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Yazdi HP, Silva WTAF, Suh A. Why Do Some Sex Chromosomes Degenerate More Slowly Than Others? The Odd Case of Ratite Sex Chromosomes. Genes (Basel) 2020; 11:E1153. [PMID: 33007827 PMCID: PMC7601716 DOI: 10.3390/genes11101153] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 01/10/2023] Open
Abstract
The hallmark of sex chromosome evolution is the progressive suppression of recombination which leads to subsequent degeneration of the non-recombining chromosome. In birds, species belonging to the two major clades, Palaeognathae (including tinamous and flightless ratites) and Neognathae (all remaining birds), show distinctive patterns of sex chromosome degeneration. Birds are female heterogametic, in which females have a Z and a W chromosome. In Neognathae, the highly-degenerated W chromosome seems to have followed the expected trajectory of sex chromosome evolution. In contrast, among Palaeognathae, sex chromosomes of ratite birds are largely recombining. The underlying reason for maintenance of recombination between sex chromosomes in ratites is not clear. Degeneration of the W chromosome might have halted or slowed down due to a multitude of reasons ranging from selective processes, such as a less pronounced effect of sexually antagonistic selection, to neutral processes, such as a slower rate of molecular evolution in ratites. The production of genome assemblies and gene expression data for species of Palaeognathae has made it possible, during recent years, to have a closer look at their sex chromosome evolution. Here, we critically evaluate the understanding of the maintenance of recombination in ratites in light of the current data. We conclude by highlighting certain aspects of sex chromosome evolution in ratites that require further research and can potentially increase power for the inference of the unique history of sex chromosome evolution in this lineage of birds.
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Affiliation(s)
| | | | - Alexander Suh
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TU, UK;
- Department of Organismal Biology—Systematic Biology, Uppsala University, SE-752 36 Uppsala, Sweden
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Yazdi HP, Ellegren H. A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution. Genome Biol Evol 2018; 10:2049-2060. [PMID: 30099482 PMCID: PMC6105114 DOI: 10.1093/gbe/evy163] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/11/2022] Open
Abstract
Recombination arrest is a necessary step for the evolution of distinct sex chromosomes. Structural changes, such as inversions, may represent the mechanistic basis for recombination suppression and comparisons of the structural organization of chromosomes as given by chromosome-level assemblies offer the possibility to infer inversions across species at some detail. In birds, deduction of the process of sex chromosome evolution has been hampered by the lack of a validated chromosome-level assembly from a representative of one of the two basal clades of modern birds, Paleognathae. We therefore developed a high-density genetic linkage map of the ostrich Z chromosome and used this to correct an existing assembly, including correction of a large chimeric superscaffold and the order and orientation of other superscaffolds. We identified the pseudoautosomal region as a 52 Mb segment (≈60% of the Z chromosome) where recombination occurred in both sexes. By comparing the order and location of genes on the ostrich Z chromosome with that of six bird species from the other major clade of birds (Neognathae), and of reptilian outgroup species, 25 Z-linked inversions were inferred in the avian lineages. We defined Z chromosome organization in an early avian ancestor and identified inversions spanning the candidate sex-determining DMRT1 gene in this ancestor, which could potentially have triggered the onset of avian sex chromosome evolution. We conclude that avian sex chromosome evolution has been characterized by a complex process of probably both Z-linked and W-linked inversions (and/or other processes). This study illustrates the need for validated chromosome-level assemblies for inference of genome evolution.
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Affiliation(s)
- Homa Papoli Yazdi
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden
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Al-Shuhaib MBS, Al-Kafajy FR, Badi MA, AbdulAzeez S, Marimuthu K, Al-Juhaishi HAI, Borgio JF. Highly deleterious variations in COX1, CYTB, SCG5, FK2, PRL and PGF genes are the potential adaptation of the immigrated African ostrich population. Comput Biol Med 2018; 100:17-26. [PMID: 29960146 DOI: 10.1016/j.compbiomed.2018.06.019] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 06/13/2018] [Accepted: 06/22/2018] [Indexed: 11/19/2022]
Abstract
Because of variable inconvenient living conditions in some places around the world, it is difficult to collect reliable physiological data for ostriches. Therefore, this study aims to provide a comprehensive in silico insight for the nature of polymorphism of important genetic loci that are related to physiological and reproductive traits. Sixty-nine mature ostriches ranging over half of Iraq were screened. Six exonic genetic loci, including cytochrome c oxidase I (COX1), cytochrome b (CYTB), secretogranin V (SCG5), feather keratin 2-like (FK2), prolactin (PRL) and placenta growth factor (PGF) were genotyped by PCR-single stranded conformation polymorphism (SSCP). Thirty-six novel SNPs, including seventeen nonsynonymous (ns) SNPs, were observed. Several computational software programs were utilized to assess the extent of the nsSNPs on their corresponding proteins structure, function and stability. The results showed several deleterious functional and stability changes in almost all the proteins studied. The total severity of each missense mutation was evaluated and compared with other nsSNPs accumulatively. It is evident from the extensive cumulative in silico computation that both p.E34D and p.E60K in PGF have the highest deleterious effect. The cumulative predictions from the present study are an impressive guide for the genotypes of African ostriches, which bypassed the expensive protocols for wet laboratory screening, to identify the effects of variants. To the best of our knowledge, this is the first investigation of its kind on the analyses and prediction outcome of missense mutations in African ostrich populations. The highly deleterious nsSNPs in the placenta growth factor are possible adaptive mutations which might be associated with adaptation in extreme and new environments. The flow and protocol of the computational predictions can be extended for various wild animals to identify the molecular nature of adaptations.
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Affiliation(s)
- Mohammed Baqur S Al-Shuhaib
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Fadhil R Al-Kafajy
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Milad Ali Badi
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, 51013, Babil, Iraq.
| | - Sayed AbdulAzeez
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
| | - Kasi Marimuthu
- Department of Biotechnology, Faculty of Applied Sciences, AIMST University, Bedong, Kedah Darul Aman, Malaysia.
| | | | - J Francis Borgio
- Department of Genetic Research, Institute for Research and Medical Consultation (IRMC), Imam Abdulrahman Bin Faisal University, Dammam, Saudi Arabia.
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Ledger JM, Malecki I, Groth DM. Characterisation of tetra-nucleotide microsatellite loci in the ostrich (Struthio camelus). Br Poult Sci 2012; 53:460-4. [PMID: 23130580 DOI: 10.1080/00071668.2012.715280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
1. Eleven polymorphic tetra-nucleotide microsatellite loci were identified in the ostrich (Struthio camelus) using a selective enrichment protocol. 2. The average number of alleles observed was 6·6 with an average heterozygosity of 0·4. 3. The population was found to be in Hardy-Weinberg equilibrium and two of the loci had a greater than 95% probability of having null alleles. 4. These microsatellite loci will add to the existing pool of markers available for the ostrich and help to facilitate analysis of population structure and pedigree determination.
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Affiliation(s)
- J M Ledger
- School of Animal Biology, University of Western Australia, Hackett Drive, Crawley, Western Australia 6009.
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Kawka M, Horbańczuk JO, Jaszczak K, Pierzchała M, Cooper RG. A search for genetic markers associated with egg production in the ostrich (Struthio camelus). Mol Biol Rep 2012; 39:7881-5. [PMID: 22544574 PMCID: PMC3383961 DOI: 10.1007/s11033-012-1632-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2011] [Accepted: 04/16/2012] [Indexed: 11/26/2022]
Abstract
The aim of the current study was to search for genetic markers, microsatellite loci associated with laying performance in ostriches. The material consisted of two groups of ostrich hens characterized by high or low laying performance (over 75 and less than 25 eggs per season, respectively). The investigation covered 30 microsatellite loci characteristic for the ostrich (the CAU group) and led to identification of significant differences in allele and genotype frequencies between the two groups of hens considered. Out of a total of 30 microsatellite loci examined, 28 showed different alleles in relation to analyzed performance groups. In hens of high laying performance (HP group, n = 12), specific alleles occurred in 23 microsatellite loci (40 alleles of 243 identified), while in those of low egg production (LP group, n = 12), they occurred in 22 (51 alleles of 243 identified). The results indicate the usefulness of the microsatellite loci as the potential genetic markers associated with laying performance that can be applied for genetic improvement of ostrich flocks.
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Affiliation(s)
- M Kawka
- Institute of Genetics and Animal Breeding of the Polish Academy of Sciences, Jastrzębiec, Poland.
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Kawka M, Parada R, Jaszczak K, Horbańczuk JO. The use of microsatellite polymorphism in genetic mapping of the ostrich (Struthio camelus). Mol Biol Rep 2011; 39:3369-74. [PMID: 21717061 PMCID: PMC3271206 DOI: 10.1007/s11033-011-1107-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 06/17/2011] [Indexed: 11/25/2022]
Abstract
The aim of this study was to determine microsatellite polymorphism in ostriches and using it in creation the genetic map of the ostrich. The polymorphism analysis covered 30 microsatellite markers characteristic of ostrich, for the CAU (China Agricultural University) group. The material consisted of 150 ostriches (Struthio camelus). The 30 microsatellite loci was examined and a total of 343 alleles was identified. The number of alleles at a single locus ranged from 5 at locus CAU78 to 34 at locus CAU85. The values for the observed heterozygosity Ho ranged from 0.467 (locus CAU78) to 0.993 (locus CAU16), whereas for the expected heterozygosity He - from 0.510 (locus CAU78) to 0.953 (locus CAU85). Analyzing the individual loci, the highest PIC value, more than 0.7 was observed for: loci CAU85 (0.932), CAU64 (0.861) and CAU32, 75 (0.852), respectively. It should be noted, that the microsatellite markers used in our study were very polymorphic as evidenced by the large number of detected alleles and high rates of heterozygosity, PIC and PE as well. The analysed microsatellite markers may be used in genetic linkage mapping of ostrich, the construction of a comparative genetic map with other ratites, such as emu and rhea, and population genetics studies or phylogenetic studies of these birds.
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Affiliation(s)
- M Kawka
- Polish Academy of Sciences Institute of Genetics and Animal Breeding, Jastrzębiec 05-552, Wólka Kosowska, Poland.
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Allentoft ME, Oskam C, Houston J, Hale ML, Gilbert MTP, Rasmussen M, Spencer P, Jacomb C, Willerslev E, Holdaway RN, Bunce M. Profiling the dead: generating microsatellite data from fossil bones of extinct megafauna--protocols, problems, and prospects. PLoS One 2011; 6:e16670. [PMID: 21304955 PMCID: PMC3031614 DOI: 10.1371/journal.pone.0016670] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2010] [Accepted: 12/31/2010] [Indexed: 11/19/2022] Open
Abstract
We present the first set of microsatellite markers developed exclusively for an extinct taxon. Microsatellite data have been analysed in thousands of genetic studies on extant species but the technology can be problematic when applied to low copy number (LCN) DNA. It is therefore rarely used on substrates more than a few decades old. Now, with the primers and protocols presented here, microsatellite markers are available to study the extinct New Zealand moa (Aves: Dinornithiformes) and, as with single nucleotide polymorphism (SNP) technology, the markers represent a means by which the field of ancient DNA can (preservation allowing) move on from its reliance on mitochondrial DNA. Candidate markers were identified using high throughput sequencing technology (GS-FLX) on DNA extracted from fossil moa bone and eggshell. From the ‘shotgun’ reads, >60 primer pairs were designed and tested on DNA from bones of the South Island giant moa (Dinornis robustus). Six polymorphic loci were characterised and used to assess measures of genetic diversity. Because of low template numbers, typical of ancient DNA, allelic dropout was observed in 36–70% of the PCR reactions at each microsatellite marker. However, a comprehensive survey of allelic dropout, combined with supporting quantitative PCR data, allowed us to establish a set of criteria that maximised data fidelity. Finally, we demonstrated the viability of the primers and the protocols, by compiling a full Dinornis microsatellite dataset representing fossils of c. 600–5000 years of age. A multi-locus genotype was obtained from 74 individuals (84% success rate), and the data showed no signs of being compromised by allelic dropout. The methodology presented here provides a framework by which to generate and evaluate microsatellite data from samples of much greater antiquity than attempted before, and opens new opportunities for ancient DNA research.
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Affiliation(s)
- Morten E. Allentoft
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- * E-mail: (MEA); (MB)
| | - Charlotte Oskam
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
| | - Jayne Houston
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
| | - Marie L. Hale
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - M. Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Morten Rasmussen
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Peter Spencer
- Wildlife Identification Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
| | - Christopher Jacomb
- Southern Pacific Archaeological Research, Department of Anthropology, University of Otago, Dunedin, New Zealand
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Richard N. Holdaway
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
- Palaecol Research Ltd, Christchurch, New Zealand
| | - Michael Bunce
- Ancient DNA Laboratory, School of Biological Sciences and Biotechnology, Murdoch University, Perth, Western Australia, Australia
- * E-mail: (MEA); (MB)
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Breeder Welfare: The Past, Present and Future. Anim Welf 2011. [DOI: 10.1007/978-3-642-19297-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Miller JM, Hallager S, Monfort SL, Newby J, Bishop K, Tidmus SA, Black P, Houston B, Matthee CA, Fleischer RC. Phylogeographic analysis of nuclear and mtDNA supports subspecies designations in the ostrich (Struthio camelus). CONSERV GENET 2010. [DOI: 10.1007/s10592-010-0149-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Cloete SWP, Engelbrecht A, Olivier JJ, Bunter KL. Deriving a preliminary breeding objective for commercial ostriches: an overview. ACTA ACUST UNITED AC 2008. [DOI: 10.1071/ea08135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Ostrich farmers rely on skins and meat as their most important sources of revenue, with feathers being of secondary importance. This paper provides a summary of parameter estimates (heritabilities and genetic correlations) estimated from the resource flock held at the Oudtshoorn Research Farm. Traits considered were egg production, chick production, mature liveweight, offspring slaughter weight and skin traits. Feather weight of mature breeding birds was not included, as revenue received for this commodity is comparatively low, and mostly reliant on quality. All the traits considered were moderately to highly heritable, and reproduction traits in particular were highly variable. No substantial unfavourable genetic correlations were noted, and worthwhile gains in all traits appear to be achievable within a selection objective based on economic principles. Economic weights for key traits were obtained from a bio-economical input–output simulation model that was prepared for the industry. A simple preliminary selection index including chick production (as a hen reproductive trait) and slaughter weight (as a measure of growth) appears to be adequate for the present needs, given the limited availability of routinely recorded traits. A key performance trait that is currently missing from the economic assessment is chick survival, which is known to be low and highly variable among ostrich flocks. Further information will be added as it becomes available.
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