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Zhang L, Su B, Huang J, Zhang L, Chang Y, Hu G. Fine Mapping of QTLs for Alkaline Tolerance in Crucian Carp ( Carassius auratus) Using Genome-Wide SNP Markers. Genes (Basel) 2024; 15:751. [PMID: 38927687 PMCID: PMC11202869 DOI: 10.3390/genes15060751] [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: 04/29/2024] [Revised: 06/06/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024] Open
Abstract
Crucian carp (Carassius auratus) is widely distributed in the world and has become an economically freshwater fish. The population in Lake Dali Nur can tolerate the extreme alkaline environment with alkalinity over 50 mmol/L (pH 9.6), thus providing a special model for exploring alkali-tolerant molecular markers in an extremely alkaline environment. In this study, we constructed a high-density and high-resolution linkage map with 16,224 SNP markers based on genotyping-by-sequencing (GBS) consisting of 152 progenies and conducted QTL studies for alkali-tolerant traits. The total length of the linkage map was 3918.893 cM, with an average distance of 0.241 cM. Two QTLs for the ammonia-N-tolerant trait were detected on LG27 and LG45. A QTL for the urea-N-tolerant trait was detected on LG27. Interestingly, mapping the two QTLs on LG27 revealed that the mapped genes were both located in the intron of CDC42. GO functional annotation and KEGG enrichment analysis results indicated that the biological functions might be involved in the cell cycle, cellular senescence, MAPK, and Ras signaling pathways. These findings suggest that CDC42 may play an important role in the process of dealing with extremely alkaline environments.
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Affiliation(s)
- Liang Zhang
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin 150070, China;
| | - Baofeng Su
- Key Laboratory of Fish Stress Resistance Breeding and Germplasm Characteristics on Special Habitats Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin 150070, China; (B.S.); (J.H.); (L.Z.)
- School of Fisheries, Aquaculture and Aquatic Sciences, Auburn University, Auburn, AL 36849, USA
| | - Jing Huang
- Key Laboratory of Fish Stress Resistance Breeding and Germplasm Characteristics on Special Habitats Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin 150070, China; (B.S.); (J.H.); (L.Z.)
| | - Limin Zhang
- Key Laboratory of Fish Stress Resistance Breeding and Germplasm Characteristics on Special Habitats Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin 150070, China; (B.S.); (J.H.); (L.Z.)
| | - Yumei Chang
- Key Laboratory of Fish Stress Resistance Breeding and Germplasm Characteristics on Special Habitats Heilongjiang Province, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin 150070, China; (B.S.); (J.H.); (L.Z.)
| | - Guo Hu
- Key Laboratory of Freshwater Aquatic Biotechnology and Breeding, Ministry of Agriculture and Rural Affairs, Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin 150070, China;
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Construction of Three High-Density Genetic Linkage Maps and Dynamic QTL Mapping of Growth Traits in Yellow River Carp ( Cyprinus carpio haematopterus). Curr Issues Mol Biol 2021; 43:2276-2288. [PMID: 34940134 PMCID: PMC8928983 DOI: 10.3390/cimb43030160] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/14/2021] [Accepted: 12/15/2021] [Indexed: 12/01/2022] Open
Abstract
To provide the theoretical basis for researching growth, development, and molecular marker-assisted breeding of the economically important Yellow River carp (Cyprinus carpio haematopterus) using dynamic quantitative trait locus (QTL) mapping, we constructed three genetic linkage maps from 207 progeny using a new modified genotyping-by-sequencing method. The three maps contained 16,886, 16,548, and 7482 single nucleotide polymorphism markers, respectively, with an average interval of 0.36 cM, 0.45 cM, and 1.00 cM. We identified 148 QTLs related to four growth traits that were located on 25 chromosomes from three growth stages of Yellow River carp. A total of 32, 36, 43, and 37 QTLs were associated with body length, height, width, and weight, respectively. Among them, 47 QTLs were detected for only one growth trait in one stage, but all of the other QTLs were co-localized. Of the 14 main QTLs, 13 were located on chromosome 12, which suggests the presence of growth-related genes on this chromosome. We then detected 17 candidate genes within 50 K upstream and downstream of the 14 main QTLs. This is the first report of the dynamic QTL mapping of growth traits of Yellow River carp, and the results can be used in future studies of growth, development, and molecular-assisted breeding of this species.
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Zenger KR, Khatkar MS, Jones DB, Khalilisamani N, Jerry DR, Raadsma HW. Genomic Selection in Aquaculture: Application, Limitations and Opportunities With Special Reference to Marine Shrimp and Pearl Oysters. Front Genet 2019; 9:693. [PMID: 30728827 PMCID: PMC6351666 DOI: 10.3389/fgene.2018.00693] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 12/11/2018] [Indexed: 11/20/2022] Open
Abstract
Within aquaculture industries, selection based on genomic information (genomic selection) has the profound potential to change genetic improvement programs and production systems. Genomic selection exploits the use of realized genomic relationships among individuals and information from genome-wide markers in close linkage disequilibrium with genes of biological and economic importance. We discuss the technical advances, practical requirements, and commercial applications that have made genomic selection feasible in a range of aquaculture industries, with a particular focus on molluscs (pearl oysters, Pinctada maxima) and marine shrimp (Litopenaeus vannamei and Penaeus monodon). The use of low-cost genome sequencing has enabled cost-effective genotyping on a large scale and is of particular value for species without a reference genome or access to commercial genotyping arrays. We highlight the pitfalls and offer the solutions to the genotyping by sequencing approach and the building of appropriate genetic resources to undertake genomic selection from first-hand experience. We describe the potential to capture large-scale commercial phenotypes based on image analysis and artificial intelligence through machine learning, as inputs for calculation of genomic breeding values. The application of genomic selection over traditional aquatic breeding programs offers significant advantages through being able to accurately predict complex polygenic traits including disease resistance; increasing rates of genetic gain; minimizing inbreeding; and negating potential limiting effects of genotype by environment interactions. Further practical advantages of genomic selection through the use of large-scale communal mating and rearing systems are highlighted, as well as presenting rate-limiting steps that impact on attaining maximum benefits from adopting genomic selection. Genomic selection is now at the tipping point where commercial applications can be readily adopted and offer significant short- and long-term solutions to sustainable and profitable aquaculture industries.
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Affiliation(s)
- Kyall R Zenger
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia
| | - Mehar S Khatkar
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - David B Jones
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia
| | - Nima Khalilisamani
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
| | - Dean R Jerry
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, Australia.,ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Tropical Futures Institute, James Cook University Singapore, Singapore, Singapore
| | - Herman W Raadsma
- ARC Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, Australia.,Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Camden, NSW, Australia
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Su S, Li H, Du F, Zhang C, Li X, Jing X, Liu L, Li Z, Yang X, Xu P, Yuan X, Zhu J, Bouzoualegh R. Combined QTL and Genome Scan Analyses With the Help of 2b-RAD Identify Growth-Associated Genetic Markers in a New Fast-Growing Carp Strain. Front Genet 2018; 9:592. [PMID: 30581452 PMCID: PMC6293859 DOI: 10.3389/fgene.2018.00592] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Accepted: 11/15/2018] [Indexed: 11/17/2022] Open
Abstract
Common carp is one of the oldest and most popular cultured freshwater fish species both globally and in China. In a previous study, we used a carp strain with a long breeding tradition in China, named Huanghe, to create a new fast-growing strain by selection for fast growth for 6 years. The growth performance at 8 months of age has been improved by 20.84%. To achieve this, we combined the best linear unbiased prediction with marker-assisted selection techniques. Recent progress in genome-wide association studies and genomic selection in livestock breeding inspired common carp breeders to consider genome-based breeding approaches. In this study, we developed a 2b-RAD sequence assay as a means of investigating the quantitative trait loci in common carp. A total of 4,953,017,786 clean reads were generated for 250 specimens (average reads/specimen = 19,812,071) with BsaXI Restriction Enzyme. From these, 56,663 SNPs were identified, covering 50 chromosomes and 3,377 scaffolds. Principal component analysis indicated that selection and control groups are relatively clearly distinct. Top 1% of Fst values was selected as the threshold signature of artificial selection. Among the 244 identified loci, genes associated with sex-related factors and nutritional metabolism (especially fat metabolism) were annotated. Eighteen QTL were associated with growth parameters. Body length at 3 months of age and body weight (both at 3 and 8 months) were controlled by polygenic effects, but body size (length, depth, width) at 8 months of age was controlled mainly by several loci with major effects. Importantly, a single shared QTL (IGF2 gene) partially controlled the body length, depth, and width. By merging the above results, we concluded that mainly the genes related to neural pathways, sex and fatty acid metabolism contributed to the improved growth performance of the new Huanghe carp strain. These findings are one of the first investigations into the potential use of genomic selection in the breeding of common carp. Moreover, our results show that combining the Fst, QTL mapping and CRISPR–Cas9 methods can be an effective way to identify important novel candidate molecular markers in economic breeding programs.
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Affiliation(s)
- Shengyan Su
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Hengde Li
- Ministry of Agriculture Key Laboratory of Aquatic Genomics, CAFS Key Laboratory of Aquatic Genomics and Beijing Key Laboratory of Fishery Biotechnology, Center for Applied Aquatic Genomics, Chinese Academy of Fishery Sciences, Beijing, China
| | - Fukuan Du
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Chengfeng Zhang
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinyuan Li
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xiaojun Jing
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Liyue Liu
- China Zebrafish Resource Center, Wuhan, China
| | - Zhixun Li
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Xingli Yang
- Henan Academy of Fishery Sciences, Zhengzhou, China
| | - Pao Xu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Xinhua Yuan
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Jian Zhu
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China.,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
| | - Raouf Bouzoualegh
- Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, China
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Zhong Z, Niu P, Wang M, Huang G, Xu S, Sun Y, Xu X, Hou Y, Sun X, Yan Y, Wang H. Targeted disruption of sp7 and myostatin with CRISPR-Cas9 results in severe bone defects and more muscular cells in common carp. Sci Rep 2016; 6:22953. [PMID: 26976234 PMCID: PMC4791634 DOI: 10.1038/srep22953] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/29/2016] [Indexed: 12/30/2022] Open
Abstract
The common carp (Cyprinus carpio) as one of the most important aquaculture fishes produces over 3 million metric tones annually, approximately 10% the annual production of the all farmed freshwater fish worldwide. However, the tetraploidy genome and long generation-time of the common carp have made its breeding and genetic studies extremely difficult. Here, TALEN and CRISPR-Cas9, two versatile genome-editing tools, are employed to target common carp bone-related genes sp7, runx2, bmp2a, spp1, opg, and muscle suppressor gene mstn. TALEN were shown to induce mutations in the target coding sites of sp7, runx2, spp1 and mstn. With CRISPR-Cas9, the two common carp sp7 genes, sp7a and sp7b, were mutated individually, all resulting in severe bone defects; while mstnba mutated fish have grown significantly more muscle cells. We also employed CRISPR-Cas9 to generate double mutant fish of sp7a;mstnba with high efficiencies in a single step. These results demonstrate that both TALEN and CRISPR-Cas9 are highly efficient tools for modifying the common carp genome, and open avenues for facilitating common carp genetic studies and breeding.
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Affiliation(s)
- Zhaomin Zhong
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China.,School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Pengfei Niu
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China.,School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Mingyong Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China.,School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Guodong Huang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China.,School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Shuhao Xu
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China.,School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Yi Sun
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China.,School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Xiaona Xu
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China.,School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Yi Hou
- School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
| | - Xiaowen Sun
- Heilongjiang River Fisheries Research Institute of Chinese Academy of Fishery Sciences, Harbin, China
| | - Yilin Yan
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China.,School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China.,Institute of Neuroscience, University of Oregon, Eugene, Oregon 97403, USA
| | - Han Wang
- Center for Circadian Clocks, Soochow University, Suzhou 215123, Jiangsu, China.,School of Biology &Basic Medical Sciences, Medical College, Soochow University, Suzhou 215123, Jiangsu, China
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Laghari MY, Lashari P, Zhang X, Xu P, Narejo NT, Liu Y, Mehboob S, Al-Ghanim K, Zhang Y, Sun X. Mapping QTLs for swimming ability related traits in Cyprinus carpio L. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2014; 16:629-637. [PMID: 24985693 DOI: 10.1007/s10126-014-9578-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 05/30/2014] [Indexed: 06/03/2023]
Abstract
Body height (BH), head length (HL), snout length (SL), and tail length (TL) are important traits related with swimming ability of fish. Therefore, improving these traits will increase the production which is the basic goal of aquaculture breeding. To understand the genetic basis of swimming ability related traits in Cyprinus carpio L., a high-density linkage map spanning 3,301 cM in 50 linkage groups was utilized for quantitative trait locus (QTL) mapping. Mapping family comprised 190 offspring and 627 molecular markers were genotyped with average distance of 5.6 cM. A total of 15 QTLs including four (qBH13, qBH30, qBH33, qBH48) for BH, four (qHL10, qHL18, qHL29, qHL48) for HL, three (qSL24, qSL27, qSL45) for SL, and four (qTL15, qTL17, qTL18, qTL44) for TL were detected on 13 linkage groups LG10, LG13, LG15, LG17, LG18, LG24, LG27, LG29, LG30, LG33, LG44, LG45, and LG48. Each LG consisted on single QTL except LG18 and LG48. LG18 was found with two QTLs associated with HL and TL. While LG48 was comprised, the QTLs related with BH and HL. The phenotype variance was recorded from 12.6 to 40.6 %. Five QTLs, qHL48, qSL45, qTL15, qTL18, and qTL44, explained phenotype variance of >20 % with a significant levels of 0.047, 0.049, 0.037, 0.025, and 0.023, respectively. The neighbored loci of these QTLs were considered as main region of chromosomes controlling the traits. These identified genetic regions will be the main source of discovering gene(s) associated with swimming ability related traits in C. carpio L.
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