Aug 2026· The Plant Genome· Vol 19· 0 citations· 61 references
Medicine
Abstract
Abstract Red clover (Trifolium pratense L.) is a globally important temperate forage legume. Its symbiosis with soil‐borne rhizobia enables nitrogen fixation, and its ability to produce quality forage under diverse soil conditions enhances pasture productivity, particularly during water deficits. With increasing climate‐related stresses, harnessing adaptive traits absent in current cultivars is critical. Genebanks conserve diverse red clover germplasm, providing genetic variation for agronomic and adaptive traits. In this study, we introgressed novel germplasm into locally adapted cultivars to track the inheritance of allelic variants using genotyping‐by‐sequencing. Multi‐location, multi‐year trials evaluated half‐sib families (generation two [Gen 2]) two generations removed from the exotic germplasm (genereation zero [Gen 0]) against local cultivars. Several Gen 2 populations matched or outperformed local cultivars and exhibited a moderate family mean heritability (h 2 > 0.40) for most traits. Integrating genomic, phenotypic, and environmental data, 77 bioclimatic‐associated single nucleotide polymorphisms (SNPs) were identified, of which 35 SNPs and 27 associated genes were significantly linked to trait expression. By using the original germplasm (Gen 0) as a training population and the derived half‐sib families (Gen 2) as a validation population, genomic prediction models were developed to calculate prediction accuracies for key agronomic traits. Biomass and plot density traits showed high predictive abilities and the highest prediction accuracies across generations. This study demonstrates a route by which genetic diversity from genebanks can be successfully incorporated into local populations, enabling evaluation and selection of key traits. The identified molecular markers and genomic prediction models provide a pathway to efficiently develop climate‐adaptive red clover cultivars.
Horticultural crops, particularly Solanaceae and Cucurbitaceae, represent a major component of global vegetable production and are increasingly exposed to climate variability and environmental constraints. Landraces and crop wild relatives constitute essential reservoirs of adaptive genetic diversity; however, their effective utilization in breeding programs remains limited by fragmented characterization, incomplete passport information, and reliance on labor-intensive morphological descriptors. These limitations hinder the systematic exploitation of conserved germplasm and restrict its integration into modern predictive breeding frameworks. Recent advances in high-throughput phenotyping, genomics, and multi-omics technologies have created new opportunities to bridge the gap between genotype and phenotype. Next-generation phenomics enables non-destructive, high-resolution quantification of plant physiological and structural traits across environments, while genomic approaches, including whole-genome resequencing, support comprehensive assessment of genetic diversity. Pangenome frameworks further extend this resolution by capturing core and variable genomic fractions, collectively defining the species variome and enabling improved identification of structural and allelic variants associated with adaptive traits. The integration of phenomic and genomic datasets through multi-omics approaches enhances the functional interpretation of trait-associated variation and strengthens the predictive capacity of breeding strategies. In this context, the genome as a functional passport constitutes a unified reference layer linking germplasm identity with genomic, phenotypic, and functional trait information, thereby enabling more systematic germplasm characterization, reduced redundancy, and improved identification of elite parental material. This mini-review highlights how the integration of phenomics, pangenomics, and multi-omics enables the transition from descriptive germplasm cataloguing toward more systematic, data-driven, and predictive breeding systems for the development of climate-resilient horticultural crops.
P. Mylona, L. Barchi, Luciana Gaccione et al.· Frontiers in Plant Science· 0 citations
This review critically evaluates the transition from conventional phenotypic selection to data-driven breeding strategies, examining genomic selection (GS), genome-wide association studies (GWAS), multi-omics integration, CRISPR/Cas9 genome editing, and high-throughput phenotyping (HTP) within the context of polyploid crop improvement.
Muhammad Abu Bakar Ghalib, Ayesha Khawar, M. Ramzan et al.· Discover Plants· 0 citations
This work used a combination of the latest genome sequencing and resequencing approaches to assemble a high-quality reference genome for Malus angustifolia, a native apple to the Southeastern U.S., and resequence its germplasm to enable genome-wide association study identify regions and structural variants associated with abiotic stress resistance.
B. Mansfeld, Zoë Migicovsky, J. Brock et al.· Horticulture Research· 0 citations
Neglected and underutilized crops have great potential to diversify agroecosystems and human diets but require genetic improvement to make them economically viable alternatives to major crops. Common buckwheat (
Fagopyrum esculentum
Moench) is valued for its excellent nutritional quality, its ecological importance and its benefits on crop rotation and soil health. However, low and highly variable yields, along with uneven seed ripening, have limited the crop’s usage in farming systems, highlighting the need for improved varieties. The availability of genetic resources and detailed genetic characterization are prerequisites for efficient breeding strategies.
In this study, we elucidate the genetic diversity and phylogeography of a global germplasm collection comprising 170 common buckwheat accessions, including nine self-compatible accessions and eleven accessions with determinate growth habit. The collection was genetically characterized using double digest restriction-site associated DNA sequencing to generate accession-specific genome-wide allele frequency fingerprints (GWAFFs).
Using accurate and repeatable GWAFFs based on 52,182 genome sites, an analysis of genetic admixture revealed seven subclusters within the collection. Our results show that common buckwheat accessions collected in specific regions of the world usually trace back to a single subcluster. Western Europe is an exception, as accessions from several different subcluster have been integrated into local cropping and food systems.
These findings illustrate that most breeding programs for common buckwheat rely on only a fraction of the available genetic diversity. Therefore, the introduction of genetic material from different sources could increase the diversity of many local breeding programs. The precise genetic characterization of the collection with GWAFFs opens opportunities to apply modern breeding strategies such as genomics-assisted selection. True-to-type seed of 81 accessions of the collection were deposited in the Swiss National Gene Bank and are publicly available for cultivation and use in research and breeding.
Fabian Hess, Lukas Kronenberg, Steven Yates et al.· Frontiers in Plant Science· 0 citations
We provide quantitative evidence that rye chromosome arm 1RS exerts background- and context-dependent effects on yield, stability, and grain protein content in contemporary elite winter wheat. Integrated multi-environment analyses demonstrate that translocation lines exhibit pronounced yield stability across 14 contrasting environments, with ‘Insave’- and ‘Petkus’-derived segments contributing through distinct performance profiles relevant for climate-resilient wheat breeding. Climate extremes increasingly threaten wheat production and yield stability globally. Rye (Secale cereale L.) chromosome arm 1RS has long been deployed in wheat breeding, yet its agronomic performance under drought and its interaction with elite genetic backgrounds remain insufficiently characterized. We evaluated 1RS translocations in elite German winter wheat using integrated molecular diversity analyses, multi-environment field phenotyping, and genomic modeling. Under near-optimal precipitation in 2021, matching the 1961–1990 reference period, the investigated winter wheat panel exhibited considerable genetic variation for yield and agronomic traits, indicating that high yield potential is still present in current German winter wheat breeding germplasm. In contrast, severe drought conditions in 2022 resulted in a 13.7% average yield decline, underscoring the sensitivity of current germplasm to drought stress. We show that 1RS translocations exhibit background-dependent effects on grain yield and stability. In particular, T1AL.1RS rye translocation originating from ‘Insave’ rye and stacked T1AL.1RS/T1BL.1RS translocations combining ‘Insave’ and ‘Petkus’ rye segments demonstrated favorable yield performance under drought conditions, although effects were context-dependent. Genetic modeling confirmed a significant interaction between 1RS translocations and the wheat genetic background, indicating that deployment of 1RS requires consideration of recipient genetic background. Our results highlight substantial response diversity within elite germplasm and demonstrate that targeted introgression of rye chromatin can contribute to improved climate resilience when systematically introgressed into adapted genetic backgrounds. The robust multi-environment field evaluation provides a strong foundation for interpreting translocation effects in modern elite germplasm. Complementary trait-level analyses, particularly root phenotyping and evaluation of double 1RS translocations within uniform genetic backgrounds, will further elucidate the physiological mechanisms underlying the observed responses.
Yeneneh Bekele-Reba, L. Bülow, A. Zaar et al.· Theoretical and Applied Gene...· 0 citations
Pulses have a vital and diverse role in agricultural systems and the food habits of people around the world. Among them, cowpea is a traditional and important pulse crop. It is a potential source of vegetable protein for the majority of Kerala's population. Crop improvement programmes aim to breed crops for diverse objectives, and developing high-yielding cowpea genotypes is a major and challenging objective in any breeding programme. To identify potential segregants with high yield and yield-contributing characters from an inter-varietal cross of cowpea, an experiment was conducted in the Department of Plant Breeding and Genetics, Kerala Agricultural University during 2023. In this research, the advanced generation of a cross between Vellayani Jyothika, a high-yielding variety susceptible to pod borer, and EC 98668, an exotic germplasm line resistant to pod borer but with low yield, was evaluated for genetic variability and to isolate promising segregants with high seed yield and yield-contributing characters. Parameters such as phenotypic coefficient of variance (PCV), genotypic coefficient of variance (GCV), heritability (H2) and genetic advance (GA) were estimated for nine quantitative characters from 230 plants belonging to 23 families. Grain yield per plant, number of pods per plant, plant height and pod length recorded high PCV and GCV, which indicated the existence of ample variability for these traits in the population; the narrow differences between PCV and GCV indicated a negligible environmental effect on trait expression. Number of pods per plant, plant height, pod length, seeds per pod, 100 seed weight and grain yield per plant recorded high heritability alongside high GAM. This indicates lower environmental influence and strong, fixable additive genetic variance in trait expression. Segregants with high yield and yield-contributing characters were identified and advanced to subsequent generations.
Anju M. Job, Jiji Jospeh, C. Beena et al.· Journal of Advances in Biolo...· 0 citations
We use cookies to run the site and, with your consent, for analytics and to show ads.
See our Cookie Policy.
