1
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Wersebe MJ, Sherman RE, Jeyasingh PD, Weider LJ. The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex. Mol Ecol 2023; 32:1478-1496. [PMID: 35119153 DOI: 10.1111/mec.16383] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/16/2022] [Accepted: 01/28/2022] [Indexed: 11/24/2022]
Abstract
Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, Daphnia pulicaria and Daphnia pulex. First, we assembled a phased chromosome-scale genome assembly using trio-binning for D. pulicaria and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity. Finally, we used a ddRADseq data set with broad geographic sampling of D. pulicaria, D. pulex, and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in D. pulicaria, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are probably driven by selection on D. pulicaria, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.
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Affiliation(s)
- Matthew J Wersebe
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
| | - Ryan E Sherman
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Punidan D Jeyasingh
- Department of Integrative Biology, Oklahoma State University, Stillwater, Oklahoma, USA
| | - Lawrence J Weider
- Department of Biology, Program in Ecology and Evolutionary Biology, University of Oklahoma, Norman, Oklahoma, USA
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2
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Ghosh A, Johnson MG, Osmanski AB, Louha S, Bayona-Vásquez NJ, Glenn TC, Gongora J, Green RE, Isberg S, Stevens RD, Ray DA. A High-Quality Reference Genome Assembly of the Saltwater Crocodile, Crocodylus porosus, Reveals Patterns of Selection in Crocodylidae. Genome Biol Evol 2020; 12:3635-3646. [PMID: 31821505 PMCID: PMC6946029 DOI: 10.1093/gbe/evz269] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/14/2022] Open
Abstract
Crocodilians are an economically, culturally, and biologically important group. To improve researchers’ ability to study genome structure, evolution, and gene regulation in the clade, we generated a high-quality de novo genome assembly of the saltwater crocodile, Crocodylus porosus, from Illumina short read data from genomic libraries and in vitro proximity-ligation libraries. The assembled genome is 2,123.5 Mb, with N50 scaffold size of 17.7 Mb and N90 scaffold size of 3.8 Mb. We then annotated this new assembly, increasing the number of annotated genes by 74%. In total, 96% of 23,242 annotated genes were associated with a functional protein domain. Furthermore, multiple noncoding functional regions and mappable genetic markers were identified. Upon analysis and overlapping the results of branch length estimation and site selection tests for detecting potential selection, we found 16 putative genes under positive selection in crocodilians, 10 in C. porosus and 6 in Alligator mississippiensis. The annotated C. porosus genome will serve as an important platform for osmoregulatory, physiological, and sex determination studies, as well as an important reference in investigating the phylogenetic relationships of crocodilians, birds, and other tetrapods.
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Affiliation(s)
- Arnab Ghosh
- Department of Biological Sciences, Texas Tech University
| | | | | | - Swarnali Louha
- Department of Environmental Health Science and Institute of Bioinformatics, University of Georgia
| | - Natalia J Bayona-Vásquez
- Department of Environmental Health Science and Institute of Bioinformatics, University of Georgia
| | - Travis C Glenn
- Department of Environmental Health Science and Institute of Bioinformatics, University of Georgia
| | - Jaime Gongora
- Sydney School of Veterinary Science, University of Sydney, Australia
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz
| | - Sally Isberg
- Sydney School of Veterinary Science, University of Sydney, Australia.,Centre for Crocodile Research, University of Sydney and Charles Darwin University, Australia
| | | | - David A Ray
- Department of Biological Sciences, Texas Tech University
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3
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The effectiveness of microsatellite DNA as a genetic tool in crocodilian conservation. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01164-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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4
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Abstract
Sex differences in overall recombination rates are well known, but little theoretical or empirical attention has been given to how and why sexes differ in their recombination landscapes: the patterns of recombination along chromosomes. In the first scientific review of this phenomenon, we find that recombination is biased toward telomeres in males and more uniformly distributed in females in most vertebrates and many other eukaryotes. Notable exceptions to this pattern exist, however. Fine-scale recombination patterns also frequently differ between males and females. The molecular mechanisms responsible for sex differences remain unclear, but chromatin landscapes play a role. Why these sex differences evolve also is unclear. Hypotheses suggest that they may result from sexually antagonistic selection acting on coding genes and their regulatory elements, meiotic drive in females, selection during the haploid phase of the life cycle, selection against aneuploidy, or mechanistic constraints. No single hypothesis, however, can adequately explain the evolution of sex differences in all cases. Sex-specific recombination landscapes have important consequences for population differentiation and sex chromosome evolution.
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Affiliation(s)
- Jason M. Sardell
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
| | - Mark Kirkpatrick
- Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712
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5
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Sexual antagonism and the instability of environmental sex determination. Nat Ecol Evol 2018; 2:343-351. [PMID: 29335574 DOI: 10.1038/s41559-017-0427-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 11/22/2017] [Indexed: 11/08/2022]
Abstract
The sex of an organism can be determined by its genetics or its early environment. Across the animal kingdom, genetic sex determination (GSD) is far more common than environmental sex determination (ESD). Here, we propose an explanation for this pattern: the coupling of genes that bias offspring sex ratios towards one sex with genes that are beneficial in that sex but costly in the other. Gradual strengthening of the sex-specific tendency of this association eventuates in a neo-sex chromosome; that is, GSD. Our model predicts to which system of heterogamety ESD will evolve when nesting behaviour is an important determinant of brood sex ratios. It explains the puzzling observation in some GSD species of sex reversal induced by extreme environments. The model also suggests an approach to discovering sex-determining genes in ESD species.
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6
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Lapbenjakul S, Thapana W, Twilprawat P, Muangmai N, Kanchanaketu T, Temsiripong Y, Unajak S, Peyachoknagul S, Srikulnath K. High genetic diversity and demographic history of captive Siamese and Saltwater crocodiles suggest the first step toward the establishment of a breeding and reintroduction program in Thailand. PLoS One 2017; 12:e0184526. [PMID: 28953895 PMCID: PMC5617146 DOI: 10.1371/journal.pone.0184526] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/25/2017] [Indexed: 01/08/2023] Open
Abstract
The Siamese crocodile (Crocodylus siamensis) and Saltwater crocodile (C. porosus) are two of the most endangered animals in Thailand. Their numbers have been reduced severely by hunting and habitat fragmentation. A reintroduction plan involving captive-bred populations that are used commercially is important and necessary as a conservation strategy to aid in the recovery of wild populations. Here, the genetic diversity and population structure of 69 individual crocodiles, mostly members of captive populations, were analyzed using both mitochondrial D-loop DNA and microsatellite markers. The overall haplotype diversity was 0.924–0.971 and the mean expected heterozygosity across 22 microsatellite loci was 0.578–0.701 for the two species. This agreed with the star-like shaped topology of the haplotype network, which suggests a high level of genetic diversity. The mean ratio of the number of alleles to the allelic range (M ratio) for the populations of both species was considerably lower than the threshold of 0.68, which was interpreted as indicative of a historical genetic bottleneck. Microsatellite markers provided evidence of introgression for three individual crocodiles, which suggest that hybridization might have occurred between C. siamensis and C. porosus. D-loop sequence analysis detected bi-directional hybridization between male and female individuals of the parent species. Therefore, identification of genetically non-hybrid and hybrid individuals is important for long-term conservation management. Relatedness values were low within the captive populations, which supported their genetic integrity and the viability of a breeding and reintroduction management plan. This work constitutes the first step in establishing an appropriate source population from a scientifically managed perspective for an in situ/ex situ conservation program and reintroduction of crocodile individuals to the wild in Thailand.
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Grants
- Kasetsart University Research and Development Institute (KURDI)
- the Graduate School, Kasetsart University
- Professor Motivation (PM), Faculty of Science, Kasetsart University
- Special Track Staff (STS), Faculty of Science, Kasetsart University
- Science Research Fund (ScRF), Faculty of Science, Kasetsart University
- the Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University
- The graduate scholarship provided by the National Research Council of Thailand (NRCT) as of fiscal year 2017, the Graduate School, Kasetsart University
- the Science Achievement Scholarship of Thailand (SAST), the Office of the Higher Education Commission, Thailand
- the Center of Excellence on Agricultural Biotechnology, Science and Technology Postgraduate Education and Research Development Office, Office of Higher Education Commission, Ministry of Education
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Affiliation(s)
- Sorravis Lapbenjakul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
| | - Watcharaporn Thapana
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, Thailand
| | - Panupon Twilprawat
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Narongrit Muangmai
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
- Department of Fishery Biology, Faculty of Fisheries, Kasetsart University, Bangkok, Thailand
| | - Thiti Kanchanaketu
- Division of Genetics, Department of Science, Faculty of Liberal Arts and Science, Kasetsart University (Kamphaeng Saen Campus), Kamphaeng Saen, Nakhon Pathom, Thailand
| | | | - Sasimanas Unajak
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, Thailand
- Department of Biology, Faculty of Science, Naresuan University, Muang Phitsanulok, Phitsanulok, Thailand
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, Thailand
- Animal Breeding and Genetics Consortium of Kasetsart University (ABG-KU), Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University (CASTNAR, NRU-KU), Kasetsart University, Bangkok, Thailand
- Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, Thailand
- * E-mail:
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7
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Lisachov AP, Trifonov VA, Giovannotti M, Ferguson-Smith MA, Borodin PM. Immunocytological analysis of meiotic recombination in two anole lizards (Squamata, Dactyloidae). COMPARATIVE CYTOGENETICS 2017; 11:129-141. [PMID: 28919954 PMCID: PMC5599703 DOI: 10.3897/compcytogen.v11i1.10916] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 01/16/2017] [Indexed: 05/13/2023]
Abstract
Although the evolutionary importance of meiotic recombination is not disputed, the significance of interspecies differences in the recombination rates and recombination landscapes remains under-appreciated. Recombination rates and distribution of chiasmata have been examined cytologically in many mammalian species, whereas data on other vertebrates are scarce. Immunolocalization of the protein of the synaptonemal complex (SYCP3), centromere proteins and the mismatch-repair protein MLH1 was used, which is associated with the most common type of recombination nodules, to analyze the pattern of meiotic recombination in the male of two species of iguanian lizards, Anolis carolinensis Voigt, 1832 and Deiroptyx coelestinus (Cope, 1862). These species are separated by a relatively long evolutionary history although they retain the ancestral iguanian karyotype. In both species similar and extremely uneven distributions of MLH1 foci along the macrochromosome bivalents were detected: approximately 90% of crossovers were located at the distal 20% of the chromosome arm length. Almost total suppression of recombination in the intermediate and proximal regions of the chromosome arms contradicts the hypothesis that "homogenous recombination" is responsible for the low variation in GC content across the anole genome. It also leads to strong linkage disequilibrium between the genes located in these regions, which may benefit conservation of co-adaptive gene arrays responsible for the ecological adaptations of the anoles.
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Affiliation(s)
- Artem P. Lisachov
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia
| | - Vladimir A. Trifonov
- Institute of Molecular and Cellular Biology, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia
- Novosibirsk State University, Novosibirsk 630090, Russia
| | - Massimo Giovannotti
- Dipartimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy
| | - Malcolm A. Ferguson-Smith
- Cambridge Resource Centre for Comparative Genomics, Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge CB3 0ES, UK
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8
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Wang L, Bai B, Liu P, Huang SQ, Wan ZY, Chua E, Ye B, Yue GH. Construction of high-resolution recombination maps in Asian seabass. BMC Genomics 2017; 18:63. [PMID: 28068919 PMCID: PMC5223582 DOI: 10.1186/s12864-016-3462-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022] Open
Abstract
Background A high-density genetic map is essential for de novo genome assembly, fine mapping QTL for important complex traits, comparative genomic studies and understanding the mechanisms of genome evolution. Although a number of genomic resources are available in Asian seabass (Lates calcarifer), a high-density linkage map is still lacking. To facilitate QTL mapping for marker-assisted selection and genome assembly, and to understand the genome-wide recombination rates, we constructed high density linkage maps using three families and genotyping by sequencing. Results A high-density consensus linkage map consisting of 8, 274 markers was constructed based on sex-averaged genetic maps. The genetic maps were then aligned and integrated with the current genome assembly of Asian seabass. More than 90% of the genome contig sequences were anchored onto the consensus genetic map. Evidence of assembly errors in the current genome assembly was identified. A fragment of up to 2.5 Mb belonging to LG14 was assembled into Chr15. The length of family-specific sex-averaged maps ranged from 1348.96 to 1624.65 cM. Female maps were slightly longer than male maps using common markers. Female-to-male ratios were highly variable both across chromosomes within each family and throughout three families for each chromosome. However, the distribution patterns of recombination along chromosomes were similar between sexes across the whole genome. The overall recombination rates were significantly correlated with genome-wide GC content and the correlations were revealed to be stronger in females than in males. Conclusions These high-density genetic maps provide not only essential tools for facilitating de novo genome assembly and comparative genomic studies in teleosts, but also critical resources for fine mapping QTL and genome-wide association mapping for economically important traits in Asian seabass. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3462-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Le Wang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Bin Bai
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Peng Liu
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore
| | - Shu Qing Huang
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Zi Yi Wan
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore.,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore
| | - Elaine Chua
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Baoqing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore
| | - Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604, Singapore. .,Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore, 117543, Singapore. .,School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551, Singapore.
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9
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Kessuwan K, Kubota S, Liu Q, Sano M, Okamoto N, Sakamoto T, Yamashita H, Nakamura Y, Ozaki A. Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016; 18:57-84. [PMID: 26511529 PMCID: PMC4705122 DOI: 10.1007/s10126-015-9673-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/14/2015] [Indexed: 06/05/2023]
Abstract
To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F1 family. Genome-wide and chromosome-wide significances of growth-related quantitative trait loci (QTLs) (body weight (BW) and total length (TL)) were detected using non-parametric mapping, Kruskal-Wallis (K-W) analysis, simple interval mapping (IM) and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39 cM and covered 84.68 and 83.21% of the genome, with an average interval of 4.1 and 4.0 cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17F that identified for 1% of the genome-wide significance and accounted for 14.6-18.9 and 14.7-18.5% of the phenotypic variance, and several putative QTL with 5% chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5% as well as a chromosome-wide value of 5%. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies, and potentially useful in MAS breeding.
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Affiliation(s)
- Kanonkporn Kessuwan
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- Department of Fisheries, Coastal Fisheries Research and Development Bureau, 50 Kaset Klang Jatujak, Bangkok, 10900, Thailand
| | - Satoshi Kubota
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Qi Liu
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- Center for Marine Ranching Engineering Science Research of Liaoning, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, China
| | - Motohiko Sano
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Nobuaki Okamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Takashi Sakamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Hirofumi Yamashita
- Ehime Research Institute of Agriculture, Forestry and Fisheries, Fisheries Research Center, 5516 Shitaba, Uwajima-shi, Ehime, 798-0104, Japan
| | - Yoji Nakamura
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Akiyuki Ozaki
- National Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minamiise-cho, Watarai-gun, Mie, 516-0193, Japan.
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10
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Kessuwan K, Kubota S, Liu Q, Sano M, Okamoto N, Sakamoto T, Yamashita H, Nakamura Y, Ozaki A. Detection of Growth-Related Quantitative Trait Loci and High-Resolution Genetic Linkage Maps Using Simple Sequence Repeat Markers in the Kelp Grouper (Epinephelus bruneus). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2016:10.1007/s10126-015-9679-z. [PMID: 26743358 DOI: 10.1007/s10126-015-9679-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 09/14/2015] [Indexed: 10/22/2022]
Abstract
To initiate breeding programs for kelp grouper (Epinephelus bruneus), the establishment of genetic linkage maps becomes essential accompanied by the search for quantitative trait loci (QTLs) that may be utilized in selection programs. We constructed a high-resolution genetic linkage map using 1055 simple sequence repeat (SSR) markers in an F1 family. Genome-wide and chromosome-wide significances of growth-related QTLs (body weight: BW and total length: TL) were detected using non-parametric mapping, Kruskal-Wallis analysis, simple interval mapping (IM), and a permutation test (PT). Two stages and two families of fish were used to confirm the QTL regions. Ultimately, 714 SSR markers were matched that evenly covered the 24 linkage groups. In total, 509 and 512 markers were localized to the female and male maps, respectively. The genome lengths were approximately 1475.95 and 1370.39 cM and covered 84.68 and 83.21 % of the genome, with an average interval of 4.1 and 4.0 cM, in females and males, respectively. One major QTL affecting BW and TL was found on linkage group EBR 17 F that identified for 1 % of the genome-wide significance and accounted for 14.6-18.9 % and 14.7-18.5 % of the phenotypic variance, and several putative QTL with 5 % chromosome-wide significance were detected on eight linkage groups. Furthermore, the confirmed results of the regions harboring the major and putative QTLs showed consistent significant experiment-wide values of 1 and 5 % as well as a chromosome-wide value of 5 %. We identified growth-related QTLs that could be applied to find candidate genes for growth traits in further studies and potentially useful in marker assisted selection (MAS) breeding.
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Affiliation(s)
- Kanonkporn Kessuwan
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- Department of Fisheries, Coastal Fisheries Research and Development Bureau, 50 Kaset Klang Jatujak, Bangkok, 10900, Thailand
| | - Satoshi Kubota
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Qi Liu
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- Center for Marine Ranching Engineering Science Research of Liaoning, Dalian Ocean University, 52 Heishijiao Street, Dalian, 116023, China
| | - Motohiko Sano
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Nobuaki Okamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Takashi Sakamoto
- Faculty of Marine Science, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo, 108-8477, Japan
| | - Hirofumi Yamashita
- Ehime Research Institute of Agriculture, Forestry and Fisheries, Fisheries Research Center, 5516 Shitaba, Uwajima-shi, Ehime, 798-0104, Japan
| | - Yoji Nakamura
- National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa-ku, Yokohama, Kanagawa, 236-8648, Japan
| | - Akiyuki Ozaki
- National Research Institute of Aquaculture, Fisheries Research Agency, 422-1 Nakatsuhamaura, Minamiise-cho, Watarai-gun, Mie, 516-0193, Japan.
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11
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Jones DB, Jerry DR, Khatkar MS, Raadsma HW, Zenger KR. A high-density SNP genetic linkage map for the silver-lipped pearl oyster, Pinctada maxima: a valuable resource for gene localisation and marker-assisted selection. BMC Genomics 2013; 14:810. [PMID: 24252414 PMCID: PMC4046678 DOI: 10.1186/1471-2164-14-810] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 11/18/2013] [Indexed: 11/26/2022] Open
Abstract
Background The silver-lipped pearl oyster, Pinctada maxima, is an important tropical aquaculture species extensively farmed for the highly sought "South Sea" pearls. Traditional breeding programs have been initiated for this species in order to select for improved pearl quality, but many economic traits under selection are complex, polygenic and confounded with environmental factors, limiting the accuracy of selection. The incorporation of a marker-assisted selection (MAS) breeding approach would greatly benefit pearl breeding programs by allowing the direct selection of genes responsible for pearl quality. However, before MAS can be incorporated, substantial genomic resources such as genetic linkage maps need to be generated. The construction of a high-density genetic linkage map for P. maxima is not only essential for unravelling the genomic architecture of complex pearl quality traits, but also provides indispensable information on the genome structure of pearl oysters. Results A total of 1,189 informative genome-wide single nucleotide polymorphisms (SNPs) were incorporated into linkage map construction. The final linkage map consisted of 887 SNPs in 14 linkage groups, spans a total genetic distance of 831.7 centimorgans (cM), and covers an estimated 96% of the P. maxima genome. Assessment of sex-specific recombination across all linkage groups revealed limited overall heterochiasmy between the sexes (i.e. 1.15:1 F/M map length ratio). However, there were pronounced localised differences throughout the linkage groups, whereby male recombination was suppressed near the centromeres compared to female recombination, but inflated towards telomeric regions. Mean values of LD for adjacent SNP pairs suggest that a higher density of markers will be required for powerful genome-wide association studies. Finally, numerous nacre biomineralization genes were localised providing novel positional information for these genes. Conclusions This high-density SNP genetic map is the first comprehensive linkage map for any pearl oyster species. It provides an essential genomic tool facilitating studies investigating the genomic architecture of complex trait variation and identifying quantitative trait loci for economically important traits useful in genetic selection programs within the P. maxima pearling industry. Furthermore, this map provides a foundation for further research aiming to improve our understanding of the dynamic process of biomineralization, and pearl oyster evolution and synteny. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-810) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David B Jones
- Centre for Sustainable Tropical Fisheries & Aquaculture, The School of Marine and Tropical Biology, James Cook University, Townsville, QLD, Australia.
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References. Mol Ecol 2012. [DOI: 10.1002/9780470979365.refs] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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St John JA, Braun EL, Isberg SR, Miles LG, Chong AY, Gongora J, Dalzell P, Moran C, Bed'hom B, Abzhanov A, Burgess SC, Cooksey AM, Castoe TA, Crawford NG, Densmore LD, Drew JC, Edwards SV, Faircloth BC, Fujita MK, Greenwold MJ, Hoffmann FG, Howard JM, Iguchi T, Janes DE, Khan SY, Kohno S, de Koning AJ, Lance SL, McCarthy FM, McCormack JE, Merchant ME, Peterson DG, Pollock DD, Pourmand N, Raney BJ, Roessler KA, Sanford JR, Sawyer RH, Schmidt CJ, Triplett EW, Tuberville TD, Venegas-Anaya M, Howard JT, Jarvis ED, Guillette LJ, Glenn TC, Green RE, Ray DA. Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes. Genome Biol 2012; 13:415. [PMID: 22293439 PMCID: PMC3334581 DOI: 10.1186/gb-2012-13-1-415] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis gangeticus) genomes. The status of these projects and our planned analyses are described.
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Luck NL, Thomas KC, Morin-Adeline VE, Barwick S, Chong AY, Carpenter EL, Wan L, Willet CE, Langford-Salisbury SM, Abdelsayd M, Ang RA, Atkinson SJ, Barcelo FG, Booth ME, Bradbury EJ, Branighan TL, Brown J, Castillo LE, Chandler ND, Chong JY, Collits KJ, Cook E, Cruz RE, Farrugia CA, Fletcher JL, Fletcher S, Gamaliel NS, Gurr JF, Hallett NJ, Hargreaves G, Harris T, Hollings S, Hopcroft RL, Johinke D, Kern PL, Kiddell JL, Kilby KE, Kragic B, Kwan JH, Lee JI, Liang JM, Lillie MC, Lui BC, Luk SW, Lun KH, Marshall KL, Marzec JA, Masters KT, Mazurkijevic LJ, Medlock J, Meoli C, Morris KM, Noh YH, Okazaki H, Orourke TJ, Payne EM, Powell DJ, Quinlivan AR, Reeves TJ, Robson K, Robson KL, Royle LJ, Stevenson R, Sellens T, Sun Z, Sutton AL, Swan A, Tang JM, Tinker JE, Tomlinson SC, Wilkin T, Wright AL, Xiao ST, Yang J, Yee C, Jaratlerdsiri W, Isberg SR, Miles L, Higgins D, Lane A, Gongora J. Mitochondrial DNA analyses of the saltwater crocodile (Crocodylus porosus) from the Northern Territory of Australia. AUST J ZOOL 2012. [DOI: 10.1071/zo12008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The saltwater crocodile is distributed throughout south-east Asia and Australia. In Australia, it is most abundant in the Northern Territory and Queensland, where it is sustainably farmed for its skins and meat. The aim of this study was to elucidate the relationships and genetic structure among saltwater crocodiles from the Northern Territory of Australia using mitochondrial control region sequences from 61 individuals, representing nine river basins and six of unknown origin, as well as published sequences from other regions. Eight mitochondrial control region haplotypes were identified among both published and novel sequences. Three of the haplotypes appear to be restricted to specimens from northern Australia, with a single haplotype being the most widely dispersed across all river basins. Although Analysis of Molecular Variance provides some support for differentiation among river basins, the frequency of shared haplotypes among these geographical units and median-joining network analysis do not support a clear genetic structure or phylogeographic pattern for saltwater crocodiles in the Northern Territory. The results of this study will assist in furthering our understanding of the genetic diversity of wild saltwater crocodile populations used for ranching in the Northern Territory, as well as providing a framework for assessing the origin of unknown specimens in the future.
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Giraut L, Falque M, Drouaud J, Pereira L, Martin OC, Mézard C. Genome-wide crossover distribution in Arabidopsis thaliana meiosis reveals sex-specific patterns along chromosomes. PLoS Genet 2011; 7:e1002354. [PMID: 22072983 PMCID: PMC3207851 DOI: 10.1371/journal.pgen.1002354] [Citation(s) in RCA: 178] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2011] [Accepted: 09/08/2011] [Indexed: 11/19/2022] Open
Abstract
In most species, crossovers (COs) are essential for the accurate segregation of homologous chromosomes at the first meiotic division. Their number and location are tightly regulated. Here, we report a detailed, genome-wide characterization of the rate and localization of COs in Arabidopsis thaliana, in male and female meiosis. We observed dramatic differences between male and female meiosis which included: (i) genetic map length; 575 cM versus 332 cM respectively; (ii) CO distribution patterns: male CO rates were very high at both ends of each chromosome, whereas female CO rates were very low; (iii) correlations between CO rates and various chromosome features: female CO rates correlated strongly and negatively with GC content and gene density but positively with transposable elements (TEs) density, whereas male CO rates correlated positively with the CpG ratio. However, except for CpG, the correlations could be explained by the unequal repartition of these sequences along the Arabidopsis chromosome. For both male and female meiosis, the number of COs per chromosome correlates with chromosome size expressed either in base pairs or as synaptonemal complex length. Finally, we show that interference modulates the CO distribution both in male and female meiosis.
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Affiliation(s)
- Laurène Giraut
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Matthieu Falque
- UMR de Génétique Végétale du Moulon, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Gif sur Yvette, France
| | - Jan Drouaud
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Lucie Pereira
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
| | - Olivier C. Martin
- UMR de Génétique Végétale du Moulon, INRA/CNRS/Univ Paris-Sud/AgroParisTech, Gif sur Yvette, France
| | - Christine Mézard
- Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, INRA Centre de Versailles-Grignon, Versailles, France
- * E-mail:
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Stolle E, Wilfert L, Schmid-Hempel R, Schmid-Hempel P, Kube M, Reinhardt R, Moritz RFA. A second generation genetic map of the bumblebee Bombus terrestris (Linnaeus, 1758) reveals slow genome and chromosome evolution in the Apidae. BMC Genomics 2011; 12:48. [PMID: 21247459 PMCID: PMC3034698 DOI: 10.1186/1471-2164-12-48] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2010] [Accepted: 01/19/2011] [Indexed: 12/30/2022] Open
Abstract
Background The bumblebee Bombus terrestris is an ecologically and economically important pollinator and has become an important biological model system. To study fundamental evolutionary questions at the genomic level, a high resolution genetic linkage map is an essential tool for analyses ranging from quantitative trait loci (QTL) mapping to genome assembly and comparative genomics. We here present a saturated linkage map and match it with the Apis mellifera genome using homologous markers. This genome-wide comparison allows insights into structural conservations and rearrangements and thus the evolution on a chromosomal level. Results The high density linkage map covers ~ 93% of the B. terrestris genome on 18 linkage groups (LGs) and has a length of 2'047 cM with an average marker distance of 4.02 cM. Based on a genome size of ~ 430 Mb, the recombination rate estimate is 4.76 cM/Mb. Sequence homologies of 242 homologous markers allowed to match 15 B. terrestris with A. mellifera LGs, five of them as composites. Comparing marker orders between both genomes we detect over 14% of the genome to be organized in synteny and 21% in rearranged blocks on the same homologous LG. Conclusions This study demonstrates that, despite the very high recombination rates of both A. mellifera and B. terrestris and a long divergence time of about 100 million years, the genomes' genetic architecture is highly conserved. This reflects a slow genome evolution in these bees. We show that data on genome organization and conserved molecular markers can be used as a powerful tool for comparative genomics and evolutionary studies, opening up new avenues of research in the Apidae.
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Affiliation(s)
- Eckart Stolle
- Institut für Biologie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany.
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A garter snake transcriptome: pyrosequencing, de novo assembly, and sex-specific differences. BMC Genomics 2010; 11:694. [PMID: 21138572 PMCID: PMC3014983 DOI: 10.1186/1471-2164-11-694] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2010] [Accepted: 12/07/2010] [Indexed: 12/19/2022] Open
Abstract
Background The reptiles, characterized by both diversity and unique evolutionary adaptations, provide a comprehensive system for comparative studies of metabolism, physiology, and development. However, molecular resources for ectothermic reptiles are severely limited, hampering our ability to study the genetic basis for many evolutionarily important traits such as metabolic plasticity, extreme longevity, limblessness, venom, and freeze tolerance. Here we use massively parallel sequencing (454 GS-FLX Titanium) to generate a transcriptome of the western terrestrial garter snake (Thamnophis elegans) with two goals in mind. First, we develop a molecular resource for an ectothermic reptile; and second, we use these sex-specific transcriptomes to identify differences in the presence of expressed transcripts and potential genes of evolutionary interest. Results Using sex-specific pools of RNA (one pool for females, one pool for males) representing 7 tissue types and 35 diverse individuals, we produced 1.24 million sequence reads, which averaged 366 bp in length after cleaning. Assembly of the cleaned reads from both sexes with NEWBLER and MIRA resulted in 96,379 contigs containing 87% of the cleaned reads. Over 34% of these contigs and 13% of the singletons were annotated based on homology to previously identified proteins. From these homology assignments, additional clustering, and ORF predictions, we estimate that this transcriptome contains ~13,000 unique genes that were previously identified in other species and over 66,000 transcripts from unidentified protein-coding genes. Furthermore, we use a graph-clustering method to identify contigs linked by NEWBLER-split reads that represent divergent alleles, gene duplications, and alternatively spliced transcripts. Beyond gene identification, we identified 95,295 SNPs and 31,651 INDELs. From these sex-specific transcriptomes, we identified 190 genes that were only present in the mRNA sequenced from one of the sexes (84 female-specific, 106 male-specific), and many highly variable genes of evolutionary interest. Conclusions This is the first large-scale, multi-organ transcriptome for an ectothermic reptile. This resource provides the most comprehensive set of EST sequences available for an individual ectothermic reptile species, increasing the number of snake ESTs 50-fold. We have identified genes that appear to be under evolutionary selection and those that are sex-specific. This resource will assist studies on gene expression and comparative genomics, and will facilitate the study of evolutionarily important traits at the molecular level.
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Rodriguez D, Forstner MRJ, Moler PE, Wasilewski JA, Cherkiss MS, Densmore III LD. Effect of human-mediated migration and hybridization on the recovery of the American crocodile in Florida (USA). CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0153-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Janes DE, Organ CL, Fujita MK, Shedlock AM, Edwards SV. Genome evolution in Reptilia, the sister group of mammals. Annu Rev Genomics Hum Genet 2010; 11:239-64. [PMID: 20590429 DOI: 10.1146/annurev-genom-082509-141646] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The genomes of birds and nonavian reptiles (Reptilia) are critical for understanding genome evolution in mammals and amniotes generally. Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in the comparative genomics era. The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral amniote genome--predicted to be large and to possess a diverse repeat landscape on par with mammals and a birdlike sex chromosome system--to the small and highly streamlined genomes of birds. Reptilia exhibit a wide range of evolutionary rates of different subgenomes and, from isochores to mitochondrial DNA, provide a critical contrast to the genomic paradigms established in mammals.
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Affiliation(s)
- Daniel E Janes
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
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Poissant J, Hogg JT, Davis CS, Miller JM, Maddox JF, Coltman DW. Genetic linkage map of a wild genome: genomic structure, recombination and sexual dimorphism in bighorn sheep. BMC Genomics 2010; 11:524. [PMID: 20920197 PMCID: PMC3091677 DOI: 10.1186/1471-2164-11-524] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2010] [Accepted: 09/28/2010] [Indexed: 12/23/2022] Open
Abstract
Background The construction of genetic linkage maps in free-living populations is a promising tool for the study of evolution. However, such maps are rare because it is difficult to develop both wild pedigrees and corresponding sets of molecular markers that are sufficiently large. We took advantage of two long-term field studies of pedigreed individuals and genomic resources originally developed for domestic sheep (Ovis aries) to construct a linkage map for bighorn sheep, Ovis canadensis. We then assessed variability in genomic structure and recombination rates between bighorn sheep populations and sheep species. Results Bighorn sheep population-specific maps differed slightly in contiguity but were otherwise very similar in terms of genomic structure and recombination rates. The joint analysis of the two pedigrees resulted in a highly contiguous map composed of 247 microsatellite markers distributed along all 26 autosomes and the X chromosome. The map is estimated to cover about 84% of the bighorn sheep genome and contains 240 unique positions spanning a sex-averaged distance of 3051 cM with an average inter-marker distance of 14.3 cM. Marker synteny, order, sex-averaged interval lengths and sex-averaged total map lengths were all very similar between sheep species. However, in contrast to domestic sheep, but consistent with the usual pattern for a placental mammal, recombination rates in bighorn sheep were significantly greater in females than in males (~12% difference), resulting in an autosomal female map of 3166 cM and an autosomal male map of 2831 cM. Despite differing genome-wide patterns of heterochiasmy between the sheep species, sexual dimorphism in recombination rates was correlated between orthologous intervals. Conclusions We have developed a first-generation bighorn sheep linkage map that will facilitate future studies of the genetic architecture of trait variation in this species. While domestication has been hypothesized to be responsible for the elevated mean recombination rate observed in domestic sheep, our results suggest that it is a characteristic of Ovis species. However, domestication may have played a role in altering patterns of heterochiasmy. Finally, we found that interval-specific patterns of sexual dimorphism were preserved among closely related Ovis species, possibly due to the conserved position of these intervals relative to the centromeres and telomeres. This study exemplifies how transferring genomic resources from domesticated species to close wild relative can benefit evolutionary ecologists while providing insights into the evolution of genomic structure and recombination rates of domesticated species.
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Affiliation(s)
- Jocelyn Poissant
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada.
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Abstract
The recent generation of a genetic linkage map for the saltwater crocodile (Crocodylus porosus) has now made it possible to carry out the systematic searches necessary for the identification of quantitative trait loci (QTL) affecting traits of economic, as well as evolutionary, importance in crocodilians. In this study, we conducted genome-wide scans for two commercially important traits, inventory head length (which is highly correlated with growth rate) and number of scale rows (SR, a skin quality trait), for the existence of QTL in a commercial population of saltwater crocodiles at Darwin Crocodile Farm, Northern Territory, Australia. To account for the uncommonly large difference in sex-specific recombination rates apparent in the saltwater crocodile, a duel mapping strategy was employed. This strategy employed a sib-pair analysis to take advantage of our full-sib pedigree structure, together with a half-sib analysis to account for, and take advantage of, the large difference in sex-specific recombination frequencies. Using these approaches, two putative QTL regions were identified for SR on linkage group 1 (LG1) at 36 cM, and on LG12 at 0 cM. The QTL identified in this investigation represent the first for a crocodilian and indeed for any non-avian member of the Class Reptilia. Mapping of QTL is an important first step towards the identification of genes and causal mutations for commercially important traits and the development of selection tools for implementation in crocodile breeding programmes for the industry.
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