TL;DR
The development and use of MGMs in the studies on conifers, one of the most important plant groups, is the primary focus of this review and an analysis of history of MGM development, their classification and characteristics, and examples of MGMs most frequently used in studies of conifer species.
This narrative review synthesizes major advances in sheep genetic mapping, functional genomics, and GS relevant to economically important traits to provide researchers, breeders, and students with a balanced, evidence-based resource to guide future genomic improvements in sustainable sheep production.
BACKGROUND Information on the genetic variation and phylogenetic relationships of white lupin (Lupinus albus L.) can support the increasing plant breeding effort on this crop. This study aimed to: (a) assess the genetic variation relative to germplasm type (landrace, modern cultivar or wild type), landrace region of origin, landrace accession within region, and genotype within landrace accession; (b) explore landrace phylogenetic relationships; and (c) assess the consistency between molecular and morphophysiological diversity. RESULTS A landrace collection of 112 accessions classified into 11 regional pools and a set of modern cultivars underwent genotyping-by-sequencing characterization (genotyping four plants per landrace) and evaluation of 11 morphophysiological traits. Molecular data of four wild-type accessions were added. Multi-dimensional scaling indicated a sharp genetic distinctness of wild-type material and a fairly modest diversity of modern cultivars relative to landraces. Mantel's test revealed low consistency between molecular and morphophysiological diversity. Overall, landrace germplasm exhibited high genetic differentiation. The size of variance components in an analysis of molecular variance ranked as: genotype within landrace > landrace within regional pool > regional pool. Cluster analysis, nucleotide diversity, number of private alleles, phylogeny and migration analyses suggested a dual or divergent crop domestication in Greece and Italy, followed by migration of Greek germplasm into North-Eastern Africa and the Near East, extensive migration of Italian germplasm in the Mediterranean basin, and hybridization of the two genetic pools in various regions. CONCLUSIONS Our results increase our knowledge of white lupin diversity and phylogeny and can help optimize the exploitation of genetic resources.
This comprehensive review demonstrates that shifting from reactive field evaluation to marker-driven, genomics-assisted precision design provides the definitive molecular framework required to engineer high-yielding, climate-resilient, and disease-proof cacao cultivars, thereby permanently safeguarding the long-term economic sustainability of global cocoa supply chains.
Molecular characterization of wheat varieties is of high importance for wheat breeding. In the present study, 1883 Chinese wheat cultivars released between 1971 and 2025 were genotyped using a wheat 90K SNP array. Analysis of genetic diversity indicated a consistent A > B > D pattern, with the D subgenome showing the lowest genetic diversity and fastest LD decay (4.2 Mb), indicating diminished genetic diversity driven by breeding and selection. Population structure analysis revealed ten genetic clusters with clear ecological preferences, whereas genetic differentiation was weak (FST < 0.05) and gene flow extensive (Nem > 1), indicating the co-existence of strong ecological adaptation and frequent interregional germplasm exchange. Selective sweeps were identified on chromosome 5A (TaVRN1) and 2D (Rht8/RNHL-D1) regions controlling vernalization, plant height, and stress tolerance. Despite high gene flow, these loci for variety adaptiveness remained differentiated, highlighting the impact of artificial selection. Average pairwise genetic similarity was 0.56, but only a minority of cultivar pairs exceeded 0.98, especially in the Northeastern Spring Wheat and Middle-Lower Yangtze River Facultative Wheat regions, revealing severe genetic homogeneity from the excessive use of core parents. Nucleotide diversity increased to a peak in 2011–2015. These findings indicate that Chinese wheat cultivars still harbor significant potential for genetic improvement, highlighting the critical need to integrate exotic germplasm into core breeding parents to drive future advancements.
Superior genetic materials for developing high-resin-yield pine were derived from Pinus merkusii mother trees, which were selected through the breeding of subline populations originating from seedling seed orchards and pine plantations in East Java and Sulawesi, Indonesia. Although selection processes have been shown to reduce genetic variation, subline populations are expected to manage kinship relationships. Genetic variation in progeny-tested subline populations of high-resin-yield P. merkusii was evaluated using four microsatellite markers. The results demonstrated high genetic variation within each subline population (mean H e =0.409; range=0.392–0.425). However, the Sumedang, East Java, and Sulawesi subline populations exhibited high inbreeding potential, as indicated by elevated Fis values (0.133–0.332). Genetic differentiation among the observed populations was low (F ST 0.011), suggesting close relatedness among populations. Progeny-tested subline populations of high-resin-yield P. merkusii can maintain genetic diversity and possess potential for development as ortets for vegetative propagation. Following evaluation and final roguing, conversion of the progeny test into a seed orchard can yield genetically improved seeds. To maintain genetic resources and broaden the genetic base, it is essential to increase outcrossing rates in subline populations and introduce genetic material from other populations.
Single nucleotide polymorphisms represent the most abundant form of genetic variation in plant genomes and have become fundamental markers in modern plant genetics and breeding. Increasing global demand for food, combined with the pressures of climate change, environmental stress, and declining arable land, requires accelerated crop improvement strategies that exceed the capacity of conventional breeding approaches. In this context, SNP-based genomic technologies provide high-resolution tools for analyzing genetic diversity, identifying trait-associated loci, and enhancing selection efficiency in breeding programs. This review provides a comprehensive synthesis of SNP discovery methodologies, tracing their development from early Sanger sequencing approaches to advanced next-generation sequencing technologies, including whole-genome resequencing, genotyping-by-sequencing, and high-density SNP arrays. The article further examines the diverse applications of SNP markers in plant genetics, including genetic diversity analysis, linkage mapping, genome-wide association studies, marker-assisted selection, genomic selection, and evolutionary research. Key analytical and technical challenges, particularly those related to polyploid genome complexity, large-scale genomic data processing, and accurate variant interpretation, are critically discussed. In addition, emerging developments such as graph-based pangenomes, long-read sequencing technologies, machine learning-assisted SNP prioritization, and multi-omics integration are highlighted as promising directions for future research. By integrating recent technological advances with established genomic approaches, this review emphasizes the central role of SNP-based genomics in accelerating crop improvement and enabling climate-resilient, sustainable agricultural systems that support global food security.