DNAwhisper: An Integrated Deep Learning Pyramidal Framework for Multi-Trait Genomic Prediction and Adaptive Marker...

Area of Science:

• Plant breeding and genetics
• Bioinformatics and computational biology
• Genomics and quantitative genetics

Background:

• Genomic selection (GS) is vital for enhancing genetic gain in plant breeding.
• Deep learning models offer potential for capturing complex genetic interactions, but face challenges with high-dimensional, noisy genomic data.
• Existing methods struggle to effectively identify informative markers for complex trait prediction.

Purpose of the Study:

• To introduce DNAwhisper, a novel deep learning framework for multi-trait prediction and adaptive marker prioritization in genomic selection.
• To address limitations of current deep learning applications in GS by improving feature learning and marker identification.
• To enhance the interpretability of genomic predictions and facilitate the discovery of genetic architecture.

Main Methods:

• Developed DNAwhisper, a deep learning framework featuring a cascaded GFIformer architecture with shared parameters across marker blocks for adaptive feature compression.
• Implemented pre-training on population genetic structure to regularize feature learning and establish generalizable latent representations.
• Utilized trait-guided deep supervision to extract multi-resolution importance scores from a hierarchical pyramid for marker prioritization.

Main Results:

• DNAwhisper achieved 3.0% to 10.0% higher prediction accuracy compared to baseline models across maize, wheat, tomato, and grape datasets.
• The framework successfully prioritized informative markers and identified major quantitative trait loci (QTLs) and epistatic interactions.
• Demonstrated identification of key genes like VGT1 and ZCN8 involved in maize flowering traits.

Conclusions:

• DNAwhisper offers a robust deep learning strategy for improving prediction accuracy in genomic selection.
• The framework enhances interpretability by providing multi-resolution genomic region importance scores, aiding marker prioritization.
• DNAwhisper provides a novel approach for dissecting the genetic architecture of complex traits in plants.