Biology subjects

Harper, J. F.

Publications and source records attributed to Harper, J. F..

4 recordsLinked to original sources

bioRxiv2022

The last missing piece of the Triangle of U: the evolution of the tetraploid Brassica carinata genome

Ethiopian mustard (Brassica carinata) is an ancient crop with significant potential for expanded cultivation as a biodiesel feedstock. The remarkable stress resilience of B. carinata and desirable seed fatty acid profile addresses the ongoing food vs. fuel debate as the crop is productive on marginal lands otherwise not suitable for even closely related species. B. carinata is one of six key Brassica spp. that share three major genomes: three diploid species (AA, BB, CC) that spontaneously hybridized in a pairwise manner, forming three allotetraploid species (AABB, AACC, and BBCC). Each of these genomes has been researched extensively, except for that of B. carinata. In the present study, we report a high-quality, 1.31 Gbp genome with 156.9-fold sequencing coverage for B. carinata var. Gomenzer, completing and confirming the classic Triangle of U, a theory of the evolutionary relationships among these six species that arose almost a century ago. Our assembly provides insights into the genomic features that give rise to B. carinatas superior agronomic traits for developing more climate-resilient Brassica crops with excellent oil production. Notably, we identified an expansion of transcription factor networks and agronomically-important gene families. Completing the Triangle of U comparative genomics platform allowed us to examine the dynamics of polyploid evolution and the role of subgenome dominance in domestication and agronomical improvement.

genetics↗

bioRxiv2021

Increasing seed thiamin content impacts stored carbon partitioning and subsequent seedling stress tolerance

Thiamin and thiamin pyrophosphate (TPP) are essential components for the function of enzymes involved in the metabolism of carbohydrates and amino acids in living organisms. In addition to its role as a cofactor, thiamin plays a key role in resistance against biotic and abiotic stresses in plants. Most of the studies used exogenous thiamin to enhance stress tolerance in plants. In this study, we achieved this objective by genetically engineering Arabidopsis thaliana and Camelina sativa for the seed-specific co-overexpression of the Arabidopsis thiamin biosynthetic genes Thi4, ThiC, and ThiE. Elevated thiamin content in the seeds of transgenic plants was accompanied by the enhanced expression levels of transcripts encoding thiamin cofactor-dependent enzymes. Furthermore, seed germination and root growth in thiamin over-producing lines were more tolerant to oxidative stress caused by salt and paraquat treatments. The transgenic seeds also accumulated more oil (up to16.4% in Arabidopsis and17.9% in C. sativa) and carbohydrate but less protein than the control seeds. The same results were also observed in TPP over-producing Arabidopsis plants generated by the seed-specific overexpression of TPK1. Together, our findings suggest that thiamin and TPP over-production in transgenic lines confer a boosted abiotic stress tolerance and alter the seed carbon partitioning as well.

bioengineering↗

bioRxiv2020

Enhanced reproductive thermotolerance is associated with increased accumulation of flavonols in pollen of the tomato high-pigment 2 mutant.

Climate change has created an environment where heat stress conditions are becoming more frequent as temperatures continue to rise in crop production areas around the world. This situation leads to decreased crop production due to plant sensitivity to heat stress. Reproductive success is critically dependent on plants ability to produce functional pollen grains, which are the most thermo-sensitive tissue. Flavonols are plant secondary metabolites known for their potent antioxidative activity, essential for male fertility in several species including tomato, and implicated in heat stress tolerance. Since flavonols are highly abundant in fruits of the tomato high pigment-2 (hp2) mutant, we tested the level of flavonols in pollen of this mutant, under the hypothesis that increased accumulation of flavonols would render pollen more tolerant to heat stress. Indeed, pollen from three alleles of the hp2 mutant were found to have flavonols levels increased by 40% on average compared with wild-type under moderate chronic heat stress conditions. This mutant produced on average 7.8-fold higher levels of viable pollen and displayed better germination competence under heat stress conditions. The percentage of fully seeded fruits and the number of seeds per fruit were maintained in the mutant under heat stress conditions while decreased in wild-type plants. Our results strongly suggest that increased pollen flavonols content enhances pollen thermotolerance and reproductive success under heat stress conditions. Thus, the high flavonols trait may help frame the model for improving crop resilience to heat stress.

plant biology↗

bioRxiv2020

Characterization of novel pollen-expressed transcripts reveals their potential roles in pollen heat stress response in Arabidopsis thaliana.

The male gametophyte is the most heat-sensitive of all plant tissues. In recent years, long noncoding RNAs (lncRNAs) have emerged as important components of cellular regulatory networks involved in most biological processes, including response to stress. While examining RNAseq datasets of developing and germinating Arabidopsis thaliana pollen exposed to heat stress (HS), we identified 66 novel and 246 recently-annotated intergenic expressed loci (XLOCs) of unknown function, with the majority encoding lncRNAs. Comparison to HS in cauline leaves and other RNAseq experiments, indicated 74% of the 312 XLOCs are pollen-specific, and at least 42% are HS-responsive. Phylogenetic analysis revealed 96% of the genes evolved recently in Brassicaceae. We found that 50 genes are putative targets of microRNAs, and that 30% of the XLOCs contain small open reading frames (ORFs) with homology to protein sequences. Finally, RNAseq of ribosome-protected RNA fragments together with predictions of periodic footprint of the ribosome P-sites indicated that 23 of these ORFs are likely to be translated. Our findings indicate that many of the 312 unknown genes might be functional, and play significant role in pollen biology, including the HS response.

plant biology↗