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Ning B, Li C, Zhao T, Zou Y, Zhan Y, Chang Y. Identification of Key Biomarkers of Growth-Related Traits in the Bay Scallop Argopecten irradians irradians via Multi-omics Analysis Strategies. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2025; 27:82. [PMID: 40338257 DOI: 10.1007/s10126-025-10457-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2025] [Accepted: 04/09/2025] [Indexed: 05/09/2025]
Abstract
In an attempt to promote and advance molecular-assisted selective breeding of shellfish, in this study, gills from selected (shell color as the marker trait and growth performance as the target trait) and unselected Argopecten irradians irradians were sampled. 2b-restriction site-associated DNA sequencing, genome-wide association study, comparative transcriptome, comparative small RNA transcriptome, miRNA-mRNA integrated analysis, quantitative real-time reverse transcription-polymerase chain reaction, and weighted gene co-expression network analysis were used to identify candidate SNPs, mRNAs, miRNAs, and miRNA/mRNA pairs with potential selective breeding value at a genomic scale in A. irradians irradians. The results revealed that a total of 6 significant SNPs were correlated closely with at least two examined growth-related traits. In addition, a total of 10 mRNAs and 7 miRNAs were identified to have positive correlations with shell length, shell height, shell width, total weight, and shell color. These candidate mRNAs and miRNAs may form 11 miRNA-mRNA pairs, which have great potential for developing molecular markers for molecular-assisted selective breeding of A. irradians irradians. The findings of this study will benefit the development of molecular-assisted breeding techniques in bay scallop aquaculture.
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Affiliation(s)
- Bingyu Ning
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, P. R. China
| | - Chengda Li
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, P. R. China
| | - Tanjun Zhao
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, P. R. China
- College of Life Science, Liaoning Normal University, Dalian, Liaoning, 116029, P. R. China
| | - Yang Zou
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, P. R. China
| | - Yaoyao Zhan
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, P. R. China.
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in North China's Sea, Ministry of Agriculture and Rural Affairs, Dalian Ocean University, Dalian, Liaoning, 116023, P. R. China.
- College of Life Science, Liaoning Normal University, Dalian, Liaoning, 116029, P. R. China.
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Aguilar-Camacho JM, Harry ND, Zakas C. Comparative Hox genes expression within the dimorphic annelid Streblospio benedicti reveals patterning variation during development. EvoDevo 2024; 15:12. [PMID: 39334480 PMCID: PMC11438215 DOI: 10.1186/s13227-024-00231-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Hox genes are transcriptional regulators that elicit cell positional identity along the anterior-posterior region of the body plan across different lineages of Metazoan. Comparison of Hox gene expression across distinct species reveals their evolutionary conservation; however, their gains and losses in different lineages can correlate with body plan modifications and morphological novelty. We compare the expression of 11 Hox genes found within Streblospio benedicti, a marine annelid that produces two types of offspring with distinct developmental and morphological features. For these two distinct larval types, we compare Hox gene expression through ontogeny using hybridization chain reaction (HCR) probes for in situ hybridization and RNA-seq data. We find that Hox gene expression patterning for both types is typically similar at equivalent developmental stages. However, some Hox genes have spatial or temporal differences between the larval types that are associated with morphological and life-history differences. This is the first comparison of developmental divergence in Hox gene expression within a single species and these changes reveal how body plan differences may arise in larval evolution.
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Affiliation(s)
| | - Nathan D Harry
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27607, USA
| | - Christina Zakas
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, 27607, USA.
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Mann RS, Glassford WJ. Hox genes: The original body builders. Semin Cell Dev Biol 2024; 152-153:1-3. [PMID: 37291029 PMCID: PMC10949336 DOI: 10.1016/j.semcdb.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Affiliation(s)
- Richard S Mann
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, United States; Department of Neuroscience, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, United States; Department of Systems Biology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, United States.
| | - William J Glassford
- Department of Biochemistry and Molecular Biophysics, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, United States; Department of Neuroscience, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, United States; Department of Systems Biology, Mortimer B. Zuckerman Mind Brain Behavior Institute, Columbia University, New York, NY 10027, United States
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Aguilar-Camacho JM, Harry ND, Zakas C. Comparative Hox genes expression within the dimorphic annelid Streblospio benedicti reveals patterning variation during development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.20.572624. [PMID: 38187656 PMCID: PMC10769376 DOI: 10.1101/2023.12.20.572624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Hox genes are transcriptional regulators that elicit cell positional identity along the anterior-posterior region of the body plan across different lineages of Metazoan. Comparison of Hox gene expression across distinct species reveals their evolutionary conservation, however their gains and losses in different lineages can correlate with body plan modifications and morphological novelty. We compare the expression of eleven Hox genes found within Streblospio benedicti, a marine annelid that produces two types of offspring with distinct developmental and morphological features. For these two distinct larval types, we compare Hox gene expression through ontogeny using HCR (hybridization chain reaction) probes for in-situ hybridization and RNA-seq data. We find that Hox gene expression patterning for both types is typically similar at equivalent developmental stages. However, some Hox genes have spatial or temporal differences between the larval types that are associated with morphological and life-history differences. This is the first comparison of developmental divergence in Hox genes expression within a single species and these changes reveal how body plan differences may arise in larval evolution.
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A special issue of Essays in Biochemistry on evolutionary developmental biology. Essays Biochem 2022; 66:703-705. [PMID: 36468772 DOI: 10.1042/ebc20220200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Evolutionary developmental biology (or evo devo) is a broad field that aims to understand how developmental processes evolve and how this underpins phenotypic change and organismal diversification. This encompasses a need to understand theoretical concepts in evolutionary biology and how tissues, cells, genes, proteins and regulatory elements function and evolve. The articles in this special issue review key topics in the field of evo devo including advances in theory and methodology as well as our latest knowledge about molecular, cellular and organismal functionality and diversification.
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