In vitro phenotyping and genomics: a conceptual framework linking plant tissue culture with GWAS, QTL mapping, and multi-omics
Planta, cilt.264, sa.6, 2026 (SCI-Expanded, Scopus)
- Yayın Türü: Makale / Derleme
- Cilt numarası: 264 Sayı: 6
- Basım Tarihi: 2026
- Doi Numarası: 10.1007/s00425-026-05148-y
- Dergi Adı: Planta
- Derginin Tarandığı İndeksler: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Artic & Antarctic Regions, BIOSIS, CAB Abstracts, Chemical Abstracts Core, EMBASE, Environment Index, MEDLINE, Natural Science Collection (ProQuest), Biological Science Database (ProQuest), Biomedical Reference Collection: Corporate Edition (EBSCO), Health Research Premium Collection (ProQuest), Pharma Collection (ProQuest)
- Anahtar Kelimeler: Genome-wide association study, Multi-omics, Plant tissue culture, Quantitative trait loci, Somaclonal variation
- Erciyes Üniversitesi Adresli: Evet
Özet
Main conclusion: Standardized in vitro phenotypes provide genetically tractable traits that integrate GWAS, QTL mapping, and multi-omics, enabling mechanistic insight and genetics-informed improvement of plant regeneration. Abstract: Plant tissue culture (PTC) has traditionally been employed as a technical tool for propagation, transformation, and germplasm conservation. This review reframes in vitro culture systems as quantitative phenotyping platforms that enable rigorous genetic dissection of complex traits, such as regeneration competence, stress tolerance, and developmental plasticity. By operating under highly standardized and reproducible conditions, in vitro systems reduce environmental noise and expose genotype-dependent variation that is often obscured in field or greenhouse experiments. When formalized as quantitative traits, culture responses, including callus induction, organogenesis, somatic embryogenesis, and stress survival, become amenable to genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping. Synthesizing evidence across diverse plant species, this review demonstrates that in vitro traits are genetically structured, polygenic, and biologically meaningful, reflecting coordinated regulation of hormonal signaling, chromatin accessibility, stress response pathways, and developmental gene networks. Numerous GWAS and QTL studies have identified loci and candidate genes underlying regeneration efficiency, embryogenic competence, and stress-responsive culture performance, confirming that tissue culture responsiveness is rooted in genomic architecture rather than protocol effects alone. The interpretive power of genetic mapping is substantially enhanced through integration with bioinformatic and multi-omics layers, including transcriptomics, epigenomics, proteomics, metabolomics, and network-based analyses, thereby refining candidate prioritization and facilitating mechanistic inference. This review further examines the dual role of somaclonal variation as both a constraint on clonal fidelity and a source of genetic and epigenetic diversity that can reveal cryptic genotype–phenotype relationships. Emphasis is placed on study design principles, phenotyping challenges, statistical modeling strategies, and integrative pipelines that connect genotype to in vitro phenotype and ultimately to breeding and biotechnology applications. This synthesis highlights in vitro culture systems as powerful, genetics-informed platforms for precision breeding, gene validation, and supporting efforts to more predictably and rationally manipulate complex traits, particularly in horticultural and clonally propagated crops.