1
|
Zhou M, Yao Z, Zhao M, Fang Q, Ji X, Chen H, Zhao Y. Molecular Cloning and Expression Responses of Jarid2b to High-Temperature Treatment in Nile Tilapia ( Oreochromis niloticus). Genes (Basel) 2022; 13:1719. [PMID: 36292604 PMCID: PMC9602145 DOI: 10.3390/genes13101719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 09/12/2022] [Accepted: 09/20/2022] [Indexed: 10/27/2023] Open
Abstract
Nile tilapia is a GSD + TE (Genetic Sex Determination + Temperature Effect) fish, and high-temperature treatment during critical thermosensitive periods (TSP) can induce the sex reversal of Nile tilapia genetic females, and brain transcriptomes have revealed the upregulation of Jarid2 (Jumonji and AT-rich domain containing 2) expression after 36 °C high-temperature treatment for 12 days during TSP. It was shown that JARID2 forms a complex with polycomb repressive complex 2 (PRC2) that catalyzed H3K27me3, which was strongly associated with transcriptional repression. In this study, Jarid2b was cloned and characterized in Nile tilapia, which was highly conserved among the analyzed fish species. The expression of Jarid2b was upregulated in the gonad of 21 dpf XX genetic females after 12-day high-temperature treatment and reached a similar level to that of males. Similar responses to high-temperature treatment also appeared in the brain, heart, liver, muscle, eye, and skin tissues. Interestingly, Jarid2b expression was only in response to high-temperature treatment, and not to 17α-methyltestosterone (MT) or letrozole treatments; although, these treatments can also induce the sex reversal of genetic Nile tilapia females. Further studies revealed that Jarid2b responded rapidly at the 8th hour after high-temperature treatment. Considering that JARID2 can recruit PRC2 and establish H3K27me3, we speculated that it might be an upstream gene participating in the regulation of Nile tilapia GSD + TE through regulating the H3K27 methylation level at the locus of many sex differentiation-related genes.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Yan Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian 271000, China
| |
Collapse
|
2
|
Fu G, Yuna Y. Phenotyping and phenomics in aquaculture breeding. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2021.07.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
|
3
|
Liu X, Dai S, Wu J, Wei X, Zhou X, Chen M, Tan D, Pu D, Li M, Wang D. Roles of anti-Müllerian hormone and its duplicates in sex determination and germ cell proliferation of Nile tilapia. Genetics 2021; 220:6486528. [PMID: 35100374 PMCID: PMC9208641 DOI: 10.1093/genetics/iyab237] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/17/2021] [Indexed: 12/30/2022] Open
Abstract
Duplicates of amh are crucial for fish sex determination and differentiation. In Nile tilapia, unlike in other teleosts, amh is located on X chromosome. The Y chromosome amh (amhΔ-y) is mutated with 5 bp insertion and 233 bp deletion in the coding sequence, and tandem duplicate of amh on Y chromosome (amhy) has been identified as the sex determiner. However, the expression of amh, amhΔ-y, and amhy, their roles in germ cell proliferation and the molecular mechanism of how amhy determines sex is still unclear. In this study, expression and functions of each duplicate were analyzed. Sex reversal occurred only when amhy was mutated as revealed by single, double, and triple mutation of the 3 duplicates in XY fish. Homozygous mutation of amhy in YY fish also resulted in sex reversal. Earlier and higher expression of amhy/Amhy was observed in XY gonads compared with amh/Amh during sex determination. Amhy could inhibit the transcription of cyp19a1a through Amhr2/Smads signaling. Loss of cyp19a1a rescued the sex reversal phenotype in XY fish with amhy mutation. Interestingly, mutation of both amh and amhy in XY fish or homozygous mutation of amhy in YY fish resulted in infertile females with significantly increased germ cell proliferation. Taken together, these results indicated that up-regulation of amhy during the critical period of sex determination makes it the sex-determining gene, and it functions through repressing cyp19a1a expression via Amhr2/Smads signaling pathway. Amh retained its function in controlling germ cell proliferation as reported in other teleosts, while amhΔ-y was nonfunctionalized.
Collapse
Affiliation(s)
- Xingyong Liu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Shengfei Dai
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Jiahong Wu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xueyan Wei
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xin Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Mimi Chen
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Dejie Tan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Deyong Pu
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China,Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China. ; Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China,Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China. ; Corresponding author: Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Sciences, Southwest University, Chongqing 400715, China.
| |
Collapse
|
4
|
Curzon AY, Shirak A, Benet-Perlberg A, Naor A, Low-Tanne SI, Sharkawi H, Ron M, Seroussi E. Gene Variant of Barrier to Autointegration Factor 2 ( Banf2w) Is Concordant with Female Determination in Cichlids. Int J Mol Sci 2021; 22:7073. [PMID: 34209244 PMCID: PMC8268354 DOI: 10.3390/ijms22137073] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/23/2021] [Accepted: 06/27/2021] [Indexed: 11/15/2022] Open
Abstract
Oreochromis fishes exhibit variability of sex-determination (SD) genes whose characterization contributes to understanding of the sex differentiation network, and to effective tilapia farming, which requires all-male culture. However, O. niloticus (On) amh is the only master-key regulator (MKR) of SD that has been mapped (XY/XX SD-system on LG23). In O. aureus (Oa), LG3 controls a WZ/ZZ SD-system that has recently been delimited to 9.2 Mbp, with an embedded interval rich with female-specific variation, harboring two paics genes and banf2. Developing genetic markers within this interval and using a hybrid Oa stock that demonstrates no recombination repression in LG3, we mapped the critical SD region to 235 Kbp on the orthologous On physical map (p < 1.5 × 10-26). DNA-seq assembly and peak-proportion analysis of variation based on Sanger chromatograms allowed the characterization of copy-number variation (CNV) of banf2. Oa males had three exons capable of encoding 90-amino-acid polypeptides, yet in Oa females, we found an extra copy with an 89-amino-acid polypeptide and three non-conservative amino acid substitutions, designated as banf2w. CNV analysis suggested the existence of two to five copies of banf2 in diploidic Cichlidae. Disrupting the Hardy-Weinberg equilibrium (p < 4.2 × 10-3), banf2w was concordant with female determination in Oa and in three cichlids with LG3 WZ/ZZ SD-systems (O. tanganicae, O. hornorum and Pelmatolapia mariae). Furthermore, exclusive RNA-seq expression in Oa females strengthened the candidacy of banf2w as the long-sought LG3 SD MKR. As banf genes mediate nuclear assembly, chromatin organization, gene expression and gonad development, banf2w may play a fundamental role inducing female nucleus formation that is essential for WZ/ZZ SD.
Collapse
Affiliation(s)
- Arie Yehuda Curzon
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Ayana Benet-Perlberg
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Alon Naor
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Shai Israel Low-Tanne
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Haled Sharkawi
- Dor Research Station, Division of Fishery and Aquaculture, Hof HaCarmel 30820, Israel; (A.B.-P.); (A.N.); (S.I.L.-T.); (H.S.)
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Rishon LeTsiyon 7528809, Israel; (A.Y.C.); (A.S.); (M.R.)
| |
Collapse
|
5
|
Ding W, Zhang X, Zhao X, Jing W, Cao Z, Li J, Huang Y, You X, Wang M, Shi Q, Bing X. A Chromosome-Level Genome Assembly of the Mandarin Fish ( Siniperca chuatsi). Front Genet 2021; 12:671650. [PMID: 34249093 PMCID: PMC8262678 DOI: 10.3389/fgene.2021.671650] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/07/2021] [Indexed: 11/13/2022] Open
Abstract
The mandarin fish, Siniperca chuatsi, is an economically important perciform species with widespread aquaculture practices in China. Its special feeding habit, acceptance of only live prey fishes, contributes to its delicious meat. However, little is currently known about related genetic mechanisms. Here, we performed whole-genome sequencing and assembled a 758.78 Mb genome assembly of the mandarin fish, with the scaffold and contig N50 values reaching 2.64 Mb and 46.11 Kb, respectively. Approximately 92.8% of the scaffolds were ordered onto 24 chromosomes (Chrs) with the assistance of a previously established genetic linkage map. The chromosome-level genome contained 19,904 protein-coding genes, of which 19,059 (95.75%) genes were functionally annotated. The special feeding behavior of mandarin fish could be attributable to the interaction of a variety of sense organs (such as vision, smell, and endocrine organs). Through comparative genomics analysis, some interesting results were found. For example, olfactory receptor (OR) genes (especially the beta and delta types) underwent a significant expansion, and endocrinology/vision related npy, spexin, and opsin genes presented various functional mutations. These may contribute to the special feeding habit of the mandarin fish by strengthening the olfactory and visual systems. Meanwhile, previously identified sex-related genes and quantitative trait locis (QTLs) were localized on the Chr14 and Chr17, respectively. 155 toxin proteins were predicted from mandarin fish genome. In summary, the high-quality genome assembly of the mandarin fish provides novel insights into the feeding habit of live prey and offers a valuable genetic resource for the quality improvement of this freshwater fish.
Collapse
Affiliation(s)
- Weidong Ding
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Xiaomeng Zhao
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Wu Jing
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Zheming Cao
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| | - Jia Li
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China
| | - Xinxin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Min Wang
- BGI Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, China
| | - Xuwen Bing
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi, China
| |
Collapse
|
6
|
Abstract
Chromosome size and morphology vary within and among species, but little is known about the proximate or ultimate causes of these differences. Cichlid fish species in the tribe Oreochromini share an unusual giant chromosome that is ∼3 times longer than the other chromosomes. This giant chromosome functions as a sex chromosome in some of these species. We test two hypotheses of how this giant sex chromosome may have evolved. The first hypothesis proposes that it evolved by accumulating repetitive elements as recombination was reduced around a dominant sex determination locus, as suggested by canonical models of sex chromosome evolution. An alternative hypothesis is that the giant sex chromosome originated via the fusion of an autosome with a highly repetitive B chromosome, one of which carried a sex determination locus. We test these hypotheses using comparative analysis of chromosome-scale cichlid and teleost genomes. We find that the giant sex chromosome consists of three distinct regions based on patterns of recombination, gene and transposable element content, and synteny to the ancestral autosome. The WZ sex determination locus encompasses the last ∼105 Mb of the 134-Mb giant chromosome. The last 47 Mb of the giant chromosome shares no obvious homology to any ancestral chromosome. Comparisons across 69 teleost genomes reveal that the giant sex chromosome contains unparalleled amounts of endogenous retroviral elements, immunoglobulin genes, and long noncoding RNAs. The results favor the B chromosome fusion hypothesis for the origin of the giant chromosome.
Collapse
Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Frances E Clark
- Department of Biology, University of Maryland, College Park, MD, USA
| | - Reade B Roberts
- Department of Biological Sciences, North Carolina State University, Raleigh, NC, USA
| | - Luohao Xu
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Qi Zhou
- Department of Neuroscience and Developmental Biology, University of Vienna, Vienna, Austria
- MOE Laboratory of Biosystems Homeostasis & Protection, Life Sciences Institute, Zhejiang University, Hangzhou, China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), School of Life Sciences, Southwest University, Chongqing, China
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
| |
Collapse
|
7
|
Structure and Sequence of the Sex Determining Locus in Two Wild Populations of Nile Tilapia. Genes (Basel) 2020; 11:genes11091017. [PMID: 32872430 PMCID: PMC7563666 DOI: 10.3390/genes11091017] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/15/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
In domesticated strains of the Nile tilapia, phenotypic sex has been linked to genetic variants on linkage groups 1, 20 and 23. This diversity of sex-loci might reflect a naturally polymorphic sex determination system in Nile tilapia, or it might be an artefact arising from the process of domestication. Here, we searched for sex-determiners in wild populations from Kpandu, Lake Volta (Ghana-West Africa), and from Lake Koka (Ethiopia-East Africa) that have not been subjected to any genetic manipulation. We analysed lab-reared families using double-digest Restriction Associated DNA sequencing (ddRAD) and analysed wild-caught males and females with pooled whole-genome sequencing (WGS). Strong sex-linked signals were found on LG23 in both populations, and sex-linked signals with LG3 were observed in Kpandu samples. WGS uncovered blocks of high sequence coverage, suggesting the presence of B chromosomes. We confirmed the existence of a tandem amh duplication in LG23 in both populations and determined its breakpoints between the oaz1 and dot1l genes. We found two common deletions of ~5 kb in males and confirmed the presence of both amhY and amh∆Y genes. Males from Lake Koka lack both the previously reported 234 bp deletion and the 5 bp frameshift-insertion that creates a premature stop codon in amh∆Y.
Collapse
|
8
|
Dor L, Shirak A, Curzon AY, Rosenfeld H, Ashkenazi IM, Nixon O, Seroussi E, Weller JI, Ron M. Preferential Mapping of Sex-Biased Differentially-Expressed Genes of Larvae to the Sex-Determining Region of Flathead Grey Mullet ( Mugil cephalus). Front Genet 2020; 11:839. [PMID: 32973865 PMCID: PMC7472742 DOI: 10.3389/fgene.2020.00839] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/10/2020] [Indexed: 12/23/2022] Open
Abstract
Flathead gray mullet (Mugil cephalus) is a cosmopolitan mugilid species popular in fishery and aquaculture with an economic preference for all-female population. However, it displays neither sexual dimorphisms nor heteromorphic sex chromosomes. We have previously presented a microsatellite-based linkage map for this species locating a single sex determination region (SDR) on linkage group 9 (LG9) with evidence for XX/XY sex determination (SD) mechanism. In this work, we refine the critical SDR on LG9, and propose positional- and functional- candidate genes for SD. To elucidate the genetic mechanism of SD, we assembled and compared male and female genomic sequences of 19 syntenic genes within the putative SDR on mullet's LG9, based on orthology to tilapia's LG8 (tLG8) physical map. A total of 25 sequence-based markers in 12 genes were developed. For all markers, we observed association with sex in at least one of the two analyzed M. cephalus full-sib families, but not in the wild-type population. Recombination events were inferred within families thus setting the SDR boundaries to a region orthologous to ∼0.9 Mbp with 27 genes on tLG8. As the sexual phenotype is evident only in adults, larvae were assigned into two putative sex-groups according to their paternal haplotypes, following a model of XY/XX SD-system. A total of 107 sex-biased differentially expressed genes in larvae were observed, of which 51 were mapped to tLG8 (48% enrichment), as compared to 5% in random control. Furthermore, 23 of the 107 genes displayed sex-specific expression; and 22 of these genes were positioned to tLG8, indicating 96% enrichment. Of the 27 SDR genes, BCCIP, DHX32A, DOCK1, and FSHR (GTH-RI) are suggested as positional and functional gene candidates for SD.
Collapse
Affiliation(s)
- Lior Dor
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Andrey Shirak
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Arie Y. Curzon
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
- Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Hana Rosenfeld
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Iris M. Ashkenazi
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Oriya Nixon
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat, Israel
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
| | - Joel I. Weller
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan, Israel
| |
Collapse
|
9
|
Taslima K, Wehner S, Taggart JB, de Verdal H, Benzie JAH, Bekaert M, McAndrew BJ, Penman DJ. Sex determination in the GIFT strain of tilapia is controlled by a locus in linkage group 23. BMC Genet 2020; 21:49. [PMID: 32349678 PMCID: PMC7189693 DOI: 10.1186/s12863-020-00853-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 04/15/2020] [Indexed: 12/25/2022] Open
Abstract
Background Tilapias (Family Cichlidae) are the second most important group of aquaculture species in the world. They have been the subject of much research on sex determination due to problems caused by early maturation in culture and their complex sex-determining systems. Different sex-determining loci (linkage group 1, 20 and 23) have been detected in various tilapia stocks. The ‘genetically improved farmed tilapia’ (GIFT) stock, founded from multiple Nile tilapia (Oreochromis niloticus) populations, with some likely to have been introgressed with O. mossambicus, is a key resource for tilapia aquaculture. The sex-determining mechanism in the GIFT stock was unknown, but potentially complicated due to its multiple origins. Results A bulk segregant analysis (BSA) version of double-digest restriction-site associated DNA sequencing (BSA-ddRADseq) was developed and used to detect and position sex-linked single nucleotide polymorphism (SNP) markers in 19 families from the GIFT strain breeding nucleus and two Stirling families as controls (a single XY locus had been previously mapped to LG1 in the latter). About 1500 SNPs per family were detected across the genome. Phenotypic sex in Stirling families showed strong association with LG1, whereas only SNPs located in LG23 showed clear association with sex in the majority of the GIFT families. No other genomic regions linked to sex determination were apparent. This region was validated using a series of LG23-specific DNA markers (five SNPs with highest association to sex from this study, the LG23 sex-associated microsatellite UNH898 and ARO172, and the recently isolated amhy marker for individual fish (n = 284). Conclusions Perhaps surprisingly given its multiple origins, sex determination in the GIFT strain breeding nucleus was associated only with a locus in LG23. BSA-ddRADseq allowed cost-effective analysis of multiple families, strengthening this conclusion. This technique has potential to be applied to other complex traits. The sex-linked SNP markers identified will be useful for potential marker-assisted selection (MAS) to control sex-ratio in GIFT tilapia to suppress unwanted reproduction during growout.
Collapse
Affiliation(s)
- Khanam Taslima
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK.,Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Stefanie Wehner
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - John B Taggart
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - Hugues de Verdal
- WorldFish Centre, Jalan Batu Maung, Bayan Lepas, Penang, Malaysia.,CIRAD, UMR ISEM, F-34398 Montpellier, France; ISEM, Univ Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | - John A H Benzie
- WorldFish Centre, Jalan Batu Maung, Bayan Lepas, Penang, Malaysia.,School of Biological Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | - Michaël Bekaert
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - Brendan J McAndrew
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK
| | - David J Penman
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Stirling, Scotland, UK.
| |
Collapse
|
10
|
Mapping of the Sex Determining Region on Linkage Group 12 of Guppy ( Poecilia reticulata). G3-GENES GENOMES GENETICS 2019; 9:3867-3875. [PMID: 31551287 PMCID: PMC6829149 DOI: 10.1534/g3.119.400656] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Poecilia reticulata is one of the most popular ornamental fish species with a higher demand for males due to their large colorful fins. The objectives of this study were mapping of the sex-determining (SD) region on linkage group 12 of guppy, and identification of a sex specific marker. We generated eight polymorphic microsatellite markers distributed along the distal 5.4 Mbp sequence of the previously identified SD region on linkage group (LG) 12. The markers were tested for association with sex in 156 individuals of the Red Blonde and Flame strains, and 126 progeny of four full-sibs Red Blonde families. A male-specific allele was found for microsatellite gu1066 at position of 25.3 Mbp on LG12 for both strains, and gu832 at position 24.4 Mbp for the Flame strain. Thus, a region of 0.9 Mbp between these markers, harboring 27 annotated genes, was selected for analysis. Based on association of copy number variation and sex determination we mapped a duplicated region between LGs 9 and 12, of 1.26 Mbp, containing 59 genes on LG12. The common interval between the segment bounded by gu1066 and gu832, and the duplicated region of 0.43 Mbp on LG12 harbors 11 genes of which 6 have multiple copies (54%). Growth arrest and DNA damage inducible gamma-like (GADD45G-like) is a plausible positional and functional candidate gene for its role in male fertility. We characterized the genomic structure of the gene in guppy, and found two isoforms; but no sex-biased differences were evident in genomic sequence and gene expression.
Collapse
|
11
|
Gammerdinger WJ, Conte MA, Sandkam BA, Ziegelbecker A, Koblmüller S, Kocher TD. Novel Sex Chromosomes in 3 Cichlid Fishes from Lake Tanganyika. J Hered 2019; 109:489-500. [PMID: 29444291 DOI: 10.1093/jhered/esy003] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 01/18/2018] [Indexed: 12/12/2022] Open
Abstract
African cichlids are well known for their adaptive radiations, but it is now apparent that they also harbor an extraordinary diversity of sex chromosome systems. In this study, we sequenced pools of males and females from species in 3 different genera of cichlids from Lake Tanganyika. We then searched for regions that were differentiated following the patterns expected for sex chromosomes. We report 2 novel sex chromosomes systems, an XY system on LG19 in Tropheus sp. "black" and a ZW system on LG7 in Hemibates stenosoma. We also identify a ZW system on LG5 in Cyprichromis leptosoma that may be convergent with a system previously described in Lake Malawi cichlids. Our data also identify candidate single nucleotide polymorphisms for the blue/yellow tail color polymorphism observed among male C. leptosoma.
Collapse
Affiliation(s)
| | - Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD, USA
| | | | | | - Stephan Koblmüller
- Institute of Zoology, University of Graz, Universitätsplatz, Graz, Austria
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD, USA
| |
Collapse
|
12
|
Dong C, Jiang P, Zhang J, Li X, Li S, Bai J, Fan J, Xu P. High-Density Linkage Map and Mapping for Sex and Growth-Related Traits of Largemouth Bass ( Micropterus salmoides). Front Genet 2019; 10:960. [PMID: 31649731 PMCID: PMC6796248 DOI: 10.3389/fgene.2019.00960] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/09/2019] [Indexed: 11/13/2022] Open
Abstract
The largemouth bass is an important species, and its culture has risen sharply with the surge in fish aquaculture in China. Due to the lack of selective breeding technology for the largemouth bass, the growth rate and disease resistance are low, its sexual maturation is slow, and other serious problems are contributing to a sharp decline in the safety and quality of largemouth bass products in recent decades. Therefore, comprehensive breeding programs to improve the economic performance and promote the modern industrial development of largemouth bass must be considered a priority. Here, a total of 152 adult largemouth bass, including two parents and 150 progenies, were selected to produce the genetic mapping family. Then, a high-density linkage map was constructed based on restriction site–associated DNA sequencing using 6,917 single-nucleotide polymorphisms (SNPs) located in 24 linkage groups (LGs). The total genetic length of the linkage map was 1,261.96 cM, and the length of each LG varied from 24.72 cM for LG02 to 117.53 cM for LG16, with an average length of 52.58 cM and an average SNP number of 286. Thirteen significant quantitative trait loci (QTLs) for sex determination were located on LG04, LG05, LG08, LG12, LG15, LG21, and LG23. An informative QTL cluster that included six QTLs was detected on LG12. However, one notable QTL, which accounted for 71.48% of the total phenotypic variation, was located in the region of 1.85 cM on LG05. In addition, 32 identified QTLs were related to growth, including body weight, body length, body height, and head length. The QTLs for these growth-related traits are located in 13 LG regions and have little effect on phenotypic variation. This high-density genetic linkage map will enable the fine-mapping of economic traits and support the future genome assembly of the largemouth bass. Additionally, our study will be useful for future selective culture of largemouth bass and could potentially be used in molecular-assisted breeding of largemouth bass for aquaculture.
Collapse
Affiliation(s)
- Chuanju Dong
- Pearl River Fisheries Research Institute, CAFS, Guangzhou, China.,College of Fisheries, Henan Normal University, Xinxiang, China.,Key Laboratory of Tropical and Subtropical Fishery Resource Application and Cultivation, Ministry of Agriculture, Pearl River Fisheries Research Institute, CAFS, Guangzhou, China
| | - Peng Jiang
- Pearl River Fisheries Research Institute, CAFS, Guangzhou, China
| | - Jiangfan Zhang
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Xuejun Li
- College of Fisheries, Henan Normal University, Xinxiang, China
| | - Shengjie Li
- Pearl River Fisheries Research Institute, CAFS, Guangzhou, China.,College of Fisheries, Henan Normal University, Xinxiang, China
| | - Junjie Bai
- Pearl River Fisheries Research Institute, CAFS, Guangzhou, China
| | - Jiajia Fan
- Pearl River Fisheries Research Institute, CAFS, Guangzhou, China
| | - Peng Xu
- College of Fisheries, Henan Normal University, Xinxiang, China.,State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, China
| |
Collapse
|
13
|
Cáceres G, López ME, Cádiz MI, Yoshida GM, Jedlicki A, Palma-Véjares R, Travisany D, Díaz-Domínguez D, Maass A, Lhorente JP, Soto J, Salas D, Yáñez JM. Fine Mapping Using Whole-Genome Sequencing Confirms Anti-Müllerian Hormone as a Major Gene for Sex Determination in Farmed Nile Tilapia ( Oreochromis niloticus L.). G3 (BETHESDA, MD.) 2019; 9:3213-3223. [PMID: 31416805 PMCID: PMC6778786 DOI: 10.1534/g3.119.400297] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 07/27/2019] [Indexed: 02/06/2023]
Abstract
Nile tilapia (Oreochromis niloticus) is one of the most cultivated and economically important species in world aquaculture. Intensive production promotes the use of monosex animals, due to an important dimorphism that favors male growth. Currently, the main mechanism to obtain all-male populations is the use of hormones in feeding during larval and fry phases. Identifying genomic regions associated with sex determination in Nile tilapia is a research topic of great interest. The objective of this study was to identify genomic variants associated with sex determination in three commercial populations of Nile tilapia. Whole-genome sequencing of 326 individuals was performed, and a total of 2.4 million high-quality bi-allelic single nucleotide polymorphisms (SNPs) were identified after quality control. A genome-wide association study (GWAS) was conducted to identify markers associated with the binary sex trait (males = 1; females = 0). A mixed logistic regression GWAS model was fitted and a genome-wide significant signal comprising 36 SNPs, spanning a genomic region of 536 kb in chromosome 23 was identified. Ten out of these 36 genetic variants intercept the anti-Müllerian (Amh) hormone gene. Other significant SNPs were located in the neighboring Amh gene region. This gene has been strongly associated with sex determination in several vertebrate species, playing an essential role in the differentiation of male and female reproductive tissue in early stages of development. This finding provides useful information to better understand the genetic mechanisms underlying sex determination in Nile tilapia.
Collapse
Affiliation(s)
- Giovanna Cáceres
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile
| | - María E López
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - María I Cádiz
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Programa de Doctorado en Ciencias Silvoagropecuarias y Veterinarias, Campus Sur, Universidad de Chile, Santa Rosa 11315, La Pintana, Santiago, Chile
| | - Grazyella M Yoshida
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
- Benchmark Genetics Chile, Puerto Montt, Chile
| | - Ana Jedlicki
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile
| | - Ricardo Palma-Véjares
- Centro para la Regulación del Genoma, and
- Centro de Modelamiento Matemático UMI CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Dante Travisany
- Centro para la Regulación del Genoma, and
- Centro de Modelamiento Matemático UMI CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Diego Díaz-Domínguez
- Centro para la Regulación del Genoma, and
- Centro de Modelamiento Matemático UMI CNRS 2807, Universidad de Chile, Santiago, Chile
| | - Alejandro Maass
- Centro para la Regulación del Genoma, and
- Centro de Modelamiento Matemático UMI CNRS 2807, Universidad de Chile, Santiago, Chile
| | | | - Jose Soto
- Grupo Acuacorporación Internacional (GACI), Cañas, Costa Rica, and
| | - Diego Salas
- Grupo Acuacorporación Internacional (GACI), Cañas, Costa Rica, and
| | - José M Yáñez
- Facultad de Ciencias Veterinarias y Pecuarias, Universidad de Chile, Santiago, Chile,
- Núcleo Milenio INVASAL, Concepción, Chile
| |
Collapse
|
14
|
Sissao R, D'Cotta H, Baroiller JF, Toguyeni A. Mismatches between the genetic and phenotypic sex in the wild Kou population of Nile tilapia Oreochromis niloticus. PeerJ 2019; 7:e7709. [PMID: 31579600 PMCID: PMC6754722 DOI: 10.7717/peerj.7709] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 08/20/2019] [Indexed: 11/20/2022] Open
Abstract
Sex determination and sex chromosomes can be very diverse between teleost species. The group of tilapias shows a polymorphism in sex determination not only between closely related species but also between domestic strains within a species. In the Nile tilapia, the major effect genes and therefore the Y chromosome have been located on either linkage group 1 (LG1) or LG23 depending on the strains. In a Japanese strain, the sex determinant of LG23 (the amhY gene) has been identified as a duplicated amh (anti-Müllerian hormone) gene, with its gametolog found on the X chromosome (amhX). AmhY is located in tandem with the amhΔY gene (a truncated form) on the Y chromosome. X and Y chromosome markers based on the amh genes have been validated only on a few domestic strains but not in wild populations. Here, we used four of these markers in order to examine (1) the possible variation in sex determination of a wild population of Nile tilapia living in Lake Kou (Burkina Faso), (2) putative polymorphisms for these amh copies and (3) the existence of sex reversed individuals in the wild. Our genotyping of 91 wild Kou individuals with the amh sex-diagnostic markers of LG23 showed that while phenotypic females were all XX, phenotypic males were either XY or XX. Progeny testing of eight of these XX males revealed that one of these males consistently sired all-female progenies, suggesting that it is a wild sex reversed male (which could result from high temperature effects). The other XX males gave balanced sex ratios, suggesting that sex is controlled by another locus (possibly on another LG) which may be epistatically dominant over the LG23 locus. Finally, identification of unexpected amh genotypes was found for two individuals. They produced either balanced or female-biased sex ratios, depending on the breeder with whom they were crossed, suggesting possible recombination between the X and the Y chromosomes.
Collapse
Affiliation(s)
- Rokyatou Sissao
- Unité de recherche aquaculture et biodiversité aquatique/Laboratoire d'études et de recherche sur les ressources naturelles et sciences de l'environnement, Université Nazi BONI, Bobo-Dioulasso, Burkina Faso.,Institut de l'environnement et de recherches agricoles, Centre national de la recherche scientifique et technologique, Bobo-Dioulasso, Burkina Faso.,Centre international de recherche-développement sur l'élevage en zone subhumide, Bobo-Dioulasso, Burkina Faso
| | - Helena D'Cotta
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,UMR ISEM, CIRAD, Montpellier, France
| | - Jean-François Baroiller
- ISEM, Université de Montpellier, CNRS, IRD, EPHE, Montpellier, France.,UMR ISEM, CIRAD, Montpellier, France
| | - Aboubacar Toguyeni
- Unité de recherche aquaculture et biodiversité aquatique/Laboratoire d'études et de recherche sur les ressources naturelles et sciences de l'environnement, Université Nazi BONI, Bobo-Dioulasso, Burkina Faso.,Centre international de recherche-développement sur l'élevage en zone subhumide, Bobo-Dioulasso, Burkina Faso
| |
Collapse
|
15
|
Guo L, Xu YH, Zhang N, Zhou FL, Huang JH, Liu BS, Jiang SG, Zhang DC. A High-Density Genetic Linkage Map and QTL Mapping for Sex in Black Tiger Shrimp ( Penaeus monodon). Front Genet 2019; 10:326. [PMID: 31024632 PMCID: PMC6465554 DOI: 10.3389/fgene.2019.00326] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Accepted: 03/26/2019] [Indexed: 12/20/2022] Open
Abstract
The black tiger shrimp, Penaeus monodon, is important in both fishery and aquaculture and is the second-most widely cultured shrimp species in the world. However, the current strains cannot meet the market needs in various cultural environments, and the genome resources for P. monodon are still lacking. Restriction-site associated DNA sequencing (RADseq) has been widely used in genetic linkage map construction and in quantitative trait loci (QTL) mapping. We constructed a high-density genetic linkage map with RADseq in a full-sib family. This map contained 6524 single nucleotide polymorphisms (SNPs) and 2208 unique loci. The total length was 3275.4 cM, and the genetic distance was estimated to be 1.1 Mb/cM. The sex trait is a dichotomous phenotype, and the same interval was detected as a QTL using QTL mapping and genome-wide association analysis. The most significant locus explained 77.4% of the phenotype variance. The sex locus was speculated to be the same in this species based on the sequence alignments in Mozambique, India, and Hawaii populations. The constructed genetic linkage map provided a valuable resource for QTL mapping, genome assembly, and genome comparison for shrimp. The demonstrated common sex locus is a step closer to locating the underlying gene.
Collapse
Affiliation(s)
- Liang Guo
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Yu-Hui Xu
- Biomarker Technologies Corporation, Beijing, China
| | - Nan Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Fa-Lin Zhou
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Jian-Hua Huang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Bao-Suo Liu
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Shi-Gui Jiang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| | - Dian-Chang Zhang
- Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture and Rural Affairs, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China.,Guangdong Provincial Engineer Technology Research Center of Marine Biological Seed Industry, Guangzhou, China
| |
Collapse
|
16
|
Conte MA, Joshi R, Moore EC, Nandamuri SP, Gammerdinger WJ, Roberts RB, Carleton KL, Lien S, Kocher TD. Chromosome-scale assemblies reveal the structural evolution of African cichlid genomes. Gigascience 2019; 8:giz030. [PMID: 30942871 PMCID: PMC6447674 DOI: 10.1093/gigascience/giz030] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 01/11/2019] [Accepted: 03/07/2019] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND African cichlid fishes are well known for their rapid radiations and are a model system for studying evolutionary processes. Here we compare multiple, high-quality, chromosome-scale genome assemblies to elucidate the genetic mechanisms underlying cichlid diversification and study how genome structure evolves in rapidly radiating lineages. RESULTS We re-anchored our recent assembly of the Nile tilapia (Oreochromis niloticus) genome using a new high-density genetic map. We also developed a new de novo genome assembly of the Lake Malawi cichlid, Metriaclima zebra, using high-coverage Pacific Biosciences sequencing, and anchored contigs to linkage groups (LGs) using 4 different genetic maps. These new anchored assemblies allow the first chromosome-scale comparisons of African cichlid genomes. Large intra-chromosomal structural differences (∼2-28 megabase pairs) among species are common, while inter-chromosomal differences are rare (<10 megabase pairs total). Placement of the centromeres within the chromosome-scale assemblies identifies large structural differences that explain many of the karyotype differences among species. Structural differences are also associated with unique patterns of recombination on sex chromosomes. Structural differences on LG9, LG11, and LG20 are associated with reduced recombination, indicative of inversions between the rock- and sand-dwelling clades of Lake Malawi cichlids. M. zebra has a larger number of recent transposable element insertions compared with O. niloticus, suggesting that several transposable element families have a higher rate of insertion in the haplochromine cichlid lineage. CONCLUSION This study identifies novel structural variation among East African cichlid genomes and provides a new set of genomic resources to support research on the mechanisms driving cichlid adaptation and speciation.
Collapse
Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Rajesh Joshi
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Emily C Moore
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | | | | | - Reade B Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC 27695, USA
| | - Karen L Carleton
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Sigbjørn Lien
- Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, PO Box 5003, Ås, Norway
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| |
Collapse
|
17
|
Zhang S, Zhang X, Chen X, Xu T, Wang M, Qin Q, Zhong L, Jiang H, Zhu X, Liu H, Shao J, Zhu Z, Shi Q, Bian W, You X. Construction of a High-Density Linkage Map and QTL Fine Mapping for Growth- and Sex-Related Traits in Channel Catfish ( Ictalurus punctatus). Front Genet 2019; 10:251. [PMID: 30984241 PMCID: PMC6448050 DOI: 10.3389/fgene.2019.00251] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/06/2019] [Indexed: 12/11/2022] Open
Abstract
A high-density genetic linkage map is of particular importance in the fine mapping for important economic traits and whole genome assembly in aquaculture species. The channel catfish (Ictalurus punctatus), a species native to North America, is one of the most important commercial freshwater fish in the world. Outside of the United States, China has become the major producer and consumer of channel catfish after experiencing rapid development in the past three decades. In this study, based on restriction site associated DNA sequencing (RAD-seq), a high-density genetic linkage map of channel catfish was constructed by using single nucleotide polymorphisms (SNPs) in a F1 family composed of 156 offspring and their two parental individuals. A total of 4,768 SNPs were assigned to 29 linkage groups (LGs), and the length of the linkage map reached 2,480.25 centiMorgans (cM) with an average distance of 0.55 cM between loci. Based on this genetic linkage map, 223 genomic scaffolds were anchored to the 29 LGs of channel catfish, and a total length of 704.66 Mb was assembled. Quantitative trait locus (QTL) mapping and genome-wide association analysis identified 10 QTLs of sex-related and six QTLs of growth-related traits at LG17 and LG28, respectively. Candidate genes associated with sex dimorphism, including spata2, spata5, sf3, zbtb38, and fox, were identified within QTL intervals on the LG17. A sex-linked marker with simple sequence repeats (SSR) in zbtb38 gene of the LG17 was validated for practical verification of sex in the channel catfish. Thus, the LG17 was considered as a sex-related LG. Potential growth-related genes were also identified, including important regulators such as megf9, npffr1, and gas1. In a word, we constructed the high-density genetic linkage map and developed the sex-linked marker in channel catfish, which are important genetic resources for future marker-assisted selection (MAS) of this economically important teleost.
Collapse
Affiliation(s)
- Shiyong Zhang
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinhui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Xiaohui Chen
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Tengfei Xu
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Minghua Wang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Qin Qin
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Liqiang Zhong
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Hucheng Jiang
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xiaohua Zhu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Hongyan Liu
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Junjie Shao
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China
| | - Zhifei Zhu
- BGI-Zhenjiang Institute of Hydrobiology, Zhenjiang, China
| | - Qiong Shi
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| | - Wenji Bian
- National Genetic Breeding Center of Channel Catfish, Freshwater Fisheries Research Institute of Jiangsu Province, Nanjing, China.,The Jiangsu Provincial Platform for Conservation and Utilization of Agricultural Germplasm, Nanjing, China
| | - Xinxin You
- BGI Education Center, University of Chinese Academy of Sciences, Shenzhen, China.,Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Beijing Genomics Institute, Shenzhen, China
| |
Collapse
|
18
|
Chen CH, Li BJ, Gu XH, Lin HR, Xia JH. Marker-assisted selection of YY supermales from a genetically improved farmed tilapia-derived strain. Zool Res 2019; 40:108-112. [PMID: 30213922 PMCID: PMC6378562 DOI: 10.24272/j.issn.2095-8137.2018.071] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/30/2018] [Indexed: 11/29/2022] Open
Abstract
Genetically improved farmed tilapia (GIFT) and GIFT-derived strains account for the majority of farmed tilapia worldwide. As male tilapias grow much faster than females, they are often considered more desirable in the aquacultural industry. Sex reversal of females to males using the male sex hormone 17-α-methyltestosterone (MT) is generally used to induce phenotypic males during large-scale production of all male fingerlings. However, the widespread use of large quantities of sex reversal hormone in hatcheries may pose a health risk to workers and ecological threats to surrounding environments. Breeding procedures to produce genetically all-male tilapia with limited or no use of sex hormones are therefore urgently needed. In this study, by applying marker-assisted selection (MAS) for the selection of YY supermales from a GIFT-derived strain, we identified 24 XY pseudofemale and 431 YY supermale tilapias. Further performance evaluation on the progenies of the YY supermales resulted in male rates of 94.1%, 99.5% and 99.6%, respectively, in three populations, and a daily increase in body weight of 1.4 g at 3 months (n=997). Our study established a highly effective MAS procedure in the selection of YY supermales from a GIFT-derived strain. Furthermore, the development of MAS-selected YY supermales will help reduce the utilization of hormones for controlling sex in the tilapia aquaculture.
Collapse
Affiliation(s)
- Chao-Hao Chen
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou Guangdong 510275, China
| | - Bi-Jun Li
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou Guangdong 510275, China
| | - Xiao-Hui Gu
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou Guangdong 510275, China
| | - Hao-Ran Lin
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou Guangdong 510275, China
| | - Jun-Hong Xia
- State Key Laboratory of Biocontrol, Institute of Aquatic Economic Animals and Guangdong Provincial Key Laboratory for Aquatic Economic Animals, College of Life Sciences, Sun Yat-Sen University, Guangzhou Guangdong 510275, China; E-mail:
| |
Collapse
|
19
|
Joshi R, Árnyasi M, Lien S, Gjøen HM, Alvarez AT, Kent M. Development and Validation of 58K SNP-Array and High-Density Linkage Map in Nile Tilapia ( O. niloticus). Front Genet 2018; 9:472. [PMID: 30374365 PMCID: PMC6196754 DOI: 10.3389/fgene.2018.00472] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 09/24/2018] [Indexed: 11/22/2022] Open
Abstract
Despite being the second most important aquaculture species in the world accounting for 7.4% of global production in 2015, tilapia aquaculture has lacked genomic tools like SNP-arrays and high-density linkage maps to improve selection accuracy and accelerate genetic progress. In this paper, we describe the development of a genotyping array containing more than 58,000 SNPs for Nile tilapia (Oreochromis niloticus). SNPs were identified from whole genome resequencing of 32 individuals from the commercial population of the Genomar strain, and were selected for the SNP-array based on polymorphic information content and physical distribution across the genome using the Orenil1.1 genome assembly as reference sequence. SNP-performance was evaluated by genotyping 4991 individuals, including 689 offspring belonging to 41 full-sib families, which revealed high-quality genotype data for 43,588 SNPs. A preliminary genetic linkage map was constructed using Lepmap2 which in turn was integrated with information from the O_niloticus_UMD1 genome assembly to produce an integrated physical and genetic linkage map comprising 40,186 SNPs distributed across 22 linkage groups (LGs). Around one-third of the LGs showed a different recombination rate between sexes, with the female being greater than the male map by a factor of 1.2 (1632.9 to 1359.6 cM, respectively), with most LGs displaying a sigmoid recombination profile. Finally, the sex-determining locus was mapped to position 40.53 cM on LG23, in the vicinity of the anti-Müllerian hormone (amh) gene. These new resources has the potential to greatly influence and improve the genetic gain when applying genomic selection and surpass the difficulties of efficient selection for invasively measured traits in Nile tilapia.
Collapse
Affiliation(s)
- Rajesh Joshi
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Mariann Árnyasi
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | - Hans Magnus Gjøen
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Matthew Kent
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
| |
Collapse
|
20
|
Gammerdinger WJ, Kocher TD. Unusual Diversity of Sex Chromosomes in African Cichlid Fishes. Genes (Basel) 2018; 9:E480. [PMID: 30287777 PMCID: PMC6210639 DOI: 10.3390/genes9100480] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 09/26/2018] [Accepted: 10/01/2018] [Indexed: 11/30/2022] Open
Abstract
African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade.
Collapse
Affiliation(s)
- William J Gammerdinger
- Institute of Science and Technology (IST) Austria, Am Campus 1, 3400 Klosterneuburg, Austria.
| | - Thomas D Kocher
- Department of Biology, University of Maryland, College Park, MD 20742, USA.
| |
Collapse
|
21
|
Quantitative trait loci on LGs 9 and 14 affect the reproductive interaction between two Oreochromis species, O. niloticus and O. aureus. Heredity (Edinb) 2018; 122:341-353. [PMID: 30082919 DOI: 10.1038/s41437-018-0131-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Revised: 07/11/2018] [Accepted: 07/17/2018] [Indexed: 11/08/2022] Open
Abstract
Effective farming of tilapia requires all-male culture, characterized by uniformity and high growth rate. Males of O. aureus (Oa) and females of O. niloticus (On) produce all-male offspring, but there is a behavioral reproductive barrier between the two species that prevents mass production. In crosses between Oa and On broodstocks, few hybrid females are attracted to the Oa male nests (denoted responders), and if they harbor the On alleles for the sex determination (SD) sites on linkage groups (LGs) 1, 3, and 23, all-male progeny are produced. Yet, without controlling for the alleles underlying SD, the parental stocks gradually lose their capability for all-male production. Hypothesizing that marker-assisted selection for female responders would allow production of sustainable broodstocks, we applied genotyping-by-sequencing to generate 4983 informative SNPs from 13 responding and 28 non-responding females from two full-sib families. Accounting for multiple comparisons in a genome-wide association study, seven SNPs met a false discovery rate of 0.061. Lowest nominal probabilities were on LGs 9 and 14, for which microsatellite DNA markers were designed within the candidate genes PTGDSL and CASRL, respectively. By increasing the sample size to 22 responders and 47 non-responders and by genotyping additional established microsatellites, we confirmed the association of these LGs with female responsiveness. The combined effects of microsatellites GM171 and CARSL-LOC100690618 on LGs 9 and 14 explained 37% of the phenotypic variance of reproductive interaction (p < 0.0001). Based on these findings, we propose a strategy for mass production of all-male tilapia hybrids through selection for genomic loci affecting SD and female responsiveness.
Collapse
|
22
|
Feulner PGD, Schwarzer J, Haesler MP, Meier JI, Seehausen O. A Dense Linkage Map of Lake Victoria Cichlids Improved the Pundamilia Genome Assembly and Revealed a Major QTL for Sex-Determination. G3 (BETHESDA, MD.) 2018; 8:2411-2420. [PMID: 29760203 PMCID: PMC6027883 DOI: 10.1534/g3.118.200207] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 05/13/2018] [Indexed: 01/09/2023]
Abstract
Genetic linkage maps are essential for comparative genomics, high quality genome sequence assembly and fine scale quantitative trait locus (QTL) mapping. In the present study we identified and genotyped markers via restriction-site associated DNA (RAD) sequencing and constructed a genetic linkage map based on 1,597 SNP markers of an interspecific F2 cross of two closely related Lake Victoria cichlids (Pundamilia pundamilia and P sp. 'red head'). The SNP markers were distributed on 22 linkage groups and the total map size was 1,594 cM with an average marker distance of 1.01 cM. This high-resolution genetic linkage map was used to anchor the scaffolds of the Pundamilia genome and estimate recombination rates along the genome. Via QTL mapping we identified a major QTL for sex in a ∼1.9 Mb region on Pun-LG10, which is homologous to Oreochromis niloticus LG 23 (Ore-LG23) and includes a well-known vertebrate sex-determination gene (amh).
Collapse
Affiliation(s)
- Philine G D Feulner
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
| | - Julia Schwarzer
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
- Zoologisches Forschungsmuseum Alexander Koenig, 53113 Bonn, Germany
| | - Marcel P Haesler
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
| | - Joana I Meier
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Centre of Ecology, Evolution and Biogeochemistry, EAWAG Swiss Federal Institute of Aquatic Science and Technology, 6047 Kastanienbaum, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, 3012 Switzerland
| |
Collapse
|
23
|
Wessels S, Krause I, Floren C, Schütz E, Beck J, Knorr C. ddRADseq reveals determinants for temperature-dependent sex reversal in Nile tilapia on LG23. BMC Genomics 2017; 18:531. [PMID: 28705237 PMCID: PMC5513378 DOI: 10.1186/s12864-017-3930-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 07/07/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In Nile tilapia sex determination is governed by a male heterogametic system XX/XY either on LG1 or LG23. The latter carries a Y-specific duplicate of the amh gene, which is a testis-determining factor. Allelic variants in the amh gene demonstrated to be major triggers for autosomal and temperature-dependent sex reversal. Further, QTL on LG23 and LG20 show a temperature-responsiveness with influence on the phenotypic sex relative to the sex chromosomes. Here we present a ddRADseq based approach to identify genomic regions that show unusual large differentiation in terms of fixation index (FST) between temperature-treated pseudomales and non-masculinized females using a comparative genome-scan. Genome-wide associations were identified for the temperature-dependent sex using a genetically all-female population devoid of amh-ΔY. RESULTS Twenty-two thousand three hundred ninety-two SNPs were interrogated for the comparison of temperature-treated pseudomales and females, which revealed the largest differentiation on LG23. Outlier FST-values (0.35-0.44) were determined for six SNPs in the genomic interval (9,190,077-11,065,693) harbouring the amh gene (9,602,693-9,605,808), exceeding the genome-wide low FST of 0.013. Association analysis with a set of 9104 selected SNPs confirmed that the same genomic region on LG23 exerts a significant effect on the temperature-dependent sex. CONCLUSIONS This study highlights the role of LG23 in sex determination, harbouring major determinants for temperature-dependent sex reversal in Nile tilapia. Furthermore FST outlier detection proves a powerful tool for detection of sex-determining regions in fish genomes.
Collapse
Affiliation(s)
- Stephan Wessels
- Department of Animal Sciences, Division of Aquaculture and Water Ecology, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany.
| | - Ina Krause
- Department of Animal Sciences, Division of Aquaculture and Water Ecology, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Claudia Floren
- Department of Animal Sciences, Division of Livestock Biotechnology and Reproduction, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany
| | - Ekkehard Schütz
- Institute of Veterinary Medicine, University of Goettingen, 37077, Goettingen, Germany.,Chronix Biomedical GmbH, 37077, Goettingen, Germany
| | - Jule Beck
- Chronix Biomedical GmbH, 37077, Goettingen, Germany
| | - Christoph Knorr
- Department of Animal Sciences, Division of Livestock Biotechnology and Reproduction, University of Goettingen, Burckhardtweg 2, 37077, Goettingen, Germany
| |
Collapse
|
24
|
Construction of a high-density linkage map and mapping of sex determination and growth-related loci in the mandarin fish (Siniperca chuatsi). BMC Genomics 2017; 18:446. [PMID: 28587594 PMCID: PMC5461734 DOI: 10.1186/s12864-017-3830-3] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 05/30/2017] [Indexed: 11/10/2022] Open
Abstract
Background The mandarin fish (Siniperca chuatsi) is an important and widely cultured fish in China. However, the lack of selective breeding of mandarin fish in previous decades has resulted in a decline in the growth rate of pond-cultured fish, a shortened period of sexual maturity, and reduced disease resistance; these issues seriously affect the quality and safety of the fish products. Therefore, it is necessary to establish a selective breeding program for the mandarin fish to improve the economical traits of the fish and to sustain the development of the mandarin fish industry. Results We constructed a high-density linkage map for it based on double digest restriction site associated DNA sequencing (ddRAD-Sequencing). This map contained 3283 dimorphic single nucleotide polymorphism markers and 24 linkage groups (LGs). The total map-length was 1972.01 cM, with an average interlocus distance of 0.61 cM. One significant quantitative trait locus (QTL) for sex determination trait was detected on LG23, which was supported by five markers, clustered between 60.27 and 68.71 cM. The highest logarithm of odds value (17.73) was located at 60.27 cM, near the marker r1_73194, accounting for 53.3% of the phenotypic variance. Genotypes of all the male fish on r1_33008 were homozygous, whereas those of all females were heterozygous. Thus, LG23 was considered a sex-related linkage group. Eleven significant QTLs, for three growth traits, at two growth stages and the increased values were distributed on four LGs; their contributions to the phenotypic variation were quite low (12.4–17.2%), suggesting that multiple genes affected the growth traits. Conclusion This high-resolution genetic map provides a valuable resource for fine-mapping of important traits and for identification of sex-related markers that should facilitate breeding of all-female mandarin fish for aquaculture and mechanistic studies on sex determination. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3830-3) contains supplementary material, which is available to authorized users.
Collapse
|
25
|
Conte MA, Gammerdinger WJ, Bartie KL, Penman DJ, Kocher TD. A high quality assembly of the Nile Tilapia (Oreochromis niloticus) genome reveals the structure of two sex determination regions. BMC Genomics 2017; 18:341. [PMID: 28464822 PMCID: PMC5414186 DOI: 10.1186/s12864-017-3723-5] [Citation(s) in RCA: 119] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 04/25/2017] [Indexed: 12/20/2022] Open
Abstract
Background Tilapias are the second most farmed fishes in the world and a sustainable source of food. Like many other fish, tilapias are sexually dimorphic and sex is a commercially important trait in these fish. In this study, we developed a significantly improved assembly of the tilapia genome using the latest genome sequencing methods and show how it improves the characterization of two sex determination regions in two tilapia species. Results A homozygous clonal XX female Nile tilapia (Oreochromis niloticus) was sequenced to 44X coverage using Pacific Biosciences (PacBio) SMRT sequencing. Dozens of candidate de novo assemblies were generated and an optimal assembly (contig NG50 of 3.3Mbp) was selected using principal component analysis of likelihood scores calculated from several paired-end sequencing libraries. Comparison of the new assembly to the previous O. niloticus genome assembly reveals that recently duplicated portions of the genome are now well represented. The overall number of genes in the new assembly increased by 27.3%, including a 67% increase in pseudogenes. The new tilapia genome assembly correctly represents two recent vasa gene duplication events that have been verified with BAC sequencing. At total of 146Mbp of additional transposable element sequence are now assembled, a large proportion of which are recent insertions. Large centromeric satellite repeats are assembled and annotated in cichlid fish for the first time. Finally, the new assembly identifies the long-range structure of both a ~9Mbp XY sex determination region on LG1 in O. niloticus, and a ~50Mbp WZ sex determination region on LG3 in the related species O. aureus. Conclusions This study highlights the use of long read sequencing to correctly assemble recent duplications and to characterize repeat-filled regions of the genome. The study serves as an example of the need for high quality genome assemblies and provides a framework for identifying sex determining genes in tilapia and related fish species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3723-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Matthew A Conte
- Department of Biology, University of Maryland, 20742, College Park, MD, USA
| | | | - Kerry L Bartie
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - David J Penman
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK
| | - Thomas D Kocher
- Department of Biology, University of Maryland, 20742, College Park, MD, USA.
| |
Collapse
|
26
|
Lin G, Chua E, Orban L, Yue GH. Mapping QTL for Sex and Growth Traits in Salt-Tolerant Tilapia (Oreochromis spp. X O. mossambicus). PLoS One 2016; 11:e0166723. [PMID: 27870905 PMCID: PMC5117716 DOI: 10.1371/journal.pone.0166723] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 11/02/2016] [Indexed: 11/18/2022] Open
Abstract
In aquaculture, growth and sex are economically important traits. To accelerate genetic improvement in increasing growth in salt-tolerant tilapia, we conducted QTL mapping for growth traits and sex with an F2 family, including 522 offspring and two parents. We used 144 polymorphic microsatellites evenly covering the genome of tilapia to genotype the family. QTL analyses were carried out using interval mapping for all individuals, males and females in the family, respectively. Using all individuals, three suggestive QTL for body weight, body length and body thickness respectively were detected in LG20, LG22 and LG12 and explained 2.4% to 3.1% of phenotypic variance (PV). When considering only males, five QTL for body weight were detected on five LGs, and explained 4.1 to 6.3% of PV. Using only females from the F2 family, three QTL for body weight were detected on LG1, LG6 and LG8, and explained 7.9-14.3% of PV. The QTL for body weight in males and females were located in different LGs, suggesting that in salt-tolerant tilapia, different set of genes 'switches' control the growth in males and females. QTL for sex were mapped on LG1 and LG22, indicating multigene sex determination in the salt-tolerant tilapia. This study provides new insights on the locations and effects of QTL for growth traits and sex, and sets the foundation for fine mapping for future marker-assisted selection for growth and sex in salt-tolerant tilapia aquaculture.
Collapse
Affiliation(s)
- Grace Lin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Elaine Chua
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
| | - Laszlo Orban
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- Department of Animal Sciences and Breeding, Georgikon Faculty, University of Pannonia, Deák Ferenc utca 16, H-8230 Keszthely, Hungary
- Centre for Comparative Genomics, Murdoch University, Murdoch, 6150 Australia
| | - Gen Hua Yue
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 117543, Singapore
- * E-mail:
| |
Collapse
|
27
|
Roberts NB, Juntti SA, Coyle KP, Dumont BL, Stanley MK, Ryan AQ, Fernald RD, Roberts RB. Polygenic sex determination in the cichlid fish Astatotilapia burtoni. BMC Genomics 2016; 17:835. [PMID: 27784286 PMCID: PMC5080751 DOI: 10.1186/s12864-016-3177-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/18/2016] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The East African riverine cichlid species Astatotilapia burtoni serves as an important laboratory model for sexually dimorphic physiology and behavior, and also serves as an outgroup species for the explosive adaptive radiations of cichlid species in Lake Malawi and Lake Victoria. An astounding diversity of genetic sex determination systems have been revealed within the adaptive radiation of East African cichlids thus far, including polygenic sex determination systems involving the epistatic interaction of multiple, independently segregating sex determination alleles. However, sex determination has remained unmapped in A. burtoni. Here we present mapping results supporting the presence of multiple, novel sex determination alleles, and thus the presence of polygenic sex determination in A. burtoni. RESULTS Using mapping in small families in conjunction with restriction-site associated DNA sequencing strategies, we identify associations with sex at loci on linkage group 13 and linkage group 5-14. Inheritance patterns support an XY sex determination system on linkage group 5-14 (a chromosome fusion relative to other cichlids studied), and an XYW system on linkage group 13, and these associations are replicated in multiple families. Additionally, combining our genetic data with comparative genomic analysis identifies another fusion that is unassociated with sex, with linkage group 8-24 and linkage group 16-21 fused in A. burtoni relative to other East African cichlid species. CONCLUSIONS We identify genetic signals supporting the presence of three previously unidentified sex determination alleles at two loci in the species A. burtoni, strongly supporting the presence of polygenic sex determination system in the species. These results provide a foundation for future mapping of multiple sex determination genes and their interactions. A better understanding of sex determination in A. burtoni provides important context for their use in behavioral studies, as well as studies of the evolution of genetic sex determination and sexual conflicts in East African cichlids.
Collapse
Affiliation(s)
- Natalie B. Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - Scott A. Juntti
- Department of Biology, Stanford University, Stanford, CA USA
| | - Kaitlin P. Coyle
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - Bethany L. Dumont
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - M. Kaitlyn Stanley
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | - Allyson Q. Ryan
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| | | | - Reade B. Roberts
- Department of Biological Sciences and W. M. Keck Center for Behavioral Biology, North Carolina State University, Raleigh, NC USA
| |
Collapse
|
28
|
Sun X, Fernando R, Dekkers J. Contributions of linkage disequilibrium and co-segregation information to the accuracy of genomic prediction. Genet Sel Evol 2016; 48:77. [PMID: 27729012 PMCID: PMC5060012 DOI: 10.1186/s12711-016-0255-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 09/30/2016] [Indexed: 01/09/2023] Open
Abstract
Background Traditional genomic prediction models using multiple regression on single nucleotide polymorphisms (SNPs) genotypes exploit associations between genotypes of quantitative trait loci (QTL) and SNPs, which can be created by historical linkage disequilibrium (LD), recent co-segregation (CS) and pedigree relationships. Results from field data analyses show that prediction accuracy is usually much higher for individuals that are close relatives of the training population than for distantly related individuals. A possible reason is that historical LD between QTL and SNPs is weak and, for close relatives, prediction accuracy of SNP models is mainly contributed by pedigree relationships and CS. Information from pedigree relationships decreases fast over generations and only contributes to within-family prediction. Information from CS is affected by family structures and effective population size, and can have a substantial contribution to prediction accuracy when modeled explicitly. Results In this study, a method to explicitly model CS was developed by following the transmission of putative QTL alleles using allele origins at SNPs. Bayesian hierarchical models that combine information from LD and CS (LD-CS model) were developed for genomic prediction in pedigree populations. Contributions of LD and CS information to prediction accuracy across families and generations without retraining were investigated in simulated half-sib datasets and deep pedigrees with different recent effective population sizes, respectively. Results from half-sib datasets showed that when historical LD between QTL and SNPs is low, accuracy of the LD model decreased when the training data size is increased by adding independent sire families, but accuracies from the CS and LD-CS models increased and plateaued rapidly. Results from deep pedigree datasets show that the LD model had high accuracy across generations only when historical LD between QTL and SNPs was high. Modeling CS explicitly resulted in higher accuracy than the LD model across generations when the mating design generated many close relatives. Conclusions Our results suggest that modeling CS explicitly improves accuracy of genomic prediction when historical LD between QTL and SNPs is low. Modeling both LD and CS explicitly is expected to improve accuracy when recent effective population size is small, or when the training data include many independent families. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0255-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiaochen Sun
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA, 50011, USA.
| | - Rohan Fernando
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA, 50011, USA
| | - Jack Dekkers
- Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, Ames, IA, 50011, USA
| |
Collapse
|
29
|
Ma K, Liao M, Liu F, Ye B, Sun F, Yue GH. Charactering the ZFAND3 gene mapped in the sex-determining locus in hybrid tilapia (Oreochromis spp.). Sci Rep 2016; 6:25471. [PMID: 27137111 PMCID: PMC4853787 DOI: 10.1038/srep25471] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 04/18/2016] [Indexed: 01/01/2023] Open
Abstract
Zinc finger AN1-type domain 3 (ZFAND3) is essential for spermatogenesis in mice. However, its function in teleosts remains unclear. In this study, we characterized the ZFAND3 gene (termed as OsZFAND3) in an important food fish, tilapia. The OsZFAND3 cDNA sequence is 1,050 bp in length, containing an ORF of 615 bp, which encodes a putative peptide of 204 amino acid residues. Quantitative real-time PCR revealed that the OsZFAND3 transcripts were exclusively expressed in the testis and ovary. In situ hybridization showed that the high expression of OsZFAND3 transcripts was predominantly localized in the spermatocyte and spermatid. These results suggest that OsZFAND3 is involved in male germ cell maturation. Three single nucleotide polymorphisms (SNPs) were detected in the introns of OsZFAND3. The OsZFAND3 gene was mapped in the sex-determining locus on linkage group 1 (LG1). The three SNPs in the OsZFAND3 gene were strictly associated with sex phenotype, suggesting that the OsZFAND3 gene is tightly linked to the sex-determining locus. Our study provides new insights into the functions of the OsZFAND3 gene in tilapia and a foundation for further detailed analysis of the OsZFAND3 gene in sex determination and differentiation.
Collapse
Affiliation(s)
- Keyi Ma
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Minghui Liao
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Feng Liu
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Baoqing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Fei Sun
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Republic of Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Republic of Singapore
| |
Collapse
|
30
|
Genome-Wide Mapping of Growth-Related Quantitative Trait Loci in Orange-Spotted Grouper (Epinephelus coioides) Using Double Digest Restriction-Site Associated DNA Sequencing (ddRADseq). Int J Mol Sci 2016; 17:501. [PMID: 27058532 PMCID: PMC4848957 DOI: 10.3390/ijms17040501] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Revised: 03/28/2016] [Accepted: 03/29/2016] [Indexed: 12/19/2022] Open
Abstract
Mapping of quantitative trait loci (QTL) is essential for the discovery of genetic structures that related to complex quantitative traits. In this study, we identified 264,072 raw SNPs (single-nucleotide polymorphisms) by double digest restriction site associated DNA sequencing (ddRADseq), and utilized 3029 of these SNPs to construct a genetic linkage map in orange-spotted grouper (Epinephelus coioides) using a regression mapping algorithm. The genetic map contained 24 linkage groups (LGs) spanning a total genetic distance of 1231.98 cM. Twenty-seven significant growth-related QTLs were identified. Furthermore, we identified 17 genes (fez2, alg3, ece2, arvcf, sla27a4, sgk223, camk2, prrc2b, mchr1, sardh, pappa, syk, tert, wdrcp91, ftz-f1, mate1 and notch1) including three (tert, ftz-f1 and notch1) that have been reported to be involved in fish growth. To summarize, we mapped growth-related QTLs in the orange-spotted grouper. These QTLs will be useful in marker-assisted selection (MAS) efforts to improve growth-related traits in this economically important fish.
Collapse
|
31
|
Figueras A, Robledo D, Corvelo A, Hermida M, Pereiro P, Rubiolo JA, Gómez-Garrido J, Carreté L, Bello X, Gut M, Gut IG, Marcet-Houben M, Forn-Cuní G, Galán B, García JL, Abal-Fabeiro JL, Pardo BG, Taboada X, Fernández C, Vlasova A, Hermoso-Pulido A, Guigó R, Álvarez-Dios JA, Gómez-Tato A, Viñas A, Maside X, Gabaldón T, Novoa B, Bouza C, Alioto T, Martínez P. Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life. DNA Res 2016; 23:181-92. [PMID: 26951068 PMCID: PMC4909306 DOI: 10.1093/dnares/dsw007] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/03/2016] [Indexed: 01/25/2023] Open
Abstract
The turbot is a flatfish (Pleuronectiformes) with increasing commercial value, which has prompted active genomic research aimed at more efficient selection. Here we present the sequence and annotation of the turbot genome, which represents a milestone for both boosting breeding programmes and ascertaining the origin and diversification of flatfish. We compare the turbot genome with model fish genomes to investigate teleost chromosome evolution. We observe a conserved macrosyntenic pattern within Percomorpha and identify large syntenic blocks within the turbot genome related to the teleost genome duplication. We identify gene family expansions and positive selection of genes associated with vision and metabolism of membrane lipids, which suggests adaptation to demersal lifestyle and to cold temperatures, respectively. Our data indicate a quick evolution and diversification of flatfish to adapt to benthic life and provide clues for understanding their controversial origin. Moreover, we investigate the genomic architecture of growth, sex determination and disease resistance, key traits for understanding local adaptation and boosting turbot production, by mapping candidate genes and previously reported quantitative trait loci. The genomic architecture of these productive traits has allowed the identification of candidate genes and enriched pathways that may represent useful information for future marker-assisted selection in turbot.
Collapse
Affiliation(s)
- Antonio Figueras
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Diego Robledo
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - André Corvelo
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain New York Genome Center, 101 Avenue of the Americas, New York, NY 10013, USA
| | - Miguel Hermida
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Patricia Pereiro
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Juan A Rubiolo
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Jèssica Gómez-Garrido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Laia Carreté
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Xabier Bello
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Marta Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Ivo Glynne Gut
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Marina Marcet-Houben
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Gabriel Forn-Cuní
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Beatriz Galán
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - José Luis García
- Centro de Investigaciones Biológicas (CIB), Consejo Superior de Investigaciones Científicas, Madrid 28040, Spain
| | - José Luis Abal-Fabeiro
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Belen G Pardo
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Xoana Taboada
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Carlos Fernández
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Anna Vlasova
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Antonio Hermoso-Pulido
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Roderic Guigó
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - José Antonio Álvarez-Dios
- Departamento de Matemática Aplicada, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Antonio Gómez-Tato
- Departamento de Xeometría e Topoloxía, Facultade de Matemáticas, Universidade de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ana Viñas
- Departamento de Xenética, Facultade de Bioloxía (CIBUS), Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Xulio Maside
- Departamento de Anatomía Patolóxica e Ciencias Forenses, Grupo de Medicina Xenómica, CIMUS, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain Xenómica Comparada de Parasitos Humanos, Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela 15706, Spain
| | - Toni Gabaldón
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluís Companys 23, 08010 Barcelona, Spain
| | - Beatriz Novoa
- Instituto de Investigaciones Marinas (IIM), Consejo Superior de Investigaciones Científicas (CSIC), Vigo 36208, Spain
| | - Carmen Bouza
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| | - Tyler Alioto
- Centre Nacional d'Anàlisi Genòmica (CNAG-CRG), Centre de Regulació Genómica, Parc Científic de Barcelona, Barcelona 08028, Spain
| | - Paulino Martínez
- Departamento de Xenética, Facultade de Veterinaria, Universidade de Santiago de Compostela, Lugo 27002, Spain
| |
Collapse
|
32
|
Li M, Sun Y, Zhao J, Shi H, Zeng S, Ye K, Jiang D, Zhou L, Sun L, Tao W, Nagahama Y, Kocher TD, Wang D. A Tandem Duplicate of Anti-Müllerian Hormone with a Missense SNP on the Y Chromosome Is Essential for Male Sex Determination in Nile Tilapia, Oreochromis niloticus. PLoS Genet 2015; 11:e1005678. [PMID: 26588702 PMCID: PMC4654491 DOI: 10.1371/journal.pgen.1005678] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 10/26/2015] [Indexed: 12/20/2022] Open
Abstract
Variation in the TGF-β signaling pathway is emerging as an important mechanism by which gonadal sex determination is controlled in teleosts. Here we show that amhy, a Y-specific duplicate of the anti-Müllerian hormone (amh) gene, induces male sex determination in Nile tilapia. amhy is a tandem duplicate located immediately downstream of amhΔ-y on the Y chromosome. The coding sequence of amhy was identical to the X-linked amh (amh) except a missense SNP (C/T) which changes an amino acid (Ser/Leu92) in the N-terminal region. amhy lacks 5608 bp of promoter sequence that is found in the X-linked amh homolog. The amhΔ-y contains several insertions and deletions in the promoter region, and even a 5 bp insertion in exonVI that results in a premature stop codon and thus a truncated protein product lacking the TGF-β binding domain. Both amhy and amhΔ-y expression is restricted to XY gonads from 5 days after hatching (dah) onwards. CRISPR/Cas9 knockout of amhy in XY fish resulted in male to female sex reversal, while mutation of amhΔ-y alone could not. In contrast, overexpression of Amhy in XX fish, using a fosmid transgene that carries the amhy/amhΔ-y haplotype or a vector containing amhy ORF under the control of CMV promoter, resulted in female to male sex reversal, while overexpression of AmhΔ-y alone in XX fish could not. Knockout of the anti-Müllerian hormone receptor type II (amhrII) in XY fish also resulted in 100% complete male to female sex reversal. Taken together, these results strongly suggest that the duplicated amhy with a missense SNP is the candidate sex determining gene and amhy/amhrII signal is essential for male sex determination in Nile tilapia. These findings highlight the conserved roles of TGF-β signaling pathway in fish sex determination. Unlike mammals, the identity of the master sex-determining gene varies among fish species, and it is not yet clear if there is a common molecular pathway regulating gonadal sex determination across teleosts. Here we show that a Y-linked duplicate of the anti-Mullerian hormone (amhy) is essential for male sex determination in tilapia. Mutation of amhy resulted in male to female sex reversal, while overexpression of it resulted in female to male sex reversal. A missense single nucleotide polymorphisms (SNP) (C/T) in the open reading frame (ORF) of amhy might contribute to male sex determination in tilapia. Knockout of the anti-Müllerian hormone receptor type II (amhrII) also resulted in male to female sex reversal. Taken the amhy in Patagonian pejerrey, amhrII in Takifugu rubripes, gsdfY in Oryzias luzonensis into consideration, these data highlight an important role for TGF-β signaling in teleost sex determination.
Collapse
Affiliation(s)
- Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Yunlv Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Jiue Zhao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Hongjuan Shi
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Sheng Zeng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Kai Ye
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Dongneng Jiang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Linyan Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Lina Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
| | - Yoshitaka Nagahama
- Solution-Oriented Research for Science and Technology (SORST), Laboratory of Reproductive Biology, National Institute for Basic Biology, Okazaki, Japan; South Ehime Fisheries Research Center, Ehime University, Matsuyama, Japan
| | - Thomas D. Kocher
- Department of Biology, University of Maryland, College Park, Maryland, United States of America
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, China
- * E-mail:
| |
Collapse
|
33
|
Pfennig F, Standke A, Gutzeit HO. The role of Amh signaling in teleost fish--Multiple functions not restricted to the gonads. Gen Comp Endocrinol 2015; 223:87-107. [PMID: 26428616 DOI: 10.1016/j.ygcen.2015.09.025] [Citation(s) in RCA: 97] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 09/24/2015] [Accepted: 09/25/2015] [Indexed: 12/16/2022]
Abstract
This review summarizes the important role of Anti-Müllerian hormone (Amh) during gonad development in fishes. This Tgfβ-domain bearing hormone was named after one of its known functions, the induction of the regression of Müllerian ducts in male mammalian embryos. Later in development it is involved in male and female gonad differentiation and extragonadal expression has been reported in mammals as well. Teleosts lack Müllerian ducts, but they have amh orthologous genes. amh expression is reported from 21 fish species and possible regulatory interactions with further factors like sex steroids and gonadotropic hormones are discussed. The gonadotropin Fsh inhibits amh expression in all fish species studied. Sex steroids show no consistent influence on amh expression. Amh is produced in male Sertoli cells and female granulosa cells and inhibits germ cell proliferation and differentiation as well as steroidogenesis in both sexes. Therefore, Amh might be a central player in gonad development and a target of gonadotropic Fsh. Furthermore, there is evidence that an Amh-type II receptor is involved in germ cell regulation. Amh and its corresponding type II receptor are also present in brain and pituitary, at least in some teleosts, indicating additional roles of Amh effects in the brain-pituitary-gonadal axis. Unraveling Amh signaling is important in stem cell research and for reproduction as well as for aquaculture and in environmental science.
Collapse
Affiliation(s)
- Frank Pfennig
- Institut für Zoologie, TU Dresden, D-01062 Dresden, Germany.
| | - Andrea Standke
- Institut für Zoologie, TU Dresden, D-01062 Dresden, Germany
| | | |
Collapse
|
34
|
Böhne A, Sengstag T, Salzburger W. Comparative transcriptomics in East African cichlids reveals sex- and species-specific expression and new candidates for sex differentiation in fishes. Genome Biol Evol 2015; 6:2567-85. [PMID: 25364805 PMCID: PMC4202336 DOI: 10.1093/gbe/evu200] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Males and females of the same species differ largely in gene expression, which accounts for most of the morphological and physiological differences and sex-specific phenotypes. Here, we analyzed sex-specific gene expression in the brain and the gonads of cichlid fishes from Lake Tanganyika belonging to four different lineages, so-called tribes (Eretmodini, Ectodini, Haplochromini, and Lamprologini), using the outgroup Nile tilapia (Oreochromis niloticus) as reference. The comparison between male and female brains revealed few differences between the sexes, consistent in all investigated species. The gonads, on the other hand, showed a large fraction of differentially expressed transcripts with the majority of them showing the same direction of expression in all four species. All here-studied cichlids, especially the three investigated mouth-breeding species, showed a trend toward more male- than female biased transcripts. Transcripts, which were female-biased in expression in all four species, were overrepresented on linkage group (LG)1 in the reference genome and common male-biased transcripts showed accumulation on LG23, the presumable sex chromosomes of the Nile tilapia. Sex-specific transcripts contained candidate genes for sex determination and differentiation in fishes,especially members of the transforming growth factor-b-superfamily and the Wnt-pathway and also prominent members of the sox-, dm-domain-, and high mobility group-box families. We further confirmed our previous finding on species/lineage-specific gene expression shifts in the sex steroid pathway, including synthesizing enzymes as the aromatase cyp19a1 and estrogen and androgen receptors.
Collapse
Affiliation(s)
- Astrid Böhne
- Zoological Institute, University of Basel, Switzerland
- *Corresponding author: E-mail:
| | - Thierry Sengstag
- SIB Swiss Institute of Bioinformatics and sciCORE Computing Center, University of Basel, Switzerland
| | | |
Collapse
|
35
|
Sex Control in Fish: Approaches, Challenges and Opportunities for Aquaculture. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2015. [DOI: 10.3390/jmse3020329] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
36
|
Palaiokostas C, Bekaert M, Khan MGQ, Taggart JB, Gharbi K, McAndrew BJ, Penman DJ. A novel sex-determining QTL in Nile tilapia (Oreochromis niloticus). BMC Genomics 2015; 16:171. [PMID: 25888226 PMCID: PMC4358704 DOI: 10.1186/s12864-015-1383-x] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Accepted: 02/23/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Fish species often exhibit significant sexual dimorphism for commercially important traits. Accordingly, the control of phenotypic sex, and in particular the production of monosex cultures, is of particular interest to the aquaculture industry. Sex determination in the widely farmed Nile tilapia (Oreochromis niloticus) is complex, involving genomic regions on at least three chromosomes (chromosomes 1, 3 and 23) and interacting in certain cases with elevated early rearing temperature as well. Thus, sex ratios may vary substantially from 50%. RESULTS This study focused on mapping sex-determining quantitative trait loci (QTL) in families with skewed sex ratios. These included four families that showed an excess of males (male ratio varied between 64% and 93%) when reared at standard temperature (28°C) and a fifth family in which an excess of males (96%) was observed when fry were reared at 36°C for ten days from first feeding. All the samples used in the current study were genotyped for two single-nucleotide polymorphisms (rs397507167 and rs397507165) located in the expected major sex-determining region in linkage group 1 (LG 1). The only misassigned individuals were phenotypic males with the expected female genotype, suggesting that those offspring had undergone sex-reversal with respect to the major sex-determining locus. We mapped SNPs identified from double digest Restriction-site Associated DNA (ddRAD) sequencing in these five families. Three genetic maps were constructed consisting of 641, 175 and 1,155 SNPs from the three largest families. QTL analyses provided evidence for a novel genome-wide significant QTL in LG 20. Evidence was also found for another sex-determining QTL in the fifth family, in the proximal region of LG 1. CONCLUSIONS Overall, the results from this study suggest that these previously undetected QTLs are involved in sex determination in the Nile tilapia, causing sex reversal (masculinisation) with respect to the XX genotype at the major sex-determining locus in LG 1.
Collapse
Affiliation(s)
- Christos Palaiokostas
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
| | - Michaël Bekaert
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
| | - Mohd G Q Khan
- Department of Fisheries Biology and Genetics, Bangladesh Agricultural University, Mymensingh, Bangladesh.
| | - John B Taggart
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
| | - Karim Gharbi
- Edinburgh Genomics, Ashworth Laboratories, King's Buildings, University of Edinburgh, Edinburgh, EH9 3JT, Scotland, UK.
| | - Brendan J McAndrew
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
| | - David J Penman
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK9 4LA, Scotland, UK.
| |
Collapse
|
37
|
Liu F, Sun F, Xia JH, Li J, Fu GH, Lin G, Tu RJ, Wan ZY, Quek D, Yue GH. A genome scan revealed significant associations of growth traits with a major QTL and GHR2 in tilapia. Sci Rep 2014; 4:7256. [PMID: 25435025 PMCID: PMC4248272 DOI: 10.1038/srep07256] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Accepted: 11/04/2014] [Indexed: 12/02/2022] Open
Abstract
Growth is an important trait in animal breeding. However, the genetic effects underpinning fish growth variability are still poorly understood. QTL mapping and analysis of candidate genes are effective methods to address this issue. We conducted a genome-wide QTL analysis for growth in tilapia. A total of 10, 7 and 8 significant QTLs were identified for body weight, total length and standard length at 140 dph, respectively. The majority of these QTLs were sex-specific. One major QTL for growth traits was identified in the sex-determining locus in LG1, explaining 71.7%, 67.2% and 64.9% of the phenotypic variation (PV) of body weight, total length and standard length, respectively. In addition, a candidate gene GHR2 in a QTL was significantly associated with body weight, explaining 13.1% of PV. Real-time qPCR revealed that different genotypes at the GHR2 locus influenced the IGF-1 expression level. The markers located in the major QTL for growth traits could be used in marker-assisted selection of tilapia. The associations between GHR2 variants and growth traits suggest that the GHR2 gene should be an important gene that explains the difference in growth among tilapia species.
Collapse
Affiliation(s)
- Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Fei Sun
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Jun Hong Xia
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Jian Li
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Gui Hong Fu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Grace Lin
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Rong Jian Tu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Zi Yi Wan
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Delia Quek
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore
| | - Gen Hua Yue
- 1] Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Republic of Singapore [2] Department of Biological Sciences, National University of Singapore, 14 Science Drive, Singapore 117543
| |
Collapse
|
38
|
Structure and decay of a proto-Y region in Tilapia, Oreochromis niloticus. BMC Genomics 2014; 15:975. [PMID: 25404257 PMCID: PMC4251933 DOI: 10.1186/1471-2164-15-975] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 10/29/2014] [Indexed: 12/30/2022] Open
Abstract
Background Sex-determination genes drive the evolution of adjacent chromosomal regions. Sexually antagonistic selection favors the accumulation of inversions that reduce recombination in regions adjacent to the sex-determination gene. Once established, the clonal inheritance of sex-linked inversions leads to the accumulation of deleterious alleles, repetitive elements and a gradual decay of sex-linked genes. This in turn creates selective pressures for the evolution of mechanisms that compensate for the unequal dosage of gene expression. Here we use whole genome sequencing to characterize the structure of a young sex chromosome and quantify sex-specific gene expression in the developing gonad. Results We found an 8.8 Mb block of strong differentiation between males and females that corresponds to the location of a previously mapped sex-determiner on linkage group 1 of Oreochromis niloticus. Putatively disruptive mutations are found in many of the genes within this region. We also found a significant female-bias in the expression of genes within the block of differentiation compared to those outside the block of differentiation. Eight candidate sex-determination genes were identified within this region. Conclusions This study demonstrates a block of differentiation on linkage group 1, suggestive of an 8.8 Mb inversion encompassing the sex-determining locus. The enrichment of female-biased gene expression inside the proposed inversion suggests incomplete dosage compensation. This study helps establish a model for studying the early-to-intermediate stages of sex chromosome evolution. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-975) contains supplementary material, which is available to authorized users.
Collapse
|
39
|
Martínez P, Viñas AM, Sánchez L, Díaz N, Ribas L, Piferrer F. Genetic architecture of sex determination in fish: applications to sex ratio control in aquaculture. Front Genet 2014; 5:340. [PMID: 25324858 PMCID: PMC4179683 DOI: 10.3389/fgene.2014.00340] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 09/10/2014] [Indexed: 01/05/2023] Open
Abstract
Controlling the sex ratio is essential in finfish farming. A balanced sex ratio is usually good for broodstock management, since it enables to develop appropriate breeding schemes. However, in some species the production of monosex populations is desirable because the existence of sexual dimorphism, primarily in growth or first time of sexual maturation, but also in color or shape, can render one sex more valuable. The knowledge of the genetic architecture of sex determination (SD) is convenient for controlling sex ratio and for the implementation of breeding programs. Unlike mammals and birds, which show highly conserved master genes that control a conserved genetic network responsible for gonad differentiation (GD), a huge diversity of SD mechanisms has been reported in fish. Despite theory predictions, more than one gene is in many cases involved in fish SD and genetic differences have been observed in the GD network. Environmental factors also play a relevant role and epigenetic mechanisms are becoming increasingly recognized for the establishment and maintenance of the GD pathways. Although major genetic factors are frequently involved in fish SD, these observations strongly suggest that SD in this group resembles a complex trait. Accordingly, the application of quantitative genetics combined with genomic tools is desirable to address its study and in fact, when applied, it has frequently demonstrated a multigene trait interacting with environmental factors in model and cultured fish species. This scenario has notable implications for aquaculture and, depending upon the species, from chromosome manipulation or environmental control techniques up to classical selection or marker assisted selection programs, are being applied. In this review, we selected four relevant species or fish groups to illustrate this diversity and hence the technologies that can be used by the industry for the control of sex ratio: turbot and European sea bass, two reference species of the European aquaculture, and salmonids and tilapia, representing the fish for which there are well established breeding programs.
Collapse
Affiliation(s)
- Paulino Martínez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de CompostelaLugo, Spain
| | - Ana M. Viñas
- Departamento de Genética, Facultad de Biología, Universidad de Santiago de CompostelaSantiago de Compostela, Spain
| | - Laura Sánchez
- Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de CompostelaLugo, Spain
| | - Noelia Díaz
- Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| | | | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones CientíficasBarcelona, Spain
| |
Collapse
|
40
|
Eshel O, Shirak A, Dor L, Band M, Zak T, Markovich-Gordon M, Chalifa-Caspi V, Feldmesser E, Weller JI, Seroussi E, Hulata G, Ron M. Identification of male-specific amh duplication, sexually differentially expressed genes and microRNAs at early embryonic development of Nile tilapia (Oreochromis niloticus). BMC Genomics 2014; 15:774. [PMID: 25199625 PMCID: PMC4176596 DOI: 10.1186/1471-2164-15-774] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2014] [Accepted: 08/18/2014] [Indexed: 12/17/2022] Open
Abstract
Background The probable influence of genes and the environment on sex determination in Nile tilapia suggests that it should be regarded as a complex trait. Detection of sex determination genes in tilapia has both scientific and commercial importance. The main objective was to detect genes and microRNAs that were differentially expressed by gender in early embryonic development. Results Artificial fertilization of Oreochromis niloticus XX females with either sex-reversed ΔXX males or genetically-modified YY ‘supermales’ resulted in all-female and all-male embryos, respectively. RNA of pools of all-female and all-male embryos at 2, 5 and 9 dpf were used as template for a custom Agilent eArray hybridization and next generation sequencing. Fifty-nine genes differentially expressed between genders were identified by a false discovery rate of p < 0.05. The most overexpressed genes were amh and tspan8 in males, and cr/20β-hsd, gpa33, rtn4ipl and zp3 in females (p < 1 × 10−9). Validation of gene expression using qPCR in embryos and gonads indicated copy number variation in tspan8, gpa33, cr/20β-hsd and amh. Sequencing of amh identified a male-specific duplication of this gene, denoted amhy, differing from the sequence of amh by a 233 bp deletion on exonVII, hence lacking the capability to encode the protein motif that binds to the transforming growth factor beta receptor (TGF-β domain). amh and amhy segregated in the mapping family in full concordance with SD-linked marker on LG23 signifying the QTL for SD. We discovered 831 microRNAs in tilapia embryos of which nine had sexually dimorphic expression patterns by a false discovery rate of p < 0.05. An up-regulated microRNA in males, pma-mir-4585, was characterized with all six predicted target genes including cr/20β-hsd, down-regulated in males. Conclusions This study reports the first discovery of sexually differentially expressed genes and microRNAs at a very early stage of tilapia embryonic development, i.e. from 2 dpf. Genes with sexually differential expression patterns are enriched for copy number variation. A novel male-specific duplication of amh, denoted amhy, lacking the TGF-β domain was identified and mapped to the QTL region on LG23 for SD, thus indicating its potential role in SD. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-774) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Micha Ron
- Institute of Animal Science, ARO, The Volcani Center, Bet Dagan 50250, Israel.
| |
Collapse
|
41
|
Wessels S, Sharifi RA, Luehmann LM, Rueangsri S, Krause I, Pach S, Hoerstgen-Schwark G, Knorr C. Allelic variant in the anti-Müllerian hormone gene leads to autosomal and temperature-dependent sex reversal in a selected Nile tilapia line. PLoS One 2014; 9:e104795. [PMID: 25157978 PMCID: PMC4144872 DOI: 10.1371/journal.pone.0104795] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 07/18/2014] [Indexed: 11/18/2022] Open
Abstract
Owing to the demand for sustainable sex-control protocols in aquaculture, research in tilapia sex determination is gaining momentum. The mutual influence of environmental and genetic factors hampers disentangling the complex sex determination mechanism in Nile tilapia (Oreochromis niloticus). Previous linkage analyses have demonstrated quantitative trait loci for the phenotypic sex on linkage groups 1, 3, and 23. Quantitative trait loci for temperature-dependent sex reversal similarly reside on linkage group 23. The anti-Müllerian hormone gene (amh), located in this genomic region, is important for sexual fate in higher vertebrates, and shows sexually dimorphic expression in Nile tilapia. Therefore this study aimed at detecting allelic variants and marker-sex associations in the amh gene. Sequencing identified six allelic variants. A significant effect on the phenotypic sex for SNP ss831884014 (p<0.0017) was found by stepwise logistic regression. The remaining variants were not significantly associated. Functional annotation of SNP ss831884014 revealed a non-synonymous amino acid substitution in the amh protein. Consequently, a fluorescence resonance energy transfer (FRET) based genotyping assay was developed and validated with a representative sample of fish. A logistic linear model confirmed a highly significant effect of the treatment and genotype on the phenotypic sex, but not for the interaction term (treatment: p<0.0001; genotype: p<0.0025). An additive genetic model proved a linear allele substitution effect of 12% in individuals from controls and groups treated at high temperature, respectively. Moreover, the effect of the genotype on the male proportion was significantly higher in groups treated at high temperature, giving 31% more males on average of the three genotypes. In addition, the groups treated at high temperature showed a positive dominance deviation (+11.4% males). In summary, marker-assisted selection for amh variant ss831884014 seems to be highly beneficial to increase the male proportion in Nile tilapia, especially when applying temperature-induced sex reversal.
Collapse
Affiliation(s)
- Stephan Wessels
- Department of Animal Sciences - Aquaculture and Water Ecology, Goettingen University, Goettingen, Germany
- * E-mail:
| | - Reza Ahmad Sharifi
- Department of Animal Sciences - Animal Breeding and Genetics, Goettingen University, Goettingen, Germany
| | - Liane Magdalena Luehmann
- Department of Animal Sciences - Aquaculture and Water Ecology, Goettingen University, Goettingen, Germany
| | - Sawichaya Rueangsri
- Department of Animal and Aquatic Sciences, Faculty of Agriculture, Chiang Mai University, Chiang Mai, Thailand
| | - Ina Krause
- Department of Animal Sciences - Aquaculture and Water Ecology, Goettingen University, Goettingen, Germany
| | - Sabrina Pach
- Department of Animal Sciences - Molecular Biology and Molecular Diagnostics of Livestock, Goettingen University, Goettingen, Germany
| | - Gabriele Hoerstgen-Schwark
- Department of Animal Sciences - Aquaculture and Water Ecology, Goettingen University, Goettingen, Germany
| | - Christoph Knorr
- Department of Animal Sciences - Livestock Biotechnology and Reproduction, Goettingen University, Goettingen, Germany
| |
Collapse
|
42
|
Fine mapping and evolution of the major sex determining region in turbot (Scophthalmus maximus). G3-GENES GENOMES GENETICS 2014; 4:1871-80. [PMID: 25106948 PMCID: PMC4199694 DOI: 10.1534/g3.114.012328] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fish sex determination (SD) systems are varied, suggesting evolutionary changes including either multiple evolution origins of genetic SD from nongenetic systems (such as environmental SD) and/or turnover events replacing one genetic system by another. When genetic SD is found, cytological differentiation between the two members of the sex chromosome pair is often minor or undetectable. The turbot (Scophthalmus maximus), a valuable commercial flatfish, has a ZZ/ZW system and a major SD region on linkage group 5 (LG5), but there are also other minor genetic and environmental influences. We here report refined mapping of the turbot SD region, supported by comparative mapping with model fish species, to identify the turbot master SD gene. Six genes were located to the SD region, two of them associated with gonad development (sox2 and dnajc19). All showed a high association with sex within families (P = 0), but not at the population level, so they are probably partially sex-linked genes, but not SD gene itself. Analysis of crossovers in LG5 using two families confirmed a ZZ/ZW system in turbot and suggested a revised map position for the master gene. Genetic diversity and differentiation for 25 LG5 genetic markers showed no differences between males and females sampled from a wild population, suggesting a recent origin of the SD region in turbot. We also analyzed associations with markers of the most relevant sex-related linkage groups in brill (S. rhombus), a closely related species to turbot; the data suggest that an ancient XX/XY system in brill changed to a ZZ/ZW mechanism in turbot.
Collapse
|
43
|
Dor L, Shirak A, Gorshkov S, Band MR, Korol A, Ronin Y, Curzon A, Hulata G, Seroussi E, Ron M. Construction of a microsatellites-based linkage map for the white grouper (Epinephelus aeneus). G3 (BETHESDA, MD.) 2014; 4:1455-64. [PMID: 24902605 PMCID: PMC4132176 DOI: 10.1534/g3.114.011387] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/01/2014] [Indexed: 02/06/2023]
Abstract
The white grouper (Epinephelus aeneus) is a promising candidate for domestication and aquaculture due to its fast growth, excellent taste, and high market price. A linkage map is an essential framework for mapping quantitative trait loci for economic traits and the study of genome evolution. DNA of a single individual was deep-sequenced, and microsatellite markers were identified in 177 of the largest scaffolds of the sequence assembly. The success rate of developing polymorphic homologous markers was 94.9% compared with 63.1% of heterologous markers from other grouper species. Of the 12 adult mature fish present in the broodstock tank, two males and two females were identified as parents of the assigned offspring by parenthood analysis using 34 heterologous markers. A single full-sib family of 48 individuals was established for the construction of first-generation linkage maps based on genotyping data of 222 microsatellites. The markers were assigned to 24 linkage groups in accordance to the 24 chromosomal pairs. The female and male maps consisting of 203 and 202 markers spanned 1053 and 886 cM, with an average intermarker distance of 5.8 and 5.0 cM, respectively. Mapping of markers to linkage groups ends was enriched by using markers originating from scaffolds harboring telomeric repeat-containing RNA. Comparative mapping showed high synteny relationships among the white grouper, kelp grouper (E. bruneus), orange-spotted grouper (E. coioides), and Nile tilapia (Oreochromis niloticus). Thus, it would be useful to integrate the markers that were developed for different groupers, depending on sharing of sequence data, into a comprehensive consensus map.
Collapse
Affiliation(s)
- Lior Dor
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Sergei Gorshkov
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat 88112, Israel
| | - Mark R Band
- The Carver Biotechnology Center, University of Illinois, Urbana, Illinois 61801
| | - Abraham Korol
- University Haifa, Institute of Evolution, of Haifa 3498838, Israel
| | - Yefim Ronin
- University Haifa, Institute of Evolution, of Haifa 3498838, Israel
| | - Arie Curzon
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Gideon Hulata
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Eyal Seroussi
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
| | - Micha Ron
- Institute of Animal Science, Agricultural Research Organization, Bet Dagan 50250, Israel
| |
Collapse
|
44
|
Mapping and validation of the major sex-determining region in Nile tilapia (Oreochromis niloticus L.) Using RAD sequencing. PLoS One 2013; 8:e68389. [PMID: 23874606 PMCID: PMC3708939 DOI: 10.1371/journal.pone.0068389] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/29/2013] [Indexed: 01/17/2023] Open
Abstract
Sex in Oreochromis niloticus (Nile tilapia) is principally determined by an XX/XY locus but other genetic and environmental factors also influence sex ratio. Restriction Associated DNA (RAD) sequencing was used in two families derived from crossing XY males with females from an isogenic clonal line, in order to identify Single Nucleotide Polymorphisms (SNPs) and map the sex-determining region(s). We constructed a linkage map with 3,802 SNPs, which corresponded to 3,280 informative markers, and identified a major sex-determining region on linkage group 1, explaining nearly 96% of the phenotypic variance. This sex-determining region was mapped in a 2 cM interval, corresponding to approximately 1.2 Mb in the O. niloticus draft genome. In order to validate this, a diverse family (4 families; 96 individuals in total) and population (40 broodstock individuals) test panel were genotyped for five of the SNPs showing the highest association with phenotypic sex. From the expanded data set, SNPs Oni23063 and Oni28137 showed the highest association, which persisted both in the case of family and population data. Across the entire dataset all females were found to be homozygous for these two SNPs. Males were heterozygous, with the exception of five individuals in the population and two in the family dataset. These fish possessed the homozygous genotype expected of females. Progeny sex ratios (over 95% females) from two of the males with the "female" genotype indicated that they were neomales (XX males). Sex reversal induced by elevated temperature during sexual differentiation also resulted in phenotypic males with the "female" genotype. This study narrows down the region containing the main sex-determining locus, and provides genetic markers tightly linked to this locus, with an association that persisted across the population. These markers will be of use in refining the production of genetically male O. niloticus for aquaculture.
Collapse
|
45
|
Tao W, Yuan J, Zhou L, Sun L, Sun Y, Yang S, Li M, Zeng S, Huang B, Wang D. Characterization of gonadal transcriptomes from Nile tilapia (Oreochromis niloticus) reveals differentially expressed genes. PLoS One 2013; 8:e63604. [PMID: 23658843 PMCID: PMC3643912 DOI: 10.1371/journal.pone.0063604] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2012] [Accepted: 04/06/2013] [Indexed: 12/12/2022] Open
Abstract
Four pairs of XX and XY gonads from Nile tilapia were sequenced at four developmental stages, 5, 30, 90, and 180 days after hatching (dah) using Illumina Hiseq(TM) technology. This produced 28 Gb sequences, which were mapped to 21,334 genes. Of these, 259 genes were found to be specifically expressed in XY gonads, and 69 were found to be specific to XX gonads. Totally, 187 XX- and 1,358 XY-enhanced genes were identified, and 2,978 genes were found to be co-expressed in XX and XY gonads. Almost all steroidogenic enzymes, including cyp19a1a, were up-regulated in XX gonads at 5 dah; but in XY gonads these enzymes, including cyp11b2, were significantly up-regulated at 90 dah, indicating that, at a time critical to sex determination, the XX fish produced estrogen and the XY fish did not produce androgens. The most pronounced expression of steroidogenic enzyme genes was observed at 30 and 90 dah for XX and XY gonads, corresponding to the initiation of germ cell meiosis in the female and male gonads, respectively. Both estrogen and androgen receptors were found to be expressed in XX gonads, but only estrogen receptors were expressed in XY gonads at 5 dah. This could explain why exogenous steroid treatment induced XX and XY sex reversal. The XX-enhanced expression of cyp19a1a and cyp19a1b at all stages suggests an important role for estrogen in female sex determination and maintenance of phenotypic sex. This work is the largest collection of gonadal transcriptome data in tilapia and lays the foundation for future studies into the molecular mechanisms of sex determination and maintenance of phenotypic sex in non-model teleosts.
Collapse
Affiliation(s)
- Wenjing Tao
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| | - Jing Yuan
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| | - Linyan Zhou
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| | - Lina Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| | - Yunlv Sun
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| | - Shijie Yang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| | - Minghui Li
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| | - Sheng Zeng
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| | - Baofeng Huang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| | - Deshou Wang
- Key Laboratory of Freshwater Fish Reproduction and Development (Ministry of Education), Key Laboratory of Aquatic Science of Chongqing, School of Life Science, Southwest University, Chongqing, P.R. China
| |
Collapse
|
46
|
Kikuchi K, Hamaguchi S. Novel sex-determining genes in fish and sex chromosome evolution. Dev Dyn 2013; 242:339-53. [PMID: 23335327 DOI: 10.1002/dvdy.23927] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2012] [Revised: 12/25/2012] [Accepted: 12/26/2012] [Indexed: 12/13/2022] Open
Abstract
Although the molecular mechanisms underlying many developmental events are conserved across vertebrate taxa, the lability at the top of the sex-determining (SD) cascade has been evident from the fact that four master SD genes have been identified: mammalian Sry; chicken DMRT1; medaka Dmy; and Xenopus laevis DM-W. This diversity is thought to be associated with the turnover of sex chromosomes, which is likely to be more frequent in fishes and other poikilotherms than in therian mammals and birds. Recently, four novel candidates for vertebrate SD genes were reported, all of them in fishes. These include amhy in the Patagonian pejerrey, Gsdf in Oryzias luzonensis, Amhr2 in fugu and sdY in rainbow trout. These studies provide a good opportunity to infer patterns from the seemingly chaotic picture of sex determination systems. Here, we review recent advances in our understanding of the master SD genes in fishes.
Collapse
Affiliation(s)
- Kiyoshi Kikuchi
- Fisheries Laboratory, University of Tokyo, Hamamatsu, Shizuoka, Japan.
| | | |
Collapse
|
47
|
Liu F, Sun F, Li J, Xia JH, Lin G, Tu RJ, Yue GH. A microsatellite-based linkage map of salt tolerant tilapia (Oreochromis mossambicus x Oreochromis spp.) and mapping of sex-determining loci. BMC Genomics 2013; 14:58. [PMID: 23356773 PMCID: PMC3565888 DOI: 10.1186/1471-2164-14-58] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 01/22/2013] [Indexed: 11/16/2022] Open
Abstract
Background Tilapia is the common name for a group of cichlid fishes and is one of the most important aquacultured freshwater food fish. Mozambique tilapia and its hybrids, including red tilapia are main representatives of salt tolerant tilapias. A linkage map is an essential framework for mapping QTL for important traits, positional cloning of genes and understanding of genome evolution. Results We constructed a consensus linkage map of Mozambique tilapia and red tilapia using 95 individuals from two F1 families and 401 microsatellites including 282 EST-derived markers. In addition, we conducted comparative mapping and searched for sex-determining loci on the whole genome. These 401 microsatellites were assigned to 22 linkage groups. The map spanned 1067.6 cM with an average inter-marker distance of 3.3 cM. Comparative mapping between tilapia and stickleback, medaka, pufferfish and zebrafish revealed clear homologous relationships between chromosomes from different species. We found evidence for the fusion of two sets of two independent chromosomes forming two new chromosome pairs, leading to a reduction of 24 chromosome pairs in their ancestor to 22 pairs in tilapias. The XY sex determination locus in Mozambique tilapia was mapped on LG1, and verified in five families containing 549 individuals. The major XY sex determination locus in red tilapia was located on LG22, and verified in two families containing 275 individuals. Conclusions A first-generation linkage map of salt tolerant tilapia was constructed using 401 microsatellites. Two separate fusions of two sets of two independent chromosomes may lead to a reduction of 24 chromosome pairs in their ancestor to 22 pairs in tilapias. The XY sex-determining loci from Mozambique tilapia and red tilapia were mapped on LG1 and LG22, respectively. This map provides a useful resource for QTL mapping for important traits and comparative genome studies. The DNA markers linked to the sex-determining loci could be used in the selection of YY males for breeding all-male populations of salt tolerant tilapia, as well as in studies on mechanisms of sex determination in fish.
Collapse
Affiliation(s)
- Feng Liu
- Molecular Population Genetics Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Republic of Singapore
| | | | | | | | | | | | | |
Collapse
|
48
|
Cnaani A. The Tilapias' Chromosomes Influencing Sex Determination. Cytogenet Genome Res 2013; 141:195-205. [DOI: 10.1159/000355304] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|
49
|
Valenzuela N, Neuwald JL, Literman R. Transcriptional evolution underlying vertebrate sexual development. Dev Dyn 2012; 242:307-19. [DOI: 10.1002/dvdy.23897] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/22/2012] [Indexed: 12/30/2022] Open
Affiliation(s)
- Nicole Valenzuela
- Department of Ecology, Evolution, and Organismal Biology; Iowa State University; Ames; Iowa
| | - Jennifer L. Neuwald
- Department of Ecology, Evolution, and Organismal Biology; Iowa State University; Ames; Iowa
| | - Robert Literman
- Department of Ecology, Evolution, and Organismal Biology; Iowa State University; Ames; Iowa
| |
Collapse
|
50
|
Takahashi T, Sota T, Hori M. Genetic basis of male colour dimorphism in a Lake Tanganyika cichlid fish. Mol Ecol 2012; 22:3049-60. [PMID: 23176589 DOI: 10.1111/mec.12120] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2012] [Revised: 10/06/2012] [Accepted: 10/10/2012] [Indexed: 12/24/2022]
Abstract
Phenotypic polymorphisms can be applied to study the micro-evolutionary forces that maintain genetic variation and can mediate speciation, but it can be difficult to determine the genetic basis of polymorphisms. Recently, restriction-site-associated DNA (RAD) sequencing has become popular, which can easily produce multiple single nucleotide polymorphisms from whole genomes. Here, we combined RAD sequencing, allele-specific PCR and Sanger sequencing to determine the genetic basis underlying male colour dimorphism of a Lake Tanganyika cichlid fish, Cyprichromis leptosoma. Our analyses using both a cross-family (two parents and 12 F2 males) and 64 wild individuals do not contradict a hypothesis that two alleles of one-locus control male colour dimorphism. Also, the locus may be located on a genome region that experiences reduced levels of recombination. Although more analyses will be needed to conclude these findings, this study is the first to suggest the genetic basis of a colour polymorphism using RAD sequencing.
Collapse
Affiliation(s)
- T Takahashi
- Laboratory of Animal Ecology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake, Sakyo, Kyoto, 606-8502, Japan.
| | | | | |
Collapse
|