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At least 19 recordsLinked to original sources
PubMed2025

Leveraging local ancestry and cross-ancestry genetic architecture to improve genetic prediction of complex traits in admixed populations.

The broader application of polygenic risk score (PRS) is hindered by the limited transferability of PRS developed in Europeans to non-European populations. While many statistical methods have been developed to improve the performance of PRS in non-European populations, most of them focused on discrete genetic ancestry clusters and did not consider admixed individuals. Admixed individuals pose a unique challenge for PRS calculation due to the complexity of local ancestry and cross-ancestry effect sizes. Here, we present a statistical method called SDPR_admix for calculating PRS in admixed individuals. SDPR_admix characterizes the joint distribution of the effect sizes of a genetic variant with two ancestries to be both zero, ancestry enriched, or shared with correlation. SDPR_admix outperformed other methods in simulations and improved the prediction of real traits in European-African admixed individuals in UK Biobank when trained on the Population Architecture using Genomics and Epidemiology (PAGE) dataset (N = 13,000). Deployment of SDPR_admix on All of Us (N = 52,000) further increased the prediction accuracy by approximately 5-fold on average compared with training on PAGE. This enhancement was achieved with manageable computational time and cost, demonstrating the feasibility of training PRS models on large-scale All of Us data. We provided several examples demonstrating that both ancestral-enriched and shared effects, as included in the SDPR_admix prediction model, are helpful for improving polygenic prediction in admixed populations. We also applied SDPR_admix to construct PRS for admixed Americans with mixture of European and Amerindigenous ancestries and showed that SDPR_admix overall outperformed other methods.

Humans↗
PubMed2025

Efficient CRISPR/Cas9-mediated genome editing of phytoene desaturase in Musa-AAA: a critical step for genetic improvement of east African highland bananas.

East African highland bananas (EAHBs), locally referred to as "matooke", are an important staple crop in Uganda. The EAHBs have a triploid genome (AAA) with a large phenotypic diversity in the Great Lakes region of Africa and are challenged by both abiotic and biotic factors. The EAHBs have been improved through conventional breeding and genetic engineering though facing challenges such as genetic drag of unfavorable traits and complex regulatory processes, respectively. Therefore, a more precise approach for crop improvement such as genome editing is highly recommended. In the current study, we assessed the feasibility and applicability of the CRISPR/Cas9 mediated-genome editing in EAHBs. Two sgRNAs were designed from the Nakitembe phytoene desaturase (PDS) gene and used to edit the PDS gene in Nakitembe (NKT) and NAROBan5 (M30) cultivars. A total of 47 NKT and 130 M30 events were regenerated via agrobacterium-mediated transformation of banana embryogenic cell suspensions. Up to 100% and 94.6% albinism rates were observed in Nakitembe and M30 cultivars respectively with additional albino-variegated and variegated phenotypes observed in M30 only. Carotenoid analysis revealed a significant reduction of total carotenoid content in edited events with all complete albinos showing no detectable carotenoids implying that the carotenoid biosynthetic pathway was effectively disrupted. Sequence analysis revealed that all of the edited events had frameshift mutations leading to PDS disruption. Overall, this study presents the first report of CRISPR/Cas9 genome editing in EAHBs and more interestingly on a hybrid, M30 showing high precision and efficiency. This validated genome editing system provides a robust platform for targeted EAHB improvement.

CRISPR/Cas9↗
PubMed1978

Selection among males for the genetic improvement of female fertility.

The quantitative physiological study of genetic variation in reproductive performance has shown that differences in the litter size and incidence of lambing in sheep are associated with variation in the release of LH. This variation is detectable in young animals of both sexes, and the injection of LHRH may aid its recognition. In the male it is associated with variation in mating behavior and testis growth. The ovarian activity of both sheep and mice has been shown to change following selection for testis growth. The use of measures of testis growth as criteria for selection to improve the reproductive performance of females is discussed.

Animals↗
PubMed2026

From family trials to genomic mate allocation: statistical and genomic strategies to accelerate sugarcane genetic improvement.

Sugarcane (Saccharum spp.) underpins global sugar and bioenergy supply and is increasingly valued as a renewable biomass feedstock. Sustained improvement in commercial traits and resilience is constrained by long breeding cycles, clonal propagation, multi-stage testing, and a highly polyploid, heterozygous, and frequently aneuploid genome with substantial non-additive genetic variation. Genomic selection has demonstrated value for predicting elite-clone performance, yet its operational use remains limited at earlier decision points, including family selection, parent evaluation, and cross design. This review examines the biological, statistical, and genomic factors that shape these decisions, with emphasis on the Australian breeding context based on progeny assessment trials (PATs), clonal assessment trials (CATs), and final assessment trials (FATs). We evaluate challenges arising from family plot means, the use of different full-sib samples as nominal family replicates, spatial heterogeneity, competition, genotype-by-environment interaction, and the partitioning of additive and non-additive effects. We also assess the integration of pedigree and genomic relationship, genotype representation, allele-dosage estimation, aneuploidy, genomic prediction models, and training-population design. We then consider genomic prediction of cross performance and constrained mate allocation as approaches for improving expected family performance, accounting for cross-specific non-additive effects and managing relatedness. We propose a decision-centred framework that links family and clonal data across breeding stages, tracks the propagation of information and uncertainty, and supports parent recycling and cross allocation. We conclude with a practical research agenda for stage-integrated mixed-model and single-step analyses that connect early family evaluation with genomic prediction and cross-level decision support in sugarcane breeding.

Saccharum↗
PubMed2026

Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.

Livestock reference genomes have transformed the discovery of variants associated with production, reproduction, health, and environmental adaptation. Nevertheless, a single linear reference represents only one mosaic haplotype and incompletely captures sequence diversity within a species, particularly structural variants, copy-number changes, repeat-rich regions, and breed-specific sequences. Pangenomes address this limitation by integrating multiple high-quality assemblies or population-scale variants into a unified sequence or graph representation. Concurrently, multi-omics approaches connect genomic variation with transcriptomic, epigenomic, manuscriptproteomic, metabolomic, and microbiome responses, thereby improving biological interpretation of genotype-phenotype relationships. This review synthesizes recent progress in livestock pangenomics and multi-omics, with emphasis on cattle, goats, sheep, water buffalo, and chickens. It describes advances in long-read and haplotype-resolved sequencing, graph construction, structural-variant discovery and genotyping, functional annotation, and integrative analysis. Recent pangenome studies have uncovered substantial non-reference sequence, reduced reference bias, identified breed- and population-specific structural variants, and resolved candidate variants underlying pigmentation, body size, tail morphology, cashmere production, altitude adaptation, and other economically relevant traits. However, translation into routine breeding remains constrained by uneven population representation, inconsistent structural-variant definitions, limited functional annotation, computational demands, and insufficient validation across environments. Future progress will depend on diverse near-complete assemblies, graph-aware imputation and genomic prediction, long-read transcriptomics, single-cell and spatial omics, rigorous causal validation, and open, interoperable resources. Together, these developments can support more accurate, resilient, and biologically informed livestock improvement. Importantly, current dairy-cattle evidence indicates that pangenome-derived structural variants can substantially improve variant discovery and functional interpretation while yielding only marginal average gains in routine genomic prediction, favoring targeted augmentation rather than wholesale replacement of established SNP-based evaluations.

Animals↗
PubMed1979

Endocrine factors in genetic improvement of milk production.

The endocrine role in lactation is undisputed, but attempts to correlate milk production with various endocrine products have had limited success. Recent work has suggested that placental hormones, in particular placental lactogen, may be an important regulator of lactation capacity. In addition to concentrations of hormones in blood, it is important to consider receptors in target tissue for the hormones. The concentration of receptors in a tissue may vary with genotype of the individual or under the influence of hormonal state. Other aspects of the target tissue's system for response also must be considered.

Animals↗
PubMed1979

Factors for improved genetic counseling for retinoblastoma based on a survey of 55 families.

Of 55 families in which one or more patients with retinoblastoma were treated, five of these families involved more than one patient. The remaining 50 were sporadic cases. Two of the five familial cases involved collateral inheritance and three involved direct inheritance. Factors important for genetic counseling included the time of onset of first symptoms, the age of the father, the occurrence of a second primary tumor, unilateral vs bilateral involvement, and the cytogenetic analysis of the patient's chromosomes. Additionally, mutational mosaicism was considered as a cause for sporadic cases of retinoblastoma. Use of the risk figures derived from this study should provide more precise genetic counseling for parents, siblings, and patients with retinoblastoma.

Adolescent↗
PubMed2026

Deep tissue sequencing improves genetic diagnostic yield in focal cortical dysplasia.

Focal cortical dysplasias (FCDs) are malformations of cortical development associated with drug-resistant focal epilepsy. We analyzed surgical tissue from 25 consecutive cases recruited from adult and pediatric epilepsy surgery programs. We performed high-depth sequencing of lesional tissue, validated somatic variants using droplet digital PCR or amplicon sequencing, and investigated genotype-phenotype correlations. A pathogenic or likely pathogenic variant was detected in 64% (n = 16/25) of cases. Of these, five cases with FCDIIa or FCDIIb had germline variants in NPRL3 (n = 3) or DEPDC5 (n = 2). Somatic variants were identified in 44% (n = 11/25) of cases. The genetic yield for FCDIIb was 77% of cases having a pathogenic mTOR pathway variant detected (n = 10/13), and for FCDIIa 66% (n = 6/9). High depth sequencing approaches allowed detection of somatic variants with very low (down to 0.4%) variant allele fractions (VAFs). No pathogenic variants were detected in 3 cases with FCDI. 62% (n = 15/24) of the cases with ≥12 months follow up experienced a favourable seizure outcome (Engel 1-2) following surgery. Of note, n = 9 patients required repeat surgery to resect residual dysplasia. Determining a genetic diagnosis reveals aetiology and paves the way to precision therapies that may benefit those with FCD who do not respond to current treatments.

Humans↗
PubMed1979

Mapping chromosomal genes of Saccharomyces cerevisiae using an improved genetic mapping method.

A triploid (3n) strain of Saccharomyces cerevisiae was constructed carrying a standard marker on each of chromosomes 1 through XVII in the -/+/+ configuration. This is called a "supertriploid." Meiotic spores from this strain (n + approximately n/2) were mated with a haploid (n) carrying an unmapped mutation. Meiotic analysis of each zygote clone (2n + approximately n/2) produced in this way resulted in elimination of an average of 4.2 chromosomes as the possible location of the unmapped marker. The distribution of extra chromosomes in the 2n + approximately n/2) strains was nearly random. Meiotic segregrants of these crosses carrying the unmapped mutation in the -/+ configuration were then crossed with multiply marked haploid strains to further narrow the possible location of the unmapped mutation to a single chromosome. Scoring of markers by complemention tests was simplified by mating spore clones with mixtures of a and alpha strains, each pair carrying the same set of markers. Using this new, more rapid method ("supertriploid mapping"), eight genes required for the maintenance of the killer plasmid were located on the genetic map of S. cerevisiae.

Aneuploidy↗
PubMed2024

Genomic prediction and genome-wide association studies of morphological traits and distraction index in Korean Sapsaree dogs.

The Korean Sapsaree dog is a native breed known for its distinctive appearance and historical significance in Korean culture. The accurate estimation of breeding values is essential for the genetic improvement and conservation of such indigenous breeds. This study aimed to evaluate the accuracy of breeding values for body height, body length, chest width, hair length, and distraction index (DI) traits in Korean Sapsaree dogs. Additionally, a genome-wide association study (GWAS) was conducted to identify the genomic regions and nearby candidate genes influencing these traits. Phenotypic data were collected from 378 Korean Sapsaree dogs, and of these, 234 individuals were genotyped using the 170k Illumina CanineHD BeadChip. The accuracy of genomic predictions was evaluated using the traditional BLUP method with phenotypes only on genotyped animals (PBLUP-G), another traditional BLUP method using a pedigree-based relationship matrix (PBLUP) for all individuals, a GBLUP method based on a genomic relationship matrix, and a single-step GBLUP (ssGBLUP) method. Heritability estimates for body height, body length, chest width, hair length, and DI were 0.45, 0.39, 0.32, 0.55, and 0.50, respectively. Accuracy values varied across methods, with ranges of 0.22 to 0.31 for PBLUP-G, 0.30 to 0.57 for PBLUP, 0.31 to 0.54 for GBLUP, and 0.39 to 0.67 for ssGBLUP. Through GWAS, 194 genome-wide significant SNPs associated with studied Sapsaree traits were identified. The selection of the most promising candidate genes was based on gene ontology (GO) terms and functions previously identified to influence traits. Notable genes included CCKAR and DCAF16 for body height, PDZRN3 and CNTN1 for body length, TRIM63, KDELR2, and SUPT3H for chest width, RSPO2, EIF3E, PKHD1L1, TRPS1, and EXT1 for hair length, and DDHD1, BMP4, SEMA3C, and FOXP1 for the DI. These findings suggest that significant QTL, combined with functional candidate genes, can be leveraged to improve the genetic quality of the Sapsaree population. This study provides a foundation for more effective breeding strategies aimed at preserving and enhancing the unique traits of this Korean dog breed.

Animals↗
PubMed2026

Fourier-transform infrared-based genome-wide association study identifies candidate genes and variants for sow colostrum composition.

Sows with high prolificacy and better lactation traits are beneficial for weaned piglet number. Because the genetic basis of sow lactation traits remains elusive, genetic improvement for lactation traits lags behind that for litter traits, constraining the full realisation of genetic potential for large litters. Here, we measured 1&#xa0;060 Fourier-transform infrared (FTIR) wavenumbers and five predicted colostrum composition traits from sow colostrum samples. Heritability estimates for both the FTIR spectra and predicted traits ranged from moderate to high. Correlation analysis revealed that lactose percentage was negatively genetically correlated with the other four predicted traits (fat percentage, protein percentage, total solid content, and urea nitrogen content) and with 24&#xa0;h litter weight, which was positively genetically correlated with both protein and total solid content. Genome-wide association studies on the FTIR spectra and predicted traits identified 134 significant single-nucleotide polymorphisms (SNPs) (False discovery rate < 0.05), with most clustering on Sus scrofa chromosomes (SSC) 5 and 7. Among the candidate genes, two expressed in lactating mammary tissue have established roles in milk trait determination: (1) LALBA, which encodes a major colostrum protein and is responsible for lactose synthesis, and (2) BTN1A1, which mediates milk fat secretion. Additionally, the study detected two important candidate variants on SSC7: (1) rs691487382, which was colocalised with the expression quantitative trait locus signal for TRIM26 in the liver, a key metabolic organ supporting lactation, and (2) rs327923027, a missense variant located in a phylogenetically conserved domain of TRIM26, an E3 ubiquitin ligase implicated in liver homeostasis. Taken together, this study identifies, for the first time, candidate genes and variants for sow colostrum, providing genomic markers useful for genetic improvement.

Association analysis↗
PubMed2026

Identification of Candidate Genes Associated with Growth Traits in Procambarus clarkii Using Whole-Genome Resequencing.

Growth is a critical economic trait in all aquaculture industries. To address issues such as germplasm degradation, a comprehensive understanding of the growth and development mechanisms, along with genetic improvement strategies, for Procambarus clarkii (P. clarkii) is urgently required. In this study, we performed whole-genome resequencing on 89 individuals from five cultured stocks to investigate growth traits (body length) and identified a total of 46,919,297 high-quality single nucleotide polymorphisms (SNPs). Based on these SNPs, we conducted principal component analysis (PCA), phylogenetic analysis, and population genetic structure analysis. Furthermore, we performed selective sweep analysis (using FST, Pi, and XP-CLR) and a genome-wide association study (GWAS) to identify genetic variants associated with growth traits. The results revealed significant genetic differentiation among the five cultured stocks, with the Ma'anshan cultured stock exhibiting the fastest linkage disequilibrium (LD) decay. Additionally, long-term aquaculture in different geographical regions resulted in distinct genetic differences among cultured stocks. Through selective sweep analysis, the intersection of FST, Pi, and XP-CLR across the five populations yielded several growth-related candidate genes: Nephrin, Somatostatin, zinc finger protein 154, and yeti. Subsequent the GWAS identified two candidate genes associated with growth traits: Cullin-associated and neddylation-dissociated protein 1 (CAND1) and Baculoviral IAP repeat-containing protein 8 (BIRC8). These genes are presumed to play pivotal roles in the growth and development of P. clarkii. Overall, our findings provide new insights into the genetic mechanisms underlying growth and development in P. clarkii, and these identified genes serve as promising candidates for further functional studies and genetic improvement of this species.

Polymorphism, Single Nucleotide↗
PubMed2026

Genome-wide association study and KASP development for growth and leaf traits in Populus deltoides.

BACKGROUND: Populus deltoides is a valuable timber species of considerable importance in the study of forest genetic breeding. However, its genetic improvement continues to rely predominantly on conventional selection and hybridization strategies hampered by long breeding cycles and limited efficiency. RESULTS: A total of 209 P. deltoides accessions were genotyped using a 60K SNP (Single nucleotide polymorphism) liquid array. Following quality control, 46,031 high-quality SNPs were screened and analyzed alongside 15 phenotypic traits in a genome-wide association study (GWAS), which identified 219 SNPs significantly associated with the traits. After further screening and annotation, a final set of 57 target SNPs and 77 candidate genes was obtained. Using kompetitive allele-specific PCR (KASP) assays, we successfully developed 48 polymorphic KASP markers. Of these, 25 markers exhibited significant phenotypic differences (p&#x2009;<&#x2009;0.05) across genotype groups. CONCLUSIONS: These 25 KASP markers can serve as reliable and practical tools for phenotype-assisted selection, providing efficient molecular resources for accelerating genetic improvement and marker-assisted breeding in poplar.

Populus↗
PubMed2026

Integrating genomics, multi-omics, CRISPR and speed breeding for stress-resilient vegetable legume improvement.

Vegetable legumes are nutritionally and ecologically important crops. However, their genetic improvement has not kept pace with the increasing challenges posed by climate change due to the polygenic nature of stress tolerance, narrow genetic diversity, and the persistent gap between molecular discoveries and field-level cultivar development. Although recent reviews have examined individual genomic tools or specific stress responses, a comprehensive synthesis integrating genomics-assisted breeding, multi-omics technologies, genome editing, and speed breeding within a unified crop improvement framework has been lacking. This review addresses that gap by critically evaluating how these complementary approaches can accelerate the development of stress-resilient vegetable legumes, including pea, common bean, cowpea, faba bean, cluster bean, yard-long bean, and hyacinth bean. This review synthesizes advances in QTL mapping, genome-wide association studies, transcriptomics, metabolomics, and CRISPR-based functional genomics that have identified key regulators and pathways underlying resistance to major biotic and abiotic stresses. Rather than considering these technologies independently, the review emphasizes their convergence into a systems-level breeding framework integrating genomic discovery, functional validation, predictive breeding, and accelerated generation advancement to improve breeding efficiency. Speed breeding, enabling up to seven to eight generations annually under optimized controlled-environment experimental conditions in cowpea, is discussed as a complementary strategy with genomic selection and genome editing. The review further identifies major translational bottlenecks, including transformation recalcitrance, limited genomic resources for underutilized vegetable legumes, inadequate multi-environment validation, and fragmented omics integration, and presents an integrated systems-breeding framework to bridge the gap between gene discovery and cultivar development.

Fabaceae↗
PubMed2026

Deep learning and statistical methods identify novel asthma risk variants in Europeans.

BACKGROUND: Asthma is a common heritable respiratory disorder with a complex genetic basis. Although large-scale genome-wide association studies have identified many risk loci, the full spectrum of its polygenic architecture remains to be defined. OBJECTIVE: We refined the genetic landscape of asthma in individuals of European ancestry and improve polygenic risk prediction through statistical and deep learning-based methods. METHODS: We conducted the largest genome-wide association study meta-analysis of asthma in individuals of European ancestry, combining data from the Global Biobank Meta-analysis Initiative (121,940 cases, 1,254,131 controls) and the Million Veteran Program (36,823 cases, 398,278 controls). To enhance discovery, we applied pleiotropy-informed multitrait analysis and conditional false discovery rate approaches, each incorporating eosinophil counts as a secondary trait. In parallel, we used a Transformer-based deep learning framework to further prioritize variants and improve polygenic risk prediction. RESULTS: The meta-analysis identified 69 independent genome-wide significant loci (P&#x2009;<&#x2009;5 &#xd7; 10-8) not previously reported in asthma. Multitrait analysis of genome-wide association studies, conditional false discovery rate, and deep learning approaches uncovered additional candidate loci. Functional annotation and expression quantitative trait locus mapping implicated novel genes in immune regulation, airway remodeling, and metabolic processes. Polygenic risk score models derived from deep learning-prioritized variants outperformed those based on conventional genome-wide association study and standard statistical approaches. CONCLUSIONS: Our study yields a comprehensive map of asthma-associated loci in European ancestry populations, improves genetic risk prediction, and informs future mechanistic studies.

Humans↗
PubMed2026

Magnetic nanoparticle-mediated genetic transformation and gene editing system in loquat (Eriobotrya japonica).

Loquat (Eriobotrya japonica Lindl.) is a valuable subtropical fruit tree whose genetic improvement has been significantly constrained by the absence of an efficient genetic transformation system. Although Agrobacterium-mediated transformation is the most widely used method, it proves ineffective in loquat due to the species' recalcitrance to in vitro regeneration. Pollen-based transformation offers a promising alternative by bypassing the need for tissue culture. However, the pollen wall poses a major physical barrier to the uptake of exogenous DNA. In this study, we investigated magnetic nanoparticle (MNP)-mediated transformation as a novel strategy for loquat. We confirmed that loquat pollen contains tricolporate apertures with diameters ranging from 3.0 to 5.0 &#x3bc;m, which are structurally suitable for the entry of MNPs-DNA. Based on this finding, we developed and optimized a transformation protocol using polyethyleneimine-coated Fe3O4 nanoparticles to deliver genetic material into loquat pollen grains. Using this approach, we successfully generated stable transgenic loquat lines, including both overexpression and gene-edited mutants. To our knowledge, this is the first report of successful MNP-mediated pollen transformation in a woody plant species. This work establishes a robust and efficient genetic transformation platform for loquat, providing a valuable tool for functional genomics and molecular breeding, as well as a potentially applicable strategy for other recalcitrant woody plants.

Eriobotrya↗