Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

Gui, Jian‐Fang; Zhou, Li; Li, Xi-Yin

doi:10.1016/j.watbs.2021.11.001

Cited by 52 publications

(42 citation statements)

References 236 publications

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“…Many aquatic animals display significant growth differences between males and females; therefore, mono-sex population culture is an effective way to improve economic value ( Mei and Gui, 2015 ; Gui et al, 2022 ). Sex determination is an important research field in developmental biology and evolutionary biology, and it is a plastic developmental process ( Charlesworth and Mank, 2010 ; Li and Gui, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, sexual dimorphism was observed, and it showed that the males grow faster than the females, but the sex-determining mechanism of crayfish is still unclear. So, there is an urgent need to establish a precise breeding program to improve economic traits and promote the development of crayfish industry ( Gui et al, 2022 ). Traditional genetic breeding programs mainly rely on phenotypic trait selection, which has a long breeding cycle and low selection efficiency ( Zenger et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

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A High-Density Genetic Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Red Swamp Crayfish (Procambarus clarkii)

et al. 2022

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Red swamp crayfish (Procambarus clarkii) is a commercially important species in global aquaculture and most successfully invasive freshwater shrimp in China. In order to determine the genetic basis of growth- and sex-related traits, a high-density genetic linkage map was constructed using 2b-RAD sequencing technology in a full-sib family. The consensus map contains 4,878 SNP markers assigned to 94 linkage groups (LGs) and spanned 6,157.737 cM with an average marker interval of 1.26 cM and 96.93% genome coverage. The quantitative trait locus (QTL) mapping for growth and sex traits was performed for the first time. QTL mapping uncovers 28 QTLs for growth-related traits in nine LGs, explaining 7.9–14.4% of the phenotypic variation, and identifies some potential candidate growth-related genes such as mih, lamr, golgb1, nurf301, and tbcd1 within the QTL intervals. A single major locus for sex determination was revealed in LG20 that explains 59.3–63.7% of the phenotypic variations. Some candidate sex-related genes, such as vps4bl, ssrf, and acot1, were identified in the QTL intervals and found to be differentially expressed in the muscle tissues between the females and the males. Furthermore, the identified SNPs were revealed to be female heterozygotes, suggesting that red swamp crayfish might have the female heterogametic ZZ/ZW sex determination system. The present study provides a valuable resource for marker-assisted selection and genetic improvement and for further genetic and genomic research in red swamp crayfish.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

A High-Density Genetic Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Red Swamp Crayfish (Procambarus clarkii)

et al. 2022

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“…As a lower vertebrate, fish models were helpful in understanding sex determination and the evolutionary history of vertebrates (Conte et al, 2021; Sember et al, 2021; Tao et al, 2021; Yin & Gui, 2018). The potential of fish biology and biotechnology breeding cannot be underestimated in a challenging era of thriving genomic resources and enhancing food security (Gui et al, 2022). In most fish species, sex chromosomes are less differentiated, making it difficult to distinguish male and female based on the morphology of sex chromosomes (Nagahama et al, 2021).…”

Section: Introductionmentioning

confidence: 99%

“…

The potential of fish biology and biotechnology breeding cannot be underestimated in a challenging era of thriving genomic resources and enhancing food security (Gui et al, 2022). In most fish species, sex chromosomes are less differentiated, making it difficult to distinguish male and female based on the morphology of sex chromosomes (Nagahama et al, 2021).

…”

mentioning

confidence: 99%

Development and verification of sex‐specific molecular marker for Golden pompano ( Trachinotus blochii )

Zhang

Song

Liang

et al. 2022

Aquaculture Research

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There are common significant character differences between genders in many fish. The sex‐specific genetic markers are important tools for research and industry. Golden pompano (Trachinotus blochii) is a commercial mass‐produced species with sex growth differences. Our study includes the whole genome re‐sequencing data of T. blochii from four populations. A total of 2,183,486 high‐quality clean reads were obtained for subsequent information analysis. Association analysis of single nucleotide polymorphism markers with sex was carried out, the genome‐wide association studyGWAS was carried out using the simple linear regression model (Q), and a high‐scored site loci in LG20 exhibiting significant association with sex was found. A heterozygous mutation was observed in this site in female fish (G/A), and a homozygous mutation in males (A/A). Within the 50kb annotation interval of this variant site, hsd17b1 was found to be linked to sex‐related pathways significantly. Based on the site, we developed a simple and efficient polymerase chain reaction‐based sex‐specific molecular marker for identifying the T. blochii genetics sex. It will benefit the sex‐controlled breeding and sex development study of the golden pompano.

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“…Gibel carp, which is widely distributed across the Eurasian continent (38)(39)(40)(41)(42)(43), has been recognized as an evolutional hexaploid with over 150 chromosomes in comparison with tetraploid goldfish (C. auratus) with 100 chromosomes (44)(45)(46). Analyses of several conserved genes suggests that two extra rounds of polyploidy, an early allopolyploidy and a later autopolyploidy, had taken place during gibel carp evolution (35,36,(47)(48)(49)(50).…”

Section: Introductionmentioning

confidence: 99%

Two Duplicated Ptpn6 Homeologs Cooperatively and Negatively Regulate RLR-Mediated IFN Response in Hexaploid Gibel Carp

Tong

Zhou

et al. 2021

Front. Immunol.

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Src homology region 2 domain-containing phosphatase 1 (SHP1), encoded by the protein tyrosine phosphatase nonreceptor type 6 (ptpn6) gene, belongs to the family of protein tyrosine phosphatases (PTPs) and participates in multiple signaling pathways of immune cells. However, the mechanism of SHP1 in regulating fish immunity is largely unknown. In this study, we first identified two gibel carp (Carassius gibelio) ptpn6 homeologs (Cgptpn6-A and Cgptpn6-B), each of which had three alleles with high identities. Then, relative to Cgptpn6-B, dominant expression in adult tissues and higher upregulated expression of Cgptpn6-A induced by polyinosinic-polycytidylic acid (poly I:C), poly deoxyadenylic-deoxythymidylic (dA:dT) acid and spring viremia of carp virus (SVCV) were uncovered. Finally, we demonstrated that CgSHP1-A (encoded by the Cgptpn6-A gene) and CgSHP1-B (encoded by the Cgptpn6-B gene) act as negative regulators of the RIG-I-like receptor (RLR)-mediated interferon (IFN) response via two mechanisms: the inhibition of CaTBK1-induced phosphorylation of CaMITA shared by CgSHP1-A and CgSHP1-B, and the autophagic degradation of CaMITA exclusively by CgSHP1-A. Meanwhile, the data support that CgSHP1-A and CgSHP1-B have sub-functionalized and that CgSHP1-A overwhelmingly dominates CgSHP1-B in the process of RLR-mediated IFN response. The current study not only sheds light on the regulative mechanism of SHP1 in fish immunity, but also provides a typical case of duplicated gene evolutionary fates.

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Rethinking fish biology and biotechnologies in the challenge era for burgeoning genome resources and strengthening food security

Cited by 52 publications

References 236 publications

A High-Density Genetic Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Red Swamp Crayfish (Procambarus clarkii)

A High-Density Genetic Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Red Swamp Crayfish (Procambarus clarkii)

Development and verification of sex‐specific molecular marker for Golden pompano ( Trachinotus blochii )

Two Duplicated Ptpn6 Homeologs Cooperatively and Negatively Regulate RLR-Mediated IFN Response in Hexaploid Gibel Carp

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