Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper ( Plectropomus leopardus).

The leopard coral grouper ( Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( θπ) and fixation index ( F ST) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus.

Biokinetics and biotransformation of paralytic shellfish toxins in different tissues of Yesso scallops, Patinopecten yessoensis.

Paralytic shellfish toxins (PSTs) are a group of natural toxic substances often found in marine bivalves. Accumulation, anatomical distribution, biotransformation and depuration of PSTs in different tissues of bivalves, however, are still not very well understood. In this study, we investigated biokinetics and biotransformation of PSTs in six different tissues, namely gill, mantle, gonad, adductor muscle, kidney, and digestive gland, in Yesso scallops Patinopecten yessoensis exposed to a toxic strain of dinoflagellate Alexandrium pacificum. High daily accumulation rate (DAR) was recorded at the beginning stage of the experiment. Most of the PSTs in toxic algae ingested by scallops were retained and the toxicity level of PSTs in scallops exceeded the regulatory limit within 5 days. At the late stage of the experiment, however, DAR decreased obviously due to the removal of PSTs. Fitting results of the biokinetics model indicated that the amount of PSTs transferred from digestive gland to mantle, adductor muscle, gonad, kidney, and gill in a decreasing order, and adductor muscle, kidney, and gonad had higher removal rate than gill and mantle. Toxin profile in digestive gland was dominated by N-sulfocarbamoyl toxins 1/2 (C1/2), closely resembled that of the toxic algae. In contrast, toxin components in kidney were dominated by high-potency neosaxitoxin (NEO) and saxitoxin (STX), suggesting that the kidney be a major organ for transformation of PSTs.

Organization of the neuroepithelial actin cytoskeleton is regulated by heparan sulfation during neurulation.

Heparan sulfate and cytoskeletal actin microfilaments have both been shown to be important regulators of neural tube closure during embryonic development. To determine the functional relationship of these two molecules in formation of the spinal neural tube, we cultured ARC mouse embryos at embryonic day E8.5 in the presence of chlorate, a competitive inhibitor of glycosaminoglycan sulfation, and examined the effects on organization of actin microfilaments in the neuroepithelium. Compared against embryos cultured under control conditions, chlorate-treated embryos had shortened posterior neuropore, a loss of median hinge point formation and increased bending at the paired dorsolateral hinge points. Furthermore, apical organization of actin microfilaments in the neuroepithelial cells was absent, and this was associated with convex bending of the neuroepithelium. The results suggest that heparan sulfate is an important determinant of cytoskeletal actin organization during spinal neurulation, and that its biological action is dependent on sulfation of the heparan molecule.

[Genomic selection and its application].

Selective breeding is very important in agricultural production and breeding value estimation is the core of selective breeding. With the development of genetic markers, especially high throughput genotyping technology, it becomes available to estimate breeding value at genome level, i.e. genomic selection (GS). In this review, the methods of GS was categorized into two groups: one is to predict genomic estimated breeding value (GEBV) based on the allele effect, such as least squares, random regression - best linear unbiased prediction (RR-BLUP), Bayes and principle component analysis, etc; the other is to predict GEBV with genetic relationship matrix, which constructs genetic relationship matrix via high throughput genetic markers and then predicts GEBV through linear mixed model, i.e. GBLUP. The basic principles of these methods were also introduced according to the above two classifications. Factors affecting GS accuracy include markers of type and density, length of haplotype, the size of reference population, the extent between marker-QTL and so on. Among the methods of GS, Bayes and GBLUP are usually more accurate than the others and least squares is the worst. GBLUP is time-efficient and can combine pedigree with genotypic information, hence it is superior to other methods. Although progress was made in GS, there are still some challenges, for examples, united breeding, long-term genetic gain with GS, and disentangling markers with and without contribution to the traits. GS has been applied in animal and plant breeding practice and also has the potential to predict genetic predisposition in humans and study evolutionary dynamics. GS, which is more precise than the traditional method, is a breakthrough at measuring genetic relationship. Therefore, GS will be a revolutionary event in the history of animal and plant breeding.

Comparative Cytogenetics Analysis of Chlamys farreri, Patinopecten yessoensis, and Argopecten irradians with Ct-1 DNA by Fluorescence In Situ Hybridization.

The chromosomes of Chlamys farreri, Patinopecten yessoensis, and Argopecten irradians were studied by FISH using C. farreri C(0)t-1 DNA probes. The results showed that C(0)t-1 DNA signals spread on all chromosomes in the three scallops, whereas signal density and intensity were different strikingly. Clustering brighter signals presented in the centromeric and telomeric regions of most C. farreri chromosomes, and in the centromeric or pericentromeric regions of several P. yessoensis chromosomes. Comparative analysis of the mapping indicated a relatively higher homology in the repetitive DNA sequences of the genome between C. farreri and P. yessoensis than that between C. farreri and A. irradians. In addition, FISH showed that the distribution of C(0)t-1 DNA clustering signals in C. farreri displayed completely similar signal bands between homologous chromosomes. Based on the C(0)t-1 DNA fluorescent bands, a more exact karyotype of C. farreri has been obtained. In this study, the comparative analysis based on C(0)t-1 DNA provides a new insight into the chromosomal reconstructions during the evolution process, and it is helpful for understanding an important source of genomic diversity, species relationships, and genome evolution.

A rapid and cheap protocol for preparation of PCR templates in peanut

This paper describes a simple, low cost and reliable DNA template preparation protocol for polymerase chain reaction (PCR) using immature leaves from peanut seeds or leaves from field-grown plants. The technique may find wide utility in studies involving PCR-based molecular markers, rapid screening for transformants and gene cloning.

[MYP gene expressions at transcription level in different stages of gonad of sea urchin Strongylocentrotus intermedius and hybrids].

MYP (Major yolk protein) gene expression at transcription level in different stages of gonad of sea urchin Strongylocentrotus intermedius and hybrids (S. intermediusfemale symbolxS. nudusmale symbol) was analyzed by real-time RT-PCR. Based on normalization with 18S rRNA levels, the comparative quantities of MYP expression were determined. The expression of MYP gene in gonad showed little difference between female and male. MYP gene expression was decreased rapidly in the gonad of S. intermedius at different stages, and slowly in hybrids. The comparative quantities of MYP expression in the gonads of S. intermedius were decreased from 44.55% to 9.59% in female and from 41.17% to 1.83% in male at different stages. The comparative quantities of MYP expression in the gonads of the hybrids were decreased from 37.66% to 19.22% in female and from 36.66% to 12.55% in male at different stages. The results indicated that the difference of MYP expression was correlated with the variation caused by hybridization.

NG2 cells response to axonal alteration in the spinal cord white matter in mice with genetic disruption of neurofilament light subunit expression.

BACKGROUND: Chondroitin sulphate proteoglycan (NG2) expressing cells, morphologically characterized by multi-branched processes and small cell bodies, are the 4th commonest cell population of non-neuronal cell type in the central nervous system (CNS). They can interact with nodes of Ranvier, receive synaptic input, generate action potential and respond to some pathological stimuli, but the function of the cells is still unclear. We assumed the NG2 cells may play an active role in neuropathogenesis and aimed to determine if NG2 cells could sense and response to the alterations in the axonal contents caused by disruption of neurofilament light subunit (NFL) expression. RESULTS: In the early neuropathological development stage, our study showed that the diameter of axons of upper motor neurons of NFL-/- mice decreased significantly while the thickness of their myelin sheath increased remarkably. Although there was an obvious morphological distortion in axons with occasionally partial demyelination, no obvious changes in expression of myelin proteins was detected. Parallel to these changes in the axons and their myelination, the processes of NG2 cells were disconnected from the nodes of Ranvier and extended further, suggesting that these cells in the spinal cord white matter could sense the alteration in axonal contents caused by disruption of NFL expression before astrocytic and microglial activation. CONCLUSION: The structural configuration determined by the NFL gene may be important for maintenance of normal morphology of myelinated axons. The NG2 cells might serve as an early sensor for the delivery of information from impaired neurons to the local environment.

[AFLP analysis in populations of Strongylocentrotus intermedius, S. nudus and hybrids (S. intermedius x S. nudus)].

AFLP analysis of genetic diversity in the three populations of sea urchin Strongylocentrotus intermedius (IN), S. nudus (NU) and F1 progeny (INxNU) was carried out in this paper. In total, 272 loci were amplified with 4 primer pairs, of which 269 were polymorphic and the percentage of polymorphic loci was 98.89%. The Shannon diversity index for S. intermedius, S. nudus, and their hybrid populations was 0.2331+/-0.1273, 0.2005+/-0.1385, and 0.2625+/-0.1067, respectively. The genetic similarity within populations was 0.6876+/-0.0523, 0.6501+/-0.0548, and 0.6552+/-0.0553, respectively. AMOVA analysis indicated that 25.39% of variance was among populations and 74.61% of variance was within populations. This suggested the rich genetic diversity level within populations. Although the hybrids can be classified into two types by apparent characters, they were clustered each other by UPGMA method according to their genetic distances.

[Interleukin 10 gene -627 polymorphisms in Chinese patients with early-onset coronary heart disease].

OBJECTIVE: To investigate the relationship between interleukin 10 (IL10) gene -627 polymorphisms and serum IL10 level and early-onset coronary heart disease (CHD). METHODS: The genotype and allele frequency of IL10 gene -627 site was assayed by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). DNA samples were obtained from 163 patients with CHD and 112 controls. Serum IL10 level was detected by ELISA. RESULTS: No significant difference was found in the distribution of IL10 genotype and allele frequency between the healthy controls and the patients with CHD; Chi-square values were 1.9324 and 1.5703 respectively, P > 0.05. Stratification analyses based on different sex still found no significant difference in the distribution of IL10 genotype and allele frequency between the healthy controls and the CHD patients; the Chi-square values in male groups were 1.2708 versus 0.8595, and in female groups were 0.8254 versus 0.7127, P > 0.05. Serum IL10 level showed significant differences among AA genotype, AC genotype and CC genotype, but no significant difference was noted between healthy controls and CHD patients. CONCLUSION: These results suggest that IL10 gene -627 polymorphisms are not associated with an increased risk of CHD, but it might assume a role in IL10 gene expression.

[Maximum entropy principle and population genetic equilibrium].

A general mathematic model of population genetic equilibrium was constructed based on the maximum entropy principle. We proved that the maximum entropy probability distribution was equivalent to the Hardy-Weinberg equilibrium law. A population reached genetic equilibrium when the genotype entropy of the population reached the maximal possible value. In information theory, the entropy or the information content is used to measure the uncertainty of a system. In population genetics, we can use entropy to measure the uncertainty of the genotype of a population. The agreement of the maximum entropy principle and the hardy-Weinberg equilibrium law indicated that random crossing is an irreversible process, which increases the genotype entropy of the population, while inbreeding and selection decrease the genotype entropy of the population. In animal or plant breeding, we often use selection and/or inbreeding to decrease the entropy of a population, and use intercrossing to increase the entropy of the population. In this point of view, breeding is actually regulating the entropy of population. By applying the basic principle of informatics in population genetics, we revealed the biological significance of the genotype entropy and demonstrated that we can work over population genetic problems with the principles and methods of informatics and cybernetics.