AIMC Topic: Quantitative Trait Loci

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Revolution and advances in gene editing and genomics technology for developing climate-resilient legume crops: developments and prospects.

Plant molecular biology
Legumes are essential for agriculture and food security. Biotic and abiotic stresses pose significant challenges to legume production, lowering productivity levels. Most legumes must be genetically improved by introducing alleles that give pest and d...

Foliar disease resistance phenomics of fungal pathogens: image-based approaches for mapping quantitative resistance in cereal germplasm.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Host plant resistance is the most effective and environmentally sustainable means of reducing yield losses caused by fungal foliar pathogens of cereal species. Cereal genebank collections hold diverse pools of potentially underutilized disease resist...

Integrated phenotypic analysis, predictive modeling, and identification of novel trait-associated loci in a diverse Theobroma cacao collection.

BMC plant biology
BACKGROUND: Cacao (Theobroma cacao L.) breeding and improvement rely on understanding germplasm diversity and trait architecture. This study characterized a cacao collection (173 accessions) evaluated in Puerto Rico, examining phenotypic diversity, t...

Breeding perspectives on tackling trait genome-to-phenome (G2P) dimensionality using ensemble-based genomic prediction.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Trait Genome-to-Phenome (G2P) dimensionality and "breeding context" combine to influence the realised prediction skill of different whole genome prediction (WGP) methods. Theory and empirical evidence both suggest there is likely to be "No Free Lunch...

Identification of key genes as diagnostic biomarkers for IBD using bioinformatics and machine learning.

Journal of translational medicine
BACKGROUND: The pathogenesis of inflammatory bowel disease (IBD) involves complex molecular mechanisms, and achieving clinical remission remains challenging. This study aims to identify IBD-potential biomarkers, analyze their correlation with immune ...

Identification of MEG3 and MAPK3 as potential therapeutic targets for osteoarthritis through multiomics integration and machine learning.

Scientific reports
Knee osteoarthritis (KOA) is a prevalent degenerative joint disorder, yet its underlying molecular mechanisms remain puzzling. This study aimed to uncover the genes with a causal relationship to KOA using Mendelian randomization (MR), transcriptomic ...

Neur-Ally: a deep learning model for regulatory variant prediction based on genomic and epigenomic features in brain and its validation in certain neurological disorders.

NAR genomics and bioinformatics
Large-scale quantitative studies have identified significant genetic associations for various neurological disorders. Expression quantitative trait locusĀ (eQTL) studies have shown the effect of single-nucleotide polymorphisms (SNPs) on the differenti...

Generative prediction of causal gene sets responsible for complex traits.

Proceedings of the National Academy of Sciences of the United States of America
The relationship between genotype and phenotype remains an outstanding question for organism-level traits because these traits are generally . The challenge arises from complex traits being determined by a combination of multiple genes (or loci), whi...

Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions.

BMC genomics
Plants exhibit extensive environment-dependent intraspecific metabolic variation, which likely plays a role in determining variation in whole plant phenotypes. However, much of the work seeking to use natural variation to link genes and transcript's ...