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Plant Breeding

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Machine learning applications to improve flavor and nutritional content of horticultural crops through breeding and genetics.

Current opinion in biotechnology
Over the last decades, significant strides were made in understanding the biochemical factors influencing the nutritional content and flavor profile of fruits and vegetables. Product differentiation in the produce aisle is the natural consequence of ...

Deep learning-enabled discovery and characterization of HKT genes in Spartina alterniflora.

The Plant journal : for cell and molecular biology
Spartina alterniflora is a halophyte that can survive in high-salinity environments, and it is phylogenetically close to important cereal crops, such as maize and rice. It is of scientific interest to understand why S. alterniflora can live under suc...

Cyber-agricultural systems for crop breeding and sustainable production.

Trends in plant science
The cyber-agricultural system (CAS) represents an overarching framework of agriculture that leverages recent advances in ubiquitous sensing, artificial intelligence, smart actuators, and scalable cyberinfrastructure (CI) in both breeding and producti...

SoyDNGP: a web-accessible deep learning framework for genomic prediction in soybean breeding.

Briefings in bioinformatics
Soybean is a globally significant crop, playing a vital role in human nutrition and agriculture. Its complex genetic structure and wide trait variation, however, pose challenges for breeders and researchers aiming to optimize its yield and quality. A...

Ridge regression and deep learning models for genome-wide selection of complex traits in New Mexican Chile peppers.

BMC genomic data
BACKGROUND: Genomewide prediction estimates the genomic breeding values of selection candidates which can be utilized for population improvement and cultivar development. Ridge regression and deep learning-based selection models were implemented for ...

Genomic prediction using machine learning: a comparison of the performance of regularized regression, ensemble, instance-based and deep learning methods on synthetic and empirical data.

BMC genomics
BACKGROUND: The accurate prediction of genomic breeding values is central to genomic selection in both plant and animal breeding studies. Genomic prediction involves the use of thousands of molecular markers spanning the entire genome and therefore r...

A comparative study of 11 non-linear regression models highlighting autoencoder, DBN, and SVR, enhanced by SHAP importance analysis in soybean branching prediction.

Scientific reports
To explore a robust tool for advancing digital breeding practices through an artificial intelligence-driven phenotype prediction expert system, we undertook a thorough analysis of 11 non-linear regression models. Our investigation specifically emphas...

TrG2P: A transfer-learning-based tool integrating multi-trait data for accurate prediction of crop yield.

Plant communications
Yield prediction is the primary goal of genomic selection (GS)-assisted crop breeding. Because yield is a complex quantitative trait, making predictions from genotypic data is challenging. Transfer learning can produce an effective model for a target...

Enhancing genome-wide populus trait prediction through deep convolutional neural networks.

The Plant journal : for cell and molecular biology
As a promising model, genome-based plant breeding has greatly promoted the improvement of agronomic traits. Traditional methods typically adopt linear regression models with clear assumptions, neither obtaining the linkage between phenotype and genot...