Genome-wide identification of loci associated with growth in rainbow trout

Ali, Ali; Al-Tobasei, Rafet; Lourenço, Daniela; Leeds, Timothy D.; Kenney, Brett; Salem, Mohamed

doi:10.21203/rs.2.17035/v2

Cited by 3 publications

(4 citation statements)

References 105 publications

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“…In addition, a significant number of the genes were associated with transferase, motor, oxidoreductase, and structural molecule activities. In the cellular component category, many of the genes were associated with the cytoplasmic compartment, membranes, myosin complex, and extracellular region compartment (Supplemental 4 and 5), which is consistent with the findings of previous studies [32] .…”

Section: Snp and Indel Functional Annotationsupporting

confidence: 90%

“…Single-nucleotide polymorphisms (SNPs) are the most common form of genetic variation in humans and drive phenotypic variation. Due to evolutionary conservation, SNPs and indels (insertion and deletions) are depleted in functionally important sequence elements [32,33] . Here, using the SAMtools/Popoolation software package.…”

Section: Distribution Of Different Snp and Indel Types During Sheep F...mentioning

confidence: 99%

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Identification and functional analysis of transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing from the oocyte to the preimplantation stage of sheep by single-cell RNA sequencing

Zhang¹,

Shi²,

Zhu³

et al. 2023

Preprint

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Numerous dynamic and complicated processes characterize development from the oocyte to the embryo. However, given the importance of functional transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing during embryonic development, the effect that these features have on the blastomeres of 2-, 4-, 8-, 16-cell, and morula stages of development have not been studied. Here, we conducted a scRNA-seq survey of cells from sheep from the oocyte to the blastocyst developmental stages. We then carried out experiments to identify and functionally analyze the transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms (SNPs), and alternative splicing (AS). We founded that between the oocyte and zygote groups significantly down-regulated genes and the second-largest change in gene expression occurred between the 8- and 16-cell stages. We used various methods to construct a profile to characterize cellular and molecular features and systematically analyze the related GO and KEGG profile of cells of all stages from the oocyte to the blastocyst. This large-scale, single-cell atlas provides key cellular information and will likely assist clinical studies in improving preimplantation genetic diagnosis.

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Section: Snp and Indel Functional Annotationsupporting

confidence: 90%

Section: Distribution Of Different Snp and Indel Types During Sheep F...mentioning

confidence: 99%

Identification and functional analysis of transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing from the oocyte to the preimplantation stage of sheep by single-cell RNA sequencing

Zhang¹,

Shi²,

Zhu³

et al. 2023

Preprint

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show abstract

“…and chromosome 19 with 1,671 cSNPs (Figure 7). A larger percent of cSNPs (9.5%) were present in the downstream region (3′ UTR) of genes as compared to the upstream located cSNPs (0.24%), implying that those located downstream may play a role in microRNA and post-transcriptional regulation of gene expression (Ali et al, 2019;Ali et al, 2019Ali et al, 2020. Fewer cSNPs found to be residing in the upstream gene region might be functional SNPs modulating binding of the transcription factor and changing the gene expression abilities (Li et al, 2018).…”

Section: Csnp Identification and Annotationmentioning

confidence: 99%

Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita

Nandanpawar

Sahoo

et al. 2023

Front. Genet.

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In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes’ underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.

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“…In fishes, the major fields of interest in GWAS are growth in Atlantic salmon (Gutierrez et al, 2015), rainbow trout (Reis Neto et al, 2019), common carp (Su et al, 2020); muscle and filet yield in rainbow trout (Gonzalez-Pena et al, 2016;Salem et al, 2018;Ali et al, 2019) and Atlantic salmon (Yoshida et al, 2017); as well as disease resistance in channel catfish (Geng et al, 2015) and Atlantic salmon (Robledo et al, 2018;Hillestad et al, 2020).…”

Section: Genome-wide Association Studiesmentioning

confidence: 99%

Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals?

et al. 2021

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Due to the steadily increasing need for seafood and the plateauing output of fisheries, more fish need to be produced by aquaculture production. In parallel with the improvement of farming methods, elite food fish lines with superior traits for production must be generated by selection programs that utilize cutting-edge tools of genomics. The purpose of this review is to provide a historical overview and status report of a selection program performed on a catadromous predator, the Asian seabass (Lates calcarifer, Bloch 1790) that can change its sex during its lifetime. We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select the best possible options and avoid potential pitfalls.

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Genome-wide identification of loci associated with growth in rainbow trout

Cited by 3 publications

References 105 publications

Identification and functional analysis of transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing from the oocyte to the preimplantation stage of sheep by single-cell RNA sequencing

Identification and functional analysis of transcriptome profiles, long non-coding RNAs, single-nucleotide polymorphisms, and alternative splicing from the oocyte to the preimplantation stage of sheep by single-cell RNA sequencing

Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita

Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals?

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