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Romanov M, Sazanov A, Smirnov A. First century of chicken gene study and mapping – a look back and forward. WORLD POULTRY SCI J 2019. [DOI: 10.1079/wps20032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- M.N. Romanov
- Department of Microbiology and Molecular Genetics, 2209 Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824–4320, USA
| | - A.A. Sazanov
- All-Russian Institute of Animal Genetics and Breeding, Russian Academy of Agricultural Science, Moskovskoye shosse 55A, St Petersburg – Pushkin 189620, Russia
- Biological Research Institute, St Petersburg State University, Oranienbaumskoye shosse 2, St Petersburg – Stary Petergof 198504, Russia
| | - A.F. Smirnov
- All-Russian Institute of Animal Genetics and Breeding, Russian Academy of Agricultural Science, Moskovskoye shosse 55A, St Petersburg – Pushkin 189620, Russia
- Biological Research Institute, St Petersburg State University, Oranienbaumskoye shosse 2, St Petersburg – Stary Petergof 198504, Russia
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Dawson DA, Ball AD, Spurgin LG, Martín-Gálvez D, Stewart IRK, Horsburgh GJ, Potter J, Molina-Morales M, Bicknell AWJ, Preston SAJ, Ekblom R, Slate J, Burke T. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 2013; 14:176. [PMID: 23497230 PMCID: PMC3738869 DOI: 10.1186/1471-2164-14-176] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 02/19/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. RESULTS We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. CONCLUSIONS When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.
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Affiliation(s)
- Deborah A Dawson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Alexander D Ball
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Lewis G Spurgin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - David Martín-Gálvez
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Estación Experimental de Zonas Áridas (CSIC), Almería, E-04120, Spain
| | - Ian R K Stewart
- Department of Biology, University of Delaware, Newark, DE, 19716, USA
| | - Gavin J Horsburgh
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jonathan Potter
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mercedes Molina-Morales
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Departamento de Zoología, Universidad de Granada, Granada, E-18071, Spain
| | - Anthony W J Bicknell
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Plymouth University, Marine Biology and Ecology Research Centre, Davy Building, Drake Circus, Plymouth, PL4 8AA, UK
| | - Stephanie A J Preston
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert Ekblom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Department of Ecology and Genetics, Uppsala University, Norbyv. 18D, Uppsala, SE-75236, Sweden
| | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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Knutson TP, Chaves LD, Hall MK, Reed KM. One hundred fifty-four genetic markers for the turkey (Meleagris gallopavo). Genome 2005; 47:1015-28. [PMID: 15644959 DOI: 10.1139/g04-076] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Identifying and selectively breeding for improved traits is one of the ultimate goals of genetic research in agriculturally important species. Genome characterization and analysis are important first steps in this process. Genetic linkage maps based on the linear order of polymorphic DNA markers are typically developed through statistical analysis of inheritance patterns in pedigreed families. To develop microsatellite markers for further improvement of the turkey genetic linkage map, small-insert genomic libraries were screened for tandem repeats. Oligonuclotide primers were designed to amplify 164 microsatellite-containing fragments from genomic DNA. Genetic polymorphisms at 154 markers were determined by genotyping the F(1) individuals of two resource populations. Markers determined as segregating in the University of Minnesota/Nicholas Turkey Breeding Farms (UMN/NTBF) reference population were used to genotype F(2) individuals and a two-point linkage analysis was performed.
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Affiliation(s)
- Todd P Knutson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, 295 ASVM, 1988 Fitch Ave., University of Minnesota, St. Paul, MN 55108, USA
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Smith EJ, Geng T, Long E, Pierson FW, Sponenberg DP, Larson C, Gogal R. Molecular analysis of the relatedness of five domesticated turkey strains. Biochem Genet 2005; 43:35-47. [PMID: 15859518 DOI: 10.1007/s10528-005-1065-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Our knowledge of the genetic relatedness among the eight existing domesticated turkey strains is limited. To begin to address this paucity, genetic relatedness among five turkey strains (Blue Slate, Bourbon Red, Narragansett, Royal Palm, and Spanish Black) was investigated using three molecular marker systems: randomly amplified polymorphic DNA (RAPD), microsatellite, and SNPs derived from a sequence tagged site and a cloned RAPD fragment. The RAPD analyses were based on five primers that revealed a total of 14 informative DNA fragments in all five populations. The microsatellite analyses involved two informative alleles from three primer-pairs. A total of nine SNPs were detected, one of which appeared to be strain specific. This SNP formed the basis of a PCR-RFLP genotyping procedure developed to distinguish one of the strains from the other four. Evidence from these analyses including the SNP-based RFLP-PCR suggests that Royal Palm is distinct from the other four strains, though more closely related to Narragansett. These data provide, for the first time, molecular evidence of the potential relationships among noncommercial domesticated turkey strains.
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Affiliation(s)
- Edward J Smith
- Comparative Genomics Lab, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia 24061-0306, USA.
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Burt DW, Morrice DR, Sewalem A, Smith J, Paton IR, Smith EJ, Bentley J, Hocking PM. Preliminary linkage map of the turkey (Meleagris gallopavo) based on microsatellite markers. Anim Genet 2004; 34:399-409. [PMID: 14687069 DOI: 10.1046/j.1365-2052.2003.01033.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The turkey is an agriculturally important species for which, until now, there is no published genetic linkage map based on microsatellite markers--still the markers most used in the chicken and other farm animals. In order to increase the number of markers on a turkey genetic linkage map we decided to map new microsatellite sequences obtained from a GT-enriched turkey genomic library. In different chicken populations more than 35-55% of microsatellites are polymorphic. In the turkey populations tested here, 43% of all turkey primers tested were found to be polymorphic, in both commercial and wild type turkeys. Twenty linkage groups (including the Z chromosome) containing 74 markers have been established, along with 37 other unassigned markers. This map will lay the foundations for further genetic mapping and the identification of genes and quantitative trait loci in this economically important species. Genome comparisons, based on genetic maps, with related species such as the chicken would then also be possible. All primer information, polymerase chain reaction (PCR) conditions, allele sizes and genetic linkage maps can be viewed at http://roslin.thearkdb.org/. The DNA is also available on request through the Roslin Institute.
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Affiliation(s)
- D W Burt
- Department of Genomics and Bioinformatics, Roslin Institute (Edinburgh), Roslin, Midlothian, UK.
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Kishore VK, Velasco P, Shintani DK, Rowe J, Rosato C, Adair N, Slabaugh MB, Knapp SJ. Conserved simple sequence repeats for the Limnanthaceae (Brassicales). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:450-457. [PMID: 14647896 DOI: 10.1007/s00122-003-1447-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2002] [Accepted: 08/20/2003] [Indexed: 05/24/2023]
Abstract
The Limnanthaceae (Order Brassicales) is a family of 18 taxa of Limnanthes (meadowfoam) native to California, Oregon, and British Columbia. Cultivated meadowfoam ( L. alba Benth.), a recently domesticated plant, has been the focus of research and development as an industrial oilseed for three decades. The goal of the present research was to develop several hundred simple sequence repeat (SSR) markers for genetic mapping, molecular breeding, and genomics research in wild and cultivated meadowfoam taxa. We developed 389 SSR markers for cultivated meadowfoam by isolating and sequencing 1,596 clones from L. alba genomic DNA libraries enriched for AG(n) or AC(n) repeats, identifying one or more unique SSRs in 696 clone sequences, and designing and testing primers for 624 unique SSRs. The SSR markers were screened for cross- taxa utility and polymorphisms among ten of 17 taxa in the Limnanthaceae; 373 of these markers were polymorphic and 106 amplified loci from every taxon. Cross-taxa amplification percentages ranged from 37.3% in L. douglasii ssp. rosea (145/389) to 85.6% in L. montana (333/389). The SSR markers amplified 4,160 unique bands from 14 genotypes sampled from ten taxa (10.7 unique bands per SSR marker), of which 972 were genotype-specific. Mean and maximum haplotype heterozygosities were 0.71 and 0.90, respectively, among six L. alba genotypes and 0.63 and 0.93, respectively, among 14 genotypes (ten taxa). The SSR markers supply a critical mass of high-throughput DNA markers for biological and agricultural research across the Limnanthaceae and open the way to the development of a genetic linkage map for meadowfoam ( x = 5).
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Affiliation(s)
- V K Kishore
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
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Tang B, Huang YH, Lin L, Hu XX, Feng JD, Yao P, Zhang L, Li N. Isolation and characterization of 70 novel microsatellite markers from ostrich (Struthiocamelus) genome. Genome 2003; 46:833-40. [PMID: 14608400 DOI: 10.1139/g03-059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microsatellite markers are widely used in linkage mapping, parentage testing, population genetic studies, and molecular evolution studies in many agricultural species, while only a limited number of ostrich (Struthio camelus) microsatellites have been isolated. Thus, we constructed a random small-insert genomic library and a microsatellite-enriched library containing CA repeats. Fourteen clones containing CA repeats were isolated from 3462 clones in the non-enriched library by radioactive screening and 248 positive clones were isolated from 300 sequenced clones from the enriched library by PCR screening. After the enrichment procedures, the proportion of clones containing CA repeats was raised to 78.8%, compared with 0.4% in the non-enriched libraries, indicating that the enrichment value approaches 200 fold, which decreased the time and cost of cloning. The number of complete simple CA repeats in these positive clones ranged from 5 to 29. The primers for 94 of these microsatellites were developed and used to detect polymorphisms, of which 61 loci exhibited length polymorphisms in 17 unrelated ostrich individuals. The new polymorphic microsatellite markers we have identified and characterized will contribute to the ostrich genetic map, parentage testing, and comparative genomics between avian species.Key words: ostrich, microsatellite markers, enriched library, polymorphism.
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Affiliation(s)
- Bo Tang
- The College of Animal Science and Technology, China Agricultural University, Beijing, China
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Abstract
A primary linkage map of the domestic turkey (Meleagris gallopavo) was developed by segregation analysis of genetic markers within a backcross family. This reference family includes 84 offspring from one F1sire mated to two dams. Genomic DNA was digested using one of five restriction enzymes, and restriction fragment length polymorphisms were detected on Southern blots using probes prepared from 135 random clones isolated from a whole-embryo cDNA library. DNA sequence was subsequently determined for 114 of these cDNA clones. Sequence comparisons were done using BLAST searches of the GenBank database, and redundant sequences were eliminated. High similarity was found between 23% of the turkey sequences and mRNA sequences reported for the chicken. The current map, based on expressed genes, includes 138 loci, encompassing 113 loci arranged into 22 linkage groups and an additional 25 loci that remain unlinked. The average distance between linked markers is 6 cM and the longest linkage group (17 loci) measures 131 cM. The total map distance contained within linkage groups is 651 cM. The present map provides an important framework for future genome mapping in the turkey.Key words: genetic map, Meleagris gallopavo, expressed sequence tag, RFLP.
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Affiliation(s)
- David E Harry
- Nicholas Turkey Breeding Farms, Sonoma, CA 95746, USA.
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Abstract
Microsatellite loci continue to be important tools in genetic analysis of populations and experimental families. Twelve new microsatellite sequences for the turkey were obtained from a small insert M13 library. Polymorphism at these new loci was examined in both domestic and wild birds. Seven of 12 loci were polymorphic in domestic turkeys, whereas 10 loci were polymorphic in our sample of wild birds.
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Affiliation(s)
- K M Reed
- Department of Veterinary PathoBiology, College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota 55108, USA.
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