthermore, we test whether seed traits have been under directional selection in P. hallii using the v-test (Fraser 2020) based on trait variance in a genetic cross. Finally, we evaluate the genetic architecture of ecotypic divergence for these traits with Quantitative Trait Locus (QTL) mapping. Field experiments reveal little plasticity but support a hypothesis of local adaptation among ecotypes based on recruitment. Patterns of segregation within recombinant hybrids provides strong support for directional selection driving ecotypic divergence in seeds traits. Genetic mapping revealed a polygenic architecture with evidence of genetic correlation between seed mass, dormancy, and seedling vigor. Our results suggest that the evolution of these traits may involve constraints that affect the direction of adaptive divergence. For example, seed size and germination percentage shared two colocalized QTL with antagonistic additive effects. This supports the hypothesis of a functional genetic relationship between these traits, resulting in either large seed/strong dormancy or small seed/weak dormancy trait combinations. Overall, our study provides insights into the factors facilitating and potentially constraining ecotypic differentiation in seed traits. Impact SummarySeed size and dormancy are key functional traits with important recruitment and fitness consequences. Theory suggests tradeoffs and plasticity in offspring quantity and quality are important in seed evolution. The genetics of seed size and dormancy traits have been studied extensively, but these studies are mostly limited to model system or domesticated crops. We also know very little about the genetic architecture and evolution of seed-based life history traits especially considering adaptation to xeric and mesic habitats. Here, we explored the genetic basis of trade-offs between seed size and dormancy in a C4 perennial grass, Panicum hallii, endemic to North America. We planted seeds of recombinant inbred lines from a cross between a xeric and mesic ecotype of P.hallii and mapped quantitative trait (QTL) loci for seed size, dormancy and seedling vigor traits. We detected a genetic basis of trade-offs between seed size and dormancy, suggesting that natural selection strongly favored specific trait combinations in ecotype formation. We further explored the role of seed size variation on seedling and adult recruitment in contrasting habitats. Our data showed that seed size was under strong selection through recruitment. Overall, our results demonstrate that adaptive differentiation for seed size and early life stages are important factors in adaptation to contrasting habitats.

evolutionary biology↗

bioRxiv2020

Salt tolerance QTL derived from the Bangladeshi landrace Horkuch

Salinity has a significant negative impact on production of rice. To cope with the increased soil salinity due to climate change, we need to develop salt tolerant rice varieties that can maintain their high yield. Rice landraces indigenous to coastal Bangladesh can be a great resource to study the genetic basis of salt adaptation. In this study, we implemented a QTL analysis framework on a reciprocal mapping population between a salt tolerant landrace Horkuch and a high yieldingrice variety IR29. Our aim was to detect genetic loci that contributes to the salt adaptive responses of the two different developmental stages of rice which are very sensitive to salinity stress. We identified 14 QTL for 9 traits and found that most are unique to the specific developmental stage. In addition, we detected a significant effect of the cytoplasmic genome on the QTL model for some traits such as leaf total potassium and filled grain weight. This underscores the importance of considering cytoplasm-nuclear interaction for breeding programs. Along with this, we identified QTL co-localization for multiple traits that highlights the possible constraint of multiple QTL selection for breeding programs due to different contributions of a donor allele for different traits. HighlightsWe identified genetic loci for the salt tolerance response of two different developmental stages of the rice plant and detected significant contribution of cytoplasm-nuclear genome interaction for a few traits.

plant biology↗