Chuankun Zhu

Pseudobagrus ussuriensis is a widely cultured bagrid fish known for its delicious tastes and high nutrition values in China. As growth performances of this fish significantly declined in recent years, the breeding of new germplasm with excellent growth traits is urgently needed. In the present study, the genome-wide association study (GWAS) method was used to identify genetic sites significantly associated with five growth traits in a population with 183 individuals. A total of 2,408,557 high-quality SNPs were identified across the 26 chromosomes of the genome. Among these, 31 SNPs were found to be significantly associated with growth traits, including 12 SNPs on Chr08, Chr17 and Chr21 associated with body length, 9 SNPs from Chr07, Chr08, Chr16, Chr22 and Chr25 associated with head length, 8 SNPs on Chr03 and Chr08 associated with body weight, and 4 SNPs from Chr03, Chr04, Chr08 and Chr15 associated with condition factor. One SNP, Chr08:20667021, located at the upstream region of the pld1 gene, was significantly associated with body length, head length and body weight, and it was also validated using Sanger sequencing in 100 individuals. Within a 50 kb range upstream and downstream of the 31 significant SNPs, 71 candidate genes were identified, with 28 of them being considered as more probable growth-associated candidate genes. The results of this study showed that the majority of growth related SNPs and candidate genes clustered on Chr08, which may be dominant in the process of growth regulation. These findings provide valuable insights into the genetic mechanisms of growth and useful tools for marker-assisted selection breeding in P. ussuriensis.

Growth rate is a key trait influencing productivity in aquaculture species, and its regulation often differs between males and females. In this study, Nanopore full-length RNA sequencing was used to investigate sex-specific growth regulation in the liver and brain of Pelteobagrus ussuriensis. Male and female groups each included three fast-growing and three slow-growing individuals. In liver tissue, 332 differentially expressed genes were identified in males and 266 in females. Male-biased genes were mainly involved in lipid and cholesterol metabolism, including the peroxisome proliferator-activated receptor signaling pathway, whereas females showed broader metabolic regulation involving carbohydrate, amino acid, and lipid metabolism, as well as growth-related genes such as IGFBP1, ESR1, and PGR. In brain tissue, fewer growth-associated differences were observed, with 26 differentially expressed genes in males and 45 in females. Alternative splicing analysis revealed strong tissue specificity, with approximately 2903 events in liver and 7412 in brain, dominated by exon skipping in liver and alternative first exon usage in brain. Isoform-level analysis further identified transcript differences not detected at the gene level, highlighting the importance of transcript diversity in growth regulation.

Pseudobagrus ussuriensis is an aquaculture catfish with significant sexual dimorphism. In this study, a chromosome-level genome with a size of 741.97 Mb was assembled for female P. ussuriensis. A total of 26 chromosome-level contigs covering 97.34% of the whole-genome assembly were obtained with an N50 of 28.53 Mb and an L50 of 11. A total of 24,075 protein-coding genes were identified, with 91.54% (22,039) genes being functionally annotated. Based on the genome assembly, four chromosome evolution clusters of catfishes were identified and the formation process of P. ussuriensis chromosomes was predicted. A total of 55 sex-related quantitative trait loci (QTLs) with a phenotypic variance explained value of 100% were located on chromosome 8 (chr08). The QTLs and other previously identified sex-specific markers were located in a sex-determining region of 16.83 Mb (from 6.90 to 23.73 Mb) on chr08, which was predicted as the X chromosome. The sex-determining region comprised 554 genes, with 135 of which being differently expressed between males and females/pseudofemales, and 16 candidate sex-determining genes were screened out. The results of this study provided a useful chromosome-level genome for genetic, genomic and evolutionary studies of P. ussuriensis, and also be useful for further studies on sex-determination mechanism analysis and sex-control breeding of this fish.

DNA methylation has been found to be involved in sex determination and differentiation in many aquaculture species. The Ussuri catfish (Pseudobagrus ussuriensis) is a popular aquaculture fish in China with high economic value in which male-biased sex dimorphism was observed in terms of body size and body weight. In this study, DNA methylation-sensitive RAD sequencing (Methyl-RAD) was used to explore the epigenetic difference between adult male and female samples in brain and gonad tissues. In brain tissues, 5,442,496 methylated cytosine sites were found and 9.94% of these sites were from symmetric CCGG or CCWGG sites. Among these sites, 321 differential DNA methylation sites (DMSs) in 171 genes were identified, while in gonad tissues, 4,043,053 methylated cytosines sites were found in total and 11.70% of them were from CCGG or CCWGG. Among these sites, 78 differential DNA methylation sites were found which were located in 64 genes. We also found several sex-determination genes among these differential methylated genes, such as amh, gsdf and hsd11b2 in brain tissues and slco3a1, socs2 and trim47 in gonad tissues. These results provided evidence for understanding the function of DNA methylation in the sex differentiation in Pseudobagrus ussuriensis, which further deepens the relationship between gene regulation and epigenetics.

The growth hormone gene (gh) of Sarcocheilichthys sinensis was cloned and characterized in this study. The cDNA length of gh was 973 bp, containing a 5′-UTR of 15 bp, a 3′-UTR of 325 bp and an open reading frame of 633 bp. The genomic DNA of gh was 2135 bp in length containing five exons and four introns. The precursor peptide of gh contained 210 amino acids (aa), including a signal peptide of 22 aa (Met¹–Ala²²) and a mature region of 188 aa (Ser²³–Leu²¹⁰). The similarity and identity ranges of the gh precursor peptide with those of other cyprinids were 88.6%–99.0% and 84.8%–98.6%, respectively. The gh of S. sinensis expressed at the highest level in the pituitary, and its expression was also detected in muscle and brain. Six polymorphic sites were detected in intron 1 (g.51InDel, g.64InDel and g.242InDel), intron 2 (g.864T>C), intron 3 (g.1017InDel) and intron 4 (g.1541A>G). Among these sites, g.242InDel was significantly associated with condition factor, g.1541A>G was associated with all six growth traits, while g.864T>C was associated with sex. The data obtained herein provide useful information for further studies on the regulation mechanisms of growth and sexual growth differences in S. sinensis.

The Asian clam, Corbicula fluminea, is a commonly consumed small freshwater bivalve in East Asia. However, available genetic information of this clam is still limited. In this study, the transcriptome of female C. fluminea was sequenced using the Illumina HiSeq 2500 platform. A total of 89,563 unigenes were assembled with an average length of 859 bp, and 36.7% of them were successfully annotated. Six members of Sox gene family namely SoxB1, SoxB2, SoxC, SoxD, SoxE and SoxF were identified. Based on these genes, the divergence time of C. fluminea was estimated to be around 476 million years ago. Furthermore, a total of 3,117 microsatellites were detected with a distribution density of 1:12,960 bp. Fifty of these microsatellites were randomly selected for validation, and 45 of them were successfully amplified with 31 polymorphic ones. The data obtained in this study will provide useful information for future genetic and genomic studies in C. fluminea.

The Asian clam Corbicula fluminea is a small bivalve with high nutritional and medical values. However, natural resources of C. fluminea have declined in many areas of China including the Hongze Lake. In this study, 119 individuals from 10 sites of this lake and 2 outgroups were analyzed using a 456 bp mitochondrial cytochrome b (cytb) gene segment. Totally, 19 polymorphic sites were detected, which defined 16 haplotypes. Polymorphism varied among the 10 populations with those at the water inlet being more polymorphic. Most F_ST values among these populations were below 0.15 with the overall value of 0.060 (p < .05), meanwhile, the overall gene flow was 7.67, both of which indicated the low level of population differentiation in this lake. Neutrality test and mismatch analyses indicated that population explosion may have occurred in this lake. The results obtained in this study will provide useful information for artificial breeding and resource protection of this species in the Hongze Lake.