arXiv:2605.06762q-bio.GNcs.AI2026-05

用线性-Transformer模型提升葡萄基因型到表型预测精度,跨年表现更稳定。

A Linear-Transformer Hybrid for SNP-Based Genotype-to-Phenotype Prediction in Grapevine

  • 融合加性遗传效应与Transformer非线性互作,利用全基因组SNP数据建模
  • 在叶毛密度和绒毛密度预测中,跨年RMSE最低达0.454,准确率超74%
  • 通过注意力权重识别关键SNP,支持后续实验验证,结果可解释

可靠的基因型到表型(G2P)预测对加速育种决策和遗传增益至关重要。然而,在不同田间条件和跨年环境下测量复杂性状仍具挑战。本文提出一种线性-Transformer混合模型LiT-G2P,自动整合加性遗传方差效应与基于Transformer的非线性互作,使用全基因组单核苷酸多态性(SNPs)数据进行预测。我们在一组多样化的葡萄种质资源上评估该模型,这些材料经SNP标记基因分型,并在连续两年内测定表型,目标性状为葡萄叶片毛密度和绒毛密度。在单年及跨年测试场景中,LiT-G2P均显著优于基线模型。对于叶毛密度,其单年和跨年RMSE分别为0.469和0.454,准确率分别为79.2%和74.6%;对于绒毛密度,整体预测性能最优。此外,我们通过注意力权重提取模型优先的SNP,并开展基因型分层分析,提供可解释的候选标记用于下游验证。结果表明,将稳定加性效应与学习到的互作模式结合,可增强跨年鲁棒性,支持实际的基于SNP的基因组选择预测建模。

原文摘要 · Abstract (English)

Robust genotype-to-phenotype (G2P) prediction is essential for accelerating breeding decisions and genetic gain. However, it remains challenging to measure complex traits under variable field conditions and across years. In this study, we propose a linear-Transformer approach, LiT-G2P (Linear-Transformer Genotype-to-Phenotype), an automated predictive framework that integrates additive genetic variance effects with Transformer-based nonlinear interactions using genome-wide single-nucleotide polymorphisms (SNPs) data. We evaluated LiT-G2P on a panel of diverse grape accessions, genotyped with SNP markers and measured for phenotypes across two consecutive years. Target phenotypic traits include leaf hair density and trichome density of grapevines. Across both single-year and cross-year testing scenarios, LiT-G2P consistently improves prediction performance compared with baseline models. For hair density, LiT-G2P achieves the lowest error in both single-year and cross-year evaluations, with RMSEs of 0.469 and 0.454, respectively, while maintaining strong tolerance accuracies of 79.2% and 74.6%, respectively. For trichome density, LiT-G2P also presents the best overall G2P performance. In addition, we extract model-prioritized SNPs from attention weights and apply genotype-stratified analysis to provide interpretable candidate marker for downstream validation. These results demonstrate that integrating stable additive effects with learned interaction patterns can enhance cross-year robustness and support practical SNP-based predictive modeling for genomic selection.

基因预测Transformer葡萄育种SNP建模

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