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Wenne R. Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations. Genes (Basel) 2023; 14:genes14040808. [PMID: 37107566 PMCID: PMC10138012 DOI: 10.3390/genes14040808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/28/2023] [Accepted: 03/17/2023] [Indexed: 03/29/2023] Open
Abstract
A large number of species and taxa has been studied for genetic polymorphism. Microsatellites have been known as hypervariable neutral molecular markers with the highest resolution power in comparison with any other markers. However, the discovery of a new type of molecular marker—single nucleotide polymorphism (SNP) has put the existing applications of microsatellites to the test. To ensure good resolution power in studies of populations and individuals, a number of microsatellite loci from 14 to 20 was often used, which corresponds to about 200 independent alleles. Recently, these numbers have tended to be increased by the application of genomic sequencing of expressed sequence tags (ESTs), and the choice of the most informative loci for genotyping depends on the aims of research. Examples of successful applications of microsatellite molecular markers in aquaculture, fisheries, and conservation genetics in comparison with SNPs have been summarized in this review. Microsatellites can be considered superior markers in such topics as kinship and parentage analysis in cultured and natural populations, the assessment of gynogenesis, androgenesis and ploidization. Microsatellites can be coupled with SNPs for mapping QTL. Microsatellites will continue to be used in research on genetic diversity in cultured stocks, and also in natural populations as an economically advantageous genotyping technique.
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Affiliation(s)
- Roman Wenne
- Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
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2
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Comparative analysis of muscle nutrient in two types of hybrid bream and native bream. REPRODUCTION AND BREEDING 2022. [DOI: 10.1016/j.repbre.2022.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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3
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Gong D, Tao M, Xu L, Hu F, Wei Z, Wang S, Wang Y, Liu Q, Wu C, Luo K, Tang C, Zhou R, Zhang C, Wang Y, Liu S. An improved hybrid bream derived from a hybrid lineage of Megalobrama amblycephala (♀)×Culter alburnus (♂). SCIENCE CHINA. LIFE SCIENCES 2022; 65:1213-1221. [PMID: 34757543 DOI: 10.1007/s11427-021-2005-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/19/2021] [Indexed: 06/13/2023]
Abstract
Distant hybridization is an important technique in fish genetic breeding. In this study, based on the establishment of an allodiploid fish lineage (BT, 2n=48, F1-F6) derived from distant hybridization between female Megalobrama amblycephala (BSB, 2n=48) and male Culter alburnus (TC, 2n=48), and the backcross progeny (BTB, 2n=48) derived by backcrossing female F1 of BT to male BSB, an improved hybrid bream (BTBB, 2n=48) was obtained by backcrossing BTB (♀) to BSB (♂). Moreover, the morphological and genetic characteristics of BTBB individuals were investigated; BTBB was similar to BSB in appearance but had a higher body height than BSB. The study results regarding chromosome numbers and DNA content indicated that BTBB is a diploid hybrid fish. The 5S rDNA and Hox gene of BTBB were inherited from the original parents. Gonadal development in BTBB was normal. On the other hand, BTBB had a faster growth rate, higher muscle protein level, and lower muscle carbohydrate level than BSB. Hence, bisexual fertile BTBB is promoted and can be applied as a high-quality fish, and it can also be used as a new fish germplasm resource to develop high-quality fish further. Thus, this study is of great significance for fish genetic breeding.
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Affiliation(s)
- Dingbin Gong
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Lihui Xu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Fangzhou Hu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Zehong Wei
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Shi Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Qingfeng Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chang Wu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Kaikun Luo
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chenchen Tang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Rong Zhou
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China
| | - Yuequn Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan Normal University, Changsha, 410081, China.
- College of Life Sciences, Hunan Normal University, Changsha, 410081, China.
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Balakirev ES. Recombinant Mitochondrial Genomes Reveal Recent Interspecific Hybridization between Invasive Salangid Fishes. Life (Basel) 2022; 12:661. [PMID: 35629328 PMCID: PMC9144084 DOI: 10.3390/life12050661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 04/26/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022] Open
Abstract
The interspecific recombination of the mitochondrial (mt) genome, if not an experimental artifact, may result from interbreeding of species with broken reproductive barriers, which, in turn, is a frequent consequence of human activities including species translocations, habitat modifications, and climate change. This issue, however, has not been addressed for Protosalanx chinensis and other commercially important and, simultaneously, invasive salangid fishes that were the product of successful aquaculture in China. To assess the probability of interspecific hybridization, we analyzed the patterns of diversity and recombination in the complete mitochondrial (mt) genomes of these fishes using the GenBank resources. A sliding window analysis revealed a non-uniform distribution of the intraspecific differences in P. chinensis with four highly pronounced peaks of divergence centered at the COI, ND4L-ND4, and ND5 genes, and also at the control region. The corresponding divergent regions in P. chinensis show a high sequence similarity (99−100%) to the related salangid fishes, Neosalanx tangkahkeii and N. anderssoni. This observation suggests that the divergent regions of P. chinensis may represent a recombinant mitochondrial DNA (mtDNA) containing mt genome fragments belonging to different salangid species. Indeed, four, highly significant (pairwise homoplasy index test, P < 0.00001) signals of recombination have been revealed at coordinates closely corresponding to the divergent regions. The recombinant fragments are, however, not fixed, and different mt genomes of P. chinensis are mosaic, containing different numbers of recombinant events. These facts, along with the high similarity or full identity of the recombinant fragments between the donor and the recipient sequences, indicate a recent interspecific hybridization between P. chinensis and two Neosalanx species. Alternative hypotheses, including taxonomical misidentifications, sequence misalignments, DNA contamination, and/or artificial PCR recombinants, are not supported by the data. The recombinant fragments revealed in our study represent diagnostic genetic markers for the identification and distinguishing of hybrids, which can be used to control the invasive dynamics of hybrid salangid fishes.
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Affiliation(s)
- Evgeniy S Balakirev
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Far Eastern Branch, Russian Academy of Sciences, Vladivostok 690041, Russia
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Chu D, Wei L. Direct in vivo observation of the effect of codon usage bias on gene expression in Arabidopsis hybrids. JOURNAL OF PLANT PHYSIOLOGY 2021; 265:153490. [PMID: 34375820 DOI: 10.1016/j.jplph.2021.153490] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 08/01/2021] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
Hybrids are the perfect materials to study cis regulatory elements because the two parental alleles are subjected to identical trans environments. There has been a debate on whether synonymous codon usage could affect gene expression. In vitro experiments found that luciferase genes with enhanced codon optimality showed elevated mRNA expression. However, the underlying mechanism is still unclear, and no direct evidence is observed to support this notion. By mapping the RNA-seq data of hybrids of Arabidopsis thaliana and Arabidopsis lyrata, we quantified the allele-specific reads and estimated the relative expression of orthologous genes. We focused on orthologous genes with dN = 0 and dS > 0, which means that they only differ in synonymous codon usage. We found that orthologous genes with higher codon optimality in A. thaliana tend to have higher expression levels of the A. thaliana allele. Codon usage bias could influence gene expression. This phenomenon is not only found in in vitro experiments but also supported by in vivo observations. Therefore, synonymous mutations could have a broad impact from multiple aspects and should not be automatically ignored in genomic studies. KEY MESSAGE: In Arabidopsis hybrids, alleles with higher codon optimality tend to have higher expression levels.
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Affiliation(s)
- Duan Chu
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China
| | - Lai Wei
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China.
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Wang S, Liu Q, Huang X, Yang C, Chen L, Han M, Shu Y, Wang M, Li W, Hu F, Wen M, Luo K, Wang Y, Zhou R, Zhang C, Tao M, Zhao R, Tang C, Liu S. The rapid variation of Hox clusters reveals a clear evolutionary path in a crucian carp-like homodiploid fish lineage. REPRODUCTION AND BREEDING 2021. [DOI: 10.1016/j.repbre.2021.09.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
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7
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Wang Y, Sun W, Gu Q, Yao J, Tan H, Huang X, Qin Q, Tao M, Zhang C, Liu S. Variations in the Mitochondrial Genome of a Goldfish-Like Hybrid [Koi Carp (♀) × Blunt Snout Bream (♂)] Indicate Paternal Leakage. Front Genet 2021; 11:613520. [PMID: 33552134 PMCID: PMC7861200 DOI: 10.3389/fgene.2020.613520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/01/2020] [Indexed: 11/13/2022] Open
Abstract
Previously, a homodiploid goldfish-like fish (2n = 100; GF-L) was spontaneously generated by self-crossing a homodiploid red crucian carp-like fish (2n = 100; RCC-L), which was in turn produced via the distant hybridization of female koi carp (Cyprinus carpio haematopterus, KOC, 2n = 100) and male blunt snout bream (Megalobrama amblycephala, BSB, 2n = 48). The phenotypes and genotypes of RCC-L and GF-L differed from those of the parental species but were similar to diploid red crucian carp (2n = 100; RCC) and goldfish (2n = 100; GF), respectively. We sequenced the complete mitochondrial DNAs (mtDNAs) of the KOC, BSB, RCC-L, GF-L, and subsequent generations produced by self-crossing [the self-mating offspring of RCC-L (RCC-L-F2) to the self-mating offspring of RCC-L-F2 (RCC-L-F3) and the self-mating offspring of GF-L (GF-L-F2)]. Paternal mtDNA fragments were stably embedded in the mtDNAs of both lineages, forming chimeric DNA fragments. In addition to these chimeras, several nucleotide positions in the RCC-L and GF-L lineages differed from the parental bases, and were instead identical with RCC and GF, respectively. Moreover, RCC-L and GF-L mtDNA organization and nucleotide composition were more similar to those of RCC and GF, respectively, compared to parental mtDNA. Finally, phylogenetic analyses indicated that RCC-L and GF-L clustered with RCC and GF, not with the parental species. The molecular dating time shows that the divergence time of KOC and GF was about 21.26 Mya [95% highest posterior density (HPD): 24.41-16.67 Mya], which fell within the period of recent. The heritable chimeric DNA fragments and mutant loci identified in the mtDNA of the RCC-L and GF-L lineages provided important evidence that hybridizations might lead to changes in the mtDNA and the subsequent generation of new lineages. Our findings also demonstrated for the first time that the paternal mtDNA was transmitted into the mtDNA of homodiploid lineages (RCC-L and GF-L), which provided evidence that paternal DNA plays a role in inherited mtDNA. These evolutionary analyses in mtDNA suggest that GF might have diverged from RCC after RCC diverged from koi carp.
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Affiliation(s)
- Yude Wang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Wenzhen Sun
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qianhong Gu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Jiajun Yao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Huifang Tan
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Xu Huang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Qinbo Qin
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Min Tao
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Chun Zhang
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
| | - Shaojun Liu
- State Key Laboratory of Developmental Biology of Freshwater Fish, Engineering Research Center of Polyploid Fish Reproduction and Breeding of the State Education Ministry, College of Life Sciences, Hunan Normal University, Changsha, China
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8
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Lu M, Li XY, Li Z, Du WX, Zhou L, Wang Y, Zhang XJ, Wang ZW, Gui JF. Regain of sex determination system and sexual reproduction ability in a synthetic octoploid male fish. SCIENCE CHINA-LIFE SCIENCES 2020; 64:77-87. [PMID: 32529288 DOI: 10.1007/s11427-020-1694-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/27/2020] [Indexed: 02/08/2023]
Abstract
Polyploids in vertebrates are generally associated with unisexual reproduction, but the direct consequences of polyploidy on sex determination system and reproduction mode remain unknown. Here, we synthesized a group of artificial octoploids between unisexual gynogenetic hexaploid Carassius gibelio and sexual tetraploid Carassius auratus. The synthetic octoploids were revealed to have more than 200 chromosomes, in which 50 chromosomes including the X/Y sex determination system were identified to transfer from sexual tetraploid C. auratus into the unisexual gynogenetic hexaploid C. gibelio. Significantly, a few synthetic octoploid males were found to be fertile, and one octoploid male was confirmed to regain sexual reproduction ability, which exhibits characteristics that are the same to sexual reproduction tetraploid males, such as 1:1 sex ratio occurrence, meiosis completion and euploid sperm formation in spermatogenesis, as well as normal embryo development and gene expression pattern during embryogenesis. Therefore, the current finding provides a unique case to explore the effect of sex determination system incorporation on reproduction mode transition from unisexual gynogenesis to sexual reproduction along with genome synthesis of recurrent polyploidy in vertebrates.
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Affiliation(s)
- Meng Lu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xi-Yin Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Zhi Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Xuan Du
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Li Zhou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Juan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhong-Wei Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Jian-Fang Gui
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Wuhan, 430072, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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