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(FST)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-effectiveimputationmethods.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.

Selection of the appropriate reference genes by quantitative real-time PCR in leopard coral groupers Plectropomus leopardus

Leopard coral groupers(Plectropomus leopardus),commercially bred in South China,are a significant economical fish species.In this study,by means of quantitative real-time PCR(qRT-PCR)technology,we assessed the stability of six common reference genes expression and selected the appropriate reference genes in leopard coral groupers with or without Vibrio harveyi stimulation at different time points.These data produced by qRT-PCR was handled via the geNorm,NormFinder,and BestKeeper software.The results revealed all the examined reference genes had manifest tissue-specific expression in different tissues.Prior to V.harveyi stimulation,RPL13 gene was the appropriate reference gene among eleven tissue types(blood,spleen,hepatopancreas,kidney,stomach,gill,heart,skin,muscle,intestine,brain)in leopard coral groupers.Under V.harveyi stimulation,the most reliable reference genes varied from tissue to tissue and were closely hinged upon different time points.At 6-h post-bacterial injection,the appropriate reference genes in hepatopancreas,spleen,kidney,and gill were Actin,B2M,UBCE,and Actin,respectively.At 9-and 12-h post-bacterial injection,the appropriate reference genes in hepatopancreas,spleen,kidney,and gill were RPL13,Actin,Actin,and Actin,respectively.If one reference gene was preferable,RPL13,Actin,Actin,and Actin could be selected as the reference gene in hepatopancreas,spleen,kidney,and gill of leopard coral groupers after V.harveyi infection,respectively.Expression profiles of two target genes(IL-6 and NK-lysin)were used to further validate reliability of these selected appropriate candidates.This study will lay a solid foundation for the future research on qRTPCR analysis of gene expression in leopard coral groupers.

Differentiation of coral trout (Plectropomus leopardus) based on an analysis of morphology and complete mitochondrial DNA: Are cryptic species present?

Two morphotypes of Plectropomus leopardus have been identified; morphometric and meristic analyses show that there is no diagnostic difference between them. A difference in color pattern was the most ap- propriate phenotypic character with which to distinguish between the two morphotypes. Complete mito- chondrial DNA sequencing, however, indicated a clear difference between the two morphotypes. Barcoding analysis revealed no significant difference （P〉0.05） in CO1 or ND2 divergence among intramorphotypic individuals, even between geographically separated populations, whereas the intermorphotypic CO1 and ND2 divergences were large enough （averaging 0.95% for CO1 and 1.37% for ND2） to clearly discriminate between the two morphotypes. The color pattern difference, geographical distribution, together with the mtDNA and barcode sequencing data, suggest that the two morphotypes should be of two subspecies or even two species.

不同光照强度对豹纹鳃棘鲈生长和体色变化的影响

人工养殖条件下维持豹纹鳃棘鲈(Plectropomus leopardus)的体色是决定经济价值的关键,所以本文设计不同梯度光照强度区间的养殖环境,观察豹纹鳃棘鲈生长情况和体色变化情况。从试验结果可以看出当豹纹鳃棘鲈处于50~300 lx光照强度区间内,会一直维持较快的生长速率,体长、体重增加速率高于其他光照强度区间;而光照强度处于300~700 lx区间时,在养殖周期内积累的红色素含量最多,观察到明显的体色变化,即光照强度确实会影响豹纹鳃棘鲈色素累积,改变体色。

抗菌药物短期浸泡对东星斑抗氧化酶、物质及消化酶活性的影响

本研究对分别经过低浓度(5 mg/L)和高浓度(10 mg/L)恩诺沙星抗菌药物24 h短期浸泡处理后的东星斑(Plectropomus leopardus)抗氧化酶活力、抗氧化物质水平及消化酶活力进行了检测。实验结果表明:10mg/L恩诺沙星浸泡处理会显著影响东星斑抗氧化酶(超氧化物歧化酶SOD;过氧化氢酶CAT;过氧化物酶POD;溶菌酶LZM;谷胱甘肽过氧化物酶GSH-Px)正常活力的表达,并显著抑制抗氧化物质丙二醛(MDA)的表达;而5 mg/L恩诺沙星浸泡处理则不会。5 mg/L和10 mg/L恩诺沙星短期浸泡处理都不会对东星斑的消化酶(胃蛋白酶;脂肪酶;淀粉酶)的正常表达活性产生显著影响。因此,以低浓度恩诺沙星抗菌药物对东星斑进行短期浸泡处理以进行细菌性疾病的预防及治疗的方式不会对其本身酶活生理造成不可逆损伤,其中5 mg/L的浓度可作为该抗菌药物的安全浸泡浓度进行使用。