AIMC Topic: Genome, Plant
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Cropformer: An interpretable deep learning framework for crop genomic prediction.
Plant communications
Dec 16, 2024
Machine learning and deep learning are extensively employed in genomic selection (GS) to expedite the identification of superior genotypes and accelerate breeding cycles. However, a significant challenge with current data-driven deep learning models ...
Identification, characterization, and design of plant genome sequences using deep learning.
The Plant journal : for cell and molecular biology
Dec 12, 2024
Due to its excellent performance in processing large amounts of data and capturing complex non-linear relationships, deep learning has been widely applied in many fields of plant biology. Here we first review the application of deep learning in analy...
Machine learning-enhanced multi-trait genomic prediction for optimizing cannabinoid profiles in cannabis.
The Plant journal : for cell and molecular biology
Nov 27, 2024
Cannabis sativa L., known for its medicinal and psychoactive properties, has recently experienced rapid market expansion but remains understudied in terms of its fundamental biology due to historical prohibitions. This pioneering study implements GS ...
Exploring genomic feature selection: A comparative analysis of GWAS and machine learning algorithms in a large-scale soybean dataset.
The plant genome
Sep 10, 2024
The surge in high-throughput technologies has empowered the acquisition of vast genomic datasets, prompting the search for genetic markers and biomarkers relevant to complex traits. However, grappling with the inherent complexities of high dimensiona...
Comparison of machine learning methods for genomic prediction of selected Arabidopsis thaliana traits.
PloS one
Aug 28, 2024
We present a comparison of machine learning methods for the prediction of four quantitative traits in Arabidopsis thaliana. High prediction accuracies were achieved on individuals grown under standardized laboratory conditions from the 1001 Arabidops...
Deep learning can predict subgenome dominance in ancient but not in neo/synthetic polyploidized genomes.
The Plant journal : for cell and molecular biology
Aug 12, 2024
Deep learning offers new approaches to investigate the mechanisms underlying complex biological phenomena, such as subgenome dominance. Subgenome dominance refers to the dominant expression and/or biased fractionation of genes in one subgenome of all...
Analyzing Medicago spp. seed morphology using GWAS and machine learning.
Scientific reports
Jul 30, 2024
Alfalfa is widely recognized as an important forage crop. To understand the morphological characteristics and genetic basis of seed morphology in alfalfa, we screened 318 Medicago spp., including 244 Medicago sativa subsp. sativa (alfalfa) and 23 oth...
Machine learning for genomic and pedigree prediction in sugarcane.
The plant genome
Jun 26, 2024
Sugarcane (Saccharum spp.) plays a crucial role in global sugar production; however, the efficiency of breeding programs has been hindered by its heterozygous polyploid genomes. Considering non-additive genetic effects is essential in genome predicti...
Using a hybrid neural network architecture for DNA sequence representation: A study on N-methylcytosine sites.
Computers in biology and medicine
May 27, 2024
N-methylcytosine (4mC) is a modified form of cytosine found in DNA, contributing to epigenetic regulation. It exists in various genomes, including the Rosaceae family encompassing significant fruit crops like apples, cherries, and roses. Previous inv...
Enhancing genome-wide populus trait prediction through deep convolutional neural networks.
The Plant journal : for cell and molecular biology
May 13, 2024
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...
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