PubMed Health⌕ Search

SEARCH · PubMed Health

Results for “molecular breeding”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 19 recordsLinked to original sources
PubMed2025

Molecular breeding of tomato: Advances and challenges.

The modern cultivated tomato (Solanum lycopersicum) was domesticated from Solanum pimpinellifolium native to the Andes Mountains of South America through a "two-step domestication" process. It was introduced to Europe in the 16th century and later widely cultivated worldwide. Since the late 19th century, breeders, guided by modern genetics, breeding science, and statistical theory, have improved tomatoes into an important fruit and vegetable crop that serves both fresh consumption and processing needs, satisfying diverse consumer demands. Over the past three decades, advancements in modern crop molecular breeding technologies, represented by molecular marker technology, genome sequencing, and genome editing, have significantly transformed tomato breeding paradigms. This article reviews the research progress in the field of tomato molecular breeding, encompassing genome sequencing of germplasm resources, the identification of functional genes for agronomic traits, and the development of key molecular breeding technologies. Based on these advancements, we also discuss the major challenges and perspectives in this field.

Solanum lycopersicum↗
PubMed2025

EucaMOD: a comprehensive multi-omics database for functional genomics research and molecular breeding of fast-growing eucalyptus trees.

Eucalyptus, one of the most widely planted plantation tree species globally, is primarily found in tropical and subtropical regions and contributes significantly to economic and social benefits. With advances in sequencing technologies, there is an increasing demand for the systematic analysis of multi-omics data among Eucalyptus species to enhance genetic breeding efforts. Although several early genomic databases have been established for eucalyptus, they have not been updated in a timely manner and lack recent multi-omics data, rendering them insufficient for current research needs. To address this gap, we developed the eucalyptus multi-omics database (EucaMOD, http://eucalyptusggd.net/eucamod), a comprehensive resource for cross-omics studies. In this study, we functionally annotated 45 eucalyptus genomes and structurally annotated 15, conducting comparative genomics and pan-proteomics analyses across all genomes. Additionally, we analyzed eucalyptus transcriptome, epigenome, and variome data through standardized workflows, enabling the in-depth mining and reanalysis of multi-omics datasets. EucaMOD is the most comprehensive multi-omics database for eucalyptus to date and includes data from 45 genomes (39 species), 870 mRNA-seq samples, 17 miRNA-seq samples, 52 epigenomic datasets (histone modifications and transcription factor binding), and genetic variation data from 1219 samples. To support functional genomics and molecular breeding research, the database is organized into the following 11 modules: Home, Species, Genomics, Comparative genomics, Pan-proteomics, Transcriptomics, Epigenetics, Variomics, Tools, Download, and Help. EucaMOD also offers online analysis tools for data mining, providing free public services to aid eucalyptus gene function and genetic engineering studies.

Eucalyptus↗
PubMed2026

Integrated Genomics and Transcriptomics Reveal Stable Resistance Loci and Candidate Genes for Powdery Mildew in Wheat.

Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt), poses a substantial threat to global wheat production. Enhancing resistance through molecular breeding necessitates a comprehensive understanding of its genetic and molecular underpinnings. This study leveraged a 2-year phenotypic evaluation of 283 diverse wheat accessions combined with genome-wide association studies (GWAS) to pinpoint stable quantitative trait loci for powdery mildew resistance. We identified 52 robust resistance loci across the wheat genome, including seven novel loci consistently detected across four environments. Comparative transcriptome profiling of resistant and susceptible wheat lines revealed 95 differentially expressed genes, predominantly enriched in defense response, signal transduction, and transcription regulation pathways. By integrating the GWAS and transcriptomic data, we precisely identified three compelling candidate genes (TaPIP5K, TaPKG, and TaORR6) on chromosome 2A, which are implicated in cell wall reinforcement, jasmonic acid signaling, and reactive oxygen species scavenging, respectively. Further validation using expression analysis corroborated their pivotal roles in resistance. Our findings provide a rich repository of validated genetic markers, promising candidate genes, and superior resistant germplasms, offering critical resources to accelerate targeted molecular breeding efforts for durable powdery mildew resistance in wheat.

Blumeria graminis f. sp. tritici↗
PubMed2025

Multi-Omics Analysis of the Potential Mechanisms of Skin Albinism in Edangered Percocypris pingi: Abnormal Ubiquitination and Calcium Signal Inhibition.

Percocypris pingi is an endangered protected fish species in China. Its albino variants exhibit growth retardation and physiological abnormalities. Understanding its albinism mechanism holds significant scientific importance for molecular breeding programs and disease model development. This study integrated transcriptomic and proteomic analyses, combined with histopathological and molecular biological techniques, to systematically compare molecular differences in skin tissues between albino and wild-type P. pingi, with a focus on elucidating the multidimensional regulatory mechanisms underlying skin albinism. Our findings suggest that albinism in P. pingi is synergistically driven by hyperactivation of ubiquitin-mediated proteolysis (which suppressed TYR/TYRP1 enzymatic activity and disrupted the pH homeostasis of melanosomes), and inhibition of calcium signaling (which impeded melanin transport). This discovery provides novel insights into the mechanisms of pigment loss in fish species and offers a valuable reference for molecular breeding of endangered species as well as research on pigmentation-related disorders.

Animals↗
PubMed2025

Near-complete reference genome assembly of Hoya carnosa.

Hoya R. Br. is the largest genus in the tribe Marsdenieae (Apocynaceae), comprising 350-450 species. Hoya species are popular in horticulture for their distinctive floral traits and fragrances, primarily sourced from domestication and mutation breeding. However, the lack of molecular analysis for floral morphological traits has limited their cultivation and application. In this study, we assembled a near-complete reference genome for H. carnosa, the model species of the genus, using PacBio HiFi reads and Hi-C method. The genome size was approximately 465.7 Mb with a contig N50 of 39.3 Mb. 99.7% of the sequences were anchored to 11 pseudochromosomes, and the assembly achieved a BUSCO score of 98.5%. We predicted 24,309 protein-coding genes, of which 90.2% (21,927) were functionally annotated. This high-quality genome provides a valuable reference for the research of evolution, conservation and molecular breeding in Hoya.

Genome, Plant↗
PubMed2026

Bioinformatics in crop research: using genomic data for crop improvement.

Sustainable crop development aims to maintain or increase yields while reducing environmental impact and managing the challenges imposed by climate change. As the global population grows and arable land becomes scarcer, the integration of molecular breeding with bioinformatics has emerged as an effective strategy for long-term crop improvement. Bioinformatics enables researchers to analyze and interpret the vast quantities of genetic data generated by high-throughput sequencing, making it possible to identify molecular markers, candidate genes, and regulatory networks linked to specific agronomic traits, which breeders then translate into focused, ecologically sustainable breeding programs. This approach has enabled major progress across several fronts: the identification of genes conferring resistance to biotic stressors (pests, pathogens) and abiotic stressors (drought, salinity, heat); the development of nutrient-efficient, low-input crop varieties; the improvement of agronomic performance and nutritional quality through identification of yield- and quality-related genes; and the conservation and deployment of genetic diversity to safeguard long-term breeding sustainability. By combining genomic data with precision breeding techniques, researchers are developing crops that are better adapted to a growing population and a changing climate, positioning the integration of molecular breeding and bioinformatics as a central pillar of future global food security.

bioinformatics↗
PubMed2025

Functional analysis of a GWAS pleiotropic hotspot suggests an auxin biosynthesis gene (AhPDS1), regulating pod development in peanut (Arachis hypogaea L.).

Peanut productivity and quality improvement rely on understanding the genetic factors influencing pod and seed size. This study aims to identify genetic factors and regulatory mechanisms influencing pod and seed size in peanuts. Herein, a genome-wide association study (GWAS) was conducted using 390 accessions from 15 peanut growing regions to analyze pod and seed traits across multiple planting seasons. A significant phenotypic variation was observed, with broad-sense heritability ranging from 53.6 to 85.4%. Strong correlations between pod and seed traits further suggest potential for co-selection in breeding efforts. A pleiotropic hotspot on chromosome B06 was strongly associated with six pod and seed traits. A peanut pod size regulator AhPDS1 (PODSIZE-1, Ahy_B06g085516) homolog of Arabidopsis thaliana YUCCA4 (AtYUC4, AT5G11320), involved in auxin biosynthesis, was selected as a candidate regulating pod and seed size. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) confirmed higher AhPDS1 expression in large pod as compared with the small pod genotypes. Subcellular localization showed AhPDS1 to be predominantly cytoplasmic, and GUS reporter assays indicated widespread expression in roots, stems, leaves, flowers, and pods, suggesting a broad functional role. Further overexpression of AhPDS1 in Arabidopsis and rice enhanced pod, seed, and grain sizes via the indole-3-pyruvic acid pathway in transgene lines. These findings highlight AhPDS1 as a potential target for peanut molecular breeding, offering opportunities to enhance pod size via auxin biosynthesis and support sustainable crop improvement.

Arachis↗
PubMed2025

Genetic diversity, population structure in a historical panel of Brazilian soybean cultivars.

Soybean [Glycine max (L.) Merrill] is one of the most widely grown legumes in the world, with Brazil being its largest producer and exporter. Breeding programs in Brazil have resulted from multiple cycles of selection and recombination starting from a small number of USA cultivar ancestors in the 1950s and 1960s years. This process has led to the successful adaptation of this crop to tropical conditions, a phenomenon known as tropicalization. Many studies describe a narrow genetic background in Brazilian soybean cultivars. Various factors can affect the genetic diversity in species, especially in cultivated crops, such as the reproduction type, artificial selection, and the number and sources of variability in the breeding programs. In turns, the genetic diversity can affect the linkage disequilibrium blocks (LD) patterns and, consequently, molecular breeding strategies for selection of target loci for agronomic traits. We used high-throughput genotyping with SoySNP50K Illumina SNP markers to assess a collection of 370 Brazilian soybean accessions covering more than 60 years of soybean breeding in Brazil. Our goal was to investigate population structure and genetic diversity in the Brazilian germplasm, detect patterns of LD blocks, and identify regions presenting signals of selective swaps linked with quantitative trait loci (QTLs) of agronomic interest. Population structure analysis revealed two major groups among all genotypes, primarily differentiated by the year of release, separating old and new cultivars (before and after 2000´s years), and by growth habit (stem termination type-SST). The group I comprises about 75% of the panel and includes cultivars release before 2000`s years, including the oldest cultivars released in Brazil, most of which exhibit a determinate growth habit and maturity groups VI and VII. Group II includes only 83 materials, but shows higher levels of diversity than group I, representing most recent introductions in Brazilian germplasm. Further analysis of substructure within Group I, identified seven subgroups with no clear trend for segregation based on maturity group, STT or year of release. Instead, these subgroups were based on the contribution of key donors of disease resistance and adaptability, as soybean cultivation expanded from the South to Central region of Brazil. This finding is consistent with the history of soybean expansion in Brazil. We identified 123 genomic regions under selection among the groups of Brazilian cultivars associated with 440 quantitative trait loci (QTLs), revealing regions fixed across the breeding process associated with yield, disease resistance, water efficiency use, and others.

Glycine max↗
PubMed2026

Evolutionary expansion of the NF-Y gene family in bivalves and divergent subunit responses to thermal and pathogenic stress in the noble scallop.

Nuclear factor Y (NF-Y) is a conserved eukaryotic transcription factor complex that specifically interacts with the CCAAT motif. Prior research has demonstrated that this gene family participates in various biological processes, encompassing growth, development, and stress responses, across a broad spectrum of organisms. However, research on the role of the NF-Y family in bivalves remains limited. In this study, we comprehensively identified the NF-Y family in 34 bivalve species, and further investigated its expression in the noble scallop Chlamys nobilis. A total of 296 NF-Y genes were identified and classified into three subfamilies, NF-YA, NF-YB, and NF-YC. Phylogenetic analysis revealed that NF-YA and NF-YC have remained relatively conserved, whereas NF-YB has undergone significant expansion. Additionally, while substantial disparities in gene copy numbers exist across species, the motif composition and exon-intron structures within each subfamily demonstrate notable conservation. Tissue expression profiling revealed distinct expression patterns among CnNF-Y genes, with several members exhibiting relatively high transcript abundance in gonadal tissues. Furthermore, qRT-PCR results demonstrated that CnNF-YA2, CnNF-YB6, and CnNF-YC were significantly and continuously upregulated under heat stress. Conversely, several genes, particularly CnNF-YA2, CnNF-YB3, and CnNF-YB4, exhibited dynamic transcriptional responses to Vibrio parahaemolyticus exposure. These findings enhance our understanding of the evolutionary trajectory and functional diversification of the NF-Y gene family in bivalves, laying a theoretical foundation for future research on thermal adaptation, immune regulation, and molecular breeding in scallops.

Animals↗
PubMed2025

Development and validation of a high-density 'Amahysnp' genotyping array in grain amaranth (Amaranthus hypochondriacus).

BACKGROUND: Grain amaranth has recently gained global attention as a promising crop alternative to traditional cereals due to its nutritional value and adaptability to various growing conditions. Although gene banks conserve extensive collections of amaranth germplasm, the genomic and phenotypic characterization of these resources is limited, which hinders their full utilization in breeding programs. A major challenge is the lack of high-throughput genotyping assays essential for comprehensive genomic characterization and trait mapping. High-density SNP arrays have become standard tools for genome-wide analysis across multiple loci, enabling molecular breeding across a range of crop species. RESULTS: In this study, we developed a 64 K high-throughput SNP genotyping array named "AmahySNP", using Affymetrix® Axiom® technology. The array contains 64,069 high-density SNPs distributed across both genic (55.17%) and non-genic (44.83%) regions of the Amaranthus hypochondriacus genome. The genic region includes 8,879 genes, which consist of 4,830 single-copy genes and 4,049 multi-copy genes distributed across 16 scaffolds. These genes cover various functional regions, including exons (10.5%), introns (40.1%), 5'UTRs (1.6%), and 3'UTRs (2.9%), respectively. The AmahySNP array was effectively utilized for population structure analysis, genetic diversity studies, core development, and genome wide association studies (GWAS) in amaranth germplasm. A representative core set of 112 accessions was identified, which includes two released varieties (Annapurna and Suvarna) and 100 diverse accessions from 12 different regions, representing 12% of the total 917 accessions evaluated. Phylogenetic analysis revealed three major genetic clusters, independent of their geographical origins. GWAS conducted using 22,763 polymorphic SNPs from 540 genotypes identified 13 novel loci associated days to flowering (DTF) trait, seven of which were located within annotated genes. CONCLUSIONS: The AmahySNP 64 K SNP chip a valuable genomic tool for amaranth research and breeding with a strong potential to accelerate its genetic improvement. It enables high-throughput genotyping for a wide range of applications, including GWAS and other genomic studies, and will significantly advance the exploration of natural genetic variations. Ultimately, this resource will empower amaranth breeders to develop improved amaranth cultivars with enhanced crop yield, resilience, and nutritional quality, contributing to global food security and sustainable agriculture.

Amaranthus↗
PubMed2024

The genome of Lespedeza potaninii reveals biased subgenome evolution and drought adaptation.

Lespedeza potaninii, a xerophytic subshrub belonging to the legume family, is native to the Tengger Desert and is highly adapted to drought. It has important ecological value due to its drought adaptability, but the underlying molecular mechanisms remain largely unknown. Here, we report a 1.24 Gb chromosome-scale assembly of the L. potaninii genome (contig N50 = 15.75 Mb). Our results indicate that L. potaninii underwent an allopolyploid event with 2 subgenomes, A and B, presenting asymmetric evolution and B subgenome dominance. We estimate that the 2 diploid progenitors of L. potaninii diverged around 3.6 million years ago (MYA) and merged around 1.0 MYA. We revealed that the expansion of hub genes associated with drought responses, such as the binding partner 1 of accelerated cell death 11 (ACD11) (BPA1), facilitated environmental adaptations of L. potaninii to desert habitats. We found a novel function of the BPA1 family in abiotic stress tolerance in addition to the known role in regulating the plant immune response, which could improve drought tolerance by positively regulating reactive oxygen species homeostasis in plants. We revealed that bZIP transcription factors could bind to the BPA1 promoter and activate its transcription. Our work fills the genomic data gap in the Lespedeza genus and the tribe Desmodieae, which should provide theoretical support both in the study of drought tolerance and in the molecular breeding of legume crops.

Genome, Plant↗
PubMed2025

A high-quality chromosome-level genome assembly and annotation of the giant freshwater prawn (Macrobrachium rosenbergii).

The giant freshwater prawn, Macrobrachium rosenbergii, is native to Southeast Asia and is used in aquacultural practices worldwide. It is considered advantageous because of its rapid growth, high nutritional value, and economic benefits. As one of the three major freshwater aquaculture shrimp sources in China, a high-quality genome resource is of great significance for promoting the germplasm improvement of varieties. This study presents a high-quality chromosome-level genome assembly of M. rosenbergii that was generated by combining PacBio, MGI, and Hi-C reads. The assembled genome was 2.96 Gb in size, with a contig N50 of 0.64 Mb and a scaffold N50 of 55.76 Mb, which was positioned on 59 pseudo-chromosomes. The Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis for genome assembly reached 94.37%. In total, 27,111 protein-coding genes were identified, of which 25,470 were functionally annotated. These results provide a foundation for future research into adaptive evolution, genomics, and molecular breeding in M. rosenbergii.

Animals↗
PubMed2026

Adaptive genomic evolution and WD40-regulated temporal dynamics of anthocyanins support leaf photoplasticity in Parrotia subaequalis.

BACKGROUND: Parrotia subaequalis, a Tertiary relict endemic to China, plays a significant role in phylogeny and adaptive evolution as a key species in the early differentiation of angiosperms. It has abundant leaf colors and great potential as an ornamental tree. RESULTS: This study assembled the first chromosome-level genome of P. subaequalis (Contig N50 = 2.15 Mb), revealing transposable element proliferation, key paleopolyploid events and dynamic gene family evolution, including the expansion of secondary metabolite transport and synthesis genes (such as WD40, 2OG-FeII_Oxy) and the contraction of gene families related to flower morphogenesis (such as F-box-like, K-box). Through integrative transcriptomics and targeted metabolomics approaches, we further revealed that the color transition of young leaves from red to green was driven by temporal accumulation differences of malvidin-3,5-O-diglucoside, whose biosynthesis is progressively down-regulated during leaf development. WGCNA revealed that a subset of WD40 genes (light-signaling, TTG1/HOS15-like, etc.) coexpresses with anthocyanin biosynthetic genes, like 4CLL9, GT1, in anthocyanin-related modules enriched for auxin signaling and hydrolase activity, suggesting a potential link between WD40 expansion and photoprotective plasticity. Relevant regulatory networks were found to complement the species-specific gene pool related to leaf color regulation. CONCLUSION: This genomic resource of P. subaequalis advanced our understanding of early angiosperm adaptation through neofunctionalized regulatory networks and established a foundation for molecular breeding aimed at enhancing environmental resilience while preserving ornamental traits.

Anthocyanins↗
PubMed2025

Molecular mechanisms and breeding strategies for heat tolerance in vegetable crops under global warming.

Extreme heat driven by climate change poses a catastrophic threat to global vegetable production, undermining nutritional security because of the heightened physiological sensitivity and succulent tissues of these crops. This review synthesizes the multistage impacts of heat stress across critical developmental phases-from germination to reproduction-emphasizing morphological impairments (such as leaf wilting and floral abortion) and physiological disruptions (including photosynthetic inhibition and oxidative damage). We systematically dissect thermotolerance mechanisms in vegetables, highlighting transcriptional reprogramming by HSFs, WRKY, and NAC transcription factors; chaperone-mediated proteostasis via HSPs; epigenetic remodeling; Ca2+-ROS signaling pathways; and the role of phase separation dynamics. Importantly, we propose six strategic pathways to develop heat-resilient vegetables: harnessing natural variation through pan-genome-driven allele mining; employing biotechnological interventions such as CRISPR-mediated editing and synthetic promoters; engineering multistress tolerance by targeting conserved 'core response' pathways; exploiting epigenetic memory to achieve transgenerational resilience; optimizing source-sink dynamics with ''Climate-Responsive Carbon Optimization; and applying plant growth regulators and nanotechnology to enhance thermotolerance. Together, these strategies chart a clear roadmap for climate-smart vegetable breeding and call for interdisciplinary collaboration to translate molecular discoveries into practical breeding approaches for sustainable food systems under escalating thermal extremes.

Journal Article↗
PubMed2025

The chromosome-level genome of Stylosanthes guianensis provides insights into genome evolution and environmental adaptation.

Stylosanthes guianensis is a leguminous forage crop of significant economic importance, primarily distributed in tropical and subtropical regions. It exhibits strong adaptability to various stresses, yet the genetic basis underlying this trait remains unclear. In this study, we constructed the first chromosome-scale reference genome of S. guianensis using a combination of Nanopore and Hi-C sequencing technologies. The assembled genome size is 1254 Mb, with 10 pseudochromosomes. Using Nanopore full-length transcriptome data, we generated high-quality transcript-level gene annotations, identifying 36 585 gene models and 110 601 transcripts. The repetitive sequences in S. guianensis account for 79.16% of the genome, with the extensive expansion of Gypsy elements in long terminal repeats contributing to its genome size enlargement. Comparative genomic and transcriptomic analyses revealed that flavonoid metabolism plays a pivotal role in stress adaptation, providing new insights into the genetic basis of stress tolerance. Additionally, we generated whole-genome methylation profiles under cold treatment and control conditions, offering valuable data for future epigenomic research. These findings provide essential molecular resources for understanding stress resilience in S. guianensis and advancing its molecular breeding.

Genome, Plant↗
PubMed2026

Identification of rice DUF1719 gene family and analysis of alkaline tolerance function of OsDUF1719.8.

Alkaline stress severely constrains the physiological metabolism and growth and development of rice through high pH and ionic toxicity. Domains of unknown function (DUF) play significant roles in plant stress responses. However, the function of the DUF1719 family (PF08224) in rice has not been reported and further research is needed. This study systematically identified the OsDUF1719 gene family in rice and investigated the function of OsDUF1719.8 under alkaline stress. The results demonstrate that the rice DUF1719 family comprises 13 protein members, all containing the PF08224 domain. It is predicted that this domain may play a role in ATPase activation. Evolutionary analysis divided DUF1719 proteins from eight grass species into six subgroups, with highly conserved gene structures, motifs, and tertiary architectures within each subgroup. Promoter analysis indicated enrichment of stress- and hormone-responsive elements, implying broad involvement in stress regulation. Expression analysis revealed that several genes, including OsDUF1719.5 and OsDUF1719.8, were upregulated under multiple abiotic stresses. Notably, OsDUF1719.8 was strongly induced during early alkaline stress. Consequently, we further analyzed the function of OsDUF1719.8 in the rice alkaline stress response. The results demonstrate that overexpression of OsDUF1719.8 enhanced rice alkaline tolerance, whereas knockout mutants exhibited stress sensitivity. OsDUF1719.8 enhances rice tolerance to alkaline stress by coordinately regulating reactive oxygen species metabolism, promoting the accumulation of osmotic adjustment compounds, and modulating ion homeostasis. This study provides the first systematic identification of the DUF1719 family and elucidates the function of OsDUF1719.8 in positively regulating rice alkaline tolerance, offering a novel gene for alkali-tolerant molecular breeding of rice.

Oryza↗
PubMed2025

A chromosome-level reference genome assembly of the Small snakehead (Channa asiatica).

The Small snakehead (Channa asiatica) is an economically important species in both aquaculture and ornamental trade, mainly distributed in South China and Southeast Asia. Despite its significance, limited genomic resources have impeded in-depth genetic studies and breeding programs. In this study, we used PacBio HiFi long-read sequencing, Illumina short-read sequencing, and Hi-C technologies to generate a high-quality chromosome-level genome of the C. asiatica. The final genome spans 659.44 Mb, with an impressive 98.18% anchored to 23 chromosomes. Notably, the contig N50 and scaffold N50 are 23.92 Mb and 29.61 Mb, validated by a BUSCO completeness score of 98.93%. Genome annotation identified 26,603 protein-coding genes, 99.29% of which were confirmed by BUSCO analysis, and 93.68% were functionally annotated. Approximately 27.72% of the genome sequences were classified as repeat elements. This high-fidelity genome assembly provides a robust foundation for advancing molecular breeding, comparative genomics, and evolutionary studies of C. asiatica and related species.

Animals↗