Aquaculture Reports最新文献

{"title":"Molecular insights into heterosis for Vibrio alginolyticus resistance in crosses between two geographically distinct wild populations of Ruditapes philippinarum","authors":"Hongda Li ,&nbsp;Hongtao Nie ,&nbsp;Bin Wang ,&nbsp;Zhongming Huo ,&nbsp;Xiwu Yan","doi":"10.1016/j.aqrep.2025.102831","DOIUrl":"10.1016/j.aqrep.2025.102831","url":null,"abstract":"<div><div>Intraspecific crossbreeding is one of the effective methods to improve the disease resistance of <em>R. philippinarum</em>, and excellent traits can usually be produced in the hybrid progeny. In this study, we conducted a challenge experiment with <em>V. alginolyticus</em> on the hybrid progeny (D♀ × W♂ (DW) and W♀ × D♂ (WD)) and inbred progeny (D♀ × D♂ (DD) and W♀ × W♂ (WW)) of <em>R. philippinarum</em> Dalian Jinshitan (Liaoning Province) and Weihai moyedao (Shandong Province) populations, and found that the hybrid progeny had heterosis in resistance to <em>V. alginolyticus</em>. To explore the molecular mechanism of this heterosis, we then performed transcriptome sequencing on the hybrid and inbred progeny challenged with <em>V. alginolyticus</em> for 48 h and those that were not stressed. The results showed that 548 and 260 differentially expressed genes were detected in the hybrid progeny DW and WD, respectively, and 399 and 520 differentially expressed genes were detected in the inbred progeny DD and WW, respectively. Among them, the mRNA expression levels of immune genes and inflammatory factors such as <em>Hsp70</em>, <em>TNFSF13</em>, <em>TRAF6</em>, <em>IFI44</em>, <em>IL17</em> in hybrid progeny were higher than those in inbred progeny, which may be one of the reasons for heterosis. Heterosis-related module (darkturquoise) was identified and the genes of this module were significantly enriched in the phagosome pathway. These results may provide a molecular basis for the superior ability of intraspecific hybrid progeny of <em>R. philippinarum</em> to survive attack by <em>V. alginolyticus</em> than their parents, thereby deepening our understanding of heterosis in <em>R. philippinarum</em>.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102831"},"PeriodicalIF":3.2,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851991","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enzymatic hydrolysis of cottonseed protein enhances appetite and intestinal health of Litopenaeus vannamei","authors":"Jili Wang ,&nbsp;Dawei Zhao ,&nbsp;Yujia Yang ,&nbsp;Tianbi Li ,&nbsp;Shipin Wang ,&nbsp;Shaoying Lv ,&nbsp;Beiping Tan ,&nbsp;Shuyan Chi","doi":"10.1016/j.aqrep.2025.102809","DOIUrl":"10.1016/j.aqrep.2025.102809","url":null,"abstract":"<div><div>This study examined the effects of enzymatic hydrolysis cottonseed protein (ECP) on the appetite and intestinal health of <em>Litopenaeus vannamei</em> (0.16 ± 0.01 g). Based on the control diet (fishmeal 18 %, crude protein 40 %, crude fat 7.5 %), 2 %, 4 %, 6 %, 8 % and 10 % of ECP were added to replace fishmeal in equal amounts to formulate six isonitrogenous and iso-lipidic experimental diets named ECP0 (Control), ECP2, ECP4, ECP6, ECP8, and ECP10, respectively. After an 8-week feeding trial, the serum orexin levels were significantly increased (<em>P</em> &lt; 0.05); and leptin, peptide YY and cholecystokinin were significantly reduced when shrimp ingested diet contained ECP， as well as their genes expression levels (<em>P</em> &lt; 0.05). Compared with the ECP0 group, the weight gain rate of the shrimps in group ECP2 had significantly increased (<em>P</em> &lt; 0.05). Besides, intestinal fold height and muscular thickness of shrimps in group ECP2 were markedly increased, and up-regulated genes expression levels for periplasmic membrane factors (<em>P</em> &lt; 0.05). Significantly increased intestinal amylase, lipase, trypsin and chymotrypsin activities were found in shrimps fed diet ECP2 and ECP4 (<em>P</em> &lt; 0.05). The addition of ECP significantly decreased <em>Vibrio</em>, <em>Photobacterium</em> and <em>Tenacibaculum</em> abundance, and increased <em>Ruegeria</em> and <em>Marivita</em> abundance in shrimp intestine (<em>P</em> &lt; 0.05), especially the supplemented 2 % ECP significantly improved the membrane transport and amino acid metabolism functions of the intestinal flora in shrimps (<em>P</em> &lt; 0.05). Therefore, the addition of 2–4 % ECP by replacing fishmeal at an equal level could enhance growth by improving appetite, intestinal morphology and the composition of gut microbiota for <em>L.vannamei</em>.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102809"},"PeriodicalIF":3.2,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851992","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Increasing reproductive capacity in female blue swimmer crabs using vitellogenesis-inhibiting hormone dsRNA","authors":"Supawadee Duangprom ,&nbsp;Siriporn Nonkhwao ,&nbsp;Jirawat Saetan ,&nbsp;Sineenart Songkoomkrong ,&nbsp;Prateep Amonruttanapun ,&nbsp;Chompunut Samhuay ,&nbsp;Benyamat Boonobrom ,&nbsp;Montakan Tamtin ,&nbsp;Prasert Sobhon ,&nbsp;Napamanee Kornthong","doi":"10.1016/j.aqrep.2025.102827","DOIUrl":"10.1016/j.aqrep.2025.102827","url":null,"abstract":"<div><div>Vitellogenesis-inhibiting hormone (VIH) is a key regulatory hormone that suppresses vitellogenin production and inhibits ovarian maturation in various crustaceans. The X-organ sinus gland complex of the eyestalks and the central nervous system (CNS) synthesizes and releases this neuropeptide. Double-stranded RNA (dsRNA) techniques have been employed to silence hormonal target transcripts through RNA interference with target genes. We investigated the impact of dsRNA-VIH on the reproductive function of female blue swimmer crabs, <em>Portunus pelagicus</em>, by evaluating its capacity to inhibit VIH in the eyestalks. A single injection of VIH dsRNA at 0.6 µg/g of body weight was injected every 14 days, which effectively suppressed VIH expression for 14 days after the injection. In the dsRNA-VIH treatment group, both the gonadosomatic index (GSI) and the vitellin (Vn) concentration in the hemolymph increased over time relative to the control groups on days 14 and 28. Moreover, dsRNA-VIH had a stimulatory impact on the expressions of other reproductive-related gene: vitellogenin (<em>Vg</em>), red pigment-concentrating hormone (<em>RPCH</em>), farnesoic acid O-methyltransferase (<em>FAMeT</em>), and estrogen sulfotransferase (<em>ESULT</em>). The findings indicate a progressive rise in the expression levels of these genes in both the brain and ventral nerve cord. Histological analysis also showed that the dsRNA-VIH group had significantly more oocytes in step 4 (Oc4) than the control group. The findings indicate that dsRNA-VIH has the capacity to reduce VIH production in the CNS, which affects the expression of other genes that are implicated in ovarian development in the blue swimmer crab.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102827"},"PeriodicalIF":3.2,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851988","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Starvation affects the intestinal oxidative stress, autophagy, microbiota and histology of Chinese soft-shelled turtle (Pelodiscus sinensis)","authors":"Xueying Shi ,&nbsp;Da Yue ,&nbsp;Qingqing Guo ,&nbsp;Xiangce Li ,&nbsp;Peiyu Zhang ,&nbsp;Haiyan Liu","doi":"10.1016/j.aqrep.2025.102835","DOIUrl":"10.1016/j.aqrep.2025.102835","url":null,"abstract":"<div><div>Chinese soft-shelled turtle (<em>Pelodiscus sinensis</em>) frequently encounters period of starvation during its life cycle, but the impact of starvation on its intestinal physiology remains unclear. This study investigated the effects of starvation on the antioxidant status, autophagy, microflora, and histological structure in the intestinal of <em>P. sinensis</em>. Turtles were subjected to starvation for 1, 4, 8, 16, and 32 days (referred to as S1, S4, S8, S16, and S32). The results of histological examination showed a progressive shortening of intestine villus and thickening of the muscle layer as starvation duration increased. The ROS and MDA contents showed a gradual increase with the prolonged starvation. The activities of SOD and GPx were significantly elevated after 16 and 32 days of starvation. Transmission electron microscopy revealed the presence of autophagosomes starting from S4, with a significant increase observed after 8 days of starvation. The mRNA expression levels of autophagy-related genes (<em>atg5, atg12, p53</em>, <em>p62</em>, and <em>lc3</em>) were significantly upregulated with the prolonged starvation, while the expressions of <em>mtor1</em> and <em>s6k1</em> were significantly decreased in S32 group. Moreover, microbiota analysis via 16S rRNA sequencing demonstrated a distinct separation between the S1 group and the starving groups. Starvation led to an increase in intestinal microbial diversity, as evidenced by an elevated Shannon index and a decreased Simpson index. At the phylum level, the abundance of Firmicutes decreased, whereas Bacteroidota and Proteobacteria increased with prolonged starvation. A Mantel test showed that the abundance of Proteobacteria was significantly positively correlated to ROS contents and the expression levels of <em>p53</em>. In conclusion, this study suggests that starvation induce the oxidative stress and autophagy, change the structure of microbiota and morphology in the gut of <em>P. sinensis</em>, and provides valuable insights to the adaptive mechanisms of this species.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102835"},"PeriodicalIF":3.2,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851993","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Non-invasive sexing of the long-spined sea urchin, Diadema setosum","authors":"Nicholas Wei Jie Mak ,&nbsp;Sze Hui Foo ,&nbsp;Shuang Song,&nbsp;Peter A. Todd","doi":"10.1016/j.aqrep.2025.102822","DOIUrl":"10.1016/j.aqrep.2025.102822","url":null,"abstract":"<div><div>Sea urchins are highly valued due to their commercial significance and essential roles in marine ecosystems. However, traditional methods for sexing sea urchins, such as spawning induction or gonad histology, are typically invasive, season-dependent, time-consuming, and labour-intensive. This study investigated non-invasive sexing techniques for <em>Diadema setosum</em> by assessing various morphological traits, performing a genome wide association study (GWAS), and testing PCR markers previously developed for <em>Mesocentrotus nudus</em>. Of the 16 morphological traits examined, only genital papillae exhibited sexual dimorphism, achieving 82.5 % accuracy for sex identification in a blinded experiment. Importantly, the sexual divergence of this trait was independent of the urchins’ reproductive status, making it a reliable year-round sexing indicator. The PCR markers from <em>M. nudus</em> did not prove applicable for <em>D. setosum</em>. However, a genomic region with 22 male-heterozygous SNPs on Scaffold 2 was identified, spanning just 1154 bp. This region holds potential for development into a PCR- or sequencing-based sexing barcode for <em>D. setosum</em>. These findings present a promising avenue for non-invasive, season-independent sex identification in this species, with potential to enhance the efficiency and sustainability of sea urchin aquaculture.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102822"},"PeriodicalIF":3.2,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851987","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of acute and chronic ammonia exposure on survival, growth and intestinal microbiota composition of hybrid carp","authors":"Yu Han ,&nbsp;Xiaoqian Li ,&nbsp;Xue Li ,&nbsp;Shidong Wang ,&nbsp;Muzi Zhang ,&nbsp;Ming Li","doi":"10.1016/j.aqrep.2025.102834","DOIUrl":"10.1016/j.aqrep.2025.102834","url":null,"abstract":"<div><div>It is very important to evaluate the growth tolerance threshold of fish under long-term low ammonia exposure for water quality management in aquaculture. This study employed a sequential method to evaluate the tolerance of hybrid carp to both acute and chronic ammonia exposure. In stage 1, we estimated the effects of acute high ammonia stress on hybrid carp and based on linear interpolation (y = 0.0047x - 0.4659, where R² = 0.9448, with y representing cumulative mortality and x representing ammonia concentration), the 96-h LC₅₀ was determined to be 206.38 mg/L of total ammonia (TA). In stage 2, the long-term low ammonia exposure ranges (&lt; 0.001 (control), 1.03 (LC₅₀/200), 2.05 (LC₅₀/100), 4.11 (LC₅₀/50), and 8.21 (LC₅₀/25) mg/L TA) were determined based on 96-h LC₅₀ value, and then a 6-week experiment was performed. The results showed that elevated ammonia concentration (&gt; 1.03 mg/L TA) significantly reduced food intake. The growth performance was inhibited at ammonia concentrations above 1.03 mg/L TA, while survival rate decreased at ammonia concentrations above 4.11 mg/L TA. The lack of free amino acids (arginine, leucine, aspartic acid, and glutamine) not only affect the fish growth, but also inhibits the key enzymes (arginase and argininosuccinic acid lyase) activity in urea cycle, resulting in a decrease in ammonia detoxification ability. Even exposure to low concentration of ammonia (2.05 mg/L TA) can reduce the activity of antioxidant enzymes (superoxide dismutase and catalase), causing liver damage and inflammation. Long-term low ammonia exposure reduces intestinal microbiota richness and diversity while increasing relative abundance of harmful bacteria, such as <em>Leifsonia</em>, <em>Aeromonas</em>, <em>Erysipelothrix</em>, and <em>Acinetobacter</em>. And the increase in relative abundance of beneficial bacteria such as <em>Cetobacterium</em> may be a coping strategy against ammonia toxicity. We recommend against exposing hybrid carp to ammonia concentrations exceeding 1.03 mg/L TA for prolonged periods of time.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102834"},"PeriodicalIF":3.2,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global analysis of transcriptome and metabolomics revealed that fatty acid synthesis and urea cycle process regulate the growth of chinese soft-shelled turtle","authors":"Tong Zhou ,&nbsp;Guobin Chen ,&nbsp;Lihuan Cao ,&nbsp;Jizeng Cao ,&nbsp;Huizi Ji ,&nbsp;Guiwei Zou ,&nbsp;Hongwei Liang","doi":"10.1016/j.aqrep.2025.102814","DOIUrl":"10.1016/j.aqrep.2025.102814","url":null,"abstract":"<div><div>The Chinese soft-shelled turtle (<em>Pelodiscus sinensis</em>) is an economically important aquatic species, with its growth influenced by genetic factors, environmental conditions, nutritional status, and intestinal microbiota. Despite its slow growth rate, typically taking 2–3 years to reach market size, understanding the molecular mechanisms that regulate its growth is critical for optimizing breeding conditions and improving aquaculture sustainability. In this study, we carried out a multi-omics analysis in individuals of <em>P. sinensis</em> aged 2, 5, and 8 months to systematically disclose the biological mechanisms and explore how these mechanisms affect its growth and adaptive ability. We found significant changes in the composition of intestinal bacteria, with <em>Fusobacteriota</em> and <em>Proteobacteria</em> dominating at the phylum level and displaying increasingly intimate interactions as growth processed. Notable enrichments were observed in pathways related to arginine biosynthesis and glycine and serine metabolism in differentially expressed genes (DEGs), as well as steroid biosynthesis and steroid hormone biosynthesis pathways in differentially expressed metabolites (DEMs). Furthermore, fatty acid synthesis and the urea cycle were identified as key metabolic pathways essential for the breeding of Chinese soft-shelled turtles. This research provides insights that can be utilized to optimize feed formulations, enhance breeding efficiency, and promote the healthy growth of <em>P. sinensis</em> in aquaculture.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102814"},"PeriodicalIF":3.2,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851989","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evaluating the response of Schizothorax prenanti to ammonia nitrogen stress using computer vision and transcriptomics","authors":"Yinhua Zhou ,&nbsp;He Gao ,&nbsp;Hejiao Li ,&nbsp;Tianyi Shen ,&nbsp;Yifan Yao ,&nbsp;Zhilei Wang ,&nbsp;Yuting Duan ,&nbsp;Junting Li ,&nbsp;Suxing Fu ,&nbsp;Shidong Liu ,&nbsp;Rongrong Liao ,&nbsp;Haiping Liu ,&nbsp;Luo Lei ,&nbsp;Chaowei Zhou","doi":"10.1016/j.aqrep.2025.102829","DOIUrl":"10.1016/j.aqrep.2025.102829","url":null,"abstract":"<div><div>The tolerance and response to ammonia nitrogen have not been studied in <em>Schizothorax prenanti</em> (<em>S. prenanti</em>), an important economic fish in southwest China. This study, for the first time, combines behavioral, histological, biochemical, and transcriptomic analyses to explore its response to ammonia nitrogen stress. Acute toxicity tests showed that the 96 h LC50 TAN (total ammonia nitrogen) in <em>S. prenanti</em> was approximately 16 mg/L (temperature = 21°C, pH = 7.5). Behavioral quantification using YOLO v8 (You Only Look Once version 8) indicated no significant impact under low-concentration stress (L, 30 % LC50); medium-concentration stress (M, 45 % LC50) significantly enhanced the swimming speed, exercise volumes, and localized activity, and high-concentration stress (H, 60 % LC50) caused abnormal behavior and restricted activity. Gill histology and TUNEL assay revealed epithelial swelling and curling of secondary filaments under low-concentration stress. Medium-concentration stress caused localized structural damage and cell apoptosis and high-concentration stress induced severe necrosis and apoptosis in the secondary filaments. Biochemical tests showed significant increases in plasma cortisol, glucose, plasma ammonia, and tumor necrosis factor-α under high-concentration stress. Gill superoxide dismutase, catalase, and total antioxidant capacity activities were significantly decreased and malondialdehyde levels were increased. Transcriptomic analysis indicated that most differentially expressed genes (DEGs) in the M and H groups were enriched in pathways related to immune response, antioxidation, carbohydrate metabolism, and amino acid metabolism. Notably, DEGs related to the TCA cycle and oxidative phosphorylation were enriched in the M group, likely to provide energy for immune response and ammonia detoxification. Suppression of antigen processing and presentation may explain why <em>S. prenanti</em> struggles to cope under high ammonia nitrogen stress. <em>S. prenanti</em> shows a certain tolerance to ammonia nitrogen, however, concentrations exceeding 9.6 mg/L result in behavioral abnormalities, gill tissue damage, oxidative stress, apoptosis, and immune suppression. The findings provide a theoretical foundation for research on the tolerance and response of <em>S. prenanti</em> to ammonia nitrogen and offer a new perspective for monitoring and managing ammonia nitrogen stress in intensive aquaculture systems.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102829"},"PeriodicalIF":3.2,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143851990","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of QTLs and candidate genes screening for hypoxia tolerance in Pacific white shrimp (Litopenaeus vannamei)","authors":"Xiawen Li ,&nbsp;Yian Zhu ,&nbsp;Zhixiang Yuan,&nbsp;Cunyu Duan,&nbsp;Yu Chen,&nbsp;Lei Yang,&nbsp;Minghui Ye,&nbsp;Wei Wang,&nbsp;Zhongduo Wang,&nbsp;Huapu Chen,&nbsp;Yulei Zhang,&nbsp;Changxu Tian","doi":"10.1016/j.aqrep.2025.102824","DOIUrl":"10.1016/j.aqrep.2025.102824","url":null,"abstract":"<div><div>The Pacific white shrimp (<em>Litopenaeus vannamei</em>, also known as <em>Peneaus vannamei</em>) is pivotal in global aquaculture, with its growth and survival significantly influenced by hypoxia conditions in farming. This study aimed to uncover the genetic basis of hypoxia tolerance to enhance farming efficiency and sustainability. We evaluated hypoxia tolerance in a shrimp mapping family and identified quantitative trait loci (QTLs) and candidate genes associated with this trait. The F₁ full-sibling family exhibited significant variation in hypoxia tolerance, with an average survival time of 13 hours at dissolved oxygen levels of 0.4 mg/L. Whole-genome sequencing of 200 offspring and their parents generated 81,892 markers for a genetic map with 44 linkage groups over 5386.79 cM. The linkage group lengths ranged from 12.79 cM to 196.86 cM, averaging 122.43 cM, with marker distances from 0.03 to 0.61 cM and highest and lowest marker densities observed in LG11 and LG44, respectively. QTL analysis revealed 8 QTLs associated with hypoxia tolerance, encompassing 78 annotated genes, 13 of which were identified as candidate genes for hypoxia tolerance. RNA-seq analysis of hypoxia-tolerant and hypoxia-intolerant individuals revealed 1973 differentially expressed genes, with GO and KEGG enrichment analyses highlighting their roles in DNA repair, RNA processing, and redox-related pathways. Integrating QTL and RNA-seq data pinpointed 11 genes with differential expression under hypoxic stress. This study not only advances the understanding of the genetic mechanisms underlying hypoxia tolerance in <em>L. vannamei</em> but also establishes a foundation for enhancing hypoxia resilience through genetic improvement.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102824"},"PeriodicalIF":3.2,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143850676","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of sex determination region and candidate genes in blotched snakehead (Channa maculata) through genome-wide association studies and transcriptome analysis","authors":"Haiyang Liu ,&nbsp;Tongxin Cui ,&nbsp;Jin Zhang ,&nbsp;Yang Zhang ,&nbsp;Qing Luo ,&nbsp;Shuzhan Fei ,&nbsp;Kunci Chen ,&nbsp;Jian Zhao ,&nbsp;Mi Ou","doi":"10.1016/j.aqrep.2025.102825","DOIUrl":"10.1016/j.aqrep.2025.102825","url":null,"abstract":"<div><div>The blotched snakehead (<em>Channa maculata</em>) is an economically significant freshwater species in China, exhibiting pronounced sexual size dimorphism, with males displaying faster growth rates and larger body sizes. Monosex farming has the potential to significantly substantially enhance aquaculture efficiency for this species. In this study, we conducted whole-genome resequencing of 45 female and 50 male blotched snakehead individuals. Genome-wide association analysis (GWAS) was performed based on genome-wide SNPs and InDels, and combined with fixation index (<em>Fst</em>) analysis between male and female groups, which identified a candidate sex-determining region located on Chr.02: 34,288,075–34,351,554 (63.479 kb). Linkage disequilibrium analysis revealed that the sex-determining region has formed a haplotype block with a state of linkage disequilibrium. Within this region, we identified six InDels larger than 15 bp and developed two sex-specific markers capable of accurately identifying the genetic sex of blotched snakehead. Additionally, we performed transcriptome analyses of male and female gonads at 120, 150, and 180 days post-fertilization (dpf). Combined with the GWAS results, we identified candidate sex-determining genes, including five male-biased genes (<em>EVM0022796</em>, <em>ITGB1BP1</em>, <em>RSAD2</em>, <em>CMPK2</em>, and <em>KIDINS220</em>) and two female-biased genes (<em>Sox11</em> and <em>DNAJC30</em>). This study enhances our understanding of the genetic basis of sex determination in blotched snakehead, providing novel insights into its genetic mechanisms. Our findings establish a solid scientific foundation for applications in monosex breeding and marker-assisted selection breeding programs in this species.</div></div>","PeriodicalId":8103,"journal":{"name":"Aquaculture Reports","volume":"42 ","pages":"Article 102825"},"PeriodicalIF":3.2,"publicationDate":"2025-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143848326","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}