Comparative analysis of genetic diversity, growth performance, disease resistance and expression of growth and immune related genes among five different stocks of Labeo rohita (Hamilton, 1822)

Kamran, Muhammad; Razzaq, Hafsa; Noorullah, Muhammad; Ahmad, Mohd Faizal; Zuberi, Amina

doi:10.1016/j.aquaculture.2023.739277

Cited by 6 publications

(4 citation statements)

References 93 publications

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“…There is a common practice of sharing brooders between hatcheries of the same province instead of another province because of geographical distance. The present investigation affirms the correlation between genetic and geographical separation, which is in line with the previous research conducted by Sultana et al (2015) and Kamran et al (2023), who observed a comparable degree of genetic resemblance among populations from three separate hatcheries located in the same province (Faisalabad, Farooqabad, and Mianchannu hatcheries). The UPGMA dendrogram classified the eight strains into two primary clusters based on genetic distance, which were subsequently divided into sub-clusters, indicating the genetic proximity of seven strains.…”

Section: Fisheries and Aquatic Sciencessupporting

confidence: 93%

“…Three heterologous microsatellite primers used by Patel et al (2010) for cross-species amplification of 34 rohu microsatellite loci in Labeo bata and some other cyprinids and a CO1 gene primer designed and used by Ward et al (2005) for the identification of 207 fish species and assessment of different stocks of farmed L. rohita (Kamran et al, 2023) were selected (Table 1). Primers were synthesized from Macrogen (Macrogen, Seoul, Korea).…”

Section: Amplification Of Dna and Pcr Conditionsmentioning

confidence: 99%

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Assessment of genetic diversity among wild and captive-bred Labeo rohita through microsatellite markers and mitochondrial DNA

Noorullah,

Zuberi,

Zaman

et al. 2023

Fish Aquat Sci

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Genetic diversity serves as the basis for selecting and genetically enhancing any culturable species in aquaculture. Here, two different strains of wild (River Ravi and River Kabul) and six captive-bred strains of Labeo rohita from various provinces were selected, and genetic diversity among them was evaluated using three different microsatellite markers, i.e., Lr-28, Lr-29, and Lr-37, and one mitochondrial CO1 (Cytochrome c oxidase subunit 1) gene. Different strains of L. rohita were collected, and part of their caudal fin was cut and preserved in ethanol for DNA extraction and determination of genetic diversity among them. Results indicated that selected markers were polymorphic with polymorphic information content (PIC) content values above 0.5 with the highest in Lr-28 followed by Lr-29 and then Lr-37. The observed heterozygosity (Ho) of all strains was higher (Avg: 0.731) but less than the expected heterozygosity (He). Moreover, TMs and WRs showed the highest He, while TKs showed the lowest, He. Overall, inbreeding coefficient (FIS) values observed for all strains with selected markers were positive. The DNA barcoding with the CO1 gene revealed genetic variation among various strains, as demonstrated by the clades in the phylogenetic tree separating the strains into two distinct clusters that then divided into sub-clusters. In conclusion, TMs showed the highest heterozygosity as compared to other strains. Overall results provide the baseline data for the initiation of the genetic improvement program.

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Section: Fisheries and Aquatic Sciencessupporting

confidence: 93%

Section: Amplification Of Dna and Pcr Conditionsmentioning

confidence: 99%

Assessment of genetic diversity among wild and captive-bred Labeo rohita through microsatellite markers and mitochondrial DNA

Noorullah,

Zuberi,

Zaman

et al. 2023

Fish Aquat Sci

Self Cite

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show abstract

“…Given these challenges, a question arises: should selection strategies focus on enhancing the overall immune response of individuals within a population or on bolstering the overall health of the entire population? Some of our own research findings suggest the potential for improvement in immunological traits to improve overall health of populations [51,76]. However, future investigations should include a broader array of crucial immunological parameters, including the Lysozyme assay, haemolysin test, haemagglutination test, bacterial agglutination test, as well as cortisol, Transferrin, and Total IgM.…”

Section: Enhancing Overall Immune Response and Epidemiological Host T...mentioning

confidence: 91%

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

Nguyen

2023

Preprint

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Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease- and species-specific and contingent upon a multitude of factors. The field of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favourable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate to high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems, AI algorithms, and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.

show abstract

“…Given these challenges, a question arises: should selection strategies focus on enhancing the overall immune response of individuals within a population or on bolstering the overall health of the entire population? Some of our own research findings suggest the potential for improvement in immunological traits to improve overall health of populations [52,77]. However, future investigations should include a broader array of crucial immunological parameters, including the lysozyme assay, hemolysin test, hemagglutination test, and bacterial agglutination test, as well as cortisol, Transferrin, and Total IgM.…”

Section: Enhancing Overall Immune Response and Epidemiological Host T...mentioning

confidence: 91%

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

Nguyen

2024

Biology

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Diseases pose a significant and pressing concern for the sustainable development of the aquaculture sector, particularly as their impact continues to grow due to climatic shifts such as rising water temperatures. While various approaches, ranging from biosecurity measures to vaccines, have been devised to combat infectious diseases, their efficacy is disease and species specific and contingent upon a multitude of factors. The fields of genetics and genomics offer effective tools to control and prevent disease outbreaks in aquatic animal species. In this study, we present the key findings from our recent research, focusing on the genetic resistance to three specific diseases: White Spot Syndrome Virus (WSSV) in white shrimp, Bacterial Necrotic Pancreatitis (BNP) in striped catfish, and skin fluke (a parasitic ailment) in yellowtail kingfish. Our investigations reveal that all three species possess substantial heritable genetic components for disease-resistant traits, indicating their potential responsiveness to artificial selection in genetic improvement programs tailored to combat these diseases. Also, we observed a high genetic association between disease traits and survival rates. Through selective breeding aimed at enhancing resistance to these pathogens, we achieved substantial genetic gains, averaging 10% per generation. These selection programs also contributed positively to the overall production performance and productivity of these species. Although the effects of selection on immunological traits or immune responses were not significant in white shrimp, they yielded favorable results in striped catfish. Furthermore, our genomic analyses, including shallow genome sequencing of pedigreed populations, enriched our understanding of the genomic architecture underlying disease resistance traits. These traits are primarily governed by a polygenic nature, with numerous genes or genetic variants, each with small effects. Leveraging a range of advanced statistical methods, from mixed models to machine and deep learning, we developed prediction models that demonstrated moderate-to-high levels of accuracy in forecasting these disease-related traits. In addition to genomics, our RNA-seq experiments identified several genes that undergo upregulation in response to infection or viral loads within the populations. Preliminary microbiome data, while offering limited predictive accuracy for disease traits in one of our studied species, underscore the potential for combining such data with genome sequence information to enhance predictive power for disease traits in our populations. Lastly, this paper briefly discusses the roles of precision agriculture systems and AI algorithms and outlines the path for future research to expedite the development of disease-resistant genetic lines tailored to our target species. In conclusion, our study underscores the critical role of genetics and genomics in fortifying the aquaculture sector against the threats posed by diseases, paving the way for more sustainable and resilient aquaculture development.

show abstract

Comparative analysis of genetic diversity, growth performance, disease resistance and expression of growth and immune related genes among five different stocks of Labeo rohita (Hamilton, 1822)

Cited by 6 publications

References 93 publications

Assessment of genetic diversity among wild and captive-bred Labeo rohita through microsatellite markers and mitochondrial DNA

Assessment of genetic diversity among wild and captive-bred Labeo rohita through microsatellite markers and mitochondrial DNA

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

Genetics and Genomics of Infectious Diseases in Key Aquaculture Species

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