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Wang W, Huang J, Hu Y, Feng J, Gao D, Fang W, Xu M, Ma C, Fu Z, Chen Q, Liang X, Lu J. Seascapes Shaped the Local Adaptation and Population Structure of South China Coast Yellowfin Seabream (Acanthopagrus latus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024; 26:60-73. [PMID: 38147145 DOI: 10.1007/s10126-023-10277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023]
Abstract
Understanding the genetic composition and regional adaptation of marine species under environmental heterogeneity and fishing pressure is crucial for responsible management. In order to understand the genetic diversity and adaptability of yellowfin seabream (Acanthopagrus latus) along southern China coast, this study was conducted a seascape genome analysis on yellowfin seabream from the ecologically diverse coast, spanning over 1600 km. A total of 92 yellowfin seabream individuals from 15 sites were performed whole-genome resequencing, and 4,383,564 high-quality single nucleotide polymorphisms (SNPs) were called. By conducting a genotype-environment association analysis, 29,951 adaptive and 4,328,299 neutral SNPs were identified. The yellowfin seabream exhibited two distinct population structures, despite high gene flow between sites. The seascape genome analysis revealed that genetic structure was influenced by a variety of factors including salinity gradients, habitat distance, and ocean currents. The frequency of allelic variation at the candidate loci changed with the salinity gradient. Annotation of these loci revealed that most of the genes are associated with osmoregulation, such as kcnab2a, kcnk5a, and slc47a1. These genes are significantly enriched in pathways associated with ion transport including G protein-coupled receptor activity, transmembrane signaling receptor activity, and transporter activity. Overall, our findings provide insights into how seascape heterogeneity affects adaptive evolution, while providing important information for regional management in yellowfin seabream populations.
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Affiliation(s)
- Wenhao Wang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Junrou Huang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Yan Hu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Jianxiang Feng
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Dong Gao
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Wenyu Fang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Meng Xu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Chunlei Ma
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Zhenqiang Fu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Qinglong Chen
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Xuanguang Liang
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China
| | - Jianguo Lu
- School of Marine Sciences, Sun Yat-sen University, Zhuhai, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China.
- Guangdong Provincial Key Laboratory of Marine Resources and Coastal Engineering, Guangzhou, Guangdong, China.
- Pearl River Estuary Marine Ecosystem Research Station, Ministry of Education, Zhuhai, China.
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2
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Li X, Kumar S, Brenneman KV, Anderson TJC. Bulk segregant linkage mapping for rodent and human malaria parasites. Parasitol Int 2022; 91:102653. [PMID: 36007706 DOI: 10.1016/j.parint.2022.102653] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 11/25/2022]
Abstract
In 2005 Richard Carter's group surprised the malaria genetics community with an elegant approach to rapidly mapping the genetic basis of phenotypic traits in rodent malaria parasites. This approach, which he termed "linkage group selection", utilized bulk pools of progeny, rather than individual clones, and exploited simple selection schemes to identify genome regions underlying resistance to drug treatment (or other phenotypes). This work was the first application of "bulk segregant" methodologies for genetic mapping in microbes: this approach is now widely used in yeast, and across multiple recombining pathogens ranging from Aspergillus fungi to Schistosome parasites. Genetic crosses of human malaria parasites (for which Richard Carter was also a pioneer) can now be conducted in humanized mice, providing new opportunities for exploiting bulk segregant approaches for a wide variety of malaria parasite traits. We review the application of bulk segregant approaches to mapping malaria parasite traits and suggest additional developments that may further expand the utility of this powerful approach.
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Affiliation(s)
- Xue Li
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA.
| | - Sudhir Kumar
- Center for Global Infectious Disease Research, Seattle Children's Research Institute, Seattle, Washington, USA
| | - Katelyn Vendrely Brenneman
- Eck Institute for Global Health, Department of Biological Sciences, University of Notre Dame, Notre Dame, IN, USA
| | - Tim J C Anderson
- Program in Disease Intervention and Prevention, Texas Biomedical Research Institute, San Antonio, TX, USA.
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3
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Genome-wide association study reveals the genetic basis of growth trait in yellow catfish with sexual size dimorphism. Genomics 2022; 114:110380. [PMID: 35533968 DOI: 10.1016/j.ygeno.2022.110380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 04/20/2022] [Accepted: 05/02/2022] [Indexed: 01/14/2023]
Abstract
Sexual size dimorphism has been widely observed in a large number of animals including fish species. Genome-wide association study (GWAS) is a powerful tool to dissect the genetic basis of complex traits, whereas the sex-differences in the genomics of animal complex traits have been ignored in the GWAS analysis. Yellow catfish (Pelteobagrus fulvidraco) is an important aquaculture fish in China with significant sexual size dimorphism. In this study, GWAS was conducted to identify candidate SNPs and genes related to body length (BL) and body weight (BW) in 125 female yellow catfish from a breeding population. In total, one BL-related SNP and three BW-related SNPs were identified to be significantly associated with the traits. Besides, one of these SNPs (Chr15:19195072) was shared in both the BW and BL traits in female yellow catfish, which was further validated in 185 male individuals and located on the exon of stat5b gene. Transgenic yellow catfish and zebrafish that expressed yellow catfish stat5b showed increased growth rate and reduction of sexual size dimorphism. These results not only reveal the genetic basis of growth trait and sexual size dimorphism in fish species, but also provide useful information for the marker-assisted breeding in yellow catfish.
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Li Z, Xu Y. Bulk segregation analysis in the NGS era: a review of its teenage years. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:1355-1374. [PMID: 34931728 DOI: 10.1111/tpj.15646] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/27/2021] [Accepted: 12/14/2021] [Indexed: 06/14/2023]
Abstract
Bulk segregation analysis (BSA) utilizes a strategy of pooling individuals with extreme phenotypes to conduct economical and rapidly linked marker screening or quantitative trait locus (QTL) mapping. With the development of next-generation sequencing (NGS) technology in the past 10 years, BSA methods and technical systems have been gradually developed and improved. At the same time, the ever-decreasing costs of sequencing accelerate NGS-based BSA application in different species, including eukaryotic yeast, grain crops, economic crops, horticultural crops, trees, aquatic animals, and insects. This paper provides a landscape of BSA methods and reviews the BSA development process in the past decade, including the sequencing method for BSA, different populations, different mapping algorithms, associated region threshold determination, and factors affecting BSA mapping. Finally, we summarize related strategies in QTL fine mapping combining BSA.
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Affiliation(s)
- Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, 830022, China
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5
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Qin H, Yu Z, Zhu Z, Lin Y, Xia J, Jia Y. The integrated analyses of metabolomics and transcriptomics in gill of GIFT tilapia in response to long term salinity challenge. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2021.02.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Palaiokostas C, Anjum A, Jeuthe H, Kurta K, Lopes Pinto F, Koning DJ. A genomic‐based vision on the genetic diversity and key performance traits in selectively bred Arctic charr (
Salvelinus alpinus
). Evol Appl 2021; 15:565-577. [PMID: 35505879 PMCID: PMC9046918 DOI: 10.1111/eva.13261] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/19/2021] [Accepted: 05/29/2021] [Indexed: 12/25/2022] Open
Abstract
Routine implementation of genomic information for guiding selection decisions is not yet common in the majority of aquaculture species. Reduced representation sequencing approaches offer a cost‐effective solution for obtaining genome‐wide information in species with a limited availability of genomic resources. In the current study, we implemented double‐digest restriction site‐associated DNA sequencing (ddRAD‐seq) on an Arctic charr strain with the longest known history of selection (approximately 40 years) aiming to improve selection decisions. In total, 1730 animals reared at four different farms in Sweden and spanning from year classes 2013–2017 were genotyped using ddRAD‐seq. Approximately 5000 single nucleotide polymorphisms (SNPs) were identified, genetic diversity‐related metrics were estimated, and genome‐wide association studies (GWAS) for body length at different time points and age of sexual maturation were conducted. Low genetic differentiation amongst animals from the different farms was observed based on both the results from pairwise Fst values and principal component analysis (PCA). The existence of associations was investigated between the mean genome‐wide heterozygosity of each full‐sib family (year class 2017) and the corresponding inbreeding coefficient or survival to the eyed stage. A moderate correlation (−0.33) was estimated between the mean observed heterozygosity of each full‐sib family and the corresponding inbreeding coefficient, while no linear association was obtained with the survival to the eyed stage. GWAS did not detect loci with major effect for any of the studied traits. However, genomic regions explaining more than 1% of the additive genetic variance for either studied traits were suggested across 14 different chromosomes. Overall, key insights valuable for future selection decisions of Arctic charr have been obtained, suggesting ddRAD as an attractive genotyping platform for obtaining genome‐wide information in a cost‐effective manner.
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Affiliation(s)
- Christos Palaiokostas
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Anam Anjum
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Henrik Jeuthe
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
- Aquaculture Center North Kälarne Sweden
| | - Khrystyna Kurta
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Fernando Lopes Pinto
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
| | - Dirk Jan Koning
- Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Uppsala Sweden
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Pappas F, Palaiokostas C. Genotyping Strategies Using ddRAD Sequencing in Farmed Arctic Charr ( Salvelinus alpinus). Animals (Basel) 2021; 11:899. [PMID: 33801139 PMCID: PMC8004150 DOI: 10.3390/ani11030899] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Revised: 03/13/2021] [Accepted: 03/16/2021] [Indexed: 12/17/2022] Open
Abstract
Incorporation of genomic technologies into fish breeding programs is a modern reality, promising substantial advances regarding the accuracy of selection, monitoring the genetic diversity and pedigree record verification. Single nucleotide polymorphism (SNP) arrays are the most commonly used genomic tool, but the investments required make them unsustainable for emerging species, such as Arctic charr (Salvelinus alpinus), where production volume is low. The requirement to genotype a large number of animals for breeding practices necessitates cost effective genotyping approaches. In the current study, we used double digest restriction site-associated DNA (ddRAD) sequencing of either high or low coverage to genotype Arctic charr from the Swedish national breeding program and performed analytical procedures to assess their utility in a range of tasks. SNPs were identified and used for deciphering the genetic structure of the studied population, estimating genomic relationships and implementing an association study for growth-related traits. Missing information and underestimation of heterozygosity in the low coverage set were limiting factors in genetic diversity and genomic relationship analyses, where high coverage performed notably better. On the other hand, the high coverage dataset proved to be valuable when it comes to identifying loci that are associated with phenotypic traits of interest. In general, both genotyping strategies offer sustainable alternatives to hybridization-based genotyping platforms and show potential for applications in aquaculture selective breeding.
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Affiliation(s)
| | - Christos Palaiokostas
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7090, 750 07 Uppsala, Sweden;
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Nyinondi CS, Mtolera MSP, Mmochi AJ, Lopes Pinto FA, Houston RD, de Koning DJ, Palaiokostas C. Assessing the genetic diversity of farmed and wild Rufiji tilapia ( Oreochromis urolepis urolepis) populations using ddRAD sequencing. Ecol Evol 2020; 10:10044-10056. [PMID: 33005362 PMCID: PMC7520224 DOI: 10.1002/ece3.6664] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 07/16/2020] [Accepted: 07/20/2020] [Indexed: 12/21/2022] Open
Abstract
Rufiji tilapia (Oreochromis urolepis urolepis) is an endemic cichlid in Tanzania. In addition to its importance for biodiversity conservation, Rufiji tilapia is also attractive for farming due to its high growth rate, salinity tolerance, and the production of all-male hybrids when crossed with Nile tilapia (Oreochromis niloticus). The aim of the current study was to assess the genetic diversity and population structure of both wild and farmed Rufiji tilapia populations in order to inform conservation and aquaculture practices. Double-digest restriction-site-associated DNA (ddRAD) libraries were constructed from 195 animals originating from eight wild (Nyamisati, Utete, Mansi, Mindu, Wami, Ruaha, Kibasira, and Kilola) and two farmed (Bwawani and Chemchem) populations. The identified single nucleotide polymorphisms (SNPs; n = 2,182) were used to investigate the genetic variation within and among the studied populations. Genetic distance estimates (F st) were low among populations from neighboring locations, with the exception of Utete and Chemchem populations (F st = 0.34). Isolation-by-distance (IBD) analysis among the wild populations did not detect any significant correlation signal (r = .05; p-value = .4) between the genetic distance and the sampling (Euclidean distance) locations. Population structure and putative ancestry were further investigated using both Bayesian (Structure) and multivariate approaches (discriminant analysis of principal components). Both analysis indicated the existence of three distinct genetic clusters. Two cross-validation scenarios were conducted in order to test the efficiency of the SNP dataset for discriminating between farmed and wild animals or predicting the population of origin. Approximately 95% of the test dataset was correctly classified in the first scenario, while in the case of predicting for the population of origin 68% of the test dataset was correctly classified. Overall, our results provide novel insights regarding the population structure of Rufiji tilapia and a new database of informative SNP markers for both conservation management and aquaculture activities.
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Affiliation(s)
- Christer S. Nyinondi
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- Institute of Marine SciencesUniversity of Dar es SalaamZanzibarTanzania
| | | | - Aviti J. Mmochi
- Institute of Marine SciencesUniversity of Dar es SalaamZanzibarTanzania
| | - Fernando A. Lopes Pinto
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Ross D. Houston
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
| | - Dirk J. de Koning
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
| | - Christos Palaiokostas
- Department of Animal Breeding and GeneticsSwedish University of Agricultural SciencesUppsalaSweden
- The Roslin Institute and Royal (Dick) School of Veterinary StudiesUniversity of EdinburghEdinburghUK
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9
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Liu Y, Wang H, Wen H, Shi Y, Zhang M, Qi X, Zhang K, Gong Q, Li J, He F, Hu Y, Li Y. First High-Density Linkage Map and QTL Fine Mapping for Growth-Related Traits of Spotted Sea bass (Lateolabrax maculatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:526-538. [PMID: 32424479 DOI: 10.1007/s10126-020-09973-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/28/2020] [Indexed: 06/11/2023]
Abstract
Possessing powerful adaptive capacity and a pleasant taste, spotted sea bass (Lateolabrax maculatus) has a broad natural distribution and is one of the most popular mariculture fish in China. However, the genetic improvement program for this fish is still in its infancy. Growth is the most economically important trait and is controlled by quantitative trait loci (QTL); thus, the identification of QTLs and genetic markers for growth-related traits is an essential step for the establishment of marker-assisted selection (MAS) breeding programs. In this study, we report the first high-density linkage map of spotted sea bass constructed by sequencing 333 F1 generation individuals in a full-sib family using 2b-RAD technology. A total of 6883 SNP markers were anchored onto 24 linkage groups, spanning 2189.96 cM with an average marker interval of 0.33 cM. Twenty-four growth-related QTLs, including 13 QTLs for body weight and 11 QTLs for body length, were successfully detected, with phenotypic variance explained (PVE) ranging from 5.1 to 8.6%. Thirty potential candidate growth-related genes surrounding the associated SNPs were involved in cell adhesion, cell proliferation, cytoskeleton reorganization, calcium channels, and neuromodulation. Notably, the fgfr4 gene was detected in the most significant QTL; this gene plays a pivotal role in myogenesis and bone growth. The results of this study may facilitate marker-assisted selection for breeding populations and establish the foundation for further genomic and genetic studies investigating spotted sea bass.
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Affiliation(s)
- Yang Liu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Haolong Wang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Haishen Wen
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yue Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361005, China
| | - Meizhao Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Xin Qi
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Kaiqiang Zhang
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Qingli Gong
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Jifang Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Feng He
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yanbo Hu
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China
| | - Yun Li
- Key Laboratory of Mariculture, Ministry of Education, Ocean University of China, Qingdao, 266003, China.
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10
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Yang Y, Wu L, Wu X, Li B, Huang W, Weng Z, Lin Z, Song L, Guo Y, Meng Z, Liu X, Xia J. Identification of Candidate Growth-Related SNPs and Genes Using GWAS in Brown-Marbled Grouper (Epinephelus fuscoguttatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2020; 22:153-166. [PMID: 31927644 DOI: 10.1007/s10126-019-09940-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
Brown-marbled grouper, Epinephelus fuscoguttatus, is not only an important commercial fish species, but also an important crossbreeding parent in grouper industry. Improvement of growth traits of this species contributes to the development of grouper breeding. Currently, the development of molecular marker associated with growth of brown-marbled grouper is rare. Thus, we performed the first genome-wide association study (GWAS) for five growth traits in 172 brown-marbled groupers with 43,688 SNPs detected by ddRAD-seq. We identified a total of 5 significant and 18 suggestive QTLs located in multiple chromosomes associated with growth traits. In the 20 kb window of the significant SNPs and suggestive SNPs, 5 and 14 potential candidate genes affecting growth were detected, respectively. Five potential candidate genes near the significantly associated SNPs were selected for expression analysis. Among of which, bmp2k, wasf1, and acyp2 involved in bone development, maintenance of mitochondrion structure, and metabolism were differentially expressed. Interestingly, the SNP 23:29601315 located in the intron of bmp2k was significantly associated with body weight, body length, body height, and body thickness and suggestively associated with total length. We verified the locus using another new group including 123 individuals. The results showed that individuals with CC genotype have better growth traits comparing other individuals. Our findings not only contribute to understanding the molecular mechanism of growth regulation, but also promote the advance of marker-assisted selection in brown-marbled grouper.
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Affiliation(s)
- Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Lina Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Xi Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Bijun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Wenhua Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Zhuoying Weng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Zixuan Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
| | - Leling Song
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Yin Guo
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China.
- Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, 510275, People's Republic of China.
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China.
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China.
- Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Guangzhou, 510275, People's Republic of China.
| | - Junhong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yat-sen University, Guangzhou, 510275, People's Republic of China
- Southern Laboratory of Ocean Science and Engineering, Zhuhai, 519000, People's Republic of China
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11
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Lv J, Sun D, Yan D, Ti X, Liu P, Li J. Quantitative Trait Loci Mapping and Marker Identification for Low Salinity Tolerance Trait in the Swimming Crab ( Portunus trituberculatus). Front Genet 2019; 10:1193. [PMID: 31850064 PMCID: PMC6900548 DOI: 10.3389/fgene.2019.01193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 10/28/2019] [Indexed: 01/17/2023] Open
Abstract
Low salinity is one of the most important abiotic factors that directly affect the abundance of the swimming crab, Portunus trituberculatus. Quantitative trait loci (QTL) mapping could be helpful in identifying the markers and genes involved in low salinity tolerance. In this study, two QTLs of low salt tolerance were mapped on linkage group 17 (LG17, 2.6-5.2 cM) based on a high-density linkage map. Ninety-five markers related to low salinity tolerance were identified via association analysis, and seventy-nine low salt-related candidate genes (including ammonium transport, aldehyde dehydrogenase, and glucosyltransferase) were screened from draft genome of the species via these markers. This represents the first report of QTL mapping for low salinity tolerance in the swimming crab, which may be useful to elucidate salinity adaptation mechanisms.
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Affiliation(s)
- Jianjian Lv
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Dongfang Sun
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Deping Yan
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Xingbin Ti
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China
| | - Ping Liu
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Jian Li
- Key Laboratory of Sustainable Development of Marine Fisheries, Ministry of Agriculture, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao, China.,Function Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
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Liu X, Li L, Li A, Li Y, Wang W, Zhang G. Transcriptome and Gene Coexpression Network Analyses of Two Wild Populations Provides Insight into the High-Salinity Adaptation Mechanisms of Crassostrea ariakensis. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:596-612. [PMID: 31165295 DOI: 10.1007/s10126-019-09896-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 03/25/2019] [Indexed: 06/09/2023]
Abstract
Crassostrea ariakensis naturally distributes in the intertidal and estuary region with relative low salinity ranging from 10 to 25‰. To understand the adaptive capacity of oysters to salinity stress, we conducted transcriptome analysis to investigate the metabolic pathways of salinity stress effectors in oysters from two different geographical sites, namely at salinities of 16, 23, and 30‰. We completed transcriptome sequencing of 18 samples and a total of 52,392 unigenes were obtained after assembly. Differentially expressed gene (DEG) analysis and weighted gene correlation network analysis (WGCNA) were performed using RNA-Seq transcriptomic data from eye-spot larvae at different salinities and from different populations. The results showed that at moderately high salinities (23 and 30‰), genes related to osmotic agents, oxidation-reduction processes, and related regulatory networks of complex transcriptional regulation and signal transduction pathways dominated to counteract the salinity stress. Moreover, there were adaptive differences in salinity response mechanisms, especially at high salinity, in oyster larvae from different populations. These results provide a framework for understanding the interactions of multiple pathways at the system level and for elucidating the complex cellular processes involved in responding to osmotic stress and maintaining growth. Furthermore, the results facilitate further research into the biological processes underlying physiological adaptations to hypertonic stress in marine invertebrates and provide a molecular basis for our subsequent search for high salinity-tolerant populations.
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Affiliation(s)
- Xingyu Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Li Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China.
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Beijing, China.
- National & Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
| | - Ao Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingxiang Li
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Beijing, China
- National & Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Wei Wang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Beijing, China
- National & Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Guofan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, Shandong, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, Shandong, China
- Center for Ocean Mega-Science, Chinese Academy of Sciences, Beijing, China
- National & Local Joint Engineering Key Laboratory of Ecological Mariculture, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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Wu L, Yang Y, Li B, Huang W, Wang X, Liu X, Meng Z, Xia J. First Genome-wide Association Analysis for Growth Traits in the Largest Coral Reef-Dwelling Bony Fishes, the Giant Grouper (Epinephelus lanceolatus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:707-717. [PMID: 31392592 DOI: 10.1007/s10126-019-09916-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 07/23/2019] [Indexed: 06/10/2023]
Abstract
The giant grouper, Epinephelus lanceolatus, is the largest coral reef-dwelling bony fish species. However, despite extremely fast growth performance and the considerable economic importance in this species, its genetic regulation of growth remains unknown. Here, we performed the first genome-wide association study (GWAS) for five growth traits in 289 giant groupers using 42,323 single nucleotide polymorphisms (SNPs) obtained by genotyping-by-sequencing (GBS). We identified a total of 36 growth-related SNPs, of which 11 SNPs reached a genome-wide significance level. The phenotypic variance explained by these SNPs varied from 7.09% for body height to 18.42% for body length. Moreover, 22 quantitative trait loci (QTLs) for growth traits, including nine significant QTLs and 13 suggestive QTLs, were found on multiple chromosomes. Interestingly, the QTL (LG17: 6934451) was shared between body weight and body height, while two significant QTLs (LG7: 22596399 and LG15: 11877836) for body length were consistent with the associated regions of total length at the genome-wide suggestive level. Eight potential candidate genes close to the associated SNPs were selected for expression analysis, of which four genes (phosphatidylinositol transfer protein cytoplasmic 1, protein tyrosine phosphatase receptor type E, alpha/beta hydrolase domain-containing protein 17C, and vascular endothelial growth factor A-A) were differentially expressed and involved in metabolism, development, response stress, etc. This study improves our understanding of the complex genetic architecture of growth in the giant grouper. The results contribute to the selective breeding of grouper species and the conservation of coral reef fishes.
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Affiliation(s)
- Lina Wu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, 510275, China
| | - Yang Yang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, 510275, China
| | - Bijun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, 510275, China
| | - Wenhua Huang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, 510275, China
| | - Xi Wang
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, 510275, China
| | - Xiaochun Liu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, 510275, China
| | - Zining Meng
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, 510275, China.
| | - Junhong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals, and the Guangdong Province Key Laboratory for Aquatic Economic Animals, Life Science School, Sun Yet-Sen University, Guangzhou, 510275, China
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