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PubMed2000

Use of microsatellite DNA markers to investigate the level of genetic diversity and population genetic structure of coconut (Cocos nucifera L.).

We have used eight pairs of simple sequence repeat (SSR) primers to analyse the genetic diversity in 130 individuals of coconut (Cocos nucifera L.) comprising 75 tall individuals and 55 dwarf individuals, representing 94 different coconut ecotypes throughout the world. A total of 51 alleles were detected, with an average of 6.4 alleles per locus. Fifty alleles were detected in tall coconuts (talls; mean alleles/locus 6.3) compared with only 26 (mean/locus 3.3) in dwarfs, and the average diversity value in talls (0.589) was also significantly higher than that in dwarfs (0.348). Using the eight SSRs we were able to uniquely discriminate 116 of the 130 individuals. A phenetic tree based on DAD (absolute distance) values clustered individuals into five groups, each mainly composed of either talls or dwarfs. These results provide evidence in support of previous hypotheses concerning the dissemination of coconut, as well as important new information for conservation and breeding purposes.

Cocos↗
PubMed2026

Genomic distribution characteristics and interspecific differences of microsatellite landscapes in Felidae.

BACKGROUND: Microsatellites within genomes play crucial roles in regulating gene expression, DNA replication, and chromosomal structure and function. Analyzing the composition and distribution patterns of microsatellites in closely related species not only reveals their evolutionary dynamics and adaptive mechanisms but also provides essential technical support for applications in genetic breeding, species conservation, and disease research. As one of the world's most captivating animal groups, the landscape patterns of microsatellites across feline genomes remain to be systematically characterized. RESULTS: This study utilized high-quality genomic data to conduct a systematic comparative analysis of microsatellite landscape distribution patterns across the genomes of 13 felid species. The findings revealed that microsatellite abundance and distribution exhibit species-specific characteristics, with a non-random genomic distribution and a negative correlation between microsatellite abundance and repeat length. The predominant distribution pattern followed the sequence: single > double > quadruple > triple > quintuple > sextuple nucleotide repeats. Microsatellite abundance peaked in intergenic regions, whereas trinucleotide repeats were more prevalent within exons. Coding regions showed a marked preference for trinucleotide and hexanucleotide repeats. Enrichment analysis of GO and KEGG pathways indicated that coding sequences containing microsatellites were primarily involved in transcription and translation processes. CONCLUSIONS: Our study elucidates the distribution patterns and characteristics of microsatellites across diverse feline species, providing significant insights into their evolutionary mechanisms and functional roles. Furthermore, these findings establish a valuable reference and foundational dataset for the future development of high-quality, species-specific microsatellite markers in felids.

Animals↗
PubMed2004

Semen collection and artificial insemination in the common piping guan (Pipile cumanensis cumanensis): potential applications for Cracidae (Aves: Galliformes).

The common piping guan (Pipile cumanensis cumanensis) is serving as a model for assisted reproductive techniques (ARTs) in Cracidae (Aves: Galliformes). Manual collection methods used in domestic birds and other exotics were modified to optimize quality and quantity of fresh semen samples. In addition, a method to subjectively assess semen quality on the basis of its color, clarity, and consistency was developed to serve as a tool when laboratory equipment is not available. In a species where only two eggs per clutch is typical, predictability of the date of the first egg is critical to ensure adequate inseminations before oviposition. An increase in both the distance between the female's pubic bones and degree of abdominal swelling indicated optimal time to initiate artificial insemination (AI) and allowed the number of semen samples used to fertilize the first egg in the clutch to be minimized while ensuring its fertility. In three separate AI trials, a total of four fertile eggs were produced, a first for cracids. Two of the four fertile eggs hatched successfully, and the chicks' parentages were confirmed using DNA fingerprinting. This study represents the first published account of the use of ARTs in Cracidae and forms the basis for future developments (e.g., AI of frozen-thawed semen) aimed at optimizing genetic management of cracids in ex situ breeding programs.

Animals↗
PubMed2005

Sustainable development of food production: a case study on scenarios for pig production.

To study future, sustainable production systems, a step-wise method was used to create three future scenarios for pig production based on different sustainability goals. The first scenario focused on animal welfare and the natural behavior of the animals. The second targeted low impacts on the environment and the efficient use of natural resources. The third scenario aimed at product quality and safety. Each scenario fulfilled different aspects of sustainability, but there were goal conflicts because no scenario fulfilled all sustainability goals. The scenarios were then parameterized. The environmental impact was calculated using the life-cycle assessment (LCA) methodology, and the economic cost was calculated from the same data set. The cost per kilo of pork was highest for the animal welfare scenario and similar for the other two scenarios. The environmental scenario had the lowest environmental impact, and the product-quality scenario the highest. The results are discussed based on different future priorities.

Animal Welfare↗
PubMed2026

[Genetic diversity analysis of Forsythia suspensa germplasm resources in Shanxi based on phenotypic traits and SNP molecular markers].

This study aimed to clarify the degree of fruit phenotypic variation and the characteristics of genetic diversity, population structure, and genetic differentiation of Forsythia suspensa resources in Shanxi, providing an important basis for germplasm conservation and breeding of superior varieties. A total of 46 F. suspensa fruits were collected, and 12 agronomic traits were measured and analyzed. The population genetic structure and genetic diversity of F. suspensa germplasm were evaluated using simplified genome sequencing technology. For the five quality traits of the 46 fruits, the Shannon-Wiener index ranged from 0.631 to 1.074, and the Simpson index ranged from 0.379 to 0.560. The seven quantitative traits exhibited abundant genetic variation, with coefficients of variation ranging from 9.764%(fruit shape index) to 45.494%(forsythin content). Principal component analysis reduced the 12 phenotypic traits to four factors, with a cumulative variance contribution of 74.547%. Sequencing data showed mean Q20 and Q30 values of 98.13% and 94.33%, respectively, with an average GC content of 35.95%. After filtering, a total of 12 347 327 high-quality single nucleotide polymorphism(SNP) loci were obtained. Based on these high-quality SNPs, principal component analysis, population structure analysis, and phylogenetic tree construction were carried out. The 46 germplasm resources were divided into four groups; however, grouping showed little relationship with geographic origin, and intermixing occurred among regions. Mantel test revealed a significant but weak positive correlation between phenotypic and genetic distances(r=0.159, P=0.001). At the molecular level, the four groups exhibited moderate genetic diversity overall, and the genetic differentiation index among populations ranged from 0.027 to 0.084, indicating low to moderate differentiation. The rich genetic diversity of the main phenotypic traits provides a solid material basis for screening superior germplasm and genetic breeding of F. suspensa.

Forsythia↗
PubMed2005

Breeding for societally important traits in pigs.

Pig breeding programs traditionally focus on the genetic improvement of production and reproduction traits that have a clear economic value. Because citizens and consumers increasingly attach value to traits that have little or no direct relationship to production costs or to the price of a product, pig breeding organizations want to pay more attention to societally important traits, such as the welfare and health of pigs, the ecological effects of pork production, and the healthiness and sensory quality of pork. Most societally important traits have an economic and a noneconomic value and are sufficiently heritable for effective genetic selection, although many genetic and phenotypic (co)-variances still have to be estimated. However, it often is not clear to a pig breeding organization how it may deal with the noneconomic value of breeding-goal traits. In this study, a retrospective selection-index method is proposed to obtain the proper weights for societally important traits in the breeding goal. First, the genetic-progress space for each breeding-goal trait is explored by increasing the weights, in a stepwise manner, to each societally important trait in the breeding goal, starting from zero. Subsequently, a pig breeding organization can adopt the resulting genetic-progress scenario that it considers most sustainable or most acceptable. The weights underlying the adopted scenario are considered to be the proper breeding-goal weights. The noneconomic value of each societally important breeding-goal trait is found by deducting its economic value from its obtained weight and is thereby expressed in monetary units. In addition to obtaining weights for societally important breeding-goal traits, the proposed method offers the possibility to estimate the societal costs of selecting for economic traits only, as well as the societal benefits and the economic costs of selecting for traits with a noneconomic value. The method is therefore a useful tool for the development of sustainable breeding goals. An example has been worked out for a sow-line breeding program.

Animal Husbandry↗
PubMed2006

Comparison of Vietnamese and European pig breeds using microsatellites.

This study characterized autochthonous pig breeds of Vietnam and compared them with breeds from other regions. A total of 343 animals were considered from 5 indigenous pig breeds of Vietnam (Muong Khuong, Co, Meo, Tap Na, and Mong Cai), 2 exotic breeds kept in Vietnam (Landrace and Yorkshire), 3 European commercial breeds (German Land-race, Piétrain, and Large White), the Chinese breed Meishan, and the European Wild Boar. Each individual was genotyped for 20 selected polymorphic microsatellite loci. The Vietnamese autochthonous breeds showed higher degrees of polymorphism, allelic diversity, and heterozygosity than the other pig breeds. Also, large genetic diversity was observed across the area of distribution, with village-specific subpopulations, which led to significant inbreeding coefficients. As expected, genetic distances showed large differences among European-based, Chinese, and Vietnamese indigenous breeds and reflected the geographical distribution of breeds. In comparison with the European breeds, the Vietnamese indigenous pig breeds harbored a considerable amount of genetic diversity and, therefore, will be of significance for livestock bioconservation.

Animals↗
PubMed2002

Temperature effect on the immune defense functions of Arctic charr Salvelinus alpinus.

The Arctic charr Salvelinus alpinus is an endangered fish species in Finland, and thus farming is carried out mainly for stocking purposes. Farmed charr are susceptible to infection with atypical Aeromonas salmonicida (aAS). Losses of valuable brood stock will severely reduce the genetic diversity of stocked charr. No commercial vaccines are available to prevent aAS infection, and vaccines against furunculosis (caused by typical A. salmonicida, tAS) do not protect the charr against aAS infection. The effects of a metabolizable oil-adjuvanted, bivalent vaccine (containing killed aAS and A. salmonicida salmonicida bacteria) on the immune system of 1 yr old hatchery-reared charr originating from Lake Inari in Northern Finland were examined. Fish vaccination in Finland generally takes place either from October to November or from February to April, when the water temperature is low (1 to 3degrees C). The water temperature starts to increase in mid-May. Therefore, we also investigated whether post-vaccination (p.v.) temperature had an influence on the immune system of this cold-water fish species. The fish were immunized intraperitoneally at 2.9 degrees C at the end of April. After 52 d, during which the water temperature increased from 2.9 to 10.0 degrees C, the charr were exposed to 1 of 3 test temperatures: 10.3, 14.1 or 18.1 degrees C. Prior to vaccination, and 49, 75 and 103 d p.v., several immune parameters were measured in both unvaccinated and vaccinated charr. Vaccination induced a significant anti-aAS-specific antibody response, and increased plasma lysozyme activity at all p.v. temperatures. The haemolytic activity of the complement system was unaffected either by vaccination or p.v. temperatures. There was a slight positive correlation between p.v. temperature and lysozyme activity of the charr. The significant increase in lysozyme activity took place in vaccinated charr in the first 49 d p.v. as water temperatures increased from 2.9 to 10 degrees C. Furthermore, the highest activity of lysozyme in the plasma was observed 49 d p.v. Our results indicate that a rise in water temperature above 10 degrees C does not significantly enhance the vaccination response of charr. This could be one reason why farmed Arctic charr, which are well adapted to a cold climate, are highly susceptible to aAS infection in the summer.

Aeromonas↗
PubMed2026

Chromosome-Level Genome Assembly and Annotation of the Chinese Lizard Gudgeon (Saurogobio dabryi).

The Chinese lizard gudgeon (Saurogobio dabryi) is an economically important freshwater species within the Cyprinidae family, abundant in the middle and lower reaches of the Yangtze River and its adjacent basins. As a promising species suitable for aquaculture in China, the lack of genomic resources has rendered the genetic breeding and conservation research. Here, we present the first chromosome-level genome assembly of S. dabryi using PacBio HiFi long reads, short reads, and Hi-C sequencing data. The final assembly reaches a total size of 1.09 Gb and Hi-C scaffolding anchors 99.55% of the assembled contigs onto 25 chromosomes, with a scaffold N50 reaching 43.15 Mb. The final genome assembly shows a BUSCO completeness of 98.39%. We annotated 659.55 Mb repetitive sequences and 26,036 protein-coding genes, 99.47% of which are functionally annotated. Comparative phylogenomic analysis clarifies the phylogenetic position of Saurogobio within Gobioninae. This high-quality genome provides a critical genetic basis for exploring cyprinid phylogeny, benthic adaptive evolution, genetic improvement, and conservation efforts of S. dabryi.

Saurogobio dabryi↗
PubMed2026

First Report and Integrated Characterization of Aeromonas veronii Associated with the Protected Fish Diptychus maculatus in Xinjiang, China.

Aeromonas veronii is a widely distributed opportunistic aquatic pathogen associated with diseases in freshwater fish. Despite the ecological and conservation significance of Diptychus maculatus, a protected cold-water fish inhabiting high-altitude ecosystems, information regarding its associated bacterial communities remains limited. This study aimed to isolate and characterize A. veronii recovered from D. maculatus and provide baseline information on its occurrence and phenotypic characteristics. Eight bacterial isolates were recovered from various tissues, including skin, gills, eye, intestine, dorsal fin, body kidney, gonad, and spleen of randomly sampled fish individuals from Xinjiang, China. Phenotypic and biochemical characterization, together with 16S rRNA sequencing, supported their identification as A. veronii, while gyrB analysis of a representative isolate provided additional species-level confirmation. Antimicrobial susceptibility testing revealed a consistent multidrug-resistance phenotype among all isolates. The isolates were susceptible to enrofloxacin, cefotaxime, ceftriaxone, and florfenicol. Intermediate responses were observed for ciprofloxacin, ofloxacin, doxycycline, oxytetracycline, and trimethoprim-sulfamethoxazole, whereas resistance was detected against norfloxacin, neomycin, penicillin, amoxicillin, tetracycline, and erythromycin. In vitro biofilm assays demonstrated weak to moderate biofilm-forming capacity among isolates. These findings provide baseline data for wildlife microbial surveillance and conservation-oriented monitoring of protected fish populations, supporting future investigations into environmental monitoring, genomic characterization, and host-microbe interactions.

Aeromonas veronii↗
PubMed1997

[Survey on medicinal resources of Syngnathidae].

A survey on medicinal resources shows 12 species belonging to 7 genera of Syngnathidae are used as traditional Chinese medicine and some problems about cultivated Haima have been discussed.

Animals↗
PubMed2004

[The analysis of genetic variability of mtDNA 12S rRNA genes in the allotetraploid, triploid crucian carp and their parents].

The complete 12S rRNA genes from the five F11 allotetraploids, two diploid gynogens, two triploid crucian carps, one red crucian carp, one xiangjiang common carp, and one Japanese crucian carp were successfully cloned and sequenced. Sequence compositions and variations were analyzed with MEGA 1.0 software. Five F11 allotetraploids shared two haplotypes, and two diploid gynogens, two triploid crucian carps, one red crucian carp, one xiangjiang common carp, one Japanese crucian carp shared one haplotype, respectively. The similarities among red crucian carp, xiangjiang common carp, allotetraploid, diploid gynogen, Japanese crucian carp, and triploid crucian carp varied from 95% to 99%. The similarities between allotetraploid, triploid crucian carp and their female parents (red crucian carp and Japanese crucian carp, respectively) were higher than those between allotetraploid, triploid crucian carp and their male parents (xiangjiang common carp and allotetraploid, respectively). Such result indicated that mitochondrial 12S rRNA genes of the allotetraploid and triploid crucian carp were inherited maternally. A phylogenetic tree was reconstructed using the neighbor joining method of the MEGA package. It was noticeable that after nine generations from F3 to F11 hybrids, the five F11 allotetraploids shared two haplotypes (AT-1 and AT-2), indicating the allotetraploid stock had the genetic diversity. The results provided some valuable information for the breeding, genetic conservation, and population rejuvenation of the tetraploid stock.

Animals↗
PubMed2006

[Whole sequence analysis of brain-derived neurotrophic factor gene in Asiatic Black Bear through faecal sampling].

Using our lab's improved protocol for faecal DNA extraction, the entire 753-bp DNA coding sequence of the nuclear brain-derived neurotrophic factor (BDNF) gene was cloned for the first time from Asiatic Black Bear Selenarctos thibetanus faecal samples with primers based on the reported sequence of the Malayan Bear BDNF gene. Hair was used as a positive control and the experiments were repeated several times to obtain reliable and identical results. Sequence analysis showed that the BDNF gene of Asiatic Black Bear was highly conserved compared to those of human and giant panda, with an identity of 94.5% and 98.9%, respectively. The deduced amino acid sequence of the mature protein was found to be identical to those of all the reported mammalians. According to gene sequence alignment, the giant panda appeared to be phylogenetically closer to Asiatic Black Bear than the lesser panda. This study represents the first time that a non-invasive method such as faecal sampling was used to analyze a functional nuclear BDNF gene of Asiatic Black Bear. It will not only provide important reference for the conservation and breeding of Asiatic Black Bear and open up new avenues of non-invasive sampling in the study of endangered wildlife, but also provide another molecular evidence for the study of relationship of Asiatic Black Bear and its related species.

Amino Acid Sequence↗