[HTML][HTML] Machine learning approaches for crop improvement: Leveraging phenotypic and genotypic big data

H Tong, Z Nikoloski - Journal of plant physiology, 2021 - Elsevier
Highly efficient and accurate selection of elite genotypes can lead to dramatic shortening of
the breeding cycle in major crops relevant for sustaining present demands for food, feed …

Genome‐wide Transcription Factor Gene Prediction and their Expressional Tissue‐Specificities in MaizeF

Y Jiang, B Zeng, H Zhao, M Zhang… - Journal of integrative …, 2012 - Wiley Online Library
Transcription factors (TFs) are important regulators of gene expression. To better understand
TF‐encoding genes in maize (Zea mays L.), a genome‐wide TF prediction was performed …

Whole transcriptome profiling of maize during early somatic embryogenesis reveals altered expression of stress factors and embryogenesis-related genes

SAGD Salvo, CN Hirsch, CR Buell, SM Kaeppler… - PloS one, 2014 - journals.plos.org
Embryogenic tissue culture systems are utilized in propagation and genetic engineering of
crop plants, but applications are limited by genotype-dependent culture response. To date …

Harnessing genetic diversity in the USDA pea germplasm collection through genomic prediction

MAA Bari, P Zheng, I Viera, H Worral, S Szwiec… - Frontiers in …, 2021 - frontiersin.org
Phenotypic evaluation and efficient utilization of germplasm collections can be time-
intensive, laborious, and expensive. However, with the plummeting costs of next-generation …

Utility of climatic information via combining ability models to improve genomic prediction for yield within the genomes to fields maize project

D Jarquin, N De Leon, C Romay, M Bohn… - Frontiers in …, 2021 - frontiersin.org
Genomic prediction provides an efficient alternative to conventional phenotypic selection for
developing improved cultivars with desirable characteristics. New and improved methods to …

Predictive breeding for maize: Making use of molecular phenotypes, machine learning, and physiological crop models

JD Washburn, MB Burch, JAV Franco - Crop Science, 2020 - Wiley Online Library
Maize (Zea mays L.) has been a focus of scientific research and breeding for over a century.
It is also one of the most economically important crops in the world, with a value of …

Multi-trait Genomic Prediction Model Increased the Predictive Ability for Agronomic and Malting Quality Traits in Barley (Hordeum vulgare L.)

M Bhatta, L Gutierrez, L Cammarota… - G3: Genes …, 2020 - academic.oup.com
Plant breeders regularly evaluate multiple traits across multiple environments, which opens
an avenue for using multiple traits in genomic prediction models. We assessed the potential …

A multi-omics integrative network map of maize

L Han, W Zhong, J Qian, M Jin, P Tian, W Zhu… - Nature …, 2023 - nature.com
Networks are powerful tools to uncover functional roles of genes in phenotypic variation at a
system-wide scale. Here, we constructed a maize network map that contains the genomic …

Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays

RS Sekhon, R Briskine, CN Hirsch, CL Myers… - PloS one, 2013 - journals.plos.org
Transcriptome analysis is a valuable tool for identification and characterization of genes and
pathways underlying plant growth and development. We previously published a microarray …

Threshold models for genome-enabled prediction of ordinal categorical traits in plant breeding

OA Montesinos-López… - G3: Genes …, 2015 - academic.oup.com
Categorical scores for disease susceptibility or resistance often are recorded in plant
breeding. The aim of this study was to introduce genomic models for analyzing ordinal …