Search Results (240)

Phyllanthus emblica L. is a nutraceutically important medicinal plant; however, the relationship between genetic variation and bioactive potential remains poorly understood. This study integrates genome-wide SNP analysis, phytochemical profiling, and functional bioassays to investigate cross-scale differentiation among fourteen cultivars. Genotyping-by-sequencing (GBS) identified 5644 high-quality SNPs from an initial dataset of 9018 SNPs, revealing moderate but structured genomic divergence (0.0275–0.0845). Phytochemical analysis of five commercial cultivars demonstrated significant variation (p < 0.05) in total phenolic content (6.58–15.53 mg GAE/gDW) and tannin content (284.52–333.81 mg TAE/gDW). Functional assays revealed strong anti-obesity potential, with crude extracts exhibiting superior α-glucosidase inhibition (up to 98.75%), while tannin-enriched extracts showed enhanced pancreatic lipase inhibition (up to 46.26%). Importantly, enzyme inhibition did not correlate directly with total phenolic or tannin content, indicating compound-specific bioactivity. LC-MS/QTOF analysis identified flavonoids (e.g., quercetin and kaempferol), phenolic acids, and other candidate metabolites potentially associated with enzyme inhibitory activity. These findings demonstrate a non-proportional association among genomic variation, metabolite composition, and functional bioactivity, suggesting that bioactivity may be influenced more strongly by compound-specific metabolite composition than by genome-wide similarity alone. Full article

Calanthe aristulifera is a critically endangered orchid species of profound horticultural and ecological significance. However, establishing its species integrity is complicated by frequent natural introgression with sympatric relatives, such as C. sieboldii and C. discolor. Because phenotypic plasticity and complex hybrid swarms often confound traditional floral phenotyping, establishing an accurate molecular diagnostic system is imperative for conservation. In this study, we developed and validated high-throughput Kompetitive Allele-Specific PCR (KASP) and rapid Sequence-Characterized Amplified Region (SCAR) markers utilizing Genotyping-by-Sequencing (GBS) data from 64 Calanthe individuals—the same dataset reported in a companion population genomic study—re-analyzed using a more stringent marker-development pipeline. From 853,301 SNPs and 55,857 InDels initially identified, we filtered 62,231 high-quality SNPs and 1271 InDels to mine fixed homozygous alleles specific to C. aristulifera. This process isolated 179 SNP and 107 InDel loci to design three KASP markers (Ca-KASP1–3) and two SCAR markers (Ca-SCAR1–2). The KASP assays demonstrated a concordance of 98.4% (63/64 individuals; 95% CI: 91.6–99.7%) with morphological pre-classification. The single discordant case (Sample 52) was independently confirmed as a heterozygous hybrid by GBS-based population genomic analysis of the same individuals, providing molecular ground truth entirely independent of morphological assessment. The combined SCAR marker system yielded 96.9% concordance (62/64; 95% CI: 89.3–99.1%). Our findings provide an essential molecular framework for assessing species integrity and guiding the restoration of endangered C. aristulifera populations. Full article

Background/Objective: Sesame (Sesamum indicum L.) is a nutritionally and economically important oilseed crop that is grown predominantly by smallholder farmers in Mozambique. However, its breeding process is constrained by a limited understanding of the genetic diversity in sesame germplasm. Therefore, this study determined the genetic diversity and population structure of a panel of 109 sesame accessions from Instituto de Investigação Agrária de Mocambique (IIAM) using DArTseq SNPs. Methods: The generated 14,763 SNPs were filtered, retaining 11,502 high-quality SNPs for this study. Results: Overall genetic diversity was moderate (mean He = 0.30, Ho = 0.30, MAF = 0.21, PIC = 0.25). Population structure analysis using sparse non-negative matrix factorization identified eight subpopulations, consistent with principal component analysis implemented via the Latent factor mixed model. Discriminant analysis of principal components (DAPC) and Ward’s hierarchical clustering based on Nei’s distance resolved the same eight clusters, although DAPC revealed overlap among clusters, consistent with extensive admixture. Analysis of molecular variance showed that 85.85% of total molecular variation was within subpopulations and 14.15% among the subpopulations. Pairwise fixation indices (ranging from 0.02 to 0.10) identified divergent subpopulations 7 and 1 as suitable candidates for hybridization. Within subpopulations, observed heterozygosity exceeded expected heterozygosity, likely reflecting residual heterozygosity in sesame landraces, admixture, reverse Wahlund effect and scoring of paralogs as heterozygous SNPs. Conclusions: Overall, this study provided insights into sesame’s genetic diversity in Mozambique, contributing to germplasm conservation and informed parental selection. Full article

Background/Objectives: Bud sports (somatic mutations) offer a quick way to develop new bougainvillea varieties by altering specific traits while keeping the desirable genetic background of the original cultivar. However, we still lack a comprehensive understanding of their genomic architecture and the molecular mechanisms behind their formation. This study aimed to characterize the population genomic characteristics of bud sports derived from the commercial variety Bougainvillea × buttiana ‘Miss Manila’. Methods: We employed genotyping by sequencing (GBS) on 39 accessions, including 27 bud sports and 12 conventional varieties. Population genomic analyses, such as principal component analysis (PCA), phylogenetic reconstruction, ADMIXTURE, and diversity statistics (π, He, Tajima’s D), were performed on 64,810 high-quality SNPs. Genome-wide scans for differentiation (FST) and selective sweeps (XP-CLR) were also conducted. Results: Bud sports showed significantly lower genetic diversity (π and He) than conventional varieties, which matches their clonal origin. PCA, phylogenetic, and ADMIXTURE analyses (optimal K = 4) revealed clear genetic differentiation and distinct population structures between the two groups. The bud sport population possessed fewer private alleles and a less negative Tajima’s D value. Genomic scans identified regions under selection in bud sports, with functional annotation pointed to genes involved in ubiquitin-mediated proteolysis and RNA transport. Notably, Bou_119143 (UDP-rhamnose rhamnosyltransferase 1) showed a high mutation frequency specifically in bud sports. Conclusions: We provide the first population-genomic evidence that bud sports of ‘Miss Manila’ are genetically distinct clonal lineages, shaped by somatic mutation and selection. These findings support bud sports as efficient sources for germplasm innovation. The identified genomic regions and candidate genes lay a foundation for future marker-assisted selection and molecular breeding in bougainvillea. Full article

In recent years, plant genotyping has been shifting from the accumulation of whole-genome data toward their effective use in breeding programs This review examines key genotyping platforms, including single-nucleotide polymorphism (SNP) arrays, reduced-representation sequencing methods such as genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), targeted genotyping approaches, and whole-genome sequencing (WGS), analyzing their informativeness, cost, and computational limitations. The transition to pangenome-based genotyping and graph genomes is discussed, as these approaches reduce reference bias and increase sensitivity for detecting structural variants, introgressions, and rare alleles that are important for adaptation and breeding. The growing role of AI/ML is highlighted in modeling complex genotype–phenotype relationships, integrating genomic and phenotypic data, and improving the accuracy and interpretability of genomic predictions. Full article

Schizothorax wangchiachii, as a cold-water fish, is a predominant or common species in high-altitude areas with large population sizes. It is among the main edible economic fish species in the production area. We used genotype sequencing (GBS) technology to analyze the genetic diversity and population structure of 10 wild populations in the Jinsha River and Yalong River basins of the upper Yangtze River. A total of 724,858 single-nucleotide polymorphisms (SNPs) were detected in these 10 wild populations. The population genetic diversity was low; however, the degree of genetic differentiation was not significant. The populations from the Jinsha River and Yalong River could not be clustered separately on the basis of the SNPs. The Panzhihua (PZH) and Wudongde (WDD) populations from the Jinsha River exhibited gene flow with the Yajiang (YJ) population from the Yalong River, and a secondary pulse of gene flow subsequently connected the PZH and WDD populations to the upper-Jinsha population Suwalong (SWL). The demographic history of S. wangchiachii, reflected in its effective population size (N_e), has been influenced by the uplift of the Qinghai–Tibet Plateau (QTP). Furthermore, the identified SNPs are functionally associated with key cellular processes, environmental adaptation, and metabolism. These findings provide critical genomic insights that can inform conservation strategies and support the sustainable utilization of wild S. wangchiachii resources. Full article

Drought is one of the major constraints to lentil production worldwide, making the development of drought-tolerant varieties essential for stable yields. Identifying genes and markers linked to drought tolerance is a crucial first step. We analyzed 90 recombinant inbred lines (RILs) derived from an interspecific cross between the drought-susceptible Lens culinaris cv. Alpo and the tolerant L. odemensis ILWL235 to investigate genomic regions associated with drought tolerance. Using 4163 high-quality SNP markers obtained through Genotyping-by-Sequencing (GBS), we constructed a linkage map showing seven groups corresponding to the lentil chromosomes. The map spans 786.82 cM and covers 3.46 G bp, representing approximately 88% of the lentil genome. To assess drought tolerance, RILs were subjected to water stress under greenhouse conditions by maintaining the soil moisture at a 40% field capacity (FC) in pots for 15 days, with the leaf relative water content (RWC) recorded every two days. Plants were phenotyped for yield, 100-seed weight, and seed number under both control and stress conditions. We identified 26 Quantitative Trait Loci (QTLs) strongly associated with drought tolerance traits and found putative candidate genes for most of them. Additional traits, including stem pigmentation, flower coloration, seed coat patterning, and seed ground color, were also mapped, and their genomic locations validated the accuracy of our linkage map. Full article

Background: The Tibetan pig, a highland breed with exceptional adaptability to harsh environments (cold, hypoxia, coarse feed) but poor growth/reproductive traits, was studied to uncover genetic mechanisms and support breeding improvements. Methods: We conducted de novo genome assembly of a male Tibetan pig using stLFR sequencing, supplemented with ONT data, and compared the assembly to the Duroc pig genome (v11.1). Results: The assembled genome (2.25 Gb, contig N50 = 136.5 Mb, GC content = 41.74%, 94.16× coverage) showed 96.9% BUSCO completeness. Structural variant (SV) analysis identified 22,008 insertions and 27,639 deletions, with an SV genotyping accuracy of 0.9735. Selective sweep analysis highlighted adaptive genes: XIRP2 (cardiac function), KSR2/CACNA1A (fat metabolism), COL11A1 (cartilage), and ADORA2A (vascular regulation). Tibetan pigs exhibited the fewest and shortest runs of homozygosity (ROHs) among four breeds, with ROH-linked SNPs implicating lipid catabolism genes (LIPE, PNPLA2, MGLL, DGAT1). An SNP-based GWAS revealed reproductive trait associations: immune gene IL2RB, energy metabolism genes PRKAG2, ADGRA1, and PTPRN2, and growth genes SLIT2 and BMP6. SV analysis identified additional candidates: energy metabolism genes HAO2 and NRG4, growth genes MTUS2 and FGF12, and immune genes SCGB1A1 and C8A. Conclusions: This study provides a chromosome-level genome assembly of a male Tibetan pig (generated from stLFR and ONT data), and, through whole-genome resequencing of 124 Tibetan sows, identifies key genetic factors underlying Tibetan pigs’ environmental adaptability and reproductive limitations, enabling genomic strategies to enhance breeding efficiency while preserving adaptive traits. Full article

Anemone davidii Franch. is an herbaceous plant with high ornamental and medicinal value belonging to the Ranunculaceae family. Understanding its genetic diversity and predicting its potential habitat shifts are crucial for its germplasm conservation. In this study, we analyzed the genetic diversity of 164 individuals from A. davidii and its relatives using genotypic sequencing (GBS) technology. The results indicated that the expected heterozygosity (He) of 12 A. davidii populations ranged from 0.074 to 0.095, while the observed heterozygosity (Ho) ranged from 0.105 to 0.127. Phylogenetic, principal component (PCA), and population structure analyses revealed clear genetic separation among A. davidii, A. griffithii, and A. scabriuscula. The 12 A. davidii populations were grouped into three genetic clusters. Six populations—CQ, ES, SNJ, SZ, TR, and WX—of Central China were clustered together. Southwestern region populations were divided into two clusters (DG, PZ, SF and DY, EMS, HY). Low genetic differentiation values (Fst, 0.018–0.053) and high levels of gene flow (Nm, 4.4678–13.639) between populations were observed in this study, indicating that genetic differentiation was lower between adjacent populations. We also used the Maximum Entropy (MaxEnt) model to predict changes in suitable distribution areas of A. davidii across four time periods and two climate scenarios (RCP4.5, RCP8.5). Compared to the Last Glacial Maximum (LGM), the current suitable habitat area has contracted. Future climate projections indicated a progressive range contraction under both scenarios. Therefore, appropriate conservation measures are needed to address its limited genetic diversity and projected habitat loss under climate change. Our findings provide insights into the population genetics of A. davidii and the impact of climate change on plants of Southwestern China. Full article

Tetraploid non-apomictic citrus genotypes are key female parents for 4x × 2x hybridizations aimed at producing seedless triploid hybrids. However, the extent to which different tetraploidization methods affect genome integrity remains insufficiently characterized at a genome-wide scale. In this study, genotyping-by-sequencing (GBS) was used to evaluate marker-based genomic stability in ten tetraploid plants of ‘Clemenules’, ‘Fina’, and ‘Marisol’ clementines obtained via colchicine treatment, in vitro adventitious organogenesis, or somatic cybridization. Diploid parental plants, two haploid plants of ‘Clemenules’ and ‘Fina’ clementines, and one doubled haploid plant of ‘Clemenules’ clementine were included, being the haploid and double haploid essential to resolve allelic phases. After quality filtering, 3333 SNP (Single Nucleotide Polymorphism) markers distributed across the nine citrus chromosomes were identified and used to compare allele dosage patterns along the genome. Across all GBS-covered regions, no major marker-based genomic gains or losses were detected in any tetraploid plant. These results indicate that, at the resolution provided by GBS, all three tetraploidization methods largely preserve chromosome structure, supporting their suitability for citrus triploid breeding programs based on 4x × 2x sexual hybridizations. Full article

Flow velocity is a key environmental factor that exerts multifaceted effects on fish growth and adaptation. Through long-term natural selection, fish have evolved adaptability to specific flow conditions, which not only relate to oxygen supply and food acquisition but also play a decisive role in reproduction, development, and population maintenance. To investigate the genomic mechanisms through which hydrodynamic environments drive divergence in closely related species, we focused on two sister species, Hemiculter bleekeri and Hemiculter leucisculus, which are adapted to contrasting flow regimes. We generated high-quality, chromosome level telomere-to-telomere (T2T) genomes and integrated comparative genomic analyses, we investigated the genetic basis underlying body shape regulation and reproductive strategies, aiming to decipher the adaptive evolutionary patterns of these species in response to differing hydrodynamic conditions from an integrated genotype phenotype perspective. We integrated PacBio HiFi, Hi-C, and Oxford Nanopore Technologies (ONT) ultra-long read sequencing data to construct high-quality T2T reference genomes for both species. The final genome assemblies are 0.998 Gb for H. bleekeri and 1.05 Gb for H. leucisculus, with each species possessing 24 chromosomes and all chromosomal sequences assembled into single contigs. Contig N50 values reached 40.45 Mb and 40.66 Mb, respectively, and both assemblies are gap-free. BUSCO assessments yielded completeness scores of 99.34% for both genomes, confirming their high continuity and accuracy. Integrated morphometric and genomic analyses revealed distinct adaptive strategies in two Hemiculter Species. H. bleekeri has evolved a streamlined body, underpinned by expansions in body shape related genes, and a pelagic egg strategy. In contrast, the adhesive egg strategy of H. leucisculus is supported by expansions in adhesion-related gene families. This divergence reflects adaptation to distinct flow velocity. By combining high-quality chromosome-level T2T genomes with morphometric and comparative genomic approaches, this study establishes a comprehensive framework for understanding the molecular mechanisms underlying adaptive evolution in freshwater fishes inhabiting contrasting flow velocity. Full article

Winterberry (Ilex verticillata) is a deciduous shrub within the Aquifoliaceae family that holds significant ornamental and medicinal value. However, the lack of systematic research on the genetic background and phylogenetic relationships among its cultivars has hindered germplasm conservation and breeding efforts. This study marks the first application of genotyping-by-sequencing (GBS) technology to analyze winterberry germplasm resources. Sequencing was performed on 79 samples from eight representative cultivars, and 3,411,968 high-quality single-nucleotide polymorphism (SNP) markers were developed using a de novo assembly strategy. Population structure analysis based on STRUCTURE indicated K = 8 as the statistically optimal number of genetic components according to the delta K statistic. However, when STRUCTURE results were interpreted together with principal component analysis (PCA) and phylogenetic reconstruction, the winterberry cultivars were consistently summarized into five major genetic clusters. Ilex verticillata ‘Winter Gold’ and I. verticillata ‘Winter Red’ shared highly consistent genetic backgrounds, indicating extremely close kinship; I. verticillata ‘Citronella’ and I. verticillata ‘Oosterwijk’ clustered closely together; I. verticillata ‘Red Sprite’ (Rizhao) and I. verticillata ‘Red Sprite’ (Dezhou), despite differing geographical origins, clustered together, demonstrating good genetic stability; and I. verticillata ‘Golden Verboom’ and I. verticillata ‘Little Goblin Red’ each formed independent genetic branches, possessing unique genetic backgrounds. This study concludes that GBS effectively reveals the complex genetic structure among winterberry cultivars. The findings not only provide accurate molecular evidence for cultivar identification and intellectual property protection but also lay a solid foundation for future hybrid breeding, including parent selection, identification of superior genes, and advancement of marker-assisted breeding. Full article

Germplasm collections are a treasure trove of humanity. The accessions constituting those collections (wild crop relatives, landraces, cultivars, etc.) contain genes and allelic variants, which evolved prior to or post domestication, in the course of adaptation and selection, and can be used in breeding to address current and future needs. Precise characterisation of genetic diversity is essential for the efficient conservation of genetic resources and their effective utilisation in crop improvement. Detailed genetic profiles resulting from DNA genotyping constitute a basis for establishing the level of genetic diversity of a collection, analysing population structure, identifying redundancies, performing genome-wide association scans (given the availability of phenotypic information), detecting loci under selection, and many other applications. To obtain an accurate picture of genetic diversity (at the DNA sequence level), robust, high-density, high-throughput, and cost-effective methods are needed. With the advances in the next-generation sequencing, new genotyping approaches emerged (such as genotyping-by-sequencing, whole genome resequencing), which provide excellent genome coverage and low cost per datapoint (with tens of thousands to millions of loci analysed in a single assay). Crop-specific, custom, microarray-based genotyping solutions were also developed. The aim of this review is to provide a comparative description of the genome-wide, high-density genotyping technologies that are most frequently used nowadays, comprising their advantages and drawbacks, as well as factors that determine, which of the methods will best suit the particular germplasm characterisation project. Further, we characterise the current role of these methods in addressing the challenges related to the effective management and use of genetic resources and present recent examples of their application in selected crop plant groups. Finally, we briefly describe constraints to germplasm characterisation and future prospects. Full article

Angiopteris fokiensis is an endangered fern with ecological and medicinal value, yet genetic studies to support its conservation have been scarce. We performed a genome survey using high-throughput sequencing, developed genomic SSR markers from a draft assembly, and genotyped 96 individuals from 10 populations in Guangdong Province. The genome size was ~4.44 Gb (1.89% heterozygosity). From a 3.58 Gb contig assembly, 4,327,181 SSR loci were identified, with 15 highly polymorphic SSR markers being developed. Genotyping showed high within-population genetic diversity, low inter-population differentiation, and 98.55% of variation within populations. Bayesian structure, principal coordinates analysis, and neighbor-joining tree analyses consistently indicated admixed genetic clusters without clear geographical division. Additionally, the analysis revealed no significant correlation between genetic and geographic distances. Conservation should prioritize intra-population diversity via in situ/ex situ strategies. This study provides the first genomic SSR resources for A. fokiensis and underscores the importance of conserving within-population genetic diversity through integrated in situ and ex situ strategies. Full article

Background/Objectives: Quasipaa spinosa, a large-sized spiny frog, has high commercial value in the food trade. Although the sexual dimorphism in body size between males and females has been investigated, the sex-determining mechanism in this frog remains unknown. Methods: This study employed a genotyping-by-sequencing (GBS) method to identify sex-associated genomic markers and elucidate the sex determination mechanism in the species. Results: We obtained 853 candidate sex-specific GBS tags, with 811 tags (95.07%) demonstrating a male heterozygous system (XX/XY). The diagnostic specificity of the nine markers was further demonstrated by PCR analysis across multiple adult individuals from seven distinct geographic populations of the frog. Four sex-specific markers were aligned with the DMRT1 gene, representing a master regulator of sex determination and gonadal differentiation across the animal kingdom. Conclusions: Our results deciphered the genetic mechanisms governing sex determination in Q. spinosa and presented effective strategies for mono-sex breeding. Full article