1
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Garcia BF, Mastrochirico-Filho VA, Gallardo-Hidalgo J, Campos-Montes GR, Medrano-Mendoza T, Rivero-Martínez PV, Caballero-Zamora A, Hashimoto DT, Yáñez JM. A high-density linkage map and sex-determination loci in Pacific white shrimp (Litopenaeus vannamei). BMC Genomics 2024; 25:565. [PMID: 38840101 PMCID: PMC11155064 DOI: 10.1186/s12864-024-10431-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
BACKGROUND Expansion of genomic resources for the Pacific white shrimp (Litopenaeus vannamei), such as the construction of dense genetic linkage maps, is crucial for the application of genomic tools in order to improve economically relevant traits. Sexual dimorphism exists in Pacific white shrimp, and the mapping of the sex-determination region in this species may help in future reproductive applications. We have constructed male, female, and sex-averaged high-density genetic maps using a 50 K single-nucleotide polymorphism (SNP) array, followed by a genome-wide association study (GWAS) to identify genomic regions associated with sex in white shrimp. RESULTS The genetic map yielded 15,256 SNPs assigned to 44 linkage groups (LG). The lengths of the male, female, and sex-averaged maps were 5,741.36, 5,461.20 and 5,525.26 cM, respectively. LG18 was found to be the largest for both sexes, whereas LG44 was the shortest for males and LG31 for females. A sex-determining region was found in LG31 with 21 statistically significant SNPs. The most important SNP was previously identified as a sex-linked marker and was able to identify 99% of the males and 88% of the females. Although other significant markers had a lower ability to determine sex, putative genes were intercepted or close to them. The oplophorus-luciferin 2-monooxygenase, serine/arginine repetitive matrix protein and spermine oxidase genes were identified as candidates with possible participation in important processes of sexual differentiation in shrimp. CONCLUSIONS Our results provide novel genomic resources for shrimp, including a high-density linkage map and new insights into the sex-determining region in L. vannamei, which may be usefulfor future genetics and reproduction applications.
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Affiliation(s)
- Baltasar F Garcia
- São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile
| | - Vito A Mastrochirico-Filho
- São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile
| | | | - Gabriel R Campos-Montes
- Departamento de El Hombre y su Ambiente, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Thania Medrano-Mendoza
- Doctorado en Ciencias Agropecuarias, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Psique Victoria Rivero-Martínez
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Alejandra Caballero-Zamora
- Departamento de Producción Agrícola y Animal, Universidad Autónoma Metropolitana, Unidad Xochimilco, Calzada del Hueso 1100, Coyoacán, CDMX, C.P. 04960, México
| | - Diogo T Hashimoto
- São Paulo State University (Unesp), Aquaculture Center of UNESP, Jaboticabal, SP, 14884-900, Brazil
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, 8820000, Chile.
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2
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Sumana SL, Wang P, Zhang C, Jing X, Zhu J, Tang Y, Liu W, Su S, Liao Y. Genetic diversity of the common carp black strain population based on mtDNA ( D-loop and cytb). Heliyon 2024; 10:e30307. [PMID: 38774331 PMCID: PMC11107203 DOI: 10.1016/j.heliyon.2024.e30307] [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: 03/22/2023] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/24/2024] Open
Abstract
The common strain black carp (Cyprinus carpio var. baisenensis) is a culturally important carp strain that is raised and cultured in Guangxi Province, China. Its color reflects the interactions between the Burau people and their surrounding environment. The population of the common carp black strain was isolated and cultured in a rice-fish integration system. To explore the genetic diversity and protection of germplasm resources, we analyzed mitochondrial DNA (mtDNA) sequences, specifically the displacement loop (D-loop) and cytochrome b (Cytb), using single-nucleotide polymorphisms (SNP). We compared these sequences with those from four other local common carp populations. The study included a total of 136 adult common carps from five strain populations: the common black carp strain (HJ = 31), Jian (F = 30), Heilongjiang (H = 10), Songpu (S = 31), and Saijiang (SJ = 34). The results of the Cytb and D-loop analyses showed that the Heilongjiang carp (H) and Saijiang (SJ) populations had the highest levels of haplotype diversity (0.867 ± 0.034785) and nucleotide diversity (π = 0.0063 ± 0.000137 and 0.0093 ± 0.000411), respectively. On the other hand, the Common carp black strain population (HJ) exhibited the lowest haplotype diversity in both Cytb and D-loop, with haplotype 2 being the most commonly observed among the populations. Private haplotypes dominated the five common carp populations, which were significantly different at P<0.001. Furthermore, analyzing the coefficient of genetic differentiation (Fst), the highest genetic difference was observed between Saijiang (SJ) and Heilongjiang (H) (Fst = 0.963), whereas the lowest was observed between Songpu (S) and the Common carp black strain population (HJ) (Fst = 0.019) for the Cytb gene sequences. For the D-loop, the Common carp black strain population (HJ) and Songpu (S) (Fst = 0.7) had the highest values, and Heilongjiang (H) and Common black carp strain (HJ) had an Fst of 0.125. Additionally, the AMOVA analysis revealed a higher level of variance for the Cytb and D-loop genes, indicating lower genetic diversity within the local carp community. On the other hand, the phylogenetic tree analysis showed that the five carp populations were closely related and formed a distinct cluster. The distinct cluster of populations suggests a common ancestor or recent gene flow, possibly due to geographic proximity or migration history, and unique genetic characteristics, possibly due to adaptations or selective pressures. The results of this study provide valuable insights into the genetic diversity of the common strain black carp, which can have implications for conservation, breeding programs, evolutionary studies, and fisheries management.
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Affiliation(s)
- Sahr Lamin Sumana
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
| | - Peipei Wang
- Guangxi Fisheries Introduction and Cultivation Center, Nanning, PR China
| | - Chengfeng Zhang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
| | - Xiaojun Jing
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Jian Zhu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Yongkai Tang
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Wenting Liu
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Shengyan Su
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, 214081, PR China
- Key Laboratory of Integrated Rice-Fish Farming Ecology, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, 214081, PR China
| | - Yu Liao
- Guangxi Fisheries Introduction and Cultivation Center, Nanning, PR China
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3
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Perez-Enriquez R, Juárez OE, Galindo-Torres P, Vargas-Aguilar AL, Llera-Herrera R. Improved genome assembly of the whiteleg shrimp Penaeus (Litopenaeus) vannamei using long- and short-read sequences from public databases. J Hered 2024; 115:302-310. [PMID: 38451162 DOI: 10.1093/jhered/esae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Abstract
The Pacific whiteleg shrimp Penaeus (Litopenaeus) vannamei is a highly relevant species for the world's aquaculture development, for which an incomplete genome is available in public databases. In this work, PacBio long-reads from 14 publicly available genomic libraries (131.2 Gb) were mined to improve the reference genome assembly. The libraries were assembled, polished using Illumina short-reads, and scaffolded with P. vannamei, Feneropenaeus chinensis, and Penaeus monodon genomes. The reference-guided assembly, organized into 44 pseudo-chromosomes and 15,682 scaffolds, showed an improvement from previous reference genomes with a genome size of 2.055 Gb, N50 of 40.14 Mb, L50 of 21, and the longest scaffold of 65.79 Mb. Most orthologous genes (92.6%) of the Arthropoda_odb10 database were detected as "complete," and BRAKER predicted 21,816 gene models; from these, we detected 1,814 single-copy orthologues conserved across the genomic references for Marsupenaeus japonicus, F. chinensis, and P. monodon. Transcriptomic-assembly data aligned in more than 99% to the new reference-guided assembly. The collinearity analysis of the assembled pseudo-chromosomes against the P. vannamei and P. monodon reference genomes showed high conservation in different sets of pseudo-chromosomes. In addition, more than 21,000 publicly available genetic marker sequences were mapped to single-site positions. This new assembly represents a step forward to previously reported P. vannamei assemblies. It will be helpful as a reference genome for future studies on the evolutionary history of the species, the genetic architecture of physiological and sex-determination traits, and the analysis of the changes in genetic diversity and composition of cultivated stocks.
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Affiliation(s)
- Ricardo Perez-Enriquez
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
| | - Oscar E Juárez
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
- Dirección de Investigación en Acuacultura, Programa de Recursos Genéticos, Instituto Mexicano de Investigación en Pesca y Acuacultura Sustentables, Coyoacán, Ciudad de México, Mexico
| | - Pavel Galindo-Torres
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
| | - Ana Luisa Vargas-Aguilar
- Aquaculture Program, Centro de Investigaciones Biológicas del Noroeste, S.C., La Paz, B.C.S., Mexico
- Departamento de Recursos del Mar, Centro de Investigación y de Estudios Avanzados, Unidad Mérida, Mérida, Yucatán, Mexico
| | - Raúl Llera-Herrera
- Functional Genomics Laboratory, Unidad Académica Mazatlán, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Mazatlán, Sinaloa, Mexico
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4
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Granillo-Luna ON, Hernandez-Aguirre LE, Peregrino-Uriarte AB, Duarte-Gutierrez J, Contreras-Vergara CA, Gollas-Galvan T, Yepiz-Plascencia G. The anaplerotic pyruvate carboxylase from white shrimp Litopenaeus vannamei: Gene structure, molecular characterization, protein modelling and expression during hypoxia. Comp Biochem Physiol A Mol Integr Physiol 2022; 269:111212. [PMID: 35417748 DOI: 10.1016/j.cbpa.2022.111212] [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: 02/10/2022] [Revised: 04/05/2022] [Accepted: 04/07/2022] [Indexed: 10/18/2022]
Abstract
Hypoxic zones are spreading worldwide in marine environments affecting many organisms. Shrimp and other marine crustaceans can withstand environmental hypoxia using several strategies, including the regulation of energy producing metabolic pathways. Pyruvate carboxylase (PC) catalyzes the first reaction of gluconeogenesis to produce oxaloacetate from pyruvate. In mammals, PC also participates in lipogenesis, insulin secretion and other processes, but this enzyme has been scarcely studied in marine invertebrates. In this work, we characterized the gene encoding PC in the white shrimp Litopenaeus vannamei, modelled the protein structure and evaluated its gene expression in hepatopancreas during hypoxia, as well as glucose and lactate concentrations. The PC gene codes for a mitochondrial protein and has 21 coding exons and 4 non-coding exons that generate three transcript variants with differences only in the 5'-UTR. Total PC expression is more abundant in hepatopancreas compared to gills or muscle, indicating tissue-specific expression. Under hypoxic conditions of 1.53 mg/L dissolved oxygen, PC expression is maintained in hepatopancreas, indicating its key role even in energy-limited conditions. Finally, both glucose and lactate concentrations were maintained under hypoxia for 24-48 h in hepatopancreas.
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Affiliation(s)
- Omar N Granillo-Luna
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Laura E Hernandez-Aguirre
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Alma B Peregrino-Uriarte
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Jorge Duarte-Gutierrez
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Carmen A Contreras-Vergara
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Teresa Gollas-Galvan
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico
| | - Gloria Yepiz-Plascencia
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A. C., Carretera Gustavo Enrique Astiazarán Rosas, no. 46, Col. La Victoria, Hermosillo, Sonora, C. P. 83304, Mexico.
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5
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Soares PET, Dantas MDA, Silva-Portela RDCB, Agnez-Lima LF, Lanza DCF. Characterization of Penaeus vannamei mitogenome focusing on genetic diversity. PLoS One 2021; 16:e0255291. [PMID: 34329352 PMCID: PMC8323954 DOI: 10.1371/journal.pone.0255291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 07/13/2021] [Indexed: 11/23/2022] Open
Abstract
The diversity of the Penaeus vannamei mitochondrial genome has still been poorly characterized, there are no validated mitochondrial markers available for populational studies, and the heteroplasmy has not yet been investigated in this species. In this study, metagenomic reads extracted from the muscle of a single individual were used to assemble the mitochondrial genome (mtDNA). These data associated with mitochondrial genomes previously described allowed to evaluate the inter-individual variability and heteroplasmy. Comparison among 45 mtDNA control regions led to the detection of conserved and variable segments and the characterization of two hypervariable regions. The analysis of diversity revealed mostly low frequency polymorphisms, and heteroplasmy was found in practically all mitochondrial genes, with a high occurrence of indels. These results indicate that the design of mitochondrial markers for P. vannamei must be done with caution. The mapping of conserved and variable regions and the characterization of heteroplasmy presented here will contribute to increasing the efficiency of mitochondrial markers for population or individual studies.
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Affiliation(s)
- Paulo Eduardo T. Soares
- Applied Molecular Biology Lab—LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Márcia Danielle A. Dantas
- Applied Molecular Biology Lab—LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
| | - Rita de Cássia B. Silva-Portela
- Laboratory of Molecular Biology and Genomics, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Lucymara F. Agnez-Lima
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
- Laboratory of Molecular Biology and Genomics, Department of Cellular Biology and Genetics, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
| | - Daniel Carlos F. Lanza
- Applied Molecular Biology Lab—LAPLIC, Department of Biochemistry, Federal University of Rio Grande do Norte, Natal, Rio Grande do Norte, Brazil
- Postgraduate Program in Biochemistry, Federal University of Rio Grande do Norte, Natal, RN, Brazil
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6
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Gonzalez-Galaviz JR, Casillas-Hernández R, Flores-Perez MB, Lares-Villa F, Bórquez-López RA, Gil-Núñez JC. Effect of genotype and protein source on performance of Pacific white shrimp ( Litopenaeus vannamei). ITALIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1080/1828051x.2020.1733444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
| | - Ramón Casillas-Hernández
- Departamento de Ciencias Agronómicas y Veterinarias del Instituto Tecnológico de Sonora, Obregón, Sonora, México
| | - María Belem Flores-Perez
- Programa de Doctorado en Ciencias especialidad Biotecnología. Departamento de Biotecnología y Ciencias Alimentarias del Instituto Tecnológico de Sonora, Obregón, Sonora, México
| | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias del Instituto Tecnológico de Sonora, Obregón, Sonora, México
| | | | - Juan Carlos Gil-Núñez
- Departamento de Ciencias Agronómicas y Veterinarias del Instituto Tecnológico de Sonora, Obregón, Sonora, México
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7
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Mangabeira-Silva IS, Soares PET, Lanza DCF. Single nucleotide polymorphism associated with disease resistance in Penaeus vannamei. J Invertebr Pathol 2020; 177:107498. [PMID: 33137318 DOI: 10.1016/j.jip.2020.107498] [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: 03/11/2020] [Revised: 10/20/2020] [Accepted: 10/23/2020] [Indexed: 10/23/2022]
Abstract
Despite the considerable number of genetic markers published for Penaeus vannamei, the classification of these markers and their standardization in specific databases is still insufficient. As a consequence, access to these markers is difficult, hampering their application in genetic association studies. In this study, all previously described single nucleotide polymorphisms (SNPs) related to resistance for P. vannamei were revised, and 512 SNPs were identified and classified in detail. We observed that most of the SNPs occurred in the proteins including Toll like receptors 1 and 3, hemocyanin large and small subunits, and anti-lipopolysaccharide factors 1 and 2, allowing to propose to use them as targets in association studies involving resistance in P. vannamei. Additionally, the potential effects of the most frequent non-synonymous coding SNPs in the secondary structure of the main target proteins were evaluated using an in silico approach. These data can serve as the starting point for the development of new genetic and computational tools as well as for the design of new association studies that involve resistance in P. vannamei.
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Affiliation(s)
- Iasmim Santos Mangabeira-Silva
- Laboratório de Biologia Molecular Aplicada - LAPLIC, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Biotecnologia, RENORBIO, Brazil
| | - Paulo Eduardo Toscano Soares
- Laboratório de Biologia Molecular Aplicada - LAPLIC, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil
| | - Daniel Carlos Ferreira Lanza
- Laboratório de Biologia Molecular Aplicada - LAPLIC, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil; Programa de Pós-Graduação em Biotecnologia, RENORBIO, Brazil; Programa de Pós-Graduação em Bioquímica, Universidade Federal do Rio Grande do Norte, Natal, RN, Brazil.
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8
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Xu J, Jiang Y, Zhao Z, Zhang H, Peng W, Feng J, Dong C, Chen B, Tai R, Xu P. Patterns of Geographical and Potential Adaptive Divergence in the Genome of the Common Carp ( Cyprinus carpio). Front Genet 2019; 10:660. [PMID: 31354795 PMCID: PMC6640160 DOI: 10.3389/fgene.2019.00660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 06/24/2019] [Indexed: 02/04/2023] Open
Abstract
The common carp, Cyprinus carpio, is a cyprinid fish species cultured in Europe and Asia. It accounts for >70% of freshwater aquaculture production worldwide. We conducted a population genomics analysis on C. carpio using high-throughput SNP genotyping of 2,198 individuals from 14 populations worldwide to determine the genetic architecture of common carp populations and the genetic bases for environmental adaptation. Structure analyses including phylogeny and principal component analysis were also conducted, showing distinct geographical patterns in European and Asian populations. The linkage disequilibrium block average lengths of the 14 populations ranged from 3.94 kb to 36.67 kb. Genes within selective sweep regions were identified by genome scanning among the different populations, including gdf6a, bmpr1b, and opsin5. Gene Ontology and KEGG enrichment analyses revealed potential trait-related loci and genes associated with body shape, scaling patterns, and skin color. This population genomics analysis may provide valuable clues for future genome-assisted breeding of C. carpio.
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Affiliation(s)
- Jian Xu
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Yanliang Jiang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Zixia Zhao
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Hanyuan Zhang
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Wenzhu Peng
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Jianxin Feng
- Henan Academy of Fishery Science, Zhengzhou, China
| | - Chuanju Dong
- College of Fishery, Henan Normal University, Xinxiang, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ruyu Tai
- Key Laboratory of Aquatic Genomics, Ministry of Agriculture, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Chinese Academy of Fishery Sciences, Beijing, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Laboratory for Marine Biology and Biotechnology, Pilot National Laboratory for Marine Science and Technology, Qingdao, China
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