scholarly journals Making waves in Breedbase: An integrated spectral data storage and analysis pipeline for plant breeding programs

tppj ◽  
2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jenna Hershberger ◽  
Nicolas Morales ◽  
Christiano C. Simoes ◽  
Bryan Ellerbrock ◽  
Guillaume Bauchet ◽  
...  
Keyword(s):  
Plant Breeding ◽  
Spectral Data ◽  
Data Storage ◽  
Analysis Pipeline ◽  
Breeding Programs

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

2020 ◽  
Author(s):  
Jenna Hershberger ◽  
Nicolas Morales ◽  
Christiano C. Simoes ◽  
Bryan Ellerbrock ◽  
Guillaume Bauchet ◽  
...  
Keyword(s):  
Plant Breeding ◽  
Open Source ◽  
Spectral Data ◽  
Data Storage ◽  
Cross Validation ◽  
R Package ◽  
List Type ◽  
Breeding Programs ◽  
Wide Range ◽  
Prediction Functions

ABSTRACTVisible 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 ideaswaves is an open-source R package for spectral data analysis in plant breedingBreeding relevant cross-validation schemes to evaluate predictive accuracy of modelsExtension of Breedbase—an open-source database—to support spectral data storageGraphical user interface developed for implementation of waves in Breedbase

Integrating Biotechnology into Woody Plant Breeding Programs

1988 ◽  
pp. 433-449 ◽  
Author(s):  
D. E. Riemenschneider ◽  
B. E. Haissig ◽  
E. T. Bingham
Keyword(s):  
Plant Breeding ◽  
Woody Plant ◽  
Breeding Programs

scholarly journals The NMR Spectral Measurement Database: A System for Organizing and Accessing NMR Spectra of Therapeutic Proteins

2021 ◽  
Vol 126 ◽  
Author(s):  
Niksa Blonder ◽  
Frank Delaglio
Keyword(s):  
Nuclear Magnetic Resonance ◽  
Magnetic Resonance ◽  
Spectral Data ◽  
Data Storage ◽  
Nmr Spectra ◽  
Therapeutic Proteins ◽  
Data Access ◽  
Protein Therapeutics ◽  
Spectral Measurement ◽  
Storage And Retrieval

The Nuclear Magnetic Resonance Spectral Measurement Database (NMR-SMDB) was developed for the purpose of organizing and searching NMR spectral data of protein therapeutics, linking spectra to corresponding sample information and enabling quick access to full datasets and entire studies. In addition to supporting internal research at the National Institute of Standards and Technology (NIST), the system could facilitate data access to stakeholders outside of NIST, and future versions of the database software itself could be installed by others for their own data storage and retrieval.

scholarly journals Review: Cost-Effective Unmanned Aerial Vehicle (UAV) Platform for Field Plant Breeding Application

2020 ◽  
Vol 12 (6) ◽  
pp. 998 ◽  
Author(s):  
GyuJin Jang ◽  
Jaeyoung Kim ◽  
Ju-Kyung Yu ◽  
Hak-Jin Kim ◽  
Yoonha Kim ◽  
...  
Keyword(s):  
Plant Breeding ◽  
Unmanned Aerial Vehicle ◽  
High Throughput ◽  
New Technologies ◽  
Cost Effective ◽  
New Wave ◽  
Breeding Programs ◽  
Modern Agriculture ◽  
Aerial Vehicle ◽  
High Throughput Phenotyping

Utilization of remote sensing is a new wave of modern agriculture that accelerates plant breeding and research, and the performance of farming practices and farm management. High-throughput phenotyping is a key advanced agricultural technology and has been rapidly adopted in plant research. However, technology adoption is not easy due to cost limitations in academia. This article reviews various commercial unmanned aerial vehicle (UAV) platforms as a high-throughput phenotyping technology for plant breeding. It compares known commercial UAV platforms that are cost-effective and manageable in field settings and demonstrates a general workflow for high-throughput phenotyping, including data analysis. The authors expect this article to create opportunities for academics to access new technologies and utilize the information for their research and breeding programs in more workable ways.

scholarly journals Physical purity and germination of sugarcane seeds (caryopses) (Saccharum spp.)

2010 ◽  
Vol 32 (2) ◽  
pp. 140-145 ◽  
Author(s):  
Juliana Terezinha Caieiro ◽  
Maristela Panobianco ◽  
João Carlos Bespalhok Filho ◽  
Osvaldo de Castro Ohlson
Keyword(s):  
Plant Breeding ◽  
Seed Viability ◽  
Germination Test ◽  
Paper Substrate ◽  
Breeding Programs ◽  
Saccharum Spp ◽  
Test Study ◽  
Alternating Temperature ◽  
Incubation Temperatures ◽  
Favorable Conditions

Plant breeding is generally done through sexual reproduction even when the species is propagated asexually for commercial exploitation, as for example, in sugarcane. Therefore, the development of procedures to evaluate sugarcane seed viability is important for plant breeding programs. The objective of this research was to develop a methodology for analyzing the viability of sugarcane seeds (Saccharum spp.). Three crosses were used, two biparental crosses and one polycross. For the germination test study, two substrates (paper and sand) and three constant incubation temperatures (25 ºC, 30 ºC and 35 ºC), in the presence of constant light and also an alternating temperatures (20-30 ºC), with 8 hours light (30 ºC) and 16 hours darkness (20 ºC), were studied. Seedlings were evaluated every five days. The results demonstrated that temperature affected sugarcane seed germination with the most favorable conditions being the alternating temperature (20-30 ºC) and the constant temperature of 30 ºC on a paper substrate.

Improvement Strategy for Mature Plant Breeding Programs

Crop Science ◽  
2000 ◽  
Vol 40 (5) ◽  
pp. 1241-1246 ◽  
Author(s):  
Michael D. Peel ◽  
Donald C. Rasmusson
Keyword(s):  
Plant Breeding ◽  
Mature Plant ◽  
Improvement Strategy ◽  
Breeding Programs

scholarly journals MoBPS - Modular Breeding Program Simulator

2020 ◽  
Vol 10 (6) ◽  
pp. 1915-1918 ◽  
Author(s):  
Torsten Pook ◽  
Martin Schlather ◽  
Henner Simianer
Keyword(s):  
Data Storage ◽  
Large Scale ◽  
R Package ◽  
Single Step ◽  
Computationally Efficient ◽  
Breeding Programs ◽  
Genetic Impact ◽  
Founder Populations ◽  
Genetic Contributions ◽  
Impact Simulations

The R-package MoBPS provides a computationally efficient and flexible framework to simulate complex breeding programs and compare their economic and genetic impact. Simulations are performed on the base of individuals. MoBPS utilizes a highly efficient implementation with bit-wise data storage and matrix multiplications from the associated R-package miraculix allowing to handle large scale populations. Individual haplotypes are not stored but instead automatically derived based on points of recombination and mutations. The modular structure of MoBPS allows to combine rather coarse simulations, as needed to generate founder populations, with a very detailed modeling of todays’ complex breeding programs, making use of all available biotechnologies. MoBPS provides pre-implemented functions for common breeding practices such as optimum genetic contributions and single-step GBLUP but also allows the user to replace certain steps with personalized and/or self-written solutions.

A new test for family-based association mapping with inbred lines from plant breeding programs

2006 ◽  
Vol 113 (6) ◽  
pp. 1121-1130 ◽  
Author(s):  
Benjamin Stich ◽  
Albrecht E. Melchinger ◽  
Hans-Peter Piepho ◽  
Martin Heckenberger ◽  
Hans P. Maurer ◽  
...  
Keyword(s):  
Association Mapping ◽  
Plant Breeding ◽  
Inbred Lines ◽  
Breeding Programs ◽  
Family Based
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