Genetic architecture of early life history traits for channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂ hybrid production

Myers, Jaelen N.; Chatakondi, Nagaraj G.; Dunham, Rex A.; Butts, Ian A. E.

doi:10.1016/j.aquaculture.2019.734436

Cited by 9 publications

(7 citation statements)

References 82 publications

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“…This analysis reveals that the maternal transcriptomic cargo contained in the eggs may vary among species. A similar conclusion was drawn by Myers et al [69], who reported that genes constituting quality markers in other species (as reported by Sullivan et al [66]) were also poorly expressed or not at all expressed in ovulated eggs of hybrid catfish until neurulation. Interspecies differences in transcript abundance in eggs between cod and rainbow trout were also reported by Wargelius et al [65].…”

Section: Candidate Markers Of Egg Qualitysupporting

confidence: 81%

Neurodevelopment vs. the immune system: complementary contributions of maternally-inherited gene transcripts and proteins to successful egg development in fish

Żarski

Cam

Fröhlich

et al. 2021

Preprint

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Background: In Metazoans, embryonic development relies on maternally-inherited mRNAs and proteins that are critical for early developmental success and known to play major roles at later stages, beyond zygotic genome activation. However, very poor concordance between transcript and protein levels in oocytes and embryos of vertebrates suggest that maternally-inherited proteins and maternally-inherited mRNAs are playing different roles in unfertilized eggs, not considered to date comprehensively. The aim of this study was to investigate the respective contribution of maternally-inherited mRNAs and maternally-inherited proteins to egg molecular cargo and to its developmental competence using pikeperch, an ecologically and commercially relevant freshwater fish species, as a model. Results: Our data shed new light on the importance of maternally-inherited mRNAs in nervous system development suggesting that neurogenesis is a major mRNA-dependent non-genetic inheritance factor. In contrast, our results highlight a specific role of maternally-inherited proteins in immune response in ovulated eggs suggesting that maternal proteins would rather contribute to developmental success through protection of the embryo against pathogens. Further analysis revealed susceptibility of the transcriptome to modifications during the post-vitellogenic processes (i.e., final oocyte maturation and ovulation), whereas proteomic cargo remains unaffected. This may negatively affect developmental competence of the egg and possibly influence further nervous system development of the embryo. Conclusions: Our study provides novel insights into the understanding of type-specific roles of maternally-inherited molecules in fish. Here we show, for the first time, that transcripts and proteins have distinct, yet complementary, functions in the egg of teleost fish. Maternally-inherited mRNAs would shape embryo neurodevelopment and possibly the future behavior of the fish, while maternally-inherited proteins would rather be responsible for protecting the embryo against pathogens. Additionally, we observed that processes directly preceding ovulation may considerably affect the reproductive success by modifying expression level of genes crucial for proper embryonic development, being novel fish egg quality markers (e.g., smarca4 or h3f3a). These results are of major importance for understanding the influence of external factors on reproductive fitness in both captive and wild-type fish species.

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Section: Candidate Markers Of Egg Qualitysupporting

confidence: 81%

Neurodevelopment vs. the immune system: complementary contributions of maternally-inherited gene transcripts and proteins to successful egg development in fish

Żarski

Cam

Fröhlich

et al. 2021

Preprint

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“…2001; Waldbieser and Bosworth 2013; Myers et al. 2020). Elemental and isotopic concentrations in hard parts represent a permanent tag with potential to identify locations inhabited by an individual fish during its life span, including natal origin (Whitledge et al.…”

Section: Origin Markersmentioning

confidence: 99%

“…Age-0 fish that were immersed for 6 h in a 700-mg/L solution of OTC buffered to a pH of 7.0 displayed 12% mortality and 100% mark visibility in both pectoral spines and otoliths after 4 weeks (Stewart and Long 2011). Genetic marking has been used sparingly for management of Blue, Channel, and Flathead Catfish fisheries, although the approach is well represented in aquaculture literature (Waldbieser et al 2001;Waldbieser and Bosworth 2013;Myers et al 2020). Elemental and isotopic concentrations in hard parts represent a permanent tag with potential to identify locations inhabited by an individual fish during its life span, including natal origin (Whitledge et al 2007).…”

Section: Origin Markersmentioning

confidence: 99%

A Review of Marking and Tagging Methods for Blue Catfish, Channel Catfish, and Flathead Catfish

Neely

Koch

Kramer

2021

N American J Fish Manag

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Catfishes (Ictaluridae) are among North America’s most important ichthyofauna for human consumption and recreation. As such, research on Blue Catfish Ictalurus furcatus, Channel Catfish I. punctatus, and Flathead Catfish Pylodictis olivaris has been abundant in historic and contemporary literature. A common technique for studying catfish involves marking or tagging fish to understand behavior, sampling efficiency, and population dynamics. Marking and tagging methods used in these studies may be divided into eight primary types, including fin clips, strap tags, anchor tags, transbody tags, injectable tags, skin alterations, origin markers, and telemetry. Each of these methods is appropriate for specific objectives and characterized by varying retention rates and data resolution (i.e., batch or individual identification) that warrant consideration when designing projects. For example, fin clips may be most appropriate as a short‐term mark requiring batch identification (e.g., stocking evaluation), whereas telemetry might be most appropriate as a long‐term tag requiring individual identification (e.g., habitat selection). This review summarizes marking and tagging methods used for evaluation of Blue, Channel, and Flathead catfish and synthesizes results using examples from previously conducted catfish research. Further discussion is included on information gaps, emerging trends, and guidance for scientists planning and conducting studies that require marking of catfish.

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“…Pathogenic infection disease is the number one cause of catfish production loss. Paternal genetic contributions from blue catfish are essential for improving industry-relevant traits [ 18 ], and F 1 hybrid catfish can reduce loss from 40% to 20% by carrying disease-resistant alleles from the blue catfish genome. Our research team, along with other researchers, has identified the genetic loci responsible for the resistance of 3 major catfish diseases, Enteric Septicemia of Catfish (ESC), columnaris, and Aeromonas diseases [ 24–27 ], and in most cases, the blue catfish allele is the resistance allele.…”

Section: Discussionmentioning

confidence: 99%

“…Collectively, these heterosis characteristics enable a commercial production rate of 13,000 kg/ha, which doubles the yield of traditional channel catfish farming [ 11 , 16 , 17 ]. In this context, paternal genetic contributions from blue catfish are essential for improving industry-relevant traits [ 18 ], and yet the blue catfish genome resources are not publicly available. A high-quality genome assembly of the blue catfish genome will provide the essential toolkit for the following research areas to enhance catfish breeding and advance the scientific knowledge of heterosis in fish.…”

Section: Introductionmentioning

confidence: 99%

Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies

Wang

Butts

et al. 2022

GigaScience

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Background The blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (Ictalurus punctatus) × male blue catfish (Ictalurusfurcatus) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel–blue hybrid also provides an excellent model to investigate molecular mechanisms of environment-dependent heterosis. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available. Results The blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% Eukaryota and 97.0% Actinopterygii BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA sequencing evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species single-nucleotide polymorphism (SNP) density is 0.32% between the most aquaculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish. Conclusions We reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing and genome engineering, and reproductive enhancement of the blue catfish and hybrid catfish.

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Genetic architecture of early life history traits for channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂ hybrid production

Cited by 9 publications

References 82 publications

Neurodevelopment vs. the immune system: complementary contributions of maternally-inherited gene transcripts and proteins to successful egg development in fish

Neurodevelopment vs. the immune system: complementary contributions of maternally-inherited gene transcripts and proteins to successful egg development in fish

A Review of Marking and Tagging Methods for Blue Catfish, Channel Catfish, and Flathead Catfish

Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies

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Genetic architecture of early life history traits for channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂ hybrid production

Cited by 9 publications

References 82 publications

Neurodevelopment vs. the immune system: complementary contributions of maternally-inherited gene transcripts and proteins to successful egg development in fish

Neurodevelopment vs. the immune system: complementary contributions of maternally-inherited gene transcripts and proteins to successful egg development in fish

A Review of Marking and Tagging Methods for Blue Catfish, Channel Catfish, and Flathead Catfish

Chromosome-level assembly and annotation of the blue catfishIctalurus furcatus, an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies

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Genetic architecture of early life history traits for channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂ hybrid production