Search Results (287)

Several single-nucleotide polymorphisms (SNPs) across the lipoprotein lipase (LPL) gene have been found to be associated with dyslipidemia and obesity. Several InDels and SNPs in exon 1, intron 2, and intron 7 have been reported; however, their association with lipid parameters and body mass index (BMI) remains unclear. Here, we aimed to investigate the relationship among LPL variants, lipid levels, and BMI in a Kuwaiti population. Sanger sequencing was performed on three targeted regions of the LPL gene. Based on the minor allele frequency, Hardy–Weinberg equilibrium, and linkage disequilibrium, five SNPs were selected and genotyped in a cohort of 688 Kuwaiti samples to investigate their association with lipid levels and BMI. A total of 30 variants (6 InDels and 24 SNPs) were identified; of them, 5 SNPs (rs1800590, rs74377536, rs8176337, rs303, and rs304) were selected for their association with BMI and lipid levels. The G-allele of rs8176337 was found to be associated with increased BMI (β = 1.41; 95% confidence interval = 0.22–2.60; p = 0.02). In addition, an association was observed for rs303 and rs304 with both cholesterol and LDL (p < 0.05). Overall, our results demonstrate an association between LPL variants and lipid levels, and the observed association between rs8176337 and BMI was novel. Full article

The date palm (Phoenix dactylifera L.) is a key crop in the arid regions of North Africa and the Middle East, with substantial socioeconomic value. Although multiple genome assemblies have been generated using next-generation sequencing (NGS) technologies, they primarily focus on Middle Eastern cultivars, leaving North African varieties unrepresented. This study aims to address this gap by sequencing and assembling the first genome of a North African date palm using Illumina sequencing technology. We present a draft genome assembly of the elite Tunisian variety Deglet Nour. By comparing it with the Barhee BC4 reference genome, we identify key genetic variants, including single nucleotide polymorphisms (SNPs) and insertions/deletions (INDELs), potentially associated with ripening processes and fruit quality. This work expands the genomic resources for date palm research, particularly for North African cultivars, and provides new insights into the nucleotide-level variability of the genes linked to key agronomic traits. Full article

The current work focused on the molecular selection of Oreochromis niloticus with improved growth performance through marker-trait associations between SNPs within the growth hormone gene (GH) and growth performance. A total of 155 fish of the same age were collected from three locations (Lake Brullus (B), the River Nile at El-Qanater El-Khairia (Q), and Lake Nasser (A)). The selected individual progenies were evaluated through gene expression analysis for growth, inflammatory, nervous, and immune-related genes. A total of nine SNPs and three InDels were significantly associated with morphometric characteristics. The phenotypic variance (R²) of the detected SNPs ranged between 2.6% and 36%. The best populations were A and Q, as they recorded the best growth performance and harboured the highest number of SNPs and InDels, in addition to a significant increase in body weight and length. Furthermore, their progenies documented the most promising gene expression patterns of all tested genes. The current research highlights the importance of molecular selection and the potential use of population-specific SNPs in tilapia breeding programs. Full article

Perkinsiodendron macgregorii, an endangered Chinese endemic tree with high ornamental and ecological value, faces extinction threats due to its poor natural regeneration and habitat degradation. Despite the urgent need for its conservation, the genetic architecture and population differentiation mechanisms of this taxon remain poorly understood, hindering science-based protection strategies. We conducted comprehensive chloroplast genomic analyses of 134 individuals from 13 natural populations to inform science-based conservation. The chloroplast genome (158,538–158,641 bp) exhibited conserved quadripartite organization, with 113 functional genes and elevated GC contents in IR regions (42.99–43.02%). Population-level screening identified 741 SNPs and 678 indels, predominantly in non-coding regions (89.8%), with three distinct phylogeographic clades revealing north-to-south genetic stratification. The northern clade (Clade A) demonstrates the highest haplotype diversity and nucleotide diversity, followed by the southern clade (Clade C), while the central clade (Clade B) exhibits signals of genetic erosion (Tajima’s D > 3.43). Based on the genetic diversity distribution and phylogenetic tree of extant P. macgregorii, we inferred that the northern populations represent ancestral groups, while the Wuyi Mountains region and Nanling Mountains region served as glacial refugia. It is imperative to implement in situ conservation in these two regions. Additionally, ex situ conservation should involve collecting seed from representative populations across all three clades and establishing isolated cultivation lines for each clade. These findings establish a genomic framework for conserving endangered plants. Full article

The eri silkworm Samia cynthia ricini (S. ricini) is an economically and scientifically significant lepidopteran species, though its genomic resources have remained limited. Here, we present a chromosome-level genome assembly for S. ricini generated through integrated long-read, short-read, and Hi-C sequencing data. The final 456.16 Mb assembly spans 14 chromosomes, exhibiting 98.5% BUSCO completeness and a 48.51% repetitive content. Functional annotation of the 15,729 protein-coding genes against five major databases (NR, SwissProt, Pfam, GO, and KEGG) revealed a maximum annotation rate of 92.71%, demonstrating high gene set quality. Comparative genomics with B. mori uncovered conserved syntenic blocks interspersed with chromosomal fusion/fission events and inversions. We further identified 4.27 million SNPs, 1.02 million InDels, and 53,367 SVs, establishing the first comprehensive variation map for this species. These genomic variations provide a foundation for marker-assisted breeding programs and trait association studies. All the genomic resources and interactive visualization tools were integrated into the SilkMeta database. This study establishes S. ricini as a pivotal resource for comparative lepidopteran genomics and accelerates molecular breeding programs for this agriculturally valuable insect. Full article

The genetic diversity of cattle plays a crucial role in adapting to environmental challenges and enhancing production traits. While research has predominantly focused on single nucleotide polymorphisms (SNPs), small indel and structural variants (SVs) also significantly contribute to genetic variation. This study investigates the distribution and functional impact of insertions and deletions in five Hubei indigenous cattle breeds. A total of 3,208,816 deletions and 2,082,604 insertions were identified, with the majority found in intergenic and intronic regions. Hotspot regions enriched in immune-related genes were identified, underscoring the role of these variants in disease resistance and environmental adaptation. Our analysis revealed a strong influence of transposable elements (TEs), particularly LINEs and SINEs, on genomic rearrangements. The variants were also found to overlap with economically important traits, such as meat quality, reproduction, and immune response. Population structure analysis revealed genetic differentiation among the breeds, with Wuling cattle showing the highest differentiation. Notably, the NOTCH2 gene was identified as a candidate for regional adaptation due to its significant differentiation across populations. These findings provide valuable genomic resources for enhancing breeding programs, aiming at improving the productivity and resilience of indigenous cattle breeds in China. Full article

Pummelo (Citrus maxima) is an ancestral species that has given rise to several major citrus varieties, such as sweet orange (C. x aurantium var. sinensis) and grapefruit (C. x aurantium var. paradisi). This species is also cultivated and its fruit consumed, particularly in Asia. Over the course of evolution, the allogamous reproduction of pummelos and the absence of asexual multiplication have contributed to its diversification. To assess its phenotypic diversity and the chemical composition of leaf and peel essential oils, genetic analysis using DNA markers is an essential prerequisite to ensure the identity and if varieties belong to this species. Fifty-eight accessions classified as grapefruits or pummelos were analyzed using 42 SSRs, 4 Indels, and 36 SNP markers. Based on the allelic composition of these markers, 20 cultivars were detected belonging to pummelos, 18 cultivars to grapefruits, and 11 were interspecific hybrids. The grapefruit inter-cultivar SSR diversity is null. The genetic origin of five interspecific hybrids is elucidated. The level of phenotypic diversity and of essential oil composition corroborate the modes of diversification, with high levels for those resulting from crosses and very low levels for the group of grapefruit mutants. Only the characteristics of breeding selection (pulp color, acidity and aspermia) are variable in grapefruits. In the composition of leaf essential oils (LEOs), nine profiles were detected in grapefruits based on variations in six compounds (neral, geranial, β-phellandrene, γ-terpinene, (E)-β-ocimene, and β-pinene). The seven interspecific hybrids involving pummelo as one parent show particular LEO profiles but without specific compounds, with the exception of p-cymenene which is present only in Wheeny. The diversity of peel essential oils in pummelos is lower, but variations in γ-terpinene, β-pinene, limonene, and myrcene make it possible to define seven profiles. With genetic verification the chemical and phenotypic diversity of the two species, pummelo and grapefruit, revealed in this study can be used as a reference for behavior in a specific environment. Full article

Nuclear receptor subfamily 4 group A member 1 (NR4A1) plays a crucial role in regulating various physiological processes. As gene mining for reproductive traits is essential, this study aimed to investigate the mRNA expression, genetic variation, and association of the NR4A1 gene with goat litter size. We examined the mRNA expression levels of the NR4A1 gene in eight different tissues of female Shaanbei White Cashmere (SBWC) goats (n = 6). Then, a novel 11-bp insertion/deletion (InDel) variant was genotyped in 1136 SBWC goats, 87 SNPs were identified through resequencing (n = 120), and selection signal analysis was undertaken. The NR4A1 gene was expressed in all examined tissues, including the ovary and the oviduct, suggesting its role in goat reproduction. Both the 11-bp InDel and 13 SNP variants showed significant association with litter size. Additionally, four potential transcription factor binding sites were predicted within the insertion allele, which may contribute to increased litter size. Selection signal analysis revealed strong pressure on the NR4A1 gene region in the Cashmere goat population. These findings suggest that NR4A1 is a promising candidate gene for improving litter size in goats and could be utilized as a genetic marker in breeding programs. Full article

During the solid-state brewing process of traditional Chinese Baijiu, lactic acid is the most abundant organic acid, which inhibits the growth and metabolism of Saccharomyces cerevisiae. To reveal the lactic acid tolerance mechanism of S. cerevisiae, the growth, metabolic performance, and antioxidant enzyme activity of S. cerevisiae NCUF309.5-44 and S. cerevisiae NCUF309.5 were measured under 4% (v/v) lactic acid stress. Additionally, whole-genome re-sequencing and transcriptomic analyses were performed to identify genetic variations and differentially expressed genes between the two strains under lactic acid stress. The results showed that, compared to the original strain, S. cerevisiae NCUF309.5-44 could adapt to the lactic acid stress faster, with a superior utilization rate of reducing sugar and a 6.43-fold higher ethanol production at 16 h. The strain primarily activated the GSH/GPx system, resulting in a 37.29% lower intracellular ROS content. A total of 1087 SNPs and 698 InDels were found between the strains, with 384 genes significantly upregulated and 254 genes downregulated in the S. cerevisiae NCUF309.5-44 under lactic acid stress. S. cerevisiae NCUF309.5-44 responded to lactic acid stress by activating the pheromone response pathway and the cell wall integrity pathway. Meanwhile, the capacity of strains to maintain the cell membrane and proton extrusion was strengthened. Additionally, its glycolysis/gluconeogenesis metabolism was also enhanced. All these mechanisms collectively contributed to improving the lactic acid tolerance of S. cerevisiae NCUF309.5-44. These findings not only enhanced our understanding of lactic acid tolerance mechanisms of S. cerevisiae NCUF309.5-44 but also paved the way for the application of this strain in optimizing Baijiu production. Full article

Chinese Cymbidium are prized for their ornamental beauty, ecological significance, and economic value. However, genomic resources crucial for breeding studies within this genus remain scarce, which has hindered the identification of key genes controlling economically important traits and posed challenges for conservation efforts. We performed a comprehensive identification of whole-genome simple sequence repeats (SSRs) and single-nucleotide polymorphism (SNP) markers using the restriction-site associated DNA sequencing (RADseq) on C. goeringii and C. faberi. A total of 49,640 SSR loci were identified across both species, with an average density of 12.7 SSRs/Mb. Among these, 17,637 SSRs were common to both C. goeringii and C. faber, while 17,676 and 14,329 SSRs were uniquely identified in C. goeringii and C. faberi, respectively. Additionally, we identified 405,416 SNPs and 26,870 InDels, with average densities of 105.2/Mb and 6.5/Mb. Furthermore, we validated two SSRs (located at Chr01:78857480-78860461 and Chr01:93382182-93384869) and developed an efficient method for identifying hybrids among the progeny resulting from crosses between C. goeringii and C. faberi. We also validated two SNP markers that showed a close association with the petal and lip length using Sanger sequencing. Our findings revealed that the Chr01_99657375 SNP achieved 73% predictive accuracy for identifying long-petal/lip phenotypes. The results are expected to greatly benefit marker-assisted breeding efforts in Cymbidium orchids and lay a solid foundation for the molecular breeding process of improving flower shape traits in orchid plants. Full article

Forensic genetics has experienced remarkable advancements over the past decades, evolving from the analysis of a limited number of DNA segments to comprehensive genome-wide investigations. This progression has significantly improved the ability to establish genetic profiles under diverse conditions and scenarios. Beyond individual identification, forensic genetics now enables the inference of physical traits (e.g., eye, hair, and skin color, as well as body composition), biogeographic ancestry, lifestyle habits such as alcohol and tobacco use, and even the transfer of genital microbiomes post-coitus, among other characteristics. Emerging trends point to a future shaped by the integration of cutting-edge technologies, including CRISPR-Cas systems, artificial intelligence, and machine learning, which promise to further revolutionize the field. This review provides a thorough exploration of forensic genetics, tracing its evolution from its foundational methods (past) to its diverse modern applications (present) and offering insights into its potential future directions. Full article

Cycads, renowned as “living fossils”, are among the most ancient extant seed plants, playing a crucial role in understanding plant evolution and sex differentiation. Despite their importance, research on their genetics and sex differentiation remains scarce. This study investigates three species, represented by six samples, collected from various regions in Fujian Province, China, using whole-genome resequencing on the Illumina platform. The sequence data underwent rigorous quality control, alignment, and variant detection, focusing on SNP and InDel distribution and annotation. Among the studied species, Cycas revoluta exhibited the highest number of SNPs and the greatest heterozygosity values. Based on SNP data, phylogenetic trees and principal component analysis revealed distinct clusters, with the three C. revoluta samples forming one cluster, while the two C. szechuanensis samples and the C. taiwaniana sample were grouped separately. Gene function using COG and GO annotations, and KEGG enrichment analysis, all highlighted differences in genomic structure and functional gene distribution between male and female cycads. Notably, genes associated with sex differentiation, such as MADS-box and auxin-responsive protein genes, were shown, while other transcription factors showed distinct annotations and enrichment patterns based on sex. This study improves our understanding of genetic variation, evolutionary relationships, and gene enrichment in cycads, providing a foundation for conservation, cultivation, and insights into sex differentiation mechanisms in these ancient plants. Full article

The Ghd7 gene in rice plays a crucial role in determining heading date, plant height, and grain yield. However, the variations in Ghd7 and their functional implications across different rice accessions are not fully understood. Based on the release of a large amount of rice genome data in recent years, we investigated Ghd7 through pan-genome analysis of 372 diverse rice varieties and figured out the structural variations (SVs) in the Ghd7 locus. However, due to the high cost of pan-genomes, most genomes are based on next-generation sequencing (NGS) data now. Therefore, we developed a method for identifying SVs using NGS data and Polymerase Chain Reaction (PCR) based on the results of pan-genome analysis and identified 977 accessions carrying such SVs of Ghd7. Furthermore, we identified 46 single-nucleotide polymorphisms (SNPs) and one insertion-deletion (InDel) in the coding region of Ghd7. They are classified into 49 haplotypes. Notably, a splice-site mutation in haplotype H6 causes aberrant mRNA splicing. Using prime editing (PE) technology, we successfully restored the functional of Ghd7 in Yixiang 1B (YX1B), delaying the heading date by approximately 16 days. This modification synchronized the heading date between YX1B and the restorer line Yahui 2115 (YH2115R), enhancing the hybrid rice seed production efficiency. In conclusion, our findings highlight the potential of integrating pan-genomics and precision gene editing to accelerate crop improvement and enhance agronomic traits. Full article

Expanding soybean planting is vital for food security both in China and globally. The 50° N latitude serves as the northern boundary of major soybean regions. However, enhancing the adaptability of soybean to photothermal conditions enables the potential to extend cultivation to higher latitudes and altitudes. Understanding the genetic basis of super-early maturity of soybean is crucial to achieving this goal. In this study, 438 soybean germplasms collected from high-latitude regions were evaluated in Heihe (HH) (50°15′ N, 127°28′ E, 154 m), Beijicun (BJC) (53°28′ N, 122°21′ E, 295 m) and Labudalin (LBDL) (50°15′ N, 120°19′ E, 577 m). Using resequencing data, we analyzed natural variation and haplotypes in 35 key genes associated with flowering time and maturity. The results showed that the relative maturity groups (RMGs) for BJC, HH, and LBDL were −1.0, 0.0, and −1.2, respectively. Among the 35 genes analyzed, 23 had identical allelic variations, while 12 genes exhibited 19 SNPs and four InDels. Functional mutations were identified in E1, E2, E3, and E4. Notably, all cultivars carried the e1-as allele of E1, which is likely critical for high-latitude adaptation. Additional mutations included a single-base substitution in E2 (16142 A > T) and E3 (5203 C > T), causing premature codon termination, along with frameshift mutations in E4 (3726 and 4099) and E3 (2649). Haplotype analysis revealed significant differences in growth stages among nine gene haplotypes. The higher frequency of early-maturing haplotypes in BJC and LBDL highlights the role of gene accumulation in soybean adaptation. These findings offer valuable insights for improving soybean maturity and expanding its cultivation in high-latitude regions of China. Full article

Background: Cucumber (Cucumis sativus L.) is an important economic crop worldwide. Response regulators (RRs) play crucial roles in plant growth, development, and responses to both biotic and abiotic stresses. Methods: Combined analysis of 182 re-sequencing and transcriptome datasets was conducted to investigate CsRR variations, with subsequent RT-qPCR experiments confirming its functional significance. Results: In this study, 18 CsRR genes were identified and classified into three groups according to their protein structures: A-ARRs (3), B-ARRs (8), and PRRs (7). Resequencing uncovered critical mutations (non-synonymous SNPs, frameshift, and stop-gain variants) in CsRR genes. Transcriptome data revealed that five genes responded to abiotic stress and four responded to biotic stress. CsPRR1 was upregulated in both resistant and susceptible lines at five dpi, downregulated in resistant plants at nine dpi, and showed no significant difference at 11 dpi. CsPRR2 was consistently upregulated in both lines at 5, 9, and 11 dpi. CsPRR3 was upregulated in resistant lines at nine dpi but downregulated at 11 dpi. CsARR8 was significantly downregulated in both lines at 9 and 11 dpi. Notably, CsPRR2 demonstrated dual functionality related to (i) the regulation of immature fruit skin color via a stop-gain InDel and (ii) resistance to Foc, as the gene was upregulated in both resistant and susceptible lines after inoculation with the pathogen. Conclusions: This study integrated resequencing and transcriptomic data to comprehensively characterize CsRR genes, establishing a foundation for further exploration of their functional mechanisms in cucumber. Full article