Biology subjects

Hulke, B. S.

Publications and source records attributed to Hulke, B. S..

6 recordsLinked to original sources

bioRxiv2026

The stability of fatty acid composition in sunflower oil is dependent on environment and affected by structural variation

In sunflower (Helianthus annuus L.), the composition of fatty acids in the seeds, primarily oleic, linoleic, stearic and palmitic acid, is of utmost importance for oil quality. Despite this, the genetic basis of this trait and its interaction with the environment is poorly understood. Understanding this interaction is critical to improvement of sunflower within the context of climate change. In this work, we incorporated fatty acid composition measurements from the sunflower SAM population and eight environments across an extensive geographic cline into GWAS. The SAM panel consists of 287 varieties representing approximately 90% of sunflower diversity, for which 2.2 million high-quality SNPs with a MAF > 5% are available. For increased power, multivariate GWAS was performed with four different inputs: (i) mean fatty acid composition within each environment, (ii) mean fatty acid composition within each environment omitting high oleic varieties, (iii) trait stability within environments quantified by standard errors among replicate samples ( stability) and (iv) Eberhart and Russells {beta} which quantifies trait stabilities across environments ({beta} stability). All four analyses yielded highly significantly associated SNPs. We found that high oleic varieties exhibited high {beta} trait stability, resulting in substantial overlap in markers between analyses (i) and (iv), with signals being fairly consistent between environments in analysis (i). For analyses (ii) and (iii), significant markers tended to vary between trials. For significant SNPs across all analyses, 147 candidate genes were identified, including promising candidates such as 15 fatty acid metabolism genes, 6 heat shock proteins and 22 transcription factors. Lastly, a large introgression consisting of two flanking inverted sequences on Chromosome 5 was found to coincide with stability in the Georgia trial, suggesting a role in FA composition stability under high heat conditions.

plant biology↗

bioRxiv2025

Glaciation history and geographic barriers shape population genetic structure and diversity of Lewis flax across western North America

Factors shaping genetic variation at the continental scale include geographic barriers, glacial cycles, and genetic constraints like mating system. We examine how such factors combine to influence diversification in Linum lewisii (Lewis flax), a perennial forb native to North America. We used whole genome sequencing, spatial analyses, and demographic inference to quantify population diversity across space and time and to test expectations about mating system evolution during range expansion. We found that Lewis flax consists of four genetic clusters that diverged during the Last Glacial Period, with the Rocky Mountains acting as a dispersal barrier. These clusters arent reflected in current taxonomy. Genomic data also suggest Lewis flax is predominantly outcrossing, despite its self-compatibility. Although it is thought to have colonized North America via Beringia, we found no evidence of northern refugia. Current northern populations apparently derive from a post-glacial range expansion, and their genomic signatures may indicate a shift towards increased selfing. The mixed mating system of Lewis flax thus interacts with glacial history and geographical barriers in a way that differs from obligate outcrossing or selfing species. This study furthermore provides foundational knowledge for its use in ecological restoration and ongoing neodomestication as a perennial oilseed food crop.

evolutionary biology↗

bioRxiv2024

Variant filters using segregation information improve mapping of nectar-production genes in sunflower (Helianthus annuus L.)

Accurate variant calling is critical for identifying the genetic basis of complex traits, yet filters used in variant detection and validation may inadvertently exclude valuable genetic information. In this study, we compare common sequencing depth filters, used to eliminate error-prone variants associated with repetitive regions and technical issues, with a biologically relevant filtering approach that targets expected population-level Mendelian segregation. The resulting variant sets were evaluated in the context of nectar volume QTL mapping in sunflower (Helianthus annuus L.). Our previous research failed to detect a significant interval containing a strong candidate gene for nectar production (HaCWINV2). We removed certain hard filters and implemented a Chi-square goodness-of-fit test to retain variants that segregate according to expected genetic ratios. We hypothesized that this will enhance mapping resolution and capture key genetic regions previously missed. We demonstrate that biologically relevant filtering retains more significant QTL and candidate genes, including HaCWINV2, while removing variants due to technical errors more effectively, and accounted for 48.55% of phenotypic variation. In finding nine putative homologs of Arabidopsis genes with nectary function within QTL regions, we demonstrate that this filtering strategy, which considers biological contexts, has a higher power of true variant detection than the commonly used variant depth filtering strategy. PLAIN LANGUAGE SUMMARYIn genomic research, identifying genetic markers is key to understanding complex traits, but traditional methods for filtering genetic data can sometimes miss important information. In this study, we explored a new data filtering approach for mapping genes related to nectar production in sunflower. We applied a more flexible filtering method that considers how markers are expected to segregate in breeding populations. Our previous work failed to identify an important gene previously hypothesized to be involved in nectar production, likely due to overly strict filtering. Our improved approach identified nine sunflower genes related to nectar production genes in the model species Arabidopsis thaliana, as compared to zero genes identified from the previous filtering strategy. This study highlights the value of using flexible, biologically relevant filtering methods, which can lead to better results in plant genomic studies. CORE IDEASO_LIDiscovering biologically meaningful variants from sequence data requires a careful and critical view of bioinformatic workflows. C_LIO_LIThe use of arbitrary filters can remove significant genomic variation that contributes to the phenotype of interest. C_LIO_LIArbitrary filters can also fail to remove variant call errors. C_LIO_LIA Chi-square filtering strategy based on segregation ratio retained a larger number of valid variants. C_LIO_LIMore candidate regions with putative nectar-related genes and better statistical support were discovered. C_LI

plant biology↗

bioRxiv2024

Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities

Associations with soil microorganisms are crucial for plants overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 common sunflower (Helianthus annuus) genotypes from 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen Sclerotinia were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions. ImportanceDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial and fungal communities are driven primarily by site soil and climatic differences, but that genotype can interact with site to influence composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen Sclerotinia sclerotiorum were widespread but significantly affected by site, while a subset were also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial and fungal community assembly, and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.

ecology↗

bioRxiv2020

Aberrant regulation of RNA splicing in sunflower hybrids may underlie intrinsic incompatibilities

Alternative spicing is an integral part of gene expression in multicellular organisms that allows for diverse mRNA transcripts and proteins to be produced from a single gene. However, most existing analyses have focused on macro-evolution, with only limited research on splice site evolution over shorter term, micro-evolutionary time scales. Here we examine splicing evolution that has occurred during domestication and observe 45 novel splice forms with strongly transgressive isoform compositions, representing 0.24% of analyzed transcripts. We identify loci associated with variation in the levels of these splice forms, finding that many novel transcripts were regulated by multiple alleles with non-additive interactions. A subset of these interactions involved the expression of individual spliceosome components. These overdominant and epistatic interactions often resulted in alteration in the protein-coding regions of the transcripts, resulting in frameshifts and truncations. By associating the splice variation in these genes with size and growth rate measurements, we found that none of the individual splice variants affected these plant traits significantly, but the cumulative expression of all aberrant transcripts did show a significant reduction in growth rate associated with higher proportions of disrupted transcripts. This demonstrates the importance of co-evolution of the different spliceosomal components and their regulators and suggests that these genes may contribute to evolution of reproductive isolation as Bateson-Dobzhansky-Muller incompatibility loci. Author summaryIn multicellular organisms, it is common that segments of pre-mRNA molecules are physically removed, and the remaining segments are spliced back together. Through splicing alternative combinations of segments together, organisms produce various mRNA molecules, and thus multiple proteins, using the information encoded in a single gene. Here, we investigated the RNA of two sunflower genotypes, one wild and one domesticated, as well as the hybrid offspring resulting from a cross between the two genotypes. We found certain mRNA molecules that were spliced exclusively in the hybrids and were absent in the examined parental lines. These unique hybrid mRNAs were predicted to be consequential for the hybrids health, and thus represented a malfunction in the mechanisms that regulate splicing. These results improve our understanding of the genetic regulation of alternative splicing and how alternative splice forms evolve. Our findings may lead to further inquiries about how aberrant splicing promotes the formation of new species in nature.

evolutionary biology↗

bioRxiv2020

Heritable associations with microbial communities are essential for necrotrophic pathogen resistance

Host-microbe interactions are increasingly recognized as important drivers of organismal health, growth, longevity, and community-scale ecological processes. However, less is known about how genetic variation affects hosts associated microbiomes and downstream phenotypes. We demonstrate that sunflower (Helianthus annuus) harbors substantial, heritable variation in microbial communities under field conditions. We show that microbial communities explain up to 77.5% of the heritable variation in resistance to root infection caused by the necrotrophic pathogen Sclerotinia sclerotiorum, and that plants grown in sterilized soil showed almost complete elimination of pathogen resistance. Association mapping revealed 69 genetic locations related to microbial abundance and Sclerotinia resistance. Although the genetic architecture is complex and quantitative, we have, in large part, elucidated previously unexplained genetic variation for resistance to this pathogen. This suggests new targets for plant breeding and demonstrates the potential for heritable microbial associations to play important roles in defense in natural and human-altered environments.

ecology↗