Linkages between core microbiome and functional convergence during artificially selecting microbial communities for benzotriazole degradation.

Enhanced approach for gears-bearings defect diagnosis based on optimized artificial neural network model and features selection graphical technique

Detection, isolation and molecular characterization of Senecavirus A in porcine semen: Implications for control programs.

A multi-omics atlas of testicular development in Leiocassis longirostris: dynamic regulation of spermatogenesis.

Integrated transcriptome and metabolome analysis reveals new insights into acclimation of sea cucumber Stichopus monotuberculatus to hypo-osmotic stress.

The maturation process in salmonids, particularly Salvelinus fontinalis , under artificial breeding conditions is associated with phenomena that reduce production yield. Triploid populations are not affected by gonadal maturation, suggesting that triploidy could mitigate these losses. However, the impact of triploidy on meat quality requires thorough evaluation. This study compares diploid males, diploid females, and triploid individuals from pre-mature spring and mature autumn populations. Post-mortem changes, sensory attributes, and nutritional characteristics of S. fontinalis fillets were assessed and correlated with biometric traits and fillet yield indices. Multivariate statistical analysis revealed significant differences between diploid and triploid groups in both seasonal trials, with fillet yield being the primary discriminating factor. Conversely, no significant differences were observed among experimental groups in meat quality parameters, including rigor index (%), pH dynamics, water-holding capacity, texture, and sensory evaluation. Given that diploid fish exhibit yield losses due to maturation while triploid fish maintain comparable meat quality, triploidy represents a promising strategy for improving production efficiency in brook trout aquaculture. • Triploidy in brook trout prevent maturation without reducing fillet quality. • Fillet yield is the main difference between diploid and triploid trout. • Meat quality traits show no significant variation across ploidy groups. • Triploid trout improve production efficiency in aquaculture systems.

Selection signatures on the autosomes and the X chromosome in the prolific Belclare sheep breed.

Vector control remains a key strategy in reducing mosquito-borne disease transmission. Understanding mosquito species distribution, diversity, and breeding habitat ecology is crucial for effective surveillance and to define targeted vector control interventions. We conducted a study to understand the diversity and habitat preferences of mosquito larvae across Cambodia during the rainy season from July to September 2024. Mosquito larvae were collected from a variety of breeding habitats located around households across all 25 provinces. The national sampling was conducted once during the rainy season in urban (city) and rural (village) areas within each province. Collected larvae were reared to adult emergence in the insectarium for morphological identification, further confirmed with molecular techniques. We found 37 mosquito species in the households, of which 12 are vectors of pathogens such as dengue and Japanese encephalitis viruses, and Plasmodium species, representing 93% of all collected mosquitoes. Larvae were predominantly found in anthropized artificial breeding habitats, accounting for 98% of all larvae collected. Notably, the two primary dengue vectors, Aedes aegypti and Ae. albopictus, were recorded from all 52 sampling locations. In addition, our study identified the presence of Aedes vittatus in 12 provinces, a new confirmed vector of dengue in Cambodia. We also recorded eight Japanese encephalitis vectors, with at least one species from all sampling sites. There were no statistically significant differences in larval mosquito biodiversity (relative abundance, number of species, Shannon and Simpson diversity indices) between cities and villages, with 15 species occurring in both environments, representing 41% of the species and 99% of all mosquitoes collected. The widespread and predominant presence of dengue and Japanese encephalitis vectors in every household confirms the endemic circulation of these diseases in Cambodia.

Grain protein content (GPC) is well-known to negatively influence the eating and cooking quality in rice. However, the genetic mechanism underlying the natural variation of GPC is very limited. Here, we identify GPC6 as a key determinant through genome-wide association analysis. GPC6 encodes a protein with a MYB-like domain, functioning as a transcriptional repressor to modulate the expression of storage protein synthesis genes (Alb1, Pro13b.5, RM1, OsGluB1b, OsGluB7) and two regulators (RISBZ1 and PDIL1-1). Further, one functional SNP (-1,471 T/C) in the GPC6 promoter was identified, which defines two haplotypes: high-expression GPC6T (Low protein) and low-expression GPC6C (High protein). Notably, the GPC6T allele has been subject to artificial selection in modern East Asian japonica rice varieties. Collectively, these findings provide a crucial foundation for understanding the genetic mechanisms underlying the rice GPC variation and an important target gene for quality improvement practice.

Plant flavor diversity arises from genomic variation across species and cultivars, yet the mechanisms linking natural genomic variation to flavor-related phenotypes remain insufficiently integrated. Here, we systematically review how diverse forms of genomic variation reshape the biosynthesis, transport, and accumulation of flavor-related metabolites, thereby driving diversification in sweetness, acidity, bitterness, piquancy, astringency, and aroma. We further integrate evidence from genomics, transcriptomics, metabolomics, and functional validation to outline a mechanistic framework linking genomic variation to the molecular and metabolic basis of flavor phenotypes. We then examine how artificial intelligence-assisted breeding and precision gene editing can accelerate the identification of causal variants and enable targeted improvement of flavor-related traits. This framework establishes plant flavor as a mechanism-based target for plant improvement, with broad implications for quality, nutrition, and sustainability.

Locomotion is both a result and an impetus of morphology; though their interplay is an essential part of natural speciation, almost all domesticated species have been selectively bred so that their morphology better suits human needs. Where many species have been bred for function, many fish in the aquarium trade have been bred for aesthetics. Domesticated male Betta splendens have been bred for their large fins and are available in many varieties, but there is a lack of literature investigating the possible effects of this artificial selection on their behavior. The exaggerated large caudal fins of domesticated Betta are an artificially selected trait that is absent in wild Betta species, leading to questions regarding the possible effects of this selection on locomotion. To measure the effects of fin morphology on swimming behavior, we used a mixed-sex sample of several varieties of B. splendens and the closely related species B. imbellis to obtain a wide phenotypic range. We found that morphological characteristics associated with caudal fin size had a significant negative relationship with burst swimming speed, with caudal fin area and propulsive area ratio explaining the most variation in speed when adjusted for species, sex, and intra-individual variation. These results are consistent with patterns seen in similar studies of other small ray-finned fish and raise questions of the mechanical and behavioral costs of selective breeding in a common aquarium fish.

Abstract Tomatoes are highly nutritious and represent one of the important vegetable fruits worldwide. Both historically and moving forward, genetic decoding and precision breeding remain fundamental to tomato improvement. Here, we summarize pivotal advances in decoding tomato genomes across domestication, improvement and evolution processes and provide a perspective on future breeding through precision design. In-depth population genetic studies have revealed how artificial selection systematically prioritized yield-related alleles at the cost of narrowing genetic diversity, especially at flavor-related loci–highlighting the urgent need to reconcile these trade-offs. Comparative genomics across species, viewed through an evolutionary lens, has uncovered critical insights into functional genes, deepening our understanding of the genetic architecture and regulatory mechanisms underlying key traits. Collectively, these advances have enabled precise identification and functional characterization of key genetic elements, paving the way for systematic re-domestication of tomato through precision genomic design. Looking ahead, more efficient and precise breeding strategies will be required to accelerate genetic gains in tomato in the coming decades. The integration of recent genomic advances, coupled with genomic selection and artificial intelligence, into genomic design breeding offers a transformative framework, unlocking unprecedented opportunities for developing highly flavorful and consumer-customized tomato varieties.

Population genomics and GWAS reveal genetic basis of shell traits in Manila clam (Ruditapes philippinarum).

The Dianthus spiculifolius chlorophyll-binding protein DsSep2 can be used as a genetic resource to create 'golden leaf' plants.

• ROH are valuable genomic tools for quantifying individual inbreeding and identifying regions under selection in livestock populations. • HRR are potentially maintained by balancing selection and linked to fitness-related traits, such as immunity and fertility. • Joint analysis of ROH and HRR enhances our understanding of genetic diversity patterns and supports the development of more sustainable breeding programs. • ROH and HRR have practical implications for managing inbreeding depression, maintaining adaptive genetic variation, and designing conservation strategies for local or endangered breeds. Advancements in high-throughput and cost-effective genotyping techniques, coupled with robust statistical methods, have greatly facilitated the investigation of the genomic architecture of farm animals. Runs of Homozygosity (ROH) and Heterozygosity-Rich Regions (HRR) are among the most informative features of animal genomes. ROH reflects inbreeding levels and historical population dynamics, whereas HRR may indicate loci under balancing selection that contribute to important functional traits. In this review, these two genetic parameters are described and discussed. We present an updated summary of ROH studies and applications in livestock species, as well as a comprehensive overview of the status of knowledge on HRR in livestock populations. Additionally, we discuss methods for the identification of ROH and HRR, and the insights they offer on the demographic history of animal species. We investigated the link between the presence, distribution, and specific characteristics of ROH and HRR, and the breeding and selection trajectories of farm animals. ROH- and HRR-abundant regions often harbour genes associated with economically important traits and local adaptation, underscoring the significant role of artificial and natural selection in shaping the genomic architecture of livestock. The increasing availability of high-density genotyping and whole-genome sequencing data allows for the finer-scale detection of ROH and HRR, enabling a more accurate identification of functionally relevant genomic regions. The future application of ROH and HRR in livestock genetics will likely move toward more integrated, data-driven strategies aimed at improving genetic resilience, productivity and sustainability.

Tyrp1 mutation drives color variation via melanin reduction and collagen deposition in Chinese soft-shelled turtles (Pelodiscus sinensis).

Comparative transcriptomic analysis of the hypothalamus between tumbler and white king pigeons.

Mice from lines selectively bred for innately high activity levels have altered behavioral and energetic responses to repeated sleep deprivation.

Ochetobibus elongatus (Kner) is a migratory fish found in the Yangtze River basin and areas south of it, and listed as a critically endangered (CR) fish on the China Red List of Vertebrates. To achieve group recovery and artificial breeding, this study investigated the dietary characteristics of O. elongatus based on high-throughput sequencing of its intestinal contents, and its digestive system morphology, and its histology. Results showed that the digestive system of O. elongatus lacked a stomach and mainly consisted of the oropharynx, pharyngeal teeth, esophagus, intestine, and anus. The gut index was 0.88, with clear segmentation of the foregut, midgut, and hindgut, and the visceral mass index was 7.35%. Histological analysis of the digestive system revealed the presence of keratinized dental plates or pharyngeal teeth in the pharynx, as well as a high density of taste bud cells in the soft palate of the oral cavity. The surface layer of the intestinal villi contained numerous mucous cells, with the average number of mucous cells per villus gradually increasing from the esophagus to the hindgut, and the foregut having the longest and most abundant mucosal folds. The esophagus exhibited well-developed circular and longitudinal muscle layers, while in the hindgut, both the circular and longitudinal muscle layers were slightly thicker than those in the midgut. High-throughput sequencing of the intestinal contents of O. elongatus revealed the following phyla based on 18S V4 meta-barcoding: Chlorophyta, Diatoms, Arthropoda, Basidiomycetes, and Ascomycetes, with the genus Hypophthalmichthys and algae being the main classifications. In contrast, based on COI meta-barcoding, the study newly identified the phyla Cnidaria and Mollusca, with the genera Chlorophyta, Scenedesmus, Pectinodesmus, and zooplankton such as Pseudodiaptomus. Metagenomic sequencing revealed that the gut microbiota at the phylum level was predominantly composed of Pseudomonadota, Ascomycota, Basidiomycota, Chytridiomycota, and Bacillota, with key genera including Cetobacter, Pseudomonas, Acinetobacter, Aeromonas, and Clostridium. This study indicates that O. elongatus is an omnivore with carnivorous tendencies. Basic biological research on O. elongatus is of great significance for the restoration of the population, artificial breeding, and the development of its artificially formulated feed. It also provides important data for the formulation of biodiversity conservation measures.

Sex determination and differentiation represent fundamental topics in reproductive biology. Sichuan taimen (Hucho bleekeri), a first-class national protected fish species in China, lacks obvious secondary sexual characteristics, making it challenging to distinguish sex without resorting to invasive methods such as dissection. This limitation presents a significant obstacle to both artificial breeding and conservation efforts for the species. Herein, we performed transcriptome and proteome sequencing to identify sex-biased genes of H. bleekeri. A total of 25258 significantly differentially expressed genes (DEGs) were identified in gonadal tissues, including 15071 up-regulated male-biased DEGs. Proteomics analysis identified 2937 differentially expressed proteins (DEPs). Integrated analysis identified several key DEGs, including sdY, CYP11A1, 3β-HSD1, CYP17A1, CYP11B, CYP19A1A, 17β-HSD1, and 17β-HSD8, in which CYP11A1, 3β-HSD1, CYP17A1, and CYP11B exhibited high expression in the testis. Furthermore, the cDNA sequence of the sdY gene was obtained, and in situ hybridization revealed that sdY is exclusively expressed in the Sertoli cells of the testis. In addition, one pair of sdY primers was designed to screen sex-linked markers, and the results confirmed that sdY can serve as a sex-specific marker in H. bleekeri. The present study would provide a foundation for future research on genes involved in sex determination, differentiation, and artificial breeding in H. bleekeri.