Evolving best practices for transcriptome-wide association studies accelerate discovery of gene-phenotype links
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Torres-Rodríguez, J. Vladimir↗
Engineering topics
Li, Delin
Publications and source records attributed to Li, Delin.
Population‐level gene expression can repeatedly link genes to functions in maize
SUMMARY Transcriptome‐wide association studies (TWAS) can provide single gene resolution for candidate genes in plants, complementing genome‐wide association studies (GWAS) but efforts in plants have been met with, at best, mixed success. We generated expression data from 693 maize genotypes, measured in a common field experiment, sampled over a 2‐h period to minimize diurnal and environmental effects, using full‐length RNA‐seq to maximize the accurate estimation of transcript abundance. TWAS could identify roughly 10 times as many genes likely to play a role in flowering time regulation as GWAS conducted data from the same experiment. TWAS using mature leaf tissue identified known true‐positive flowering time genes known to act in the shoot apical meristem, and trait data from a new environment enabled the identification of additional flowering time genes without the need for new expression data. eQTL analysis of TWAS‐tagged genes identified at least one additional known maize flowering time gene through trans ‐eQTL interactions. Collectively these results suggest the gene expression resource described here can link genes to functions across different plant phenotypes expressed in a range of tissues and scored in different experiments.
Torres‐Rodríguez, J. Vladimir↗
Genetic and Biochemical Investigation of Seed Fatty Acid Accumulation in Arabidopsis
As a vegetable oil, consisting principally of triacylglycerols, is the major storage form of photosynthetically-fixed carbon in oilseeds which are of significant agricultural and industrial value. Photosynthesis in chlorophyll-containing green seeds, along with photosynthesis in leaves and other green organs, generates ATP and reductant (NADPH and NADH) needed for seed fatty acid production. However, contribution of seed photosynthesis to fatty acid accumulation in seeds have not been well-defined. Here, we report the contribution of seed-photosynthesis to fatty acid production by probing segregating green (photosynthetically-competent) and non-green or yellow (photosynthetically-non-competent) seeds in siliques of an Arabidopsis chlorophyll synthase mutant. Using this mutant, we found that yellow seeds lacking photosynthetic capacity reached 80% of amounts of oil in green seeds at maturity. Combining this with studies using shaded siliques, we determined that seed-photosynthesis accounts for 20% and silique and leaf/stem photosynthesis each account for ~40% of the ATP and reductant for seed oil production. Transmission electron microscopy (TEM) and pyridine nucleotides and ATP analyses revealed that seed photosynthesis provides ATP and reductant for oil production mostly during early development, as evidenced by delayed oil accumulation in non-green seeds. Transcriptomic analyses suggests that the oxidative pentose phosphate pathway could be the source of carbon, energy and reductants required for fatty acid synthesis beyond the early stages of seed development.
Nwafor, Chinedu Charles↗
Droplet Growth in Undercooled Cu-Co Alloys
High undercooling usually leads to the refinement of microstructures, while an opposite tendency occurs in liquid immiscible alloys. In the Cu-Co system, there is a metastable liquid miscibility gap which may allow the study of droplet nucleation and growth by undercooling experiments. In the present work, two alloys of Cu50Co50 and Cu68Co32 (atomic) were undercooled using a melt fluxing technique in which the liquid separation temperature could be directly measured. It was observed that after separation the resultant melts were further undercooled by 315 K prior to solidification. The relationship between the largest droplet radius and undercooling was found to exhibit three regimes: a power law growth, linear growth, and saturation stage. In addition to dendrites and droplet-like morphology reported previously, an interconnected structure was formed for the Cu50Co50 alloy at intermediate undercooling. It played a crucial role in droplet coarsening at high undercooling.
Robinson, Michael B.↗
A Study of Undercooling Behavior Of Immiscible Metal Alloys in the Absence of Crucible-Induced Nucleation
The purpose of this study is to investigate the question: Would eliminating the crucible eliminate the wall-induced nucleation of one of the liquid phases in an immiscible alloy and result in undercooling of the liquid into the metastable region thereby producing significant differences in the separation process and the microstructure upon solidification. Another primary objective of this research is to study systems with a metastable miscibility gap and to directly determine the metastable liquid miscibility gap by undercooling experiments. Nucleation and growth of droplets in these undercooled metallic liquid-liquid mixtures is also being studied. Results of this investigation indicate that containerless processing of immiscibles may not promote the undercooling of the single-phase liquid into the metastable region. Although no recalescence event was observed for this liquid-liquid transition, undercooling did occur across the miscibility gap for the solidification of the Ti phase that eventually separated.
Robinson, Michael B.↗