Biology subjects

Hershberger, J.

Publications and source records attributed to Hershberger, J..

3 recordsLinked to original sources

bioRxiv2021

Transcriptome-wide association and prediction for carotenoids and tocochromanols in fresh sweet corn kernels

Sweet corn is consistently one of the most highly consumed vegetables in the U.S., providing a valuable opportunity to increase nutrient intake through biofortification. Significant variation for carotenoid (provitamin A, lutein, zeaxanthin) and tocochromanol (vitamin E, antioxidants) levels is present in temperate sweet corn germplasm, yet previous genome-wide association studies (GWAS) of these traits have been limited by low statistical power and mapping resolution. Here, we employed a high-quality transcriptomic dataset collected from fresh sweet corn kernels to conduct transcriptome-wide association studies (TWAS) and transcriptome prediction studies for 39 carotenoid and tocochromanol traits. In agreement with previous GWAS findings, TWAS detected significant associations for four causal genes, {beta}-carotene hydroxylase (crtRB1), lycopene epsilon cyclase (lcyE),{gamma} -tocopherol methyltransferase (vte4), and homogentisate geranylgeranyltransferase (hggt1) on a transcriptome-wide level. Pathway-level analysis revealed additional associations for deoxy-xylulose synthase2 (dxs2), diphosphocytidyl methyl erythritol synthase2 (dmes2), cytidine methyl kinase1 (cmk1), and geranylgeranyl hydrogenase1 (ggh1), of which, dmes2, cmk1, and ggh1 have not previously been identified through maize association studies. Evaluation of prediction models incorporating genome-wide markers and transcriptome-wide abundances revealed a trait-dependent benefit to the inclusion of both genomic and transcriptomic data over solely genomic data, but both transcriptome- and genome-wide datasets outperformed a priori candidate gene-targeted prediction models for most traits. Altogether, this study represents an important step towards understanding the role of regulatory variation in the accumulation of vitamins in fresh sweet corn kernels. Core IdeasO_LITranscriptomic data aid the study of vitamin levels in fresh sweet corn kernels. C_LIO_LIcrtRB1, lcyE, dxs2, dmes2, and cmk1 were associated with carotenoid traits. C_LIO_LIvte4, hggt1, and ggh1 were associated with tocochromanol traits. C_LIO_LITranscriptomic data boosted predictive ability over genomic data alone for some traits. C_LIO_LIJoint transcriptome- and genome-wide models achieved the highest predictive abilities. C_LI

genomics↗

bioRxiv2021

Low-cost, handheld near-infrared spectroscopy for root dry matter content prediction in cassava

Over 800 million people across the tropics rely on cassava as a major source of calories. While the root dry matter content (RDMC) of this starchy root crop is important for both producers and consumers, characterization of RDMC by traditional methods is time-consuming and laborious for breeding programs. Alternate phenotyping methods have been proposed but lack the accuracy, cost, or speed ultimately needed for cassava breeding programs. For this reason, we investigated the use of a low-cost, handheld NIR spectrometer for field-based RDMC prediction in cassava. Oven-dried measurements of RDMC were paired with 21,044 scans of roots of 376 diverse clones from 10 field trials in Nigeria and grouped into training and test sets based on cross-validation schemes relevant to plant breeding programs. Mean partial least squares regression model performance ranged from R2p = 0.62 - 0.89 for within-trial predictions, which is within the range achieved with laboratory-grade spectrometers in previous studies. Relative to other factors, model performance was highly impacted by the inclusion of samples from the same environment in both the training and test sets. Random forest variable importance analysis of root spectra revealed increased importance in a region previously identified as predictive of water content in plants (~950 - 990 nm). With appropriate model calibration, the tested spectrometer will allow for field-based collection of spectral data with a smartphone for accurate RDMC prediction and potentially other quality traits, a step that could be easily integrated into existing harvesting workflows of cassava breeding programs. CORE IDEASO_LIA low-cost, handheld near-infrared spectrometer was tested for phenotyping of cassava roots C_LIO_LIPlant breeding-relevant cross-validation schemes were used for predictions C_LIO_LIHigh prediction accuracies were achieved for cassava root dry matter content C_LIO_LIA spectral region predictive of plant water content was identified as important C_LI

plant biology↗

bioRxiv2020

Making WAVES in Breedbase: An Integrated Spectral Data Storage and Analysis Pipeline for Plant Breeding Programs

Visible and near-infrared (vis-NIRS) spectroscopy is a promising tool for increasing phenotyping throughput in plant breeding programs, but existing analysis software packages are not optimized for a breeding context. Additionally, commercial software options are often outside of budget constraints for some breeding and research programs. To that end, we developed an open-source R package, waves, for the streamlined analysis of spectral data with several cross-validation schemes to assess prediction accuracy. Waves is compatible with a wide range of spectrometer models and performs visualization, filtering, aggregation, cross-validation set formation, model training, and prediction functions for the association of vis-NIRS spectra with reference measurements. Furthermore, we have integrated this package into the Breedbase family of open-source databases, expanding the analysis capabilities of this growing digital ecosystem to a number of crop species. Taken together, the standalone and Breedbase versions of waves enhance the accessibility of tools for the analysis of spectral data during the plant breeding process. Core ideasO_LIwaves is an open-source R package for spectral data analysis in plant breeding C_LIO_LIBreeding relevant cross-validation schemes to evaluate predictive accuracy of models C_LIO_LIExtension of Breedbase--an open-source database--to support spectral data storage C_LIO_LIGraphical user interface developed for implementation of waves in Breedbase C_LI

bioinformatics↗