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Shekhar MS, Katneni VK, Jangam AK, Krishnan K, Prabhudas SK, Jani Angel JR, Sukumaran K, Kailasam M, Jena J. First Report of Chromosome-Level Genome Assembly for Flathead Grey Mullet, Mugil cephalus (Linnaeus, 1758). Front Genet 2022; 13:911446. [PMID: 35783261 PMCID: PMC9247318 DOI: 10.3389/fgene.2022.911446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/06/2022] [Indexed: 11/25/2022] Open
Affiliation(s)
- Mudagandur S. Shekhar
- Nutrition Genetics and Biotechnology Division, Indian Council of Agricultural Research-Central Institute of Brackishwater Aquaculture, Chennai, India
| | - Vinaya Kumar Katneni
- Nutrition Genetics and Biotechnology Division, Indian Council of Agricultural Research-Central Institute of Brackishwater Aquaculture, Chennai, India
- *Correspondence: Vinaya Kumar Katneni,
| | - Ashok Kumar Jangam
- Nutrition Genetics and Biotechnology Division, Indian Council of Agricultural Research-Central Institute of Brackishwater Aquaculture, Chennai, India
| | - Karthic Krishnan
- Nutrition Genetics and Biotechnology Division, Indian Council of Agricultural Research-Central Institute of Brackishwater Aquaculture, Chennai, India
| | - Sudheesh K. Prabhudas
- Nutrition Genetics and Biotechnology Division, Indian Council of Agricultural Research-Central Institute of Brackishwater Aquaculture, Chennai, India
| | - Jesudhas Raymond Jani Angel
- Nutrition Genetics and Biotechnology Division, Indian Council of Agricultural Research-Central Institute of Brackishwater Aquaculture, Chennai, India
| | - Krishna Sukumaran
- Finfish Culture Division, ICAR-Central Institute of Brackishwater Aquaculture, Chennai, India
| | - Muniyandi Kailasam
- Finfish Culture Division, ICAR-Central Institute of Brackishwater Aquaculture, Chennai, India
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Dynamics of sexual development in teleosts with a note on Mugil cephalus. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2022.03.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Curzon AY, Dor L, Shirak A, Meiri-Ashkenazi I, Rosenfeld H, Ron M, Seroussi E. A novel c.1759T>G variant in follicle-stimulating hormone-receptor gene is concordant with male determination in the flathead grey mullet (Mugil cephalus). G3-GENES GENOMES GENETICS 2021; 11:6046932. [PMID: 33589926 PMCID: PMC8022982 DOI: 10.1093/g3journal/jkaa044] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 12/08/2020] [Indexed: 12/31/2022]
Abstract
Various master key regulators (MKRs) that control a binary switch of sex determination (SD) have been found in fish; these provide an excellent model for the study of vertebrate genetic SD. The SD region in flathead grey mullet has been previously mapped to a 1 Mbp region harboring 27 genes, of which one is follicle-stimulating hormone receptor (fshr). Although this gene is involved in gonad differentiation and function, it has not been considered as an MKR of SD. We systematically investigated polymorphism in mullet fshr using DNA shotgun sequences, and compared them between males and females. Capable of encoding nonconservative amino acid substitutions, c.1732G>A and c.1759T>G exhibited association with sex on a population level (N = 83; P ≤ 6.7 × 10-19). Hence, 1732 A and 1759 G represent a male-specific haplotype of the gene, designated as "fshry." Additional flanking SNPs showed a weaker degree of association with sex, delimiting the SD critical region to 143 nucleotides on exon 14. Lack of homozygotes for fshry, and the resulting divergence from Hardy-Weinberg equilibrium (N = 170; P ≤ 3.9 × 10-5), were compatible with a male heterogametic model (XY/XX). Capable of replacing a phenylalanine with valine, c.1759T>G alters a conserved position across the sixth transmembrane domain of vertebrate FSHRs. Amino acid substitutions in this position in vertebrates are frequently associated with constant receptor activation and consequently with FSH/FSHR signaling alteration; thus, indicating a potential role of fshr as an MKR of SD.
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Affiliation(s)
- Arie Y Curzon
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel.,Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Lior Dor
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel.,Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
| | - Andrey Shirak
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel
| | - Iris Meiri-Ashkenazi
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat 88112, Israel
| | - Hana Rosenfeld
- National Center for Mariculture, Israel Oceanographic and Limnological Research, Eilat 88112, Israel
| | - Micha Ron
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel
| | - Eyal Seroussi
- Agricultural Research Organization, Institute of Animal Science, Rishon LeTsiyon, 7528809, Israel
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Ferraresso S, Bargelloni L, Babbucci M, Cannas R, Follesa MC, Carugati L, Melis R, Cau A, Koutrakis M, Sapounidis A, Crosetti D, Patarnello T. fshr: a fish sex-determining locus shows variable incomplete penetrance across flathead grey mullet populations. iScience 2021; 24:101886. [PMID: 33354664 PMCID: PMC7744951 DOI: 10.1016/j.isci.2020.101886] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/23/2020] [Accepted: 11/25/2020] [Indexed: 12/29/2022] Open
Abstract
Whole-genome sequencing data were produced from a single flathead grey mullet female and assembled into a draft genome sequence, whereas publicly available sequence data were used to obtain a male draft sequence. Two pools, each consisting of 60 unrelated individuals, respectively, of male and female fish were analyzed using Pool-Sequencing. Mapping and analysis of Pool-Seq data against the draft genome(s) revealed >30 loci potentially associated with sex, the most promising locus of which, encoding the follicle-stimulating hormone receptor (fshr) and harboring two missense variants, was genotyped on 245 fish from four Mediterranean populations. Genotype data showed that fshr represents a previously unknown sex-determining locus, although the incomplete association pattern between fshr genotype and sex-phenotype, the variability of such pattern across different populations, and the presence of other candidate loci reveal that a greater complexity underlies sex determination in the flathead grey mullet.
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Affiliation(s)
- Serena Ferraresso
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua 35020, Italy
| | - Luca Bargelloni
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua 35020, Italy
| | - Massimiliano Babbucci
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua 35020, Italy
| | - Rita Cannas
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Maria Cristina Follesa
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Laura Carugati
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Riccardo Melis
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Angelo Cau
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari 09124, Italy
| | - Manos Koutrakis
- Fisheries Research Institute, Hellenic Agricultural Organisation, Nea Peramos Kavalas 640 07, Greece
| | - Argyrios Sapounidis
- Fisheries Research Institute, Hellenic Agricultural Organisation, Nea Peramos Kavalas 640 07, Greece
| | - Donatella Crosetti
- Department BIO-AMC, Institute for Environmental Protection and Research (ISPRA), Rome 00144, Italy
| | - Tomaso Patarnello
- Department of Comparative Biomedicine and Food Science, University of Padova, Legnaro, Padua 35020, Italy
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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.
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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
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Dor L, Shirak A, Kohn YY, Gur T, Weller JI, Zilberg D, Seroussi E, Ron M. Mapping of the Sex Determining Region on Linkage Group 12 of Guppy ( Poecilia reticulata). G3 (BETHESDA, MD.) 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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 09/19/2019] [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.
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Affiliation(s)
- Lior Dor
- Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot 76100, Israel
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Andrey Shirak
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Yair Yaacov Kohn
- Central and Northern Arava Research and Development D.N. Arava Sapir, 86825 Israel, and
| | - Tal Gur
- Central and Northern Arava Research and Development D.N. Arava Sapir, 86825 Israel, and
| | - Joel Ira Weller
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Dina Zilberg
- The French Associates Institute for Agriculture and Biotechnology of Drylands, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Eyal Seroussi
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel
| | - Micha Ron
- Agricultural Research Organization (ARO), Volcani Center, Institute of Animal Science, HaMaccabim Road, P.O.B 15159, 7528809, Rishon LeTsiyon, Israel,
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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.
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