47 results on '"Gen Hua Yue"'
Search Results
2. The ornamental fighting fish is the next model organism for genetic studies
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Gen Hua Yue, Le Wang, Fei Sun, Zituo Yang, Yubang Shen, Zining Meng, and Yuzer Alfiko
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Ecology ,Management, Monitoring, Policy and Law ,Aquatic Science - Published
- 2022
3. Aquaculture species diversification in China
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Gen Hua Yue, Yi Xuan Tay, Joey Wong, Yubang Shen, and Junhong Xia
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Ecology ,Aquatic Science ,Ecology, Evolution, Behavior and Systematics - Published
- 2023
4. VNN disease and status of breeding for resistance to NNV in aquaculture
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Sek-Man Wong, Gen Hua Yue, and Zituo Yang
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Molecular breeding ,Genetics ,0303 health sciences ,Ecology ,Genome-wide association study ,04 agricultural and veterinary sciences ,Disease ,Aquatic Science ,Plant disease resistance ,Biology ,Quantitative trait locus ,Selective breeding ,Virus ,03 medical and health sciences ,Genome editing ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology - Abstract
Viral nervous necrosis (VNN) disease, caused by the nervous necrosis virus (NNV), is a devastating disease, leading to high mortality rate and huge economical loss in aquaculture. In the past 30 years, many studies on the virus, host responses to the virus infection and diagnostics have yielded a lot of knowledge on developing measures to prevent the VNN disease. Although genetic improvement of disease resistance through breeding is inheritable and has long-lasting positive effect on aquaculture, it is a very challenging task in conventional selective breeding for improving disease resistance. With the advances in mapping quantitative trait loci (QTL) and genome wide association studies (GWAS) for NNV resistance in aquaculture species, DNA markers and genes associated with NNV resistance have been identified, making the application of marker-assisted selection (MAS) and genomic selection (GS) for NNV resistance possible. A few genes for NNV resistance are identified and are being used for genome editing to rapidly improve NNV resistance. In this review, we present the current knowledge on the NNV, host responses to NNV infection, diagnostic methods and vaccines available for NNV disease. In addition, we summarize the current status of conventional and molecular breeding for NNV resistance and highlight future directions, including genome editing for improving NNV resistance in aquaculture.
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- 2022
5. LAMP for the rapid diagnosis of iridovirus in aquaculture
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Qiwei Qin, Le Wang, Yepin Yu, Fei Sun, Yanfei Wen, Zituo Yang, May Lee, and Gen Hua Yue
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food.ingredient ,Ecology ,biology ,business.industry ,Chemistry ,Iridovirus ,Loop-mediated isothermal amplification ,DNA virus ,Aquatic Science ,biology.organism_classification ,Molecular biology ,DNA extraction ,food ,Aquaculture ,Grouper ,Asian seabass ,Dna viral ,business ,Ecology, Evolution, Behavior and Systematics - Abstract
Iridoviruses are DNA virus and have caused huge economic losses in the aquaculture industry. The aim of this study was to establish a colorimetric loop-mediated isothermal amplification (LAMP) protocol for the on-site detection of Singapore grouper iridovirus (SGIV). The SGIV-VP61 gene was chosen as the target gene to develop a colorimetric LAMP assay. The optimized condition of the colorimetric LAMP assay was incubation at 63 °C for 1 h. Samples infected with SGIV could be detected with the color change from yellow into pink. The sensitivity of the developed assay is 5.66 copies/μL of the viral DNA template. This sensitivity was about 1000 times higher than that of conventional PCR while it was slightly lower than the one-step semi-nested PCR assay. A total of 60 DNA samples extracted from the fin tissue of the SGIV-infected Asian seabass were examined for SGIV by colorimetric LAMP, semi-nested PCR and conventional PCR. The results of the colorimetric LAMP assay showed 94.87 % agreement with the semi-nested PCR. In addition, the DNA extraction method using NaOH showed a better performance in the colorimetric LAMP assay. Taken together, the colorimetric LAMP established was a sensitive, rapid and specific method for the detection of SGIV. SGIV was not detected in samples randomly taken from a genetically improved line of the Asian seabass. However, some seabass obtained from the local markets were found to contain SGIV. Thus, the LAMP assay has the potential application in the diagnosis of iridovirus diseases in the aquaculture industry.
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- 2022
6. Breeding Asian seabass to increase survival against big belly disease and growth
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Peng Liu, Jun Hong Xia, Fei Sun, Le Wang, Zituo Yang, May Lee, Hong Yan Pang, Yan Fei Wen, and Gen Hua Yue
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Ecology ,Aquatic Science ,Ecology, Evolution, Behavior and Systematics - Published
- 2022
7. Genome editing and its applications in genetic improvement in aquaculture
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Yepin Yu, Gen Hua Yue, Yi Xuan Tay, and Zituo Yang
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Ecology ,Genome editing ,Aquaculture ,business.industry ,Computational biology ,Management, Monitoring, Policy and Law ,Aquatic Science ,Biology ,business ,Genome - Published
- 2021
8. pomc knockout increases growth in zebrafish
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Zituo Yang, Joey Wong, Le Wang, Fei Sun, and Gen Hua Yue
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Aquatic Science - Published
- 2023
9. Inferring the invasion mechanisms of the red swamp crayfish in China using mitochondrial DNA sequences
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Gen Hua Yue, Chunming Wang, Jun Hong Xia, Su Yin Cao, Jian-Bin Feng, and School of Biological Sciences
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Population ,Invasive Species ,Introduced species ,Aquaculture ,Aquatic Science ,Swamp ,Freshwater ecosystem ,lcsh:Aquaculture. Fisheries. Angling ,03 medical and health sciences ,education ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Procambarus clarkii ,lcsh:SH1-691 ,0303 health sciences ,education.field_of_study ,geography ,geography.geographical_feature_category ,Ecology ,biology ,Invasive species ,Route ,Biological sciences [Science] ,Biota ,04 agricultural and veterinary sciences ,Dispersal ,biology.organism_classification ,Crayfish ,Cambaridae ,040102 fisheries ,ND2 ,0401 agriculture, forestry, and fisheries ,Biological dispersal - Abstract
The red swamp crayfish, Procambarus clarkii, is a native species in north-eastern Mexico and south-central USA. P. clarkii was introduced to China in 1929 and has been used as an aquaculture species in China since 1983. It currently exists in most of the provinces of China, but threatens local fish, crustaceans, aquatic plants and local freshwater ecosystems. We examined the genetic variation in partial mitochondrial ND2 gene of 831 individuals collected from 25 P. clarkii populations in 13 provinces of China to infer the expansion pathways and mechanisms. Six haplotypes were detected. All six haplotypes appeared in four populations in Nanjing and a population located near Nanjing whereas only 1–5 of the six haplotypes were present in other populations. These data suggest that the populations in Nanjing are probably the source of all other populations in China. There were no significant relationships between geographic distances and genetic distances in 25 populations, whereas significant relationship was found in four populations in Qinhuai River covering 50 km in Nanjing. These data suggest that the expansion mainly be human-mediated in large scale, and active disposal or non-anthropogenic passive dispersal might have played an important role in expansion at a smaller scale. In some places far away from Nanjing, several haplotypes existed, suggested multiple introduction events may have happened. Although aquaculture of this species could bring huge economic benefit, its potential to negatively affect native biota and entire ecosystems should not be ignored. National University of Singapore (NUS), Temasek Laboratories Published version The research was funded by the internal fund of the Temasek Life Sciences Laboratory (Fund number: 5020).
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- 2021
10. Characterization of pIgR and its association with resistance to iridovirus in Asian seabass
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Yi Xuan Tay, Yepin Yu, Zituo Yang, Le Wang, Fei Sun, and Gen Hua Yue
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Aquatic Science - Published
- 2023
11. Characterization of GAB3 and its association with NNV resistance in the Asian seabass
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Gen Hua Yue, Sek-Man Wong, and Zituo Yang
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Fish Proteins ,0301 basic medicine ,Candidate gene ,Genome-wide association study ,Single-nucleotide polymorphism ,Aquatic Science ,Biology ,Transcriptome ,Fish Diseases ,03 medical and health sciences ,Exon ,RNA Virus Infections ,Complementary DNA ,Animals ,Environmental Chemistry ,Nodaviridae ,Gene ,Phylogeny ,GRB2 Adaptor Protein ,Genetics ,Gene Expression Profiling ,Intron ,04 agricultural and veterinary sciences ,General Medicine ,Immunity, Innate ,030104 developmental biology ,Gene Expression Regulation ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Bass - Abstract
Understanding the functions of genes related to disease resistance and identifying polymorphisms in these genes are essential in molecular breeding for disease resistance. Viral nervous necrosis (VNN) is one of the major diseases in the Asian seabass, Lates calcarifer. Our previous works on QTL mapping, GWAS and cell-line transcriptome analysis of the Asian seabass after NNV challenge revealed that the gene GAB3 might be a candidate gene for VNN resistance. In this study, we cloned and characterized GAB3, and identified SNPs in the gene of the Asian seabass. The cDNA of the gene was 2165 bp, containing an ORF of 1674 bp encoding 557 amino acids. The gene consisted of 10 exons and nine introns. It was ubiquitously expressed in normal fish. An analysis of the association between two SNPs in the second intron and NNV resistance in 1035 fish descended from 43 families revealed that the two SNPs were significantly associated with VNN resistance. After NNV infection, the expression of GAB3 was significantly increased in the brain, spleen, muscle and gut, and was suppressed in the liver. The GAB3 protein was localized in the nucleus. Overexpression of GAB3 with specific GAB3-pcDNA was positively correlated to increased viral RNA and titer in NNV-infected Asian seabass cells. Our study provides new evidence to support that GAB3 may be an important gene related to NNV resistance. In addition, the SNPs provide DNA markers for the selection of candidate genes resistance to NNV at the juvenile stage of Asian seabass.
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- 2020
12. Current Knowledge on the Biology and Aquaculture of the Endangered Asian Arowana
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Gen Hua Yue, Antonius Suwanto, Alex Chang, and A. Yuzer
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biology ,business.industry ,media_common.quotation_subject ,Endangered species ,Management, Monitoring, Policy and Law ,Aquatic Science ,biology.organism_classification ,Fishery ,Aquaculture ,Arowana ,Freshwater fish ,%22">Fish ,Reproduction ,business ,Ecology, Evolution, Behavior and Systematics ,Scleropages formosus ,media_common - Abstract
The Asian arowana (Scleropages formosus) is an ancient freshwater fish species from the Osteoglossidae family. It is a territorial and mouth-brooding fish, which inhabits slow-moving rivers and lak...
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- 2019
13. Genes for sexual body size dimorphism in hybrid tilapia (Oreochromis sp. x Oreochromis mossambicus)
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Zi Yi Wan, Gen Hua Yue, Grace Lin, and School of Biological Sciences
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Oreochromis mossambicus ,Candidate gene ,food.ingredient ,Aquatic Science ,lcsh:Aquaculture. Fisheries. Angling ,Transcriptome ,03 medical and health sciences ,food ,Body Size ,KEGG ,Gene ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,lcsh:SH1-691 ,Genetics ,0303 health sciences ,Sexual Dimorphism ,Ecology ,biology ,Biological sciences [Science] ,Tilapia ,04 agricultural and veterinary sciences ,biology.organism_classification ,Sexual dimorphism ,Oreochromis ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,human activities - Abstract
Tilapias are important aquaculture species. Male-biased sexual size dimorphism is very common and males are preferred for aquaculture in tilapia. However, the mechanisms underlying sexual dimorphism remain to be elucidated. One hundred and thirty-six sex-biased genes, of which 23 were male-biased and 113 were female-biased, were identified via reanalysis of a muscle transcriptome data using the latest reference genome assembly. These genes were mapped to KEGG pathways that are related to somatic cell metabolism, growth and differentiations, such as MAPK, FoxO4 and metabolism pathways as well as developmental processes responsible for skeletal muscle development. Pathways related to cell growth and proliferations such as MAPK signaling pathways are upregulated in males while pathways regulating cell division such as FoxO4 are upregulated in females. Sex-biased genes in tilapia skeletal muscle have higher evolution rates (dN/dS) compared to unbiased genes. Female-biased and male-biased genes showed 17.4% and 13.5% higher dN/dS, respectively, compared to unbiased genes. Our results suggest that some of the male and female sex-biased genes were under selection pressures. Three SNPs located in the promoter region of one sex-biased gene RASGRF1 on LG1 were associated with bodyweight differences in the hybrid tilapia. These sex-biased genes identified in this study may serve as candidate genes for future functional analysis on sexual size dimorphism and for developing DNA markers for selecting fast-growing saline tilapia in aquaculture. Keywords: Sexual dimorphism, Body size, RNA-Seq, Tilapia, Aquaculture, Evolution
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- 2019
14. Occurrence of dorsal fin and opercular deformities and their effects on body weight in Asian seabass
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Gen Hua Yue, Yan Fei Wen, Fei Sun, Le Wang, Zituo Yang, and Hong Yan Pang
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Aquatic Science - Published
- 2022
15. Editorial special issue: Emerging and disruptive technologies for aquaculture
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Junhong Xia, Giana Bastos Gomes, and Gen Hua Yue
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Ecology ,Aquatic Science ,Ecology, Evolution, Behavior and Systematics - Published
- 2022
16. Current status of research on aquaculture genetics and genomics-information from ISGA 2018
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Yubang Shen, Gen Hua Yue, and School of Biological Sciences
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Population genetics ,Genomics ,Aquaculture ,Aquatic Science ,Biology ,Genome ,lcsh:Aquaculture. Fisheries. Angling ,03 medical and health sciences ,Phenomics ,Genome editing ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,lcsh:SH1-691 ,Genetics ,0303 health sciences ,Ecology ,business.industry ,Biological sciences [Science] ,04 agricultural and veterinary sciences ,Quantitative genetics ,ISGA2018 ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,business ,Functional genomics - Abstract
The ISGA (International Symposium on Genetics in Aquaculture) is an important conference in the field of aquaculture genetics, which is held every three years. This year, the meeting was hosted by James Cook University, in Cairns. The conference sessions included biotechnology and functional genomics, sex control, genomic prediction, selective breeding and quantitative genetics, industrial use of genetics, genome technology, genetics of diseases and stress, genetics of nutrition, epigenetics, genomics and metabolomes, population genetics and ethics, food safety, as well as environmental risks. Many new and interesting unpublished data, including those for new aquaculture species, marker-assisted selection, genomic selection and genome editing using Crispr/Cas9 technologies, were reported at the conference. In this brief review, we highlight the novel and interesting researches on aquaculture genetics and genomics to give readers an overview of the current status and trends of aquaculture genetics and genomics research. Keywords: ISGA2018, Aquaculture, MAS, GS, Phenomics
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- 2019
17. Functional characterization of an ER-stress responding Crustin gene in Litopenaeus vannamei
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Yi-Hong Chen, Jianguo He, Gen Hua Yue, Chao-Zheng Zhang, Kai Yuan, Hong-Hui He, and Yu-Ying Lian
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0301 basic medicine ,Staphylococcus aureus ,animal structures ,Penaeidae ,Litopenaeus ,Aquatic Science ,Arthropod Proteins ,Microbiology ,03 medical and health sciences ,Immune system ,Water environment ,Animals ,Environmental Chemistry ,Amino Acid Sequence ,Phylogeny ,Innate immune system ,Base Sequence ,biology ,Effector ,Gene Expression Profiling ,fungi ,04 agricultural and veterinary sciences ,General Medicine ,biology.organism_classification ,Immunity, Innate ,Shrimp ,030104 developmental biology ,Gene Expression Regulation ,040102 fisheries ,Unfolded protein response ,0401 agriculture, forestry, and fisheries ,Vibrio parahaemolyticus ,Antimicrobial Cationic Peptides - Abstract
Shrimp in culture ponds are challenged by various pathogens as well as harsh water environment. The innate immune system and environmental stress response system of shrimp paly an important role in shrimp survival and growth. For remission the endoplasmic reticulum (ER)-stress caused by environmental stress, unfolded protein response (UPR) may reduce the synthesis of most proteins, including great mass of immune factors, which could weaken the immune function of shrimp. Therefore, how cells keep appropriate amount of immune factor synthesis under such a situation is critical important for shrimp health and growth. In this study, we cloned a new Crustin gene (LvCruU) from Litopenaeus vannamei. We showed that LvCruU has antibacterial activity, and reducing its expression would increase the cumulative mortality of L. vannamei upon the Vibrio parahemolyticus infection. In addition, we found that promoter activity of LvCruU was enhanced not only by the deformed epidermal autoregulatory factor-1 (Deaf1), but also by activating transcription factor 3 (LvATF3) of shrimp UPR. Real-time RT-PCR showed that LvCruU and LvATF3 both were induced upon UPR activation. And moreover, in Thapsigargin plus dsLvCruU injection test, we showed that down-regulation of LvCruU increased the cumulative mortality of V. parahemolyticus-infected shrimp under ER-stress. These results suggest that LvCruU work as a downstream effector of UPR, and contribute to antimicrobic immune response upon ER-stress in L. vannamei.
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- 2019
18. Identification of Pmel17 for golden skin color using linkage mapping in Mozambique tilapia
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Le Wang, Feng Liu, Fei Sun, Gang Qiao Kuang, and Gen Hua Yue
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Genetics ,Untranslated region ,endocrine system ,education.field_of_study ,Sequence analysis ,animal diseases ,education ,Population ,Aquatic Science ,Biology ,humanities ,symbols.namesake ,Genetic linkage ,Genetic marker ,Backcrossing ,Mendelian inheritance ,symbols ,human activities ,Gene - Abstract
Fish color is an important trait involved in many biological functions and related to commercial value of fish. However, our understanding of the molecular mechanisms underlying color variations in fish species is limited. In this study, we found 12 natural golden mutants in a Mozambique tilapia population. Analysis of the inheritance pattern of the golden and blackish skin colors in nine backcross families revealed that the golden phenotype is a recessive mutant determined by a single locus and follows simple Mendelian inheritance. Using linkage mapping, fine mapping and analyses of gene expressions, we uncovered that the Pmel17 gene was responsible for golden and black skin colors. Further sequence analysis of the gene discovered that an insertion in 3′ UTR of Pmel17 was fully associated with the golden skin color in 1835 tilapias. Expression analysis showed that Pmel17 with the insertion reduced the transcripts of Pmel17. These results indicate that the insertion in 3′ UTR of Pmel17 is responsible for the golden skin color in tilapia. The insertion can be used as a reliable DNA marker to accelerate the breeding for golden color.
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- 2022
19. Two SNPs in SNX2 are associated with SGIV resistance in Asian seabass
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May Lee, Fei Sun, Yepin Yu, Le Wang, Zituo Yang, and Gen Hua Yue
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Genetics ,Untranslated region ,0303 health sciences ,Gene knockdown ,food.ingredient ,biology ,Iridovirus ,04 agricultural and veterinary sciences ,Aquatic Science ,Plant disease resistance ,biology.organism_classification ,03 medical and health sciences ,food ,Genetic marker ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Grouper ,Gene ,030304 developmental biology ,Cytopathic effect - Abstract
Breeding for disease resistance is an important task for genetic improvement in aquaculture. Identification of DNA markers associated with disease resistance is a critical step towards molecular breeding for disease resistance. Iridovirus causes mass mortality in hatchery of an important food fish Asian seabass (Lates calcarifer). In this study, an SNX2 (Sorting nexin 2) homolog (LcaSNX2) from L. calcarifer was cloned. Its roles in the infection of Singapore grouper iridovirus (SGIV) were characterized. The gene contained an ORF of 1542 bp encoding 513 amino acids, a 5’ UTR of 242 bp and a 3′ UTR of 2650 bp. Two SNPs in the 3’ UTR of the gene were identified, and they were significantly associated with SGIV resistance. Thus, they provide useful DNA markers for selecting Asian seabass juveniles for resistance against SGIV. The SNX2 gene was expressed ubiquitously in healthy fish, and highly expressed in the eye, gill, fin and brain. The expression of the gene was induced after SGIV infection in vitro, suggesting that LcaSNX2 plays a role in virus-host interaction during SGIV infection. Overexpression of LcaSNX2 increased the infection and replication of SGIV. Knockdown of this gene reduced viral gene transcriptional level, cytopathic effect and virus titer, indicating that suppression of the gene reduces SGIV infection. These data indicate that LcaSNX2 gene is essential for efficient replication of SGIV.
- Published
- 2021
20. Heritability of growth traits in the Asian seabass ( Lates calcarifer )
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Hongyan Pang, Zi Yi Wan, Gen Hua Yue, Junhui Jiang, Bing Liang, Huan Sein Lim, Le Wang, Baoqing Ye, Huiming Liu, Yanfei Wen, and School of Biological Sciences
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0301 basic medicine ,Breeding program ,Offspring ,Growth ,Broodstock ,Asian Seabass ,Aquatic Science ,Biology ,Selective breeding ,lcsh:Aquaculture. Fisheries. Angling ,Heritability ,03 medical and health sciences ,Animal science ,Aquaculture ,Breeding Program ,DNA marker ,Ecology, Evolution, Behavior and Systematics ,Asian seabass ,lcsh:SH1-691 ,Genetics ,Ecology ,business.industry ,Biological sciences [Science] ,04 agricultural and veterinary sciences ,biology.organism_classification ,Lates ,030104 developmental biology ,040102 fisheries ,Trait ,0401 agriculture, forestry, and fisheries ,business - Abstract
Growth is an economically important trait in aquaculture. To improve growth trait of the Asian seabass (Lates calcarifer) we have been carrying out, since 2004, a selective breeding program. This study focuses on growth traits in the F2 fish generation, comprised of offspring from 23 mass crosses from 383 F1 brooders. Using genotyping analysis for 10 microsatellites from both brood stock and progeny we have reconstructed the pedigree of each mass-cross. For F2 generation at 90 days post hatch (dph), we have recorded body weight (BW) for 12,117 individuals and total length (TL), standard length (SL) and condition factor (Ktl and Ksl) for 3530 individuals; and all five traits for 2136 individuals at 270 dph. At 90 dph the average BW was 46.88 ± 20.95 g. Combining pedigree information, recorded growth traits and Restricted Maximum Likelihood method, we have estimated that the narrow sense heritability (h2) in F1 fish for BW, TL, SL, Ktl and Ksl was at, 90 dph, 0.12 ± 0.03, 0.11 ± 0.03, 0.10 ± 0.03, 0.20 ± 0.04 and 0.11 ± 0.03, respectively and, at 270 dph, 0.34 ± 0.07, 0.32 ± 0.07, 0.30 ± 0.06, 0.13 ± 0.04 and 0.11 ± 0.04, respectively. At 90 dph the realised heritability for BW was 0.13. Comparing with F1 generation, the growth performance of F2 fish was increased by 14.4%. Heritability of growth traits will be useful for future genetic improvement programmes of the Asian seabass. NRF (Natl Research Foundation, S’pore) Published version
- Published
- 2017
21. Current status of genome sequencing and its applications in aquaculture
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Gen Hua Yue and Le Wang
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0301 basic medicine ,Whole genome sequencing ,business.industry ,04 agricultural and veterinary sciences ,Aquatic Science ,Biology ,Genome ,DNA sequencing ,Biotechnology ,03 medical and health sciences ,030104 developmental biology ,Aquaculture ,Agriculture ,Sustainability ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Identification (biology) ,business ,Personal genomics - Abstract
Aquaculture is the fastest-growing food production sector in agriculture, with great potential to meet projected protein needs of human beings. Aquaculture is facing several challenges, including lack of a sufficient number of genetically improved species, lack of species-specific feeds, high mortality due to diseases and pollution of ecosystems. The rapid development of sequencing technologies has revolutionized biological sciences, and supplied necessary tools to tackle these challenges in aquaculture and thus ensure its sustainability and profitability. So far, draft genomes have been published in over 24 aquaculture species, and used to address important issues related to aquaculture. We briefly review the advances of next generation sequencing technologies, and summarize the status of whole genome sequencing and its general applications (i.e. establishing reference genomes and discovering DNA markers) and specific applications in tackling some important issues (e.g. breeding, diseases, sex determination & maturation) related to aquaculture. For sequencing a new genome, we recommend the use of 100–200 × short reads using Illumina and 50–60 × long reads with PacBio sequencing technologies. For identification of a large number of SNPs, resequencing pooled DNA samples from different populations is the most cost-effective way. We also discuss the challenges and future directions of whole genome sequencing in aquaculture.
- Published
- 2017
22. Characterization of a novel disease resistance gene rtp3 and its association with VNN disease resistance in Asian seabass
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Sek-Man Wong, Gen Hua Yue, Bao Qing Ye, Le Wang, Peng Liu, and Shuqing Huang
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0301 basic medicine ,Untranslated region ,Gene Expression ,Aquatic Science ,Plant disease resistance ,Biology ,Virus ,Transcriptome ,Fish Diseases ,03 medical and health sciences ,RNA Virus Infections ,0302 clinical medicine ,Expression pattern ,Animals ,Environmental Chemistry ,Nodaviridae ,Asian seabass ,Gene ,Disease Resistance ,Genetics ,Gene Expression Profiling ,General Medicine ,Perciformes ,030104 developmental biology ,030220 oncology & carcinogenesis ,Microsatellite ,Microsatellite Repeats - Abstract
Asian seabass, an important food fish in Southeast Asia, has suffered from nervous necrosis virus (NNV) infection, resulting in massive mortality of Asian seabass larvae and enormous economic losses. Identification and characterization of disease resistance genes is important. Previous transcriptome analysis of Asians seabass epithelial cells after NNV infection revealed a highly inducible gene, receptor-transporting protein 3 ( rtp3 ), indicating it could play an important role in Asian seabass – NNV interaction. To characterize this gene, we determined its expression pattern and subcellular localization. The rtp3 was highly induced in most examined tissues and organs of Asian seabass after NNV infection, and protein Rtp3 was localized in cytoplasm. Further association study in multiple families revealed that a microsatellite marker, (GT)ntt(GT)n, in the 3′ UTR of rtp3 was significantly associated with VNN disease resistance in Asian seabass. Our results imply that rtp3 may be a novel disease resistance gene in Asian seabass. This data could improve our understanding of molecular interaction between Asian seabass and NNV, and has the potential to be applied in marker-assisted selection for disease resistance breeding in Asian seabass.
- Published
- 2017
23. Who eats whom, when and why? Juvenile cannibalism in fish Asian seabass
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Xiaojun Liu, Hongyan Pang, Gen Hua Yue, Jun Hong Xia, and School of Biological Sciences
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0301 basic medicine ,Kin discrimination ,Bioinformatics analysis ,Kin recognition ,Offspring ,Zoology ,Aquatic Science ,Biology ,lcsh:Aquaculture. Fisheries. Angling ,03 medical and health sciences ,Aquaculture ,Cannibalism ,Juvenile ,Asian seabass ,Ecology, Evolution, Behavior and Systematics ,lcsh:SH1-691 ,Ecology ,business.industry ,Biological sciences [Science] ,04 agricultural and veterinary sciences ,Fish ,030104 developmental biology ,Polymorphic microsatellites ,Kinship ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Gene expression ,RNA-seq ,business - Abstract
While juvenile cannibalism plays an important role in the evolution of organisms in natural populations, it is a serious problem in aquaculture. A number of genetic and environmental factors result in different rates of cannibalism. Whether there is kin recognition in juvenile cannibalism in fish is poorly understood. We studied cannibalism and kinship recognition in juveniles of Asian seabass using molecular parentage analysis with polymorphic microsatellites. In the three mass crosses, under an ordinary feeding scheme without size grading, the rate of juvenile loss due to cannibalism was 1.08% per day. In the group without feeding for 24 h, 2.30% ± 0.43% of offspring per day were lost within 24 h due to cannibalism. We detected that juveniles avoided cannibalizing their siblings when they were not hungry, whereas cannibalism among siblings increased when they were hungry. These data suggest that there is kin discrimination in fish cannibalism. Raising genetically closely related offspring in the same tanks and appropriate levels of feeding may reduce the rate of cannibalism. We hypothesized that the chemical cues for kin discrimination might be secreted by fish skins. To test this hypothesis, we analyzed gene expression profiles in the skins of juveniles under slightly and very hungry conditions using RNA sequencing and bioinformatics analysis. Genes differently expressed under slightly and very hungry conditions were identified. Among them, genes from the trypsin family were significantly down-regulated under starved conditions, suggesting that they may play a role in kin discrimination. NRF (Natl Research Foundation, S’pore) Published version
- Published
- 2017
24. Status, challenges and trends of aquaculture in Singapore
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Yubang Shen, Gen Hua Yue, and Keyi Ma
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0303 health sciences ,Food security ,business.industry ,Fish farming ,Biosecurity ,04 agricultural and veterinary sciences ,Aquatic Science ,Biology ,Hatchery ,Fishery ,03 medical and health sciences ,Aquaculture ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Asian seabass ,business ,Cage aquaculture ,030304 developmental biology ,Grey mullet - Abstract
Singapore is a small island country with limited land and sea space for aquaculture. Foodfish production in Singapore is mainly from cage aquaculture in sea and supplied about 10% of total fish consumed. The major cultured species are Asian seabass, milk fish, grey mullet, snappers, golden pompanos, hybrid groupers and shrimps. Although small scale of its aquaculture, constrained by limited available land and coastal areas and high cost for aquaculture, the industry is thriving and transferring from low-tech to high-tech. With the strong support of the government for food security, aquaculture R&D are geared towards developing novel hatchery technologies, marker-assisted and genomic selection to accelerate genetic improvement, the establishment of high-tech aquaculture farms and ensuring biosecurity. Singapore is fast becoming global aquaculture hotspot. In this review, we summarized the status of Singapore's aquaculture production, R&D, training and education and its challenges, and suggested some ideas on the future development of Singapore's aquaculture. Singapore is well-positioned to serve as a R&D and education hub for tropical aquaculture. Its R & D on aquaculture should focus on fish reproduction, genetic improvement and high-tech aquaculture systems to improve local fish production and to supply superior fry for culture in other countries.
- Published
- 2021
25. An indel in the Suv39h1 gene is associated with resistance to iridovirus in the Asian seabass
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Le Wang, Fei Sun, Gen Hua Yue, and Yanfei Wen
- Subjects
Genetics ,0303 health sciences ,food.ingredient ,Iridovirus ,Chromosome ,04 agricultural and veterinary sciences ,Aquatic Science ,Biology ,03 medical and health sciences ,food ,Genetic marker ,Complementary DNA ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Heterochromatin organization ,Indel ,Gene ,DOT1L Gene ,030304 developmental biology - Abstract
Suv39h1 is a member of the Suv39h sub-family of histone lysine methyltransferases. The gene plays an important role in heterochromatin organization, chromosome segregation, and mitotic progression in humans and model organisms. However, its functions in food fish species remain largely unknown. We identified the full-length cDNA of the Suv39h1 in the Asian seabass, analysed its genomic structure and identified polymorphisms. The gene was expressed in all tissues examined, but highly expressed in the gill, spleen and kidney. After challenging Asian seabass juveniles with iridovirus, the expressions of the gene altered, suggesting that the gene is related to the infection by iridovirus. Three SNPs and one indel were detected in the 3’ UTR of the gene. The indel was significantly associated with the resistance against iridovirus. In silico-mapping revealed that the gene was mapped to chromosome 6, where a significant QTL for the resistance to iridovirus was located previously in the Asian seabass. Altogether, the data suggest that the gene Suv39h1 play an important role in iridovirus resistance in the Asian seabass. This study also laid the foundation for further detailed analysis of the function of the Suv39h1 gene in resistance to iridovirus. The indel may supply a useful DNA marker for selecting Asian seabass fingerlings resistant to iridovirus.
- Published
- 2020
26. Characterization of two novel gadd45a genes in hybrid tilapia and their responses to the infection of Streptococcus agalactiae
- Author
-
Yubang Shen, Gen Hua Yue, Feng Liu, and Keyi Ma
- Subjects
Fish Proteins ,0301 basic medicine ,food.ingredient ,Single-nucleotide polymorphism ,Aquaculture ,Aquatic Science ,Biology ,Plant disease resistance ,medicine.disease_cause ,Polymorphism, Single Nucleotide ,Streptococcus agalactiae ,Fish Diseases ,03 medical and health sciences ,food ,Sequence Analysis, Protein ,Streptococcal Infections ,medicine ,Animals ,Environmental Chemistry ,Pathogen ,Gene ,Phylogeny ,Regulation of gene expression ,Genetics ,Intracellular Signaling Peptides and Proteins ,Tilapia ,Cichlids ,04 agricultural and veterinary sciences ,General Medicine ,Immunity, Innate ,030104 developmental biology ,Gene Expression Regulation ,Genetic marker ,040102 fisheries ,Hybridization, Genetic ,0401 agriculture, forestry, and fisheries - Abstract
Diseases are one of the major challenges in tilapia aquaculture. Identification of DNA markers associated with disease resistance may facilitate the acceleration of the selection for disease resistance. Gadd45a (growth arrest and DNA damage 45 A), a stress-inducible gene in humans and mice, has not been studied in fish. We characterized the two prologues of Gadd45a genes in hybrid tilapia. Gadd45a1 and Gadd45a2 shared an identical gene structure and showed an amino acid sequence identity of 73.8%. Their expressions were detected in all 10 tissues examined, with the kidney and gill having high transcriptional expressions. The expression levels of Gadd45a1 were significantly lower than those of Gadd45a2 in all examined tissues. After a challenge with a bacterial pathogen Streptococcus agalactiae, the expressions of the two genes were up-regulated significantly in the spleen, kidney, liver and intestine. These findings suggest that the two Gadd45a genes play an important role in the resistance to S. agalactiae in tilapia. We identified 10 SNPs in the two genes. The SNP markers in the two Gadd45a genes could be used to examine whether they are associated with resistance to S. agalactiae.
- Published
- 2016
27. Genetic heterogeneity and local adaptation of Asian seabass across Indonesian Archipelago revealed with gene-associated SNP markers
- Author
-
Huan Sein Lim, Zi Yi Wan, Le Wang, and Gen Hua Yue
- Subjects
Genetic diversity ,education.field_of_study ,Breeding program ,Ecology ,Genetic heterogeneity ,Population ,Zoology ,Aquatic Science ,Biology ,Southeast asian ,Genetic marker ,parasitic diseases ,Microsatellite ,education ,Local adaptation - Abstract
Asian seabass is an important marine foodfish species in Asia-Pacific region. Previous studies using microsatellites and mitochondrial DNA sequences showed that the populations in Australia are significantly different from those in Southeast Asia. However, within Australian and Southeast Asian populations, there are some conflicts regarding to population differentiations. It is essential for us to use more DNA markers to examine the population structure of Asian seabass. We collected Asian seabass samples from seven wild populations distributed across Indonesian Archipelago from Southeast Asia to Australia and Papua New Guinea. We measured the genetic diversity within each population and analyzed the genetic relationships among the wild populations using 96 SNPs. We detected significant population differentiations among the seven wild populations of Asian seabass. The genetic diversity in Southeast Asian populations was significantly higher than that in Australian and Papua New Guinean populations. There were significant genetic differentiations among the Australian and Papua New Guinean populations while the differentiation in Southeast Asian populations was minor. In addition, we identified footprints of directional selection at three loci using outlier tests. Our data supply useful information about the management of wild stocks of Asian seabass and the use of wild Asian seabass to start a breeding program.
- Published
- 2015
28. The MCP-8 gene and its possible association with resistance to Streptococcus agalactiae in tilapia
- Author
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Gen Hua Yue, Xiaojun Liu, Feng Liu, Gui Hong Fu, Jun Hong Xia, and Zi Yi Wan
- Subjects
Fish Proteins ,Proteases ,food.ingredient ,medicine.medical_treatment ,Molecular Sequence Data ,Aquatic Science ,Biology ,medicine.disease_cause ,Streptococcus agalactiae ,Fish Diseases ,food ,Streptococcal Infections ,Complementary DNA ,medicine ,Animals ,Environmental Chemistry ,Gene ,Disease Resistance ,Protease ,Bacterial disease ,Tilapia ,Sequence Analysis, DNA ,General Medicine ,Mast cell ,Molecular biology ,medicine.anatomical_structure ,Tryptases - Abstract
Mast cell proteases play an important role in the regulation of the immune response. We identified the cDNA of the mast cell protease 8 (MCP-8) gene and analyzed its genomic structure in tilapia. The ORF of the MCP-8 was 768 bp, encoding 255 amino acids. Quantitative real-time PCR revealed that the MCP-8 gene was expressed predominantly in spleen, moderately in liver, blood, brain, gill, intestine, skin, and weakly expressed in kidney, muscle and eye. After a challenge with Streptococcus agalactiae, the gene was induced significantly (p0.05) in intestine, kidney, spleen and liver. Furthermore, we identified five single nucleotide polymorphisms (SNPs) in the MCP-8 gene and found that three SNPs were significantly associated (p0.05) with resistance against S. agalactiae. However, we found no association between four SNPs and growth traits (p0.05). These results suggest that the MCP-8 gene play an important role in the resistance to S. agalactiae in tilapia. The SNP markers in the MCP-8 gene associated with the resistance to the bacterial pathogen may facilitate selection of tilapia resistant to the bacterial disease.
- Published
- 2014
29. Genome-wide discovery and in silico mapping of gene-associated SNPs in Nile tilapia
- Author
-
Gen Hua Yue, Grace Lin, Gui Hong Fu, Feng Liu, Le Wang, Jun Hong Xia, Zhen Long Ng, and Zi Yi Wan
- Subjects
Genetics ,Genetic diversity ,food.ingredient ,Population genetics ,Tilapia ,Single-nucleotide polymorphism ,Aquatic Science ,Biology ,Quantitative trait locus ,biology.organism_classification ,Nile tilapia ,Oreochromis ,food ,Genetic marker ,human activities - Abstract
Single nucleotide polymorphisms (SNPs) are important DNA markers for genetic studies. However, the number of SNPs is limited in important aquaculture species. We have identified 23,535 high quality SNPs in genes of Nile tilapia ( Oreochromis niloticus ) by analyzing the available RNA-seq data. Among them, 17,699 SNPs were mapped onto 22 linkage groups (LG) using in silico mapping. The number of mapped SNPs ranged from 332 on LG2 to 1148 on LG16_21 with an average number of 805 SNPs/LG. The mapped SNPs were located in 7146 genes. This SNP resource will be useful in monitoring the genetic diversity and mapping QTL for genetic improvement of tilapia species. We further studied the relationships among individuals from four populations (GIFT, O. niloticus , Red tilapia and O. mossambicus ) using 101 SNPs from LG23. Ninety-four SNPs (~ 93%) were polymorphic in the tested populations. Red tilapia (77%) had the highest number of informative markers than GIFT (69%), Nile tilapia (56%), and Mozambique tilapia (12%). Significant population structure was detected through phylogenic and population structure analysis. The Red tilapia individuals were closely related to Mozambique tilapia, but were split into several subclades, confirming that red tilapia is a hybrid admixture of different resources of tilapias.
- Published
- 2014
30. Practical Considerations of Molecular Parentage Analysis in Fish
- Author
-
Gen Hua Yue and Jun Hong Xia
- Subjects
Aquaculture ,business.industry ,Pedigree information ,Multiplex polymerase chain reaction ,%22">Fish ,Computational biology ,Aquatic Science ,Biology ,business ,Bioinformatics ,Agronomy and Crop Science ,Genotyping - Abstract
Pedigree information is important in selective breeding programs and hatchery management of aquaculture. However, in aquaculture species, tagging of young fish with physical tags is very difficult. Molecular parentage analyses have been used in reconstructing pedigrees in aquaculture species since the 1990s. Some studies have been carried out to optimize every step to reduce the cost and improve the efficiency of molecular parentage analysis. However, molecular parentage analysis of a large number of individuals is still too expensive because some steps of molecular parentage analysis are very cost-intensive. In this review, we have summarized the techniques of major steps in parentage analysis, and provided a guide for aquaculture scientists on how to cost-effectively and rapidly extract DNA from a large number of samples, select the right types of DNA markers, optimize multiplex polymerase chain reaction, and select appropriate methods and software to analyze the genotyping data for reconstructing pedigrees. In addition, we discuss the challenges and future directions of molecular parentage analysis in aquaculture species.
- Published
- 2014
31. Recent advances of genome mapping and marker-assisted selection in aquaculture
- Author
-
Gen Hua Yue
- Subjects
business.industry ,Genome-wide association study ,Management, Monitoring, Policy and Law ,Aquatic Science ,Quantitative trait locus ,Biology ,Marker-assisted selection ,Oceanography ,Selective breeding ,Biotechnology ,Aquaculture ,Evolutionary biology ,Genetic gain ,business ,Ecology, Evolution, Behavior and Systematics ,Selection (genetic algorithm) ,Genetic association - Abstract
Aquaculture is the fastest growing sector in agriculture. Substantial genetic gains have been achieved in a few cultured species using conventional selective breeding approaches. However, the majority of fish and shellfish species remain in their wild state. Due to the recognition of the enormous potential of marker-assisted selection (MAS) to speed up genetic gain through early selection, aquaculture scientists have constructed linkage maps in over 40 species and mapped quantitative trait loci (QTL) for important traits in over 20 species since the 1990s. Although MAS and genomic selection (GS) have not been widely used in aquaculture, their application in breeding programmes is expected to be a fertile area of research. In this paper, I summarized the recent advances of linkage and QTL mapping, as well as MAS in aquaculture species. I also discussed the potentials of genome-wide association studies (GWAS) and GS in aquaculture species.
- Published
- 2013
32. Isolation and characterization of polymorphic microsatellite loci in large yellow croaker, Larimichthys crocea
- Author
-
Hua Ye, Guangtai Zhao, Gen Hua Yue, Peng Ren, and Zhiyong Wang
- Subjects
Genetics ,education.field_of_study ,biology ,Population ,Population genetics ,Locus (genetics) ,Aquatic Science ,Oceanography ,biology.organism_classification ,Null allele ,Loss of heterozygosity ,Genetic linkage ,Larimichthys crocea ,Microsatellite ,education - Abstract
An (AC)n-microsatellite-enriched library for Larimichthys crocea was constructed in this study. Primers for fifty simple sequence repeat (SSR) loci were synthesized and genotyped on 30 L. crocea individuals from Guanjingyang wild population (WP) in Fujian Province and 38 individuals from Ningbo cultured population (CP) in Zhejiang Province. Only 21 loci were successfully amplified and polymorphic in two populations. In WP, the observed heterozygosity (HO) ranged from 0.233 to 0.900 and the expected heterozygosity (HE) ranged from 0.326 to 0.893, with an average of 7.8 alleles/locus, the polymorphism information content (PIC) ranged from 0.283 to 0.866 (mean 0.731). In CP, the HO ranged from 0.189 to 0.892 and the HE ranged from 0.333 to 0.800, with an average of 4.4 alleles/locus. The probability test showed significant departures from HWE in 9 and 2 of the 21 loci in WP and in CP, respectively. Deficiency of heterozygotes at four loci showed the presence of null alleles (P
- Published
- 2012
33. Genetic Variations in Populations from Farms and Natural Habitats of Asian Green Mussel, Perna viridis, in Singapore Inferred from Nine Microsatellite Markers
- Author
-
Gen Hua Yue, Grace Lin, and Loong Chueng Lo
- Subjects
Genetic diversity ,Breeding program ,Ecology ,Genetic variation ,Microsatellite ,Species richness ,Aquatic Science ,Biology ,biology.organism_classification ,Agronomy and Crop Science ,Inbreeding ,Perna viridis ,Fixation index - Abstract
The Asian green mussel, Perna viridis, has been widely cultured in Southeast Asia as delicious seafood depending on natural spat. We analyzed the genetic diversity and population structure of three populations (two from Singapore and one from Malaysia) from natural habitats and two from Singapore farms, by genotyping a total of 262 adult individuals using nine polymorphic microsatellites. In all five populations, high allelic (number of alleles A = 11.0–14.4,allelic richness Ar = 10.4–13.9) and gene diversity (expected heterozygosity He = 0.73–0.77) were observed, whereas deficiency of heterozygosity (inbreeding index f = 0.08–0.12) was detected in all populations. Genetic differentiation among populations was low (pairwise fixation index ranged from 0.003 to 0.088), but statistically significant. The usefulness of the information about genetic variations for genetic resource management of the populations in wild habitats and farms to keep genetic variation and setting up a breeding program of Asian green mussel was discussed.
- Published
- 2012
34. Transcriptome analysis of genes responding to NNV infection in Asian seabass epithelial cells
- Author
-
Gen Hua Yue, Le Wang, Peng Liu, Sek-Man Wong, and Jimmy Kwang
- Subjects
0301 basic medicine ,Fish Proteins ,Aquatic Science ,Biology ,Quantitative trait locus ,Cell Line ,Transcriptome ,03 medical and health sciences ,Fish Diseases ,RNA Virus Infections ,Environmental Chemistry ,Animals ,Nodaviridae ,RNA, Messenger ,Gene ,Genetics ,Innate immune system ,Gene Expression Profiling ,Epithelial Cells ,04 agricultural and veterinary sciences ,General Medicine ,biology.organism_classification ,Gene expression profiling ,030104 developmental biology ,Gene Expression Regulation ,Viperin ,040102 fisheries ,0401 agriculture, forestry, and fisheries ,Bass ,IRF3 ,Microsatellite Repeats - Abstract
Asian seabass is an important food fish in Southeast Asia. Viral nervous necrosis (VNN) disease, triggered by nervous necrosis virus (NNV) infection, has caused mass mortality of Asian seabass larvae, resulting in enormous economic losses in the Asian seabass industry. In order to better understand the complex molecular interaction between Asian seabass and NNV, we investigated the transcriptome profiles of Asian seabass epithelial cells, which play an essential role in immune regulation, after NNV infection. Using the next generation sequencing (NGS) technology, we sequenced mRNA from eight samples (6, 12, 24, 48 h post-inoculation) of mock and NNV-infected Asian seabass epithelial cell line, respectively. Clean reads were de novo assembled into a transcriptome consisting of 89026 transcripts with a N50 of 2617 bp. Furthermore, 251 differentially expressed genes (DEGs) in response to NNV infection were identified. Top DEGs include protein asteroid homolog 1-like (ASTE1), receptor-transporting protein 3 (RTP3), heat shock proteins 30 (HSP30) and 70 (HSP70), Viperin, interferon regulatory factor 3 (IRF3) and other genes related to innate immunity. Our data suggest that abundant and diverse genes corresponding to NNV infection. The results of this study could also offer vital information not only for identification of novel genes involved in Asian seabass-NNV interaction, but also for our understanding of the molecular mechanism of Asian seabass' response to viral infection. In addition, 24807 simple sequence repeats (SSRs) were detected in the assembled transcriptome, providing valuable resources for studying genetic variations and accelerating quantitative trait loci (QTL) mapping for disease resistance in Asian seabass in the future.
- Published
- 2015
35. High genetic diversity and substantial population differentiation in grass carp (Ctenopharyngodon idella) revealed by microsatellite analysis
- Author
-
Gen Hua Yue, Jiale Li, Jianjun Fu, Feng Liu, Zhiyi Bai, and Jun Hong Xia
- Subjects
Genetics ,Genetic diversity ,education.field_of_study ,Animal breeding ,biology ,Population ,Zoology ,Aquatic Science ,biology.organism_classification ,Grass carp ,Genotype ,Microsatellite ,Allele ,education ,Genotyping - Abstract
Grass carp is one of the most important freshwater food fish species in the world. We studied genetic diversity and population relationships of grass carp by genotyping 507 individuals from nine populations using 10 polymorphic microsatellites. In five wild populations and four cultured populations, a total of 212 alleles were detected at the 10 loci. All wild and cultured populations in China showed high allelic ( A = 6–13.7; Ar = 6.00–8.23) and gene diversity ( Ho = 0.71–0.79 and He = 0.71–0.82), while the cultured population Cul3 located in Malaysia showed low genetic diversity ( A = 6.4; Ar = 3.89, Ho = 0.48, He = 0.55). Both AMOVA and F ST analysis revealed significant population structuring ( F IS = 0.035, P F ST = 0.081, P F IT = 0.113, P
- Published
- 2009
36. Genetic variation and population structure of Asian seabass (Lates calcarifer) in the Asia-Pacific region
- Author
-
Felicia Feng, Huansein Lim, László Orbán, Ze Yuan Zhu, Ping Gong, Hong Yan Pang, Hui Ming Liu, Renee Chou, Loong Chueng Lo, Jason Tan, Grace Lin, Gen Hua Yue, Chun Ming Wang, and Jian Li
- Subjects
education.field_of_study ,Genetic diversity ,Ecology ,Barramundi ,Population ,Zoology ,Locus (genetics) ,Aquatic Science ,Biology ,Southeast asian ,biology.organism_classification ,Genetic variation ,Genotype ,Genetic variability ,education - Abstract
Asian seabass (Lates calcarifer) is an important marine foodfish species in Southeast Asia and Australia. To facilitate a selective breeding program conducted in Singapore, we genotyped 772 Asian seabass individuals collected from five cultured stocks and four wild populations originating from Singapore, Australia, Malaysia, Thailand, Indonesia and Taiwan using 14 polymorphic microsatellites. A total of 210 alleles were detected at 14 loci across the nine populations. Cultured stocks showed much lower allelic and gene diversity (A = 3.57–8.21 alleles/locus, Ho = 0.52–0.66 and He = 0.47–0.74, respectively) than wild populations (A = 9.14–10.71 alleles/locus, Ho = 0.71–0.74 and He = 0.74–0.78, respectively). The wild population from Thailand showed the highest allele richness (AR = 8.50 alleles/locus), whereas one of the three cultured Australian stocks had the lowest one (3.57 alleles/locus). Populations from Southeast Asia were more diverse genetically (A = 13.28, AR = 10.23, Ho = 0.72 and He = 0.78) than those from Australia (7.0, 6.56, 0.59 and 0.64, respectively) and Taiwan (7.35, 7.35, 0.66 and 0.68, respectively). Nearly three quarter (73.3%) of 90 private alleles were detected in populations from Southeast Asia. Genetic differentiation among populations/stocks was statistically significant (FST = 0.124, RST = 0.159, P < 0.05). Phylogenetic analysis showed that stocks from Australia clustered into one group, while the samples from Southeast Asian and Taiwan formed another group. All these data suggest significant genetic differentiation between Australian and Southeast Asian populations/stocks, and Australian populations contain only part of genetic variation of Asian seabass, which should be taken into account in aquaculture of Asian seabass. A total of 549 individuals from the four wild populations in Southeast Asia are being used in a selective breeding program.
- Published
- 2009
37. The complete mitochondrial genome of red grouper Plectropomus leopardus and its applications in identification of grouper species
- Author
-
Ze Yuan Zhu and Gen Hua Yue
- Subjects
Leopardus ,Mitochondrial DNA ,Phylogenetic tree ,Serranidae ,biology ,Ecology ,Plectropomus ,Zoology ,Grouper ,Aquatic Science ,biology.organism_classification ,Genome ,DNA sequencing - Abstract
Aquaculture of high-value finfish species, such as groupers, is an industry of increasing importance world wide. Groupers are represented by 15 genera and 159 species. Phenotypical classification of grouper species is difficult. Mitochondrial DNA (mtDNA) sequences can be used in differentiating species. We report the first complete mitochondrial genome sequence among grouper species, the complete mtDNA of Leopard coral grouper (Plectropomus leopardus). The complete mtDNA of P. leopardus was 16,714 bp long including a 1077 bp control region, 13 protein-coding genes, two rRNA and 22 tRNA. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes of 29 fish species representing 12 suborders indicated that P. leopardus was located in the cluster of fish species from the order Perciformes, supporting the traditional taxonomic classification of fish. Using nucleotide sequences of the NADH2 genes of 49 grouper species from eight genera, we constructed phylogenetic trees showing most of these species could be differentiated with sequences of the NADH2 gene, and the P. leopardus was closely related to P. maculatus, in agreement their phenotypic similarity. We developed one duplex PCR which could differentiate the two species P. leopardus and P. maculatus based on the D-loop DNA sequences of these two species. The complete mtDNA sequence of P. leopardus and duplex PCR provide useful tools for genetic studies and aquaculture of P. leopardus.
- Published
- 2008
38. Characterization of the duodenase-1 gene and its associations with resistance to Streptococuus agalactiae in hybrid tilapia (Oreochromis spp.)
- Author
-
Yubang Shen, Gui Hong Fu, Gen Hua Yue, and Feng Liu
- Subjects
Fish Proteins ,Candidate gene ,food.ingredient ,Molecular Sequence Data ,Aquatic Science ,Plant disease resistance ,medicine.disease_cause ,Kidney ,Polymorphism, Single Nucleotide ,Streptococcus agalactiae ,Exon ,food ,Streptococcal Infections ,medicine ,Environmental Chemistry ,Animals ,Amino Acid Sequence ,RNA, Messenger ,Intestinal Mucosa ,Gene ,Disease Resistance ,Skin ,Genetics ,Bacterial disease ,biology ,Base Sequence ,Serine Endopeptidases ,Tilapia ,General Medicine ,biology.organism_classification ,Intestines ,Oreochromis ,Liver ,Spleen - Abstract
Tilapia is a group of cultured teleost fishes whose production is threatened by some diseases. Identification of DNA markers associated with disease resistance in candidate genes may facilitate to accelerate the selection of disease resistance. The gene encoding a duodenase, which can trigger immune response, has not been studied in fish. We characterized the cDNA of duodenase-1 gene of hybrid tilapia. Its ORF is 759 bp, encoding a serine protease of 252 amino acids. This gene consisted of five exons and four introns. Its expression was detected in all 10 tissues examined, and it was highly expressed in the intestine and kidney. After a challenge with the bacterial pathogen, Streptococcus agalactiae, its expression was up-regulated significantly in the intestine, liver and spleen. We identified seven SNPs in the gene and found that four of them were significantly associated with the resistance to S. agalactiae (P < 0.05). The CGTCC haplotype, CAGTC/CGGTC and CGTCC/CGTCC diplotype were significantly associated with the resistance to S. agalactiae (P = 0.00, 0.04 and < 0.0001, respectively). In addition, one SNP was associated significantly with growth traits (P < 0.05). These findings suggest that the duodenase-1 gene plays an important role in the resistance to S. agalactiae in tilapia. The SNP markers in the duodenase-1 gene associated with resistance to the bacterial pathogen, may facilitate the selection of tilapia resistant to the bacterial disease.
- Published
- 2015
39. Genetic analyses of Asian seabass stocks using novel polymorphic microsatellites
- Author
-
Renee Chou, Gen Hua Yue, Grace Lin, Yin Xue Xu, Ze Yuan Zhu, Felicia Feng, and Loong Chueng Lo
- Subjects
Genetics ,Genetic diversity ,Multiplex polymerase chain reaction ,Genotype ,Microsatellite ,Locus (genetics) ,Genomic library ,Aquatic Science ,Allele ,Biology ,Stock (geology) - Abstract
To study genetic diversity of two cultured and one wild stock of Asian seabass ( Lates calcarifer ) in South-East Asia and their relationships, thirty-six polymorphic microsatellites were isolated from partial genomic libraries. The average allele number of the 36 microsatellites present among 32 individuals, was 7.4/locus, ranging from 2 to 17. One multiplex PCR set of nine polymorphic microsatellites was used to genotype 294 individuals from three stocks. High levels of allelic and genetic diversity were observed in all three stocks (average allele number = 8.2/locus and H e = 0.75 in the wild stock; allele number = 9.6 and H e = 0.76 in Singapore stock I; and allele number = 8.0 and H e = 0.72 in Singapore stock II). F IS values within each stock were very low. Significant genetic differentiation ( F ST = 0.03, P
- Published
- 2006
40. The Complete Mitochondrial Genome Sequence and Characterization of Single-Nucleotide Polymorphisms in the Control Region of the Asian Seabass (Lates calcarifer)
- Author
-
Loong Chueng Lo, Gen Hua Yue, Grace Lin, Felicia Feng, Ze Yuan Zhu, and Renee Chou
- Subjects
Mitochondrial DNA ,Molecular Sequence Data ,single-nucleotide polymorphisms and phylogeny ,Single-nucleotide polymorphism ,Aquatic Science ,Biology ,shotgun sequencing ,DNA, Mitochondrial ,Polymerase Chain Reaction ,Polymorphism, Single Nucleotide ,Applied Microbiology and Biotechnology ,Genome ,Barramundi ,RNA, Transfer ,Gene Order ,Animals ,Gene ,Phylogeny ,Genetics ,Base Composition ,Base Sequence ,Phylogenetic tree ,mtDNA ,Shotgun sequencing ,Nucleic acid sequence ,Genes, rRNA ,Sequence Analysis, DNA ,Ribosomal RNA ,Locus Control Region ,Biological Evolution ,Mitochondria ,Perciformes ,Original Article ,Biotechnology - Abstract
We determined the complete mtDNA nucleotide sequence of Lates calcarifer using the shotgun sequencing method. The mitochondrial DNA (mtDNA) was 16,535 base pairs (bp) in length, and contained 13 protein coding genes, 22 transfer RNAs, 2 ribosomal RNAs, and one major noncoding control region (CR). The CR was unusually short at only 768 bp. A striking feature of the mitochondrial genome was the high G+C content (46.1%), which is among the highest in fish. The gene order was identical to that of a typical vertebrate. Phylogenetic analyses using concatenated amino acid sequences of 12 protein-coding genes of 30 fish species representing 14 suborders clearly showed Lates calcarifer was located in the cluster of fish species from the order Perciformes, supporting the traditional systematic classification. We characterized single-nucleotide polymorphisms (SNPs) in the CR by sequencing the complete CR of 25 individuals obtained from Australia and Singapore. A total of 68 SNPs were detected. Eighteen SNPs were fixed with alternative nucleotides in Australian and Singapore seabass, and these SNPs could be used for differentiating fish from the two countries.
- Published
- 2006
41. Monitoring the genetic diversity of three Asian arowana (Scleropages formosus) captive stocks using AFLP and microsatellites
- Author
-
Gen Hua Yue, Lian Chuan Lim, László Orbán, and Yang Li
- Subjects
Genetic diversity ,Arowana ,biology ,Effective population size ,Genetic distance ,Ecology ,Captive breeding ,Zoology ,Microsatellite ,Amplified fragment length polymorphism ,Aquatic Science ,biology.organism_classification ,Scleropages formosus - Abstract
Asian arowana (Scleropages formosus) is listed by CITES as a highly endangered fish species. The genetic diversity and population structure of three Asian arowana captive stocks was analyzed using microsatellites and AFLP markers on 32 randomly collected individuals from each stock. Six AFLP primer pairs amplified a total of 324 bands across the three sample sets. The green stock showed the highest percentage of polymorphic bands (15.6%) and expected heterozygosity (0.26), followed by the red (13.0% and 0.24), then the golden one (12.7% and 0.22). Microsatellite analysis showed high allelic and gene diversity in all three varieties. The green stock showed higher allele number (100) and higher gene diversity (0.75) than the red (98 and 0.74) and golden ones (85 and 0.71), respectively. The estimates of long-term effective population size by two different methods ranged from 4741 to 7288 and from 25,056 to 64,641, respectively. Tests of heterozygosity and allele frequency distribution indicate that a recent bottleneck in any of the three captive populations is highly unlikely. Altogether, the data suggest that the captive breeding program for conservation and sustainable use of the endangered Asian arowana will be successful. In addition, we found that the differentiation among populations was intermediate (FST=0.047, RST=0.103) and the genetic distance was the smallest between the green and red, whereas the largest between the red and golden varieties.
- Published
- 2004
42. Microsatellites within genes and ESTs of common carp and their applicability in silver crucian carp
- Author
-
Mei Yin Ho, J. Komen, Gen Hua Yue, and László Orbán
- Subjects
rapid isolation ,Population ,markers ,polymerase-chain-reaction ,Locus (genetics) ,Animal Breeding and Genomics ,Aquatic Science ,Genome ,Common carp ,Gene mapping ,carassius-auratus gibelio ,Fokkerij en Genomica ,education ,cyprinus-carpio ,Genetics ,education.field_of_study ,biology ,compact genome ,biology.organism_classification ,dna polymorphisms ,genomic DNA ,fresh-water ,WIAS ,Crucian carp ,Microsatellite ,cross-species amplification ,simple sequence repeats - Abstract
Thirty-six new microsatellites were identified from common carp (Cyprinus carpio L.) by screening through genes found in GenBank, EST sequences from a testis cDNA library and a genomic DNA library enriched for CA repeats. Eleven of the twenty-eight microsatellites identified from genes and ESTs were AT repeats, suggesting their high abundance in the genome of common carp. Characterization of the 36 microsatellites on a panel of 18 unrelated common carp individuals revealed that all, except two, were polymorphic with an average allele number of 7.3/locus (range: 2-15 alleles/locus). The microsatellites located in genes and ESTs showed higher allele number than those eight which were isolated from a genomic DNA library (7.7/locus vs. 4.9/locus df=32, P
- Published
- 2004
43. A strain-specific and a sex-associated STS marker for Asian arowana (Scleropages formosus , Osteoglossidae)
- Author
-
László Orbán, D Ong, Gen Hua Yue, C C Wong, and L C Lim
- Subjects
Genetics ,genomic DNA ,Arowana ,biology ,Genetic marker ,Strain (biology) ,%22">Fish ,Amplified fragment length polymorphism ,Aquatic Science ,biology.organism_classification ,Scleropages formosus ,RAPD - Abstract
A sex-associated amplified fragment length polymorphism and a strain-specific random amplified polymorphic DNA marker were identified from Asian arowana (dragonfish; Scleropages formosus Muller & Schlegel) by screening pooled genomic DNA samples from three different strains as well as males and females respectively. Both markers were cloned, sequenced and successfully converted into sequence-tagged-site (STS) markers. The strain-specific STS marker could be applied to differentiate the Indonesian golden strain of Asian arowana from the green and blood-red strains before the stage when colours become identifiable. Individuals from the green strain could be sexed with an efficiency of 82.7% using the sex-associated STS marker. Thus, populations with preferred sex ratios can be formed without the need of rearing a large number of fish.
- Published
- 2003
44. Genetic analysis of two common carp broodstocks by RAPD and microsatellite markers
- Author
-
Sándor Egedi, Richárd Bártfai, Gen Hua Yue, Balázs Kovács, Béla Urbányi, Gizella Tamás, László Orbán, and László Horváth
- Subjects
Genetics ,Common carp ,Genetic diversity ,Genetic marker ,Genotype ,Genetic structure ,Microsatellite ,Aquatic Science ,Biology ,Allele frequency ,RAPD - Abstract
The whole broodstock of two Hungarian common carp farms—80 and 196 individuals—was analyzed by using random amplified polymorphic DNA (RAPD) assay and microsatellite analysis. Ten polymorphic RAPD markers and four microsatellites were selected to genotype both of the stocks. As expected, microsatellite analysis revealed more detailed information on genetic diversities than RAPD assay. Results obtained with both types of DNA markers showed lack of major differences between the genetic structure of the two stocks: heterozygosity values and allele frequencies were very similar. Dendrograms created from both sets of data did not show grouping of individuals according to stocks. Genotypes from the two stocks were also compared to those from a limited number of samples collected from other hatcheries and two rivers. Allele frequencies in the groups were similar, with the exception of wild carps. An interesting observation was that three private microsatellite alleles were found in the eight wild carp individuals, compared to the seven detected in the rest of the samples tested (372 individuals).
- Published
- 2003
45. Extensive search does not identify genomic sex markers in Tetraodon nigroviridis
- Author
-
Yang Li, László Orbán, J. A. Hill, Gen Hua Yue, and F. Chen
- Subjects
Genetics ,genomic DNA ,Genetic marker ,fungi ,Amplified fragment length polymorphism ,Aquatic Science ,Biology ,Tetraodon nigroviridis ,biology.organism_classification ,Tetraodontidae ,Genome ,Ecology, Evolution, Behavior and Systematics ,RAPD - Abstract
Three methods used for comparing genomic DNA did not detect a sex-specific genomic marker in the green spotted pufferfish Tetraodon nigroviridis.
- Published
- 2002
46. Characterization of the LECT2 gene and its associations with resistance to the big belly disease in Asian seabass
- Author
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Feng Liu, Xiaojun Liu, Jun Hong Xia, Zhi Yi Bai, Gen Hua Yue, Gui Hong Fu, and Zi Yi Wan
- Subjects
DNA, Complementary ,Molecular Sequence Data ,Single-nucleotide polymorphism ,Aquatic Science ,Real-Time Polymerase Chain Reaction ,Polymorphism, Single Nucleotide ,Exon ,Fish Diseases ,Complementary DNA ,Environmental Chemistry ,Animals ,Cloning, Molecular ,Gene ,DNA Primers ,Disease Resistance ,Vibrio ,Genetics ,biology ,Base Sequence ,Vibrio harveyi ,Gene Expression Profiling ,Intracellular Signaling Peptides and Proteins ,General Medicine ,Sequence Analysis, DNA ,biology.organism_classification ,Gene expression profiling ,genomic DNA ,Open reading frame ,Gene Components ,Liver ,Vibrio Infections ,Bass ,Spleen - Abstract
Leukocyte cell-derived chemotaxin-2 (LECT2) is an important protein of the innate immune system for the defense against bacterial infection. We cloned and characterized the LECT2 gene from Asian seabass (Lates calcarifer). Its complete cDNA consisted of an open reading frame of 459 bp encoding a protein of 152 amino acids. The genomic DNA sequence of this gene consists of four exons and three introns. Quantitative real-time PCR revealed that the LECT2 gene was expressed predominantly in liver while its expression was moderate in spleen and heart, and weak in other tissues. The LECT2 transcript was up-regulated in the kidney, spleen and liver in response to a challenge with a pathogenic bacterium Vibrio harveyi. In addition, we identified three single nucleotide polymorphisms (SNPs) in the LECT2 gene, and found significant associations between these polymorphisms and resistance to the big belly disease. These results suggest that the LECT2 gene play an important role in resistance to bacterial pathogens in fish. The SNP markers in the gene associated with the resistance to bacterial pathogens may facilitate selecting Asian seabass resistant to bacterial diseases.
- Published
- 2013
47. Estimating reproductive success of brooders and heritability of growth traits in Asian sea bass (Lates calcarifer) using microsatellites
- Author
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Wen Tong Yang, Felicia Feng, Huan Sein Lim, Jason Tan, Loong Chueng Lo, Grace Lin, Ze Yuan Zhu, Chun Ming Wang, Gen Hua Yue, Renee Chou, László Orbán, and Jian Li
- Subjects
Genetics ,Animal science ,Reproductive success ,Offspring ,Genetic variation ,Additive genetic effects ,Broodstock ,Aquatic Science ,Biology ,Heritability ,Sea bass ,Selective breeding - Abstract
Asian sea bass (Lates calcarifer) is one of the most important marine food fish species in Asia and Australia. To estimate the reproductive success of broodstock and heritabilities of growth-related traits, two independent full-factorial crosses (PI and PII) were created by crossing 10 males and 10 females. At 90 days post hatch (dph), the body weight (BW) and total length (TL) of 804 individuals from PI and 900 individuals from PII were measured and tissues samples of each fish were collected. Parents and offspring were genotyped with nine polymorphic microsatellites. Out of 1704 offspring from the two crosses, 98.7% were assigned to their parents. In PI, 19 of 20 parents produced offspring, while in PII, only five parents contributed to offspring. Low contribution of parents to offspring could lead to reduced genetic variation in the next generation. Heritabilities for growth-related traits were estimated using the pedigrees reconstructed using microsatellite genotypes. The estimates of heritability were 0.22±0.16 and 0.25±0.18 for BW, 0.31±0.14 and 0.24±0.21 for TL and 0.22±0.22 and 0.15±0.09 for Fulton's condition factor in the two crosses respectively. Body weights at 90 dph and at harvest (289 dph) were significantly correlated (r=0.601, P
- Published
- 2008
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