Search Results (242)

Despite its ecological and economic importance, Hampala macrolepidota (Cyprinidae: Smiliogastrinae) remains taxonomically debated, having undergone historical reclassifications across multiple taxonomic ranks. These challenges highlight the urgent need for integrative genomic analyses to resolve its phylogeny and assess genome-wide diversity, establishing a baseline for effective management and conservation. In this study, the newly assembled mitogenome of H. macrolepidota from within its native range in Lake Dibawah, West Sumatra, Indonesia, was sequenced. The mitogenome spanned 17,104 bp, encoded 37 genes and a control region, and exhibited a nucleotide composition biased toward adenine and thymine. The protein-coding genes (PCGs) predominantly utilized ATG as the initiation codon and showed a higher proportion of hydrophobic compared to hydrophilic amino acids. The nonsynonymous (Ka) and synonymous (Ks) substitution ratios were below ‘1’, which indicates negative selection on most of the PCGs within Hampala and other Smiliogastrinae species. Mitogenome-wide analysis revealed overall high intraspecific genetic diversity (≥2.7%) in the native Indonesian population compared to mainland populations in Southeast Asia. The Bayesian and maximum-likelihood phylogenetic analyses elucidated matrilineal evolutionary relationships within the subfamily Smiliogastrinae, with the Hampala species forming a monophyletic cluster. The present mitogenome-based phylogenetic topologies also supported the taxonomic placement of several species in the revised classification, which previously were classified under the genera Puntius and Barbus, respectively. Additionally, the investigation of partial mitochondrial COI and Cytb genes further elucidated the population genetic structure of H. macrolepidota across Southeast and East Asia. The observed genetic divergence (0–4.2% in COI and 0–4.5% in Cytb), together with well-resolved phylogenetic clustering and the presence of both shared and distinct haplotypes among Indonesian samples, provides strong evidence for long-term population isolation and local adaptation. These patterns are most plausibly driven by historical hydrological dynamics, paleo-drainage connectivity, and persistent geographic barriers that have structured population divergence over time. In addition, this study emphasizes the need to generate mitogenomes of seven additional Hampala species from Southeast Asia to better understand their evolutionary patterns. Further, broader sampling of wild H. macrolepidota populations across their biogeographical range will be essential to strengthen understanding of their genetic diversity and guide effective conservation strategies. Full article

Drought and salt stresses are major abiotic factors limiting maize yield. Lignin, a key cell wall component, plays a crucial role in boosting plant stress resistance. Cinnamyl alcohol dehydrogenase (CAD) is a vital enzyme at the late stage of lignin biosynthesis; however, a systematic study of its functions in abiotic stress responses and its potential for genetic improvement in maize remains lacking. In this study, we conducted the first comprehensive, multi-dimensional analysis of the maize ZmCAD gene family, including gene identification, evolutionary relationships, protein interaction networks, and stress-responsive expression patterns. We identified 9 ZmCAD members that showed significant functional divergence in evolution, structure, and expression patterns. Expression analysis revealed complex, tissue-specific responses of ZmCAD genes to drought and salt stress, with ZmCAD6 strongly induced by drought. Importantly, through haplotype analysis of 157 waxy maize inbred lines, we successfully identified an elite haplotype (H3) of ZmCAD6 that is significantly associated with improved drought tolerance in maize. This study not only clarifies the functional differentiation mechanisms of the ZmCAD gene family but also provides the identified elite ZmCAD6-H3 haplotype as a valuable genetic resource and precise target for molecular breeding aimed at enhancing drought tolerance in maize. Full article

The Asian tiger mosquito (Aedes albopictus) is an important vector of arboviruses, including dengue, chikungunya, and Zika. Its rapid global expansion has been facilitated by climate change and human activities. Phylogenetic studies of Ae. albopictus have largely relied on mitochondrial cytochrome c oxidase subunit 1 (COX1) and NADH dehydrogenase subunit 5 (ND5) markers, while the utility of cytochrome b (CYTB) remains underexplored. We collected Ae. albopictus from 13 sites in seven provinces of South Korea and analyzed COX1, ND5, and CYTB sequences. Genetic diversity indices were calculated, and phylogenetic relationships were reconstructed using maximum-likelihood trees and haplotype networks with a dataset obtained from GenBank. COX1 revealed 46 haplotypes, including six novel variants, with the highest diversity in southern coastal regions such as Busan and Suncheon. ND5 showed limited variation, with only two haplotypes. CYTB revealed three haplotypes, including region-specific variants in Busan and Wonju, supporting its role as a complementary marker. The Busan haplotype H41 bridged domestic and international lineages, suggesting Busan as a likely entry point. This study demonstrates that integrating COX1, ND5, and CYTB improves the resolution of Ae. albopictus phylogeography in Korea and highlights the need for continued molecular surveillance to guide vector control strategies. Full article

Deep-sea hydrothermal vent fauna is often regarded as highly endemic, although exceptions have been reported. We examined genetic connectivity across broad spatial scales within the alvinocaridid genus Rimicaris, which has undergone substantial adaptive radiation worldwide. We analyzed six Rimicaris species using three genetic markers, cytochrome c oxidase subunit I (COI), 16S ribosomal rRNA gene (16S), and histone h3 (H3), and complete mitogenomes, employing newly generated sequences combined with publicly available sequence data. A genetic tree and haplotype networks were constructed, and divergence analyses were performed. Three clades of paired Rimicaris species were identified, each made up of taxa from different oceanic regions but showing relatively low COI divergence (0.35–1.90%). In Clade I, Rimicaris chacei and Rimicaris hybisae are morphologically similar and exhibit bidirectional gene flow, implying a dispersal route between the Mid-Atlantic Ridge (MAR) and the Mid-Cayman Spreading Center (MCSC). In Clade II, Rimicaris exoculata and Rimicaris kairei are morphologically, genetically, and ecologically distinct, reflecting restricted connectivity between the MAR and the Carlsberg Ridge (CR)–Central Indian Ridge (CIR). In Clade III, Rimicaris variabilis and Rimicaris cf. variabilis differ in nutritional strategies, showing a unidirectional dispersal route from the CIR to the southwestern Pacific (SWP), but morphological data to distinguish them are currently lacking. Some Rimicaris lineages maintain connectivity across distinct oceanic regions while others still form unique regional populations. This finding highlights the need for conservation strategies that incorporate both global-scale connectivity and regional endemism, rather than treating individual vent ecosystems as a single homogeneous management unit. Full article

Kongshan cattle is an indigenous breed from Sichuan Province, China, characterized by their excellent meat quality, high fertility, strong disease resistance, and remarkable environmental adaptability. However, their genomic diversity has not been systematically studied. In this work, we performed whole-genome sequencing of 30 Kongshan cattle from a breeding farm and integrated these data with 113 representative commercial and indigenous cattle breeds worldwide to investigate their population structure and genetic diversity. We further analyzed the ancestral contributions to the development of the breed. The population structure revealed that Kongshan cattle possess four types of ancestral components: East Asian indicine (0.5974), East Asian taurine (0.3464), European taurine (0.0483), and Indian indicine (0.0079). The population also exhibits high nucleotide diversity, second only to pure East Asian indicine cattle. We inferred the ancestry of each variable site in the genome and, in combination with integrated haplotype score analysis, identified candidate genes related to meat quality (ME1, ENPP2, GPD2, PDZRN4, and TMTC2), immunity (MCM6, MAP3K6, PIP4K2A, CDC6, CDC25B, PTAFR, ZC3H10, and NEK6), and environmental adaptability (KCNJ15, BECN1, AOC2, DUSP5, and ST3GAL4). These findings provide valuable insights into the evolutionary history and ancestral origins of Kongshan cattle and contribute to the broader understanding, conservation, and sustainable utilization of indigenous Chinese cattle genetic resources. Full article

(1) Background: Backcross (BC) breeding is a key technology of crop improvement, yet its efficiency largely depends on the precise assessment of the genetic background recovery. Conventional molecular marker-assisted techniques suffer from inadequate genomic coverage or an inability to resolve true chromosomal structure. (2) Methods: To address major issues in maize BC breeding, we devised a G2H block-scanning strategy. This approach converts high-density point markers into haplotype blocks, enabling precise evaluation of the genetic background in backcross progenies. A key innovation is the CFDI, which quantifies the distribution of unrecovered fragments, allowing for visual tracking of chromosomal recombination and identification of ideal individuals with both a high genetic background recovery rate and few small fragments retention. (3) Results: We validated the accuracy and effectiveness of the G2H strategy across multiple backcross generations. Through enabling a precise “point-to-line-to-area” panoramic assessment of genetic background, G2H provides a powerful tool for developing ideal breeding materials with pure genetic background and minimized linkage drag. (4) Conclusions: Notably, this strategy significantly shortens the breeding cycle by 2–3 generations compared to conventional background assessment methods, thereby accelerating precision molecular design breeding in crops. Full article

This review presents soybean responses to drought, heat, and salinity within a signal–transcript–chromatin framework. In this framework, calcium/reactive oxygen species and abscisic acid cues converge on abscisic acid-responsive element binding factor (ABF/AREB), dehydration-responsive element binding protein (DREB), NAC, and heat shock factor (HSF) families. These processes are modulated by locus-specific chromatin and non-coding RNA layers. Base-resolved methylomes reveal a high level of CG methylation in the gene body, strong CHG methylation in heterochromatin, and dynamic CHH ‘islands’ at the borders of transposable elements. CHH methylation increases over that of transposable elements during seed development, and GmDMEa editing is associated with seed size. Chromatin studies in soybean and model species implicate the reconfiguration of salt-responsive histone H3 lysine 27 trimethylation (H3K27me3) in G. max and heat-linked H2A.Z dynamics at thermoresponsive promoters characterized in Arabidopsis and other plants, suggesting that a conserved chromatin layer likely operates in soybean. miR169–NF-YA, miR398–Cu/Zn Superoxide Dismutases(CSD)/copper chaperone of CSD(CCS), miR393–transporter inhibitor response1/auxin signaling F-box (TIR1/AFB), and miR396–growth regulating factors (GRF) operate across leaves, roots, and nodules. Overexpression of lncRNA77580 enhances drought tolerance, but with context-dependent trade-offs under salinity. Single-nucleus and spatial atlases anchor these circuits in cell types and microenvironments relevant to stress and symbiosis. We present translational routes, sentinel epimarkers (bisulfite amplicons, CUT&Tag), haplotype-by-epigenotype prediction, and precise cis-regulatory editing to accelerate marker development, genomic prediction and the breeding of resilient soybean varieties with stable yields. Full article

Alfalfa (Medicago sativa L.) is a high-nutritive-value forage crop that provides livestock with abundant protein and essential nutrients. Breeding elite cultivars with superior quality has become a major goal in modern alfalfa improvement. This study systematically evaluated 12 quality-related traits under field conditions using a diverse panel of 176 alfalfa accessions and investigated the genetic basis underlying these traits. Phenotypic analysis revealed variability across all traits, with coefficients of variation ranging from 2.56% to 15.72%. Based on multi-trait clustering analysis, 16 accessions with overall superior quality were identified. Genome-wide association studies (GWAS) detected 45 significant single nucleotide polymorphisms (SNPs) and 12 structural variants (SVs). Within the associated genomic regions, eight candidate genes were prioritized. RT-qPCR validation indicated that three of these genes (Msa.H.0301430, Msa.H.0290550, and Msa.H.0313490) negatively regulate quality traits, while one gene (Msa.H.0479570) acts as a positive regulator. Haplotype analysis further revealed a positive correlation between the number of favorable haplotypes and phenotypic performance. Genomic prediction (GP) achieved accuracies ranging from 0.71 to 0.86 for the traits when incorporating the top 5000 SNPs identified from GWAS. This study provides valuable insights into the genetic architecture of quality-related traits in alfalfa and lays a solid foundation for future molecular design breeding. Full article

The genetic diversity and the genetic structure of widely distributed species are meaningful to explore plant adaptation mechanisms to the environment. This study investigated the effects of climatic factors on the genetic diversity and structure of Agropyron michnoi, and modeled its large-scale potential distribution shifts. A. michnoi was studied under different temperature and precipitation gradients on grassland of Inner Mongolia and North China using rbcL and trnL-F sequences. The results showed that the genetic diversity of A. michnoi was low and significantly influenced by precipitation. AMOVA results showed that genetic variation in A. michnoi occurred mainly within the population, accounting for 70.57%. Both Mantel test and partial Mantel test support a significant IBE pattern. STRUCTURE and UPGMA analyses divided the populations into two clusters. Population 10 was closely related to one cluster. The haplotype network shows only one cluster H1, and all other haplotypes have evolved from H1, which is likely the ancestral haplotype. A. michnoi, as a widely distributed species. Originating from a primitive haplotype. Large scale precipitation caused genetic differentiation into two genetic branches. The MaxEnt model predicts that A. michnoi’s distribution has expanded since the Last Glacial Maximum and will shift to higher elevations in the future due to climate change. Full article

The ABCB subfamily, a subset transporter of the ATP-binding cassette (ABC) superfamily, is vital for various plant life processes, especially in the transport of polar auxin and brassinosteroids. Although ABCB transporters have been characterized in diverse plant species, their specific functions in wheat remain largely unexplored. In this study, we identified 99 TaABCB members in wheat and categorized them into four groups based on their conserved domains and phylogenetic relationships. These members were found to be unevenly distributed across all 21 wheat chromosomes. We conducted a comprehensive genome-wide analysis encompassing gene structure, protein motifs, gene duplication events, collinearity, and cis-acting elements. Transcriptome analysis revealed that different TaABCB members displayed distinct expression patterns under phosphate starvation stress. Notably, we discovered that TaABCB7 might play a role in regulating wheat’s phosphate starvation. Crucially, we pinpointed an elite haplotype, H001, of the candidate gene TaABCB7, which has been progressively selected and employed in wheat breeding improvement programs. Overall, this study enhances our comprehensive understanding of TaABCB members and offers a potential gene resource for molecular marker-assisted selection breeding in wheat. Full article

Genetic diversity and population differentiation of an aquaculture population of Banggai cardinalfish (Pterapogon kauderni) introduced and maintained in Phang Nga province, Southern Thailand (A1, N = 45) was examined using control region (CR) polymorphism in comparison with three wild transplanted populations from Gilimanuk Bay (Bali), collected in 2019 (W1, N = 25), Banyuwangi (East Java), collected in 2024 (W2, N = 22), and Gilimanuk Bay (Bali), collected in 2024 (W3, N = 39). In total, 14 haplotypes were identified. Haplotype 3 was found in all populations, while haplotype 4 was found in wild transplanted but not in aquaculture populations. The remaining (12) haplotypes were private haplotypes. Of these, five private haplotypes (H5, H6, H7, H8 and H9) were found only in the A1 population. Moreover, genome-wide single nucleotide polymorphisms (SNPs) in P. kauderni from A1 (N = 21), W2 (N = 15) and W3 (N = 15) populations were also analyzed by Specific Locus Amplified Fragment-Sequencing (SLAF-Seq). In total, 648,378 SNPs were identified. By analyzing both mitochondrial DNA and SNP markers, significant genetic differences were clearly found between farmed and wild transplanted populations of P. kauderni. Reduced genetic diversity was found in a farmed population from genome-wide SNPs but not mtDNA analyses. Full article

Artemisinin-based combination therapies (ACTs) remain the cornerstone of malaria treatment in Rwanda, but the emergence of drug resistance threatens their efficacy. This study conducted genomic surveillance of Plasmodium falciparum isolates collected in Kigali between October 2021 and June 2023 to assess resistance markers. Using Oxford Nanopore Technology and Sanger sequencing methods, we analyzed 250 clinical isolates focusing on mutations in the pfcrt, pfmdr1, pfdhfr, pfdhps, and Pfkelch13 genes. Resistance-associated mutations were highly prevalent: pfcrt 76T (26%) and pfmdr1 184F (72.8%) were common, indicating continued lumefantrine pressure. All isolates carried mutations in pfdhfr and pfdhps, with the IRNI-SAEAA and IRNI-SAEGA haplotypes found in 45.6% and 24.8% of samples, respectively, suggesting sustained antifolate resistance. Pfkelch13 mutations were present in 50.4% of isolates, including validated R561H (25.6%), A675V and candidate P441L mutations. Novel haplotypes, including K189T + R561H (24.8%), were identified for the first time in Rwanda. The BTB/POZ domain mutation H384R was observed in 6.4% of isolates, raising questions about its potential functional role. These findings highlight complex and evolving resistance patterns and emphasize the urgent need for continued molecular surveillance and functional validation to inform malaria control strategies in Rwanda. Full article

Given that type 2 diabetes mellitus is common in several ciliopathies, the NME7 gene (non-metastatic cells 7), encoding a recognized member of the ciliome, was studied in connection with glucose metabolism. The aim was to find out whether the variability in the gene is associated with the response to administered glucose during the 3 h oral glucose tolerance test. The study included 1262 individuals with different levels of glucose tolerance. Glycemic curves were categorized according to their shape as monophasic, biphasic, triphasic, and more complex multiphasic. The analysis showed a significant association of five linked NME7 polymorphisms with the biphasic course of the glycemic curve, a shape that has been shown to be metabolically protective. Specifically, minor alleles of rs4656659 and rs2157597 in combination with wild-type alleles of rs10732287, rs4264046, and rs10800438 were more frequent within the biphasic category. Moreover, haplotype analysis confirmed higher insulin sensitivity in carriers of this specific haplotype. In conclusion, a cluster of five linked NME7 polymorphisms showed an association with a biphasic glycemic curve. Considering the health benefits of the biphasic curve in terms of glycoregulation and taking into account the demonstrated link of the NME7 haplotype with insulin sensitivity, variability in the NME7 gene represents another piece of the complex mosaic influencing healthy energy processing. Full article

Shanlan rice, a unique drought-resistant rice germplasm resource in Hainan Province, China, holds significant potential for rice genetic improvement and breeding innovation. However, its genetic diversity and significance in rice breeding remain inadequately explored. This study conducted a comprehensive analysis of phenolic acid profiles and antioxidant properties in the brown rice of 84 Shanlan rice accessions. It was revealed that colored Shanlan rice accessions exhibited significantly higher total phenolic content (249.00–2408.33 mg gallic acid equivalents per 100 g of rice flour (mg GAE/100 g)) and antioxidant capacity (DPPH: 680.39–809.63 micromoles of Trolox equivalent per 100 g (μmol TE/100 g); ABTS: 529.93–1917.77 μmol TE/100 g) compared to white-grained varieties. High-performance liquid chromatography (HPLC) analysis identified eight phenolic acids in the bound fractions, among which the sinapic acid (55.08 μg/g) and vanillic acid (11.72 μg/g) were predominant, accounting for over 60% of total bound phenolic acid content. A genome-wide association study (GWAS) identified 84 significant loci associated with these phenolic-related traits. A major quantitative trait locus (QTL) on chromosome 7 for free phenolic content, total phenolic content, flavonoids, and DPPH activity was co-located at the Rc gene locus, a key regulator of red pericarp pigmentation and proanthocyanidin biosynthesis. Haplotype analysis identified ten haplotypes in Rc, with the haplotype H002 showing the highest antioxidant capacity. Another QTL on chromosome 11 was associated with p-coumaric, vanillic, and sinapic acids, although no significant difference was observed in haplotype analysis. These results highlight Rc as a key genetic factor underlying antioxidant properties in rice, while other loci require further validation. This research provides a foundation for breeding health-benefit, drought-tolerant rice cultivars using Hainan’s unique germplasm. Full article

Bacterial wilt, caused by Ralstonia solanacearum, is a major constraint to tomato production globally. To uncover resistance loci and develop efficient molecular tools for breeding, we conducted disease phenotyping over two growing seasons, which revealed consistent variation in resistance and moderate broad-sense heritability (H² = 0.22–0.28), suggesting a genetic basis. A genome-wide association study (GWAS) was performed on a diverse panel of 267 tomato accessions, evaluated against two R. solanacearum strains. A major resistance locus was identified on chromosome 12, with the strongest association observed at SNP S12_2992992, located within a gene encoding a leucine-rich repeat (LRR) receptor-like protein. Haplotype analysis indicated that the resistance-associated allele is relatively rare (~13.5%) in the population, underscoring its potential value in breeding programs. Functional validation in an F₂ population derived from a cross between the susceptible ‘Seedathip6’ and the resistant ‘Hawaii 7996’ confirmed that the TT genotype at S12_2992992 was significantly associated with enhanced resistance. A Kompetitive Allele Specific PCR (KASP) marker was developed for this SNP, facilitating cost-effective and high-throughput selection. Collectively, these findings establish S12_2992992 as a robust and functionally informative marker, offering a valuable tool for accelerating bacterial wilt resistance breeding in tomato through marker-assisted selection. Full article