Search Results (435)

Banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4), poses a severe threat to global banana production, and breeding resistant cultivars remains the most effective control strategy. Mutation breeding, including radiation mutagenesis and somaclonal variation, has become a primary approach for developing resistant germplasm in triploid Cavendish bananas. However, whether secondary bud-sport selection from resistant somaclonal lines inadvertently compromises original resistance mechanisms at the molecular level remains poorly understood. In this study, we generated 44 mutants from Baxi jiao via ⁶⁰Co γ-irradiation and selected five lines with distinct phenotypic variations. We also collected somaclonal variant lines GCTCV-218, GCTCV-119, GCTCV-105, their bud-sport derivatives (NK_No.1, NTH, RK_No.1), and the radiation-induced resistant mutant ‘Zhongre No.1’. Using whole-genome resequencing and transcriptome analysis, we systematically compared the genetic and transcriptomic outcomes of these breeding strategies. Radiation mutagenesis induced substantial genomic structural variations and generated novel expression patterns of defense-related genes. In contrast, while bud-sport derivatives of GCTCV-218 remained genetically similar to their parent, they exhibited significant downregulation or loss of key resistance gene expression, particularly PR-1 family members. Our findings reveal that phenotype-driven somaclonal selection can inadvertently erode original resistance mechanisms, and we recommend prioritizing radiation mutagenesis for developing banana cultivars with stable and durable resistance to Foc TR4. Full article

The Manila clam (Ruditapes philippinarum) is an economically important bivalve widely cultured in coastal aquaculture systems of China. However, the genome-wide genetic background and germplasm differentiation of geographically distinct populations remain unclear, which constrains germplasm conservation and the development of selective breeding programs. In this study, 50 individuals from five representative coastal populations (QZ, ZZ, ZP, CL, and NH) in China were subjected to whole-genome resequencing, producing 126.67 Gb of clean data and 92,593,087 SNPs after stringent filtering. Genetic diversity analyses showed that nucleotide diversity (π) ranged from 0.2453 to 0.2588, observed heterozygosity (Ho) from 0.1316 to 0.1492, and expected heterozygosity (He) from 0.2303 to 0.2435, with the CL population exhibiting relatively lower diversity. Population differentiation was low to moderate, with pairwise F_ST values ranging from 0.0454 to 0.0557. Principal component analysis, neighbor-joining phylogenetic analysis, and Admixture clustering consistently indicated limited population structure and extensive genetic admixture. TreeMix analysis further revealed directional gene flow among populations. Rapid linkage disequilibrium decay and predominantly positive Tajima’s D values suggested relatively stable demographic histories. Despite low genome-wide differentiation, combined F_ST and nucleotide diversity ratio analyses identified localized selective sweep signals in specific genomic regions. These results provide preliminary genome-wide insights into genetic diversity, population connectivity, and candidate localized differentiation signals in R. philippinarum. Given the low sequencing depth, the findings should be interpreted as population-level observations that require further validation using higher-depth genomic datasets before being applied to germplasm conservation and selective breeding programs. Full article

Fat deposition in laying hens involves lipid synthesis, transport, storage, and allocation across multiple tissues, yet the metabolic links between abdominal fat (AF) and egg yolk (EY) lipid deposition remain unclear. Here, we integrated whole-genome resequencing data with untargeted metabolomic profiles from the liver, duodenum, ileum, cecum, and serum of 248 purebred Rhode Island Red hens at 100 weeks of age. We estimated metabolite-explained variance (me²) for 22 fat deposition-related traits, evaluated metabolite heritability, and combined Spearman correlation analysis with bidirectional generalized summary-data-based Mendelian randomization (GSMR) to identify shared metabolites and pathways associated with AF and EY traits. The me² showed clear tissue specificity, with the liver, serum, and duodenum showing significant explanatory signals for 77.3% (17/22), 72.7% (16/22), and 68.2% (15/22) of fat-related traits. Liver-, AF-, and body weight-related traits showed stronger metabolomic explanatory signals, with significant proportions of 71.4–100.0%, 28.6–100.0%, and 100.0% across tissues, respectively, whereas EY-related traits showed more restricted and tissue-specific associations (0–33.3%). Correlation analysis identified liver-enriched AF–EY shared metabolites (e.g., NADPH, cholesteryl sulfate, N6,N6,N6-trimethyllysine), most of which showed opposite association patterns between AF- and EY-related traits. Bidirectional GSMR prioritized 20 candidate metabolites with opposite putative effects on AF and EY traits, including CDP-choline, phosphorylcholine, and allantoin. Pathway integration highlighted fructose/mannose metabolism, glycerophospholipid metabolism, ABC transporters, folate/one-carbon metabolism, amino acid metabolism, and energy metabolism as core components of the AF–EY shared network. These findings reveal tissue-specific and shared metabolic bases of fat deposition and identify candidate metabolic signatures associated with lipid partitioning between abdominal fat and egg yolk in laying hens. Full article

The Tianbao melon (Cucumis melo subsp. agrestis) is a highly valued regional horticultural crop, yet its sustainable development is severely constrained by a narrow genetic base and widespread varietal admixture in the market. In this study, a panel of 32 Tianbao melon accessions was systematically evaluated by integrating field-based phenotypic assessment with genome-wide single-nucleotide polymorphism (SNP) analysis via whole-genome resequencing. Phenotypic analysis based on ten quantitative traits revealed low overall morphological variability, indicating limited discriminatory power of morphological traits alone. In contrast, 173,497 high-quality SNPs uncovered substantial hidden genetic differentiation, partitioning the accessions into four distinct genotypic groups. Notably, accessions TB-17 and TB-27, though nearly indistinguishable morphologically, exhibited clear genetic divergence in both phylogenetic and principal component analyses. Furthermore, a panel of 20 core SNPs with conserved flanking sequences was selected, generating unique molecular fingerprint profiles for all 32 accessions and achieving high discriminatory resolution (pairwise differences ranging from 10 to 13 SNPs). These findings demonstrate that the integration of phenotypic and genome-wide SNP data provides a robust framework for genetic diversity assessment and DNA fingerprinting in Tianbao melon, offering a scientific basis for cultivar identification, intellectual property protection, and precision breeding to support sustainable development of the regional melon industry. Full article

The Ili River Valley and adjacent Xinjiang regions contain introduced cattle, local cattle, and yak and therefore provide a useful regional system for examining cattle–yak genomic differentiation. Using whole-genome resequencing data from 79 individuals, we analyzed Angus (ANG), Simmental (SIM), Holstein (HOL), Xinjiang Brown Cattle (XH), Kazakh Cattle (KAZ), Altay White-headed Cattle (AWH), and yak (WY). The six domestic cattle groups were merged into a composite domestic cattle group (PTN, n = 69) and compared with WY (n = 10). Sequencing generated 2996.28 Gb of raw data and 2939.56 Gb of clean data. Alignment to the Bos taurus ARS-UCD1.2 reference genome yielded mapping rates of 96.71–99.78% and depths of 5.98×–17.26×. Genome-wide PTN-WY comparisons showed extremely high differentiation: the median weighted F_ST was 0.846 and the 95th percentile was 0.943. The joint F_ST–π scan identified 832 candidate highly differentiated windows and 533 unique ENSBTAG gene IDs, whereas the low-differentiation set contained only five windows and three genes. The longest contiguous highly differentiated segments were located on chromosomes 26, 29, 8, 21, and 7. WY had the highest median Tajima’s D (1.173) and the slowest LD decay, while KAZ had the lowest median Tajima’s D (0.345) and the fastest LD decay. Treemix supported non-tree-like covariance components, and PSMC indicated broadly similar deep-time demographic profiles across individuals. Overall, the dominant genomic signal between PTN and WY is deep phylogenetic divergence, with locally enhanced highly differentiated segments superimposed on this background. These segments were enriched for functions and pathways related to reproductive behavior, neuroendocrine regulation, circadian rhythm, and membrane transport, but they are not interpreted here as recent within-species selective sweeps. The results provide a cautious regional framework for conservation and breeding of bovine genetic resources in Xinjiang. Full article

Pumpkin (Cucurbita spp.) is a globally significant vegetable crop known for its high nutritional value and remarkable phenotypic diversity. Yet, the surge in new cultivar releases has overwhelmed traditional morphological descriptors, creating critical gaps in variety purity control and breeders’ rights enforcement. Despite the established utility of SNP markers as the gold standard for genetic analysis, a dedicated high-resolution molecular database for modern pumpkin cultivars remains unavailable. To address this gap, we conducted whole-genome resequencing (WGS) on 94 representative pumpkin cultivars (spanning C. moschata, C. maxima, and C. pepo). Clean reads were mapped to the Cucurbita maxima reference genome. We employed a stringent pipeline to identify genomic variants and utilized STRUCTURE software, Principal Component Analysis (PCA), and Neighbor-Joining (NJ) trees to evaluate population stratification. Linkage disequilibrium (LD) decay and DNA fingerprinting barcodes were also developed. A total of 8,873,150 high-quality variants were identified, including 7,345,007 SNPs and 1,528,143 InDels, with an average SNP density of 21,281.50 SNPs/Mb. Population analysis consistently categorized the 94 cultivars into two primary subpopulations (G1 and G2). The first two PCs accounted for 74.06% of the total genetic variance. Further analysis revealed that G1 possessed a more complex genetic architecture and slower LD decay compared to G2, suggesting distinct selection histories. Finally, we screened for highly informative biallelic SNPs to construct a DNA fingerprinting database, enabling precise sample discrimination through unique chromatic barcodes. This study fills a critical gap in pumpkin genomics by establishing a high-density SNP database and a robust fingerprinting system. These resources provide a definitive tool for variety certification, seed purity testing, and the advancement of molecular-assisted breeding in pumpkin. Full article

To explore the genetic diversity and evolutionary differentiation of Mastacembelus armatus from the headwaters of the Dongjiang and Ganjiang Rivers, we performed whole-genome resequencing on three populations, including Xunyushui (XW) and Jiuqu River (DN) from the Dongjiang River source as well as Taojiang River (XF) from the Ganjiang River source. We analyzed population structure, genetic differentiation, nucleotide diversity (π), pairwise FST, linkage disequilibrium, kinship, and neutrality tests (Tajima’s D, Fu and Li’s D). A total of 209.05 Gbp of clean data were obtained, with high quality and reliable alignment. Average nucleotide diversity (π) was higher in XW (0.00490 ± 0.00248) and DN (0.00478 ± 0.00312) and lower in XF (0.00463 ± 0.00158). Pairwise FST values revealed moderate differentiation between XW and DN (FST = 0.12) and strong divergence between XF and the other two populations (FST = 0.19 and 0.17). Neutrality tests showed no significant deviation from neutrality. XW and DN exhibited positive values, indicating stable demography, while XF showed negative values, suggesting a tendency of population expansion. Phylogenetic, admixture, and PCA analyses supported that all three populations belonged to one evolutionary clade with two ancestral components. XF showed the slowest linkage disequilibrium decay and distant kinship, indicating a small effective population size. Significant genetic divergence was primarily driven by geographic isolation and limited gene flow. This study reveals the genetic diversity and differentiation pattern of M. armatus and provides a genomic basis for its conservation and management. Full article

Sweet cherry (Prunus avium L.) is an economically important fruit species with considerable genetic variability, particularly among autochthonous cultivars. This study aimed to evaluate the genetic diversity and population structure of six indigenous sweet cherry cultivars from the Ohrid region in North Macedonia using whole-genome resequencing. A total of approximately 2.27 million single-nucleotide polymorphisms (SNPs) and 263 thousand insertions and deletions (InDels) were identified, indicating high genomic variability. Population structure and phylogenetic analyses revealed two distinct genetic clusters among the studied cultivars. The Ohridska bela cultivar showed the highest level of genetic differentiation, highlighting its importance as a valuable genetic resource. Functional annotation of genetic variants demonstrated significant variability in genes associated with flowering time, dormancy, and stress response, suggesting adaptation to local environmental conditions, while genes related to fruit ripening were highly conserved. Additionally, the rapid linkage disequilibrium decay confirmed the high genetic diversity within the population. These findings emphasize the importance of Macedonian autochthonous sweet cherry germplasm for breeding programs, conservation efforts, and future adaptation to changing environmental conditions. Full article

Background: Copy number variation (CNV) is an important class of structural variations (SVs) that contribute to phenotypic diversity and environmental adaptation in animals. However, large-scale population-level analyses of CNVs in goats remain limited. This study aimed to comprehensively characterize CNVs and explore their potential roles in economically important traits in Chinese goat populations. Methods: Whole-genome resequencing data from 151 individuals representing 17 Chinese goat breeds were analyzed. CNV regions (CNVRs) were identified across the genome, followed by gene annotation, functional enrichment analysis, and population differentiation analysis based on V_ST. Results: A total of 5636 CNVRs were identified from 151 individuals of 17 goat breeds, including 1365 duplication CNVRs, 4241 deletion CNVRs, and 30 both CNVRs. These CNVRs collectively spanned 2.38% of the goat genome. A total of 912 protein-coding genes overlapped with these CNVRs. After Bonferroni correction, GO enrichment analysis showed that these genes were significantly enriched in terms related to transmembrane transport, cell projection, ion binding, and ATP binding. Population differentiation analysis identified several CNVR-associated candidate genes with potential relevance to production or adaptive traits, including ABCC4, APOL3, EXOC3L4, ERG, B4GALT1, and FTH. Conclusions: This study provides a comprehensive CNVR map of Chinese goat populations and offers insights into the genetic basis of economically important traits, contributing to future genetic improvement and breeding strategies in goats. Full article

The genus Cucurbita (pumpkin), encompassing C. maxima and C. moschata, is agriculturally and nutritionally significant globally. Herein, we re-sequenced 146 germplasm accessions (51 C. moschata and 95 C. maxima) to characterize genomic variations and identify loci associated with critical traits. Population structure analysis revealed four distinct subgroups: G1 (C. moschata), and G2–G4 (C. maxima), the latter classified by rind color (green, gray, and red, respectively). A genome-wide association study (GWAS) analysis identified 26 loci associated with eight fruit quality traits (e.g., rind color, pulp thickness, starch content) and leaf traits. Selective sweep analyses revealed 18 overlapping signals between the GWAS and selective regions, highlighting convergent evolution in starch content, pulp thickness, and water content driven by artificial and natural selection. We further validated these key fruit quality candidate genes, confirming that starch, cellulose, and pulp trait-related genes exhibited genotype-specific expression consistent with the quality divergence between CMO-X and CMO-E. Notably, C. moschata exhibited higher β-carotene and water content, while C. maxima showed higher starch content, reflecting divergent selection pressures. For leaf traits, 13 loci associated with leaf length were found, including LL9.2/LW9.1 with Cmax09G001045, which regulates leaf size. A novel haplotype in Cmax09G001045 explained the small-leaf phenotype of ‘Cuili 5’. This study provides a comprehensive genomic variation map of C. maxima and C. moschata, clarifies the genetic bases of key agronomic traits, and sheds light on their domestication and selection history, offering valuable resources for molecular breeding and crop improvement. Full article

Body measurement traits are a direct production indicator reflecting growth status and guiding genetic selection. Identifying molecular markers associated with body measurement traits could accelerate animal breeding programs. The Yanqi horse, an important indigenous breed in Xinjiang, is primarily distributed in the Bayingolin Mongol Autonomous Prefecture. However, molecular markers linked to body measurement traits in Yanqi horses remain uncharacterized. In the present study, whole-genome resequencing was performed on 183 Yanqi horses, yielding 13,366,672 single-nucleotide polymorphisms (SNPs) after quality control. A genome-wide association study on withers height, body length, heart girth, and cannon bone circumference was conducted using a mixed linear model implemented in GEMMA, with population structure and relatedness controlled using principal components and a genomic kinship matrix. Bonferroni-adjusted thresholds (p < 1 × 10⁻⁷ for significant associations; p < 1 × 10⁻⁶ for suggestive associations) were applied to minimize false positives. A total of 185 single-nucleotide polymorphisms were significantly associated with body measurement traits and 359 candidate genes were annotated within 200 kb upstream and downstream of the significant loci. Among these, five genes, GABRB1, FIGN, GABRA4, ENSECAG00000051747, and COX7B2, may be implicated in the growth and development of Yanqi horses. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses indicated that these genes are primarily involved in cytoskeletal structures within muscle cells, regulation of the actin cytoskeleton, and neuroactive ligand–receptor interaction pathways. In summary, this study presents novel markers and candidate gene sets associated with body measurement traits in Yanqi horses, offering valuable insights for functional gene investigations and presenting substantial potential for accelerating the breeding of Yanqi horses. Full article

Stem lodging significantly reduces soybean yield stability, particularly under dense planting and intercropping systems. Stem breaking strength is a key component of lodging resistance, but its genetic basis remains incompletely understood. In this study, an F₂ population consisting of 167 individuals derived from a cross between nanxiadou25 (NXD25, high stem breaking strength) and Shiyuehuang (SYH, low stem breaking strength) was analyzed using bulked segregant analysis with whole-genome resequencing (BSA-Seq) to identify loci associated with stem breaking strength. The trait showed broad quantitative variation in the F₂ population, ranging from 20.1 to 673.7 N. Two extreme bulks were constructed using 30 plants with the highest values and 30 plants with the lowest values. QTL-seq detected 21 candidate intervals at the 95% confidence level, among which, three major loci on Chr07, Chr13, and Chr16 exceeded the 99% threshold and were designated qBR7.2, qBR13.1, and qBR16.1. By integrating large-effect SNP/InDel variation, marker development, RNA-seq profiling, and qRT-PCR validation, nine candidate genes were retained for further study, and three marker-linked genes were highlighted as high-priority candidates. RNA-seq identified 9617 differentially expressed genes between the two parents. In addition, three co-dominant InDel markers, Chr07_01, Chr13_17, and Chr16_83, showed phenotype-consistent polymorphism in extreme F₂ individuals. These findings provide valuable loci, candidate genes, and molecular markers for soybean lodging-resistance breeding. Full article

To assess the current genetic status of cultured populations of the speckled blue grouper (Epinephelus cyanopodus) in China and to provide a scientific basis for the selective breeding of superior strains, this study utilized single nucleotide polymorphism (SNP) loci screened via whole-genome resequencing technology to analyze the genetic diversity and population genetic structure of 90 E. cyanopodus samples collected from six cultured populations in southeastern China. Comprehensive evaluation of various genetic diversity parameters indicated that all populations exhibited moderate genetic diversity with minor differences among them. Population structure analysis revealed weak genetic differentiation among populations, suggesting that anthropogenic introduction and translocation practices may be the primary factors contributing to the unclear population genetic structure. Additionally, this study identified a number of key genes associated with energy metabolism, muscle development, and environmental adaptation. The findings provide important theoretical foundations for the broodstock selection and scientific aquaculture of E. cyanopodus. Full article

Accurate pedigree reconstruction is essential for genetic evaluation, inbreeding control, and family management in aquaculture breeding programs. In sturgeon, extremely high fecundity and communal rearing during early developmental stages often lead to the loss of family information, making reliable full-sib family assignment a critical challenge. In this study, we developed a machine learning-based framework for full-sib family assignment using simulated genotype datasets and whole-genome resequencing data from Russian sturgeon. Simulation analyses across five machine learning algorithms showed that training set size and marker density were the primary determinants of assignment accuracy. When at least 10 individuals per family were included in the training set, mean identification accuracy exceeded 99% across all evaluated scenarios, and exceeded 99.9% for all methods except XGBoost. In contrast, performance declined when the marker number was reduced to 200. At moderate marker densities (500–1000 markers), performance remained stable, with mean identification accuracy around 99% even when only 3–4 individuals per family were included in the training set. Validation using whole-genome resequencing data (sequencing depth ranging from 9.43× to 11.86×) from 582 individuals representing 19 full-sib families of Russian sturgeon confirmed the simulation findings, with several algorithms achieving assignment accuracies exceeding 99%. These results demonstrate that machine learning provides an accurate and robust approach for full-sib family assignment using genome-wide single nucleotide polymorphism (SNP) data. The proposed framework offers an effective solution for pedigree reconstruction and family identification in sturgeon breeding populations lacking reliable pedigree records. Full article

Plant height is a key component of sunflower (Helianthus annuus L.) plant architecture. It strongly influences lodging resistance, mechanized harvestability, and yield stability. However, the genetic basis of plant height in sunflowers remains underexplored. This study aimed to develop an F₂ population consisting of 715 individuals from a cross between the dwarf inbred line 150A and the tall inbred line PT326. Bulked segregant analysis coupled with whole-genome resequencing was employed to identify loci associated with plant height. Using three complementary analytical methods, a major quantitative trait locus, qPH15, was identified on chromosome 15. This locus was subsequently fine-mapped, using Kompetitive Allele Specific PCR (KASP) markers and recombinant screening in F₂ and F₃ populations, narrowing it to a 64.66-kb region containing three annotated genes. Among these, HanXRQr2_Chr15g0707451, which encodes an NAC transcription factor designated HaNAC7, was identified as the most promising candidate gene. Haplotype analysis of HaNAC7 across 148 sunflower accessions revealed 4 polymorphic sites defining 6 haplotypes with substantial differences in plant height. The shortest haplotypes, Hap2 and Hap3, were associated with reduced plant height and were predominantly found in Asian germplasm. These findings suggest that HaNAC7 is a strong candidate gene underlying qPH15 and provide useful molecular markers and favorable allelic resources for improving sunflower plant architecture. Full article