Submit to Genes Review for Genes Propose a Special Issue

Journal Menu

Journal Browser

► Journal Browser

Genetic Breeding and Genomics of Marine Shellfish

Print Special Issue Flyer
Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (20 October 2022) | Viewed by 20795

Share This Special Issue

Special Issue Editor

Prof. Dr. Donghong Niu

E-Mail Website
Guest Editor

College of Fisheries and Life Science, Shanghai Ocean University, Shanghai 201306, China
Interests: selective breeding; genetics; genomics; molecular markers; genetic diversity; shellfish

Special Issue Information

Dear Colleagues,

Shellfish constitute the second largest phylum in the world, with more than 110,000 species. As shellfish are rich in nutrition and possess a unique flavor, they have long been one of the main aquatic products in the world. The common edible shellfish mainly include abalone, oyster, scallop, mussel and clam. In recent years, the role of genetic breeding in the development of the marine shellfish culture industry has become more and more prominent. Molecular markers are one of the most powerful tools for the genetic analysis of economically important traits in aquaculture animals. Following the rapid development of next-generation sequencing (NGS), an increasing number of methodologies have been developed for the cost-effective genotyping of SNPs in aquaculture animals, such as whole-genome sequencing, restriction-site-associated DNA sequencing (RAD-seq), and GBS.

This Special Issue will cover aspects of the genetic breeding and genomics of shellfish species, such as breeding approaches, genome sequencing, gene variants, the identification of genetic markers, population genetics, functional genes related to traits, the construction of genetic linkage maps, QTL localization and the construction of shellfish genetic breeding systems. This topic will provide valuable information on genetic breeding technologies and approaches, contributing to improving breeding progress, economic traits and resistance to abiotic stresses.

Prof. Dr. Donghong Niu
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

breeding
genetics
genomics
diversity
biomarkers
QTL
shellfish

Benefits of Publishing in a Special Issue

Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
e-Book format: Special Issues with more than 10 articles can be published as dedicated e-books, ensuring wide and rapid dissemination.

Further information on MDPI's Special Issue polices can be found here.

Published Papers (10 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

17 pages, 5374 KiB

Open AccessArticle

The Inhibitory Effects of RNA-Interference-Mediated Guanylate Cyclase Knockdown on Larval Metamorphosis and Early Progeny Growth of Razor Clam

by Yuting Han, Beibei Li, Yifeng Li and Donghong Niu

Genes 2023, 14(2), 459; https://doi.org/10.3390/genes14020459 - 10 Feb 2023

Viewed by 1487

Abstract

Guanylate cyclase (GC, cGMPase) is a key enzyme in organisms, catalyzing the synthesis of cGMP from GTP, thus making cGMP work. cGMP plays a vital role in the regulation of cell and biological growth as a second messenger in signaling pathways. In this study, we screened and identified cGMPase from the razor clam Sinonovacula constricta, which encoded 1257 amino acids and was widely expressed in different tissues, especially the gill and liver. We also screened one double-stranded RNA (dsRNA), cGMPase, which was used to knockdown cGMPase at three larval metamorphosis development stages: trochophores-veliger larve, veliger larve-umbo larve, and umbo larve-creeping larvae. We showed that interference at these stages significantly inhibited larval metamorphosis and survival rates. cGMPase knockdown resulted in an average metamorphosis rate of 60% and an average mortality rate of 50% when compared with control clams. After 50 days, shell length and body weight were inhibited to 53% and 66%, respectively. Thus, cGMPase appeared to regulate metamorphosis development and growth in S. constricta. By examining the role of the key gene in the metamorphosis development of S. constricta larvae and the growth and development period, we can provide some data reference for studying the growth and development mechanism of shellfish, and the results provided basic information for the breeding of S. constricta. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Figure 1

14 pages, 1899 KiB

Open AccessArticle

Effects of L-arginine on Nitric Oxide Synthesis and Larval Metamorphosis of Mytilus coruscus

by You-Ting Zhu, Lin-Li Liang, Tian-Tian Liu, Xiao Liang and Jin-Long Yang

Genes 2023, 14(2), 450; https://doi.org/10.3390/genes14020450 - 9 Feb 2023

Cited by 1 | Viewed by 1497

Abstract

To investigate the regulatory functions of L-arginine and nitric oxide (NO) on Mytilus coruscus metamorphosis, M. coruscus larvae were exposed to an inhibitor of nitric oxide synthase (NOS), aminoguanidine hemisulfate (AGH), and a substrate for NO synthesis, L-arginine. We observed that NO levels showed a significant increase, and this trend continued with L-arginine treatment. When NOS activity was inhibited, the larvae could not synthesize NO, and metamorphosis was not inhibited even in the presence of L-arginine. On transfecting pediveliger larvae with NOS siRNA followed by L-arginine exposure, we found that the larvae did not produce NO and that the larval metamorphosis rate was significantly increased, suggesting that L-arginine regulates M. coruscus larval metamorphosis by promoting NO synthesis. Our findings improve our understanding of the effects of marine environmental factors on larval metamorphosis of mollusks. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Figure 1

15 pages, 3272 KiB

Open AccessArticle

Stage-Specific Transcriptomes of the Mussel Mytilus coruscus Reveals the Developmental Program for the Planktonic to Benthic Transition

by Yu-Qing Wang, Qi Liu, Yan Zhou, Lizhi Chen, Yue-Ming Yang, Xue Shi, Deborah M. Power and Yi-Feng Li

Genes 2023, 14(2), 287; https://doi.org/10.3390/genes14020287 - 21 Jan 2023

Cited by 6 | Viewed by 2138

Abstract

Many marine invertebrate larvae undergo complex morphological and physiological changes during the planktonic—benthic transition (a.k.a. metamorphosis). In this study, transcriptome analysis of different developmental stages was used to uncover the molecular mechanisms underpinning larval settlement and metamorphosis of the mussel, Mytilus coruscus. Analysis of highly upregulated differentially expressed genes (DEGs) at the pediveliger stage revealed enrichment of immune-related genes. The results may indicate that larvae co-opt molecules of the immune system to sense and respond to external chemical cues and neuroendocrine signaling pathways forecast and trigger the response. The upregulation of adhesive protein genes linked to byssal thread secretion indicates the anchoring capacity required for larval settlement arises prior to metamorphosis. The results of gene expression support a role for the immune and neuroendocrine systems in mussel metamorphosis and provide the basis for future studies to disentangle gene networks and the biology of this important lifecycle transformation. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Figure 1

15 pages, 13129 KiB

Open AccessArticle

AMPK Promotes Larval Metamorphosis of Mytilus coruscus

by Wen Zhang, Yuyi Wang, Xiaomeng Hu, Zhongsheng Zhou, Youting Zhu, Xiao Liang and Jin-Long Yang

Genes 2022, 13(12), 2384; https://doi.org/10.3390/genes13122384 - 16 Dec 2022

Cited by 4 | Viewed by 1714

Abstract

Metamorphosis is a critical process in the transition from planktonic life to benthic life for marine invertebrates, which is accompanied by a large amount of energy consumption. Previous studies have proved that AMP-activated protein kinase (AMPK), as a vital energy regulator, plays a prominent role in mediating the growth and development of terrestrial animals. However, its function in the growth and development of marine invertebrates, especially in metamorphosis, remains elusive. This study explored the function of AMPK in the larval metamorphosis of Mytilus coruscus. The full-length cDNA of AMPK genes in M. coruscus was cloned and characterized, which is composed of three subunits, McAMPKα, McAMPKβ, and McAMPKγ. Pharmacological tests demonstrated that through the application of an AMPK activator, AMP substantially enhanced the larval metamorphosis rate (p < 0.05). By contrast, the larval metamorphosis rate decreased significantly after being treated with the AMPK inhibitor Compound C (p < 0.05). McAMPK gene knock-down resulted in a reduction in McAMPK gene expression (p < 0.05), and the larval metamorphosis of M. coruscus was significantly restrained (p < 0.05). These results indicated that AMPK signaling is vital in the larval metamorphosis of M. coruscus, which advances further understanding in exploring the molecular mechanisms in the metamorphosis of marine invertebrate larvae. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Figure 1

17 pages, 3238 KiB

Open AccessArticle

Comparing the Efficiency of Single-Locus Species Delimitation Methods within Trochoidea (Gastropoda: Vetigastropoda)

by Bingyu Guo and Lingfeng Kong

Genes 2022, 13(12), 2273; https://doi.org/10.3390/genes13122273 - 2 Dec 2022

Cited by 12 | Viewed by 3049

Abstract

In the context of diminishing global biodiversity, the validity and practicality of species delimitation methods for the identification of many neglected and undescribed biodiverse species have been paid increasing attention. DNA sequence-based species delimitation methods are mainly classified into two categories, namely, distance-based and tree-based methods, and have been widely adopted in many studies. In the present study, we performed three distance-based (ad hoc threshold, ABGD, and ASAP) and four tree-based (sGMYC, mGMYC, PTP, and mPTP) analyses based on Trochoidea COI data and analyzed the discordance between them. Moreover, we also observed the performance of these methods at different taxonomic ranks (the genus, subfamily, and family ranks). The results suggested that the distance-based approach is generally superior to the tree-based approach, with the ASAP method being the most efficient. In terms of phylogenetic methods, the single threshold version performed better than the multiple threshold version of GMYC, and PTP showed higher efficiency than mPTP in delimiting species. Additionally, GMYC was found to be significantly influenced by taxonomic rank, showing poorer efficiency in datasets at the genus level than at higher levels. Finally, our results highlighted that cryptic diversity within Trochoidea (Mollusca: Vetigastropoda) might be underestimated, which provides quantitative evidence for excavating the cryptic lineages of these species. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Graphical abstract

14 pages, 2249 KiB

Open AccessArticle

Systematic Evaluation of Genomic Prediction Algorithms for Genomic Prediction and Breeding of Aquatic Animals

by Kuiqin Wang, Ben Yang, Qi Li and Shikai Liu

Genes 2022, 13(12), 2247; https://doi.org/10.3390/genes13122247 - 29 Nov 2022

Cited by 8 | Viewed by 2440

Abstract

The extensive use of genomic selection (GS) in livestock and crops has led to a series of genomic-prediction (GP) algorithms despite the lack of a single algorithm that can suit all the species and traits. A systematic evaluation of available GP algorithms is thus necessary to identify the optimal GP algorithm for selective breeding in aquaculture species. In this study, a systematic comparison of ten GP algorithms, including both traditional and machine-learning algorithms, was conducted using publicly available genotype and phenotype data of eight traits, including weight and disease resistance traits, from five aquaculture species. The study aimed to provide insights into the optimal algorithm for GP in aquatic animals. Notably, no algorithm showed the best performance in all traits. However, reproducing kernel Hilbert space (RKHS) and support-vector machine (SVM) algorithms achieved relatively high prediction accuracies in most of the tested traits. Bayes A and random forest (RF) better prevented noise interference in the phenotypic data compared to the other algorithms. The prediction performances of GP algorithms in the Crassostrea gigas dataset were improved by using a genome-wide association study (GWAS) to select subsets of significant SNPs. An R package, “ASGS,” which integrates the commonly used traditional and machine-learning algorithms for efficiently finding the optimal algorithm, was developed to assist the application of genomic selection breeding of aquaculture species. This work provides valuable information and a tool for optimizing algorithms for GP, aiding genetic breeding in aquaculture species. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Figure 1

19 pages, 3725 KiB

Open AccessArticle

Full Mitochondrial Genomes Reveal Species Differences between the Venerid Clams Ruditapes philippinarum and R. variegatus

by Yumei Tang, Zhongming Huo, Yang Liu, Yuhang Wang, Luya Zuo, Lei Fang, Wen Zhao, Yue Tan and Xiwu Yan

Genes 2022, 13(11), 2157; https://doi.org/10.3390/genes13112157 - 19 Nov 2022

Cited by 1 | Viewed by 1737

Abstract

In natural sea areas along the coast of China, venerid clams Ruditapes philippinarum and R. variegatus exhibit similar adult shell forms and are especially difficult to distinguish as spat and juveniles. This study used comparative mitochondrial genome analysis to reveal differences between these species. The results showed that: (1) the mitochondrial genomes of R. philippinarum and R. variegatus share a large number of similar gene clusters arranged in consistent order, yet they also display noncommon genes, with both gene rearrangements and random losses found; (2) the 13 protein-coding genes in R. philippinarum as well as two-fold and four-fold degenerate sites in R. variegatus have an evident AT bias; (3) the Ka/Ks ratio of the mitochondrial ATP8 gene was significantly higher in R. philippinarum than in R. variegatus, and an analysis of selection pressure revealed that the mitochondrial NADH dehydrogenase subunit 2 gene and NADH dehydrogenase subunit 6 gene of R. variegatus were under great selective pressure during its evolution; and finally, (4) the two species clustered into one branch on a phylogenetic tree, further affirming their phylogenetic closeness. Based on these results, we speculate that the species differences between R. variegatus and R. philippinarum are largely attributable to adaptive evolution to the environment. The present findings provide a reference for the development of germplasm identification. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Figure 1

14 pages, 10277 KiB

Open AccessArticle

Identification and Functional Analysis of MAPKAPK2 in Hyriopsis cumingii

by Yang Gu, Meiling Liu, Yayu Wang, Yingduo Huo, Zongyu Liu, Wu Jin and Guiling Wang

Genes 2022, 13(11), 2060; https://doi.org/10.3390/genes13112060 - 7 Nov 2022

Cited by 2 | Viewed by 1557

Abstract

MAPKAPK2 (MK2) is an important regulator of the p38 mitogen-activated protein kinase (p38 MAPK) pathway, which is involved in a plethora of cellular processes concluding the development of gamete cells in meiosis and resisting pathogenic bacterial infestation. Hyriopsis cumingii is a significant mussel resource in China and a good material for pearl breeding. To explore the role of MK2 in H. cumingii, MK2 was identified and cloned, whose full-length cDNA was 1568 bp, including 87 bp in 5′ UTR, 398 bp in 3′ UTR, and 1083 bp in the open reading frame (ORF) region, encoding 360 amino acids. The expression of MK2 was the highest in the gills. Meanwhile, there was a significant difference in the gonads. After Aeromonas hydrophila and Lipopolysaccharide (LPS) infestation, the transcript level of the MK2 was upregulated in the gills. It indicated that MK2 might be involved in the innate immune response of H. cumingii after a pathogenic attack. After quantifying H. cumingii of different ages, it was found that the expression of MK2 was highest at 1 year old. In situ hybridization (ISH) results showed that the blue-purple hybridization signal was very significant in the oocytes and egg membranes of the female gonads of H. cumingii. The expression of MK2 increased gradually at the age of 1 to 5 months and showed a downward trend at the age of 5 to 8 months. It was suggested that MK2 might play an important role in the formation of primitive germ cells in H. cumingii. To sum up, MK2 might not only be involved in the immune response against pathogenic bacterial infection but also might play an important role in the development of the gonads in H. cumingii. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Figure 1

19 pages, 7128 KiB

Open AccessArticle

Insights into the Deep Phylogeny and Novel Divergence Time Estimation of Patellogastropoda from Complete Mitogenomes

by Jiantong Feng, Jing Miao, Yingying Ye, Jiji Li, Kaida Xu, Baoying Guo and Xiaojun Yan

Genes 2022, 13(7), 1273; https://doi.org/10.3390/genes13071273 - 18 Jul 2022

Cited by 1 | Viewed by 2297

Abstract

To further understand the origin and evolution of Patellogastropoda, we determined the mitochondrial genome sequence of Cellana toreuma, and compared its mitogenome characteristics with the other four limpets of Nacellidae. The ratio of Ka and Ks indicated that these Nacellidae species were suffering a purifying selection, with exception of the atp6 gene. The gene sequence is basically consistent among families, while there are great differences among Lottidae species. According to the mitogenome sequences of selected gastropod species, we reconstructed a new phylogenetic tree with two methods. The data complement the mitogenome database of limpets and is a favorable research tool for the phylogenetic analysis of Gastropoda. It is found that there is a long-branch attraction (LBA) artefact in the family Lottiidae of Patellogastropoda. Therefore, the Patellogastropoda was separated by Heterobranchia, and Lottiidae is located at the root of the whole phylogenetic tree. Furthermore, we constructed the divergence time tree according to the Bayesian method and discussed the internal historical dynamics, and divergence differences among the main lineages of 12 Patellogastropoda under an uncorrelated relaxed molecular clock. In turn, we made a more comprehensive discussion on the divergence time of limpets at the molecular level. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Figure 1

19 pages, 4025 KiB

Open AccessArticle

Tissue-Specific and Time-Dependent Expressions of PC4s in Bay Scallop (Argopecten irradians irradians) Reveal Function Allocation in Thermal Response

by Ancheng Liu, Xiujiang Hou, Junhao Zhang, Wen Wang, Xuecheng Dong, Jianshu Li, Xinghai Zhu, Qiang Xing, Xiaoting Huang, Jingjie Hu and Zhenmin Bao

Genes 2022, 13(6), 1057; https://doi.org/10.3390/genes13061057 - 13 Jun 2022

Cited by 3 | Viewed by 1929

Abstract

Transcriptional coactivator p15 (PC4) encodes a structurally conserved but functionally diverse protein that plays crucial roles in RNAP-II-mediated transcription, DNA replication and damage repair. Although structures and functions of PC4 have been reported in most vertebrates and some invertebrates, the PC4 genes were less systematically identified and characterized in the bay scallop Argopecten irradians irradians. In this study, five PC4 genes (AiPC4s) were successfully identified in bay scallops via whole-genome scanning through in silico analysis. Protein structure and phylogenetic analyses of AiPC4s were conducted to determine the identities and evolutionary relationships of these genes. Expression levels of AiPC4s were assessed in embryos/larvae at all developmental stages, in healthy adult tissues and in different tissues (mantles, gills, hemocytes and hearts) being processed under 32 °C stress with different time durations (0 h, 6 h, 12 h, 24 h, 3 d, 6 d and 10 d). Spatiotemporal expression profiles of AiPC4s suggested the functional roles of the genes in embryos/larvae at all developmental stages and in healthy adult tissues in bay scallop. Expression regulations (up- and down-) of AiPC4s under high-temperature stress displayed both tissue-specific and time-dependent patterns with function allocations, revealing that AiPC4s performed differentiated functions in response to thermal stress. This work provides clues of molecular function allocation of PC4 in scallops in response to thermal stress and helps in illustrating how marine bivalves resist elevated seawater temperature. Full article

(This article belongs to the Special Issue Genetic Breeding and Genomics of Marine Shellfish)

► Show Figures

Journal Menu

Journal Browser

Genetic Breeding and Genomics of Marine Shellfish

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (10 papers)

Research

Further Information

Guidelines

MDPI Initiatives

Follow MDPI