Development and characterization of microsatellite markers in Rosy-faced and other lovebirds (Agapornis spp.) using next-generation sequencing
Agapornis are a group of small African parrots that are heavily traded around the world. They are invasive species in many places, but some of them are listed as Vulnerable or Near Threatened. However, the genetic tools for assessing inter-individual relationships, population structure, and genetic...
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| Veröffentlicht in: | Molecular biology reports 2020-08, Vol.47 (8), p.6417-6427 |
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| description | Agapornis
are a group of small African parrots that are heavily traded around the world. They are invasive species in many places, but some of them are listed as Vulnerable or Near Threatened. However, the genetic tools for assessing inter-individual relationships, population structure, and genetic diversity of these birds are very limited. Therefore, we developed polymorphic microsatellite markers in
A. roseicollis
and tested the transferability on 5 lovebird species including
A. personatus
,
A. nigrigenis
,
A. fischeri
,
A. pullarius
, and
A. canus
, and two closely related outgroups (i.e.
Bolbopsittacus lunulatus
and
Loriculus galgulus
). We first performed whole-genome re-sequencing on five individuals of
A. roseicollis
to identify potential polymorphic loci. Out of 37 loci tested in 11
A. roseicollis
, 27 loci were demonstrated to be polymorphic, with the number of the alleles ranging from 2 to 7 (mean = 3.963). The observed heterozygosity ranged from 0 to 0.875 (mean = 0.481) and expected heterozygosity ranged from 0.233 to 0.842 (mean = 0.642). Five loci (
Agro-A13
,
p
|
| doi_str_mv | 10.1007/s11033-020-05623-z |
| format | Article |
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are a group of small African parrots that are heavily traded around the world. They are invasive species in many places, but some of them are listed as Vulnerable or Near Threatened. However, the genetic tools for assessing inter-individual relationships, population structure, and genetic diversity of these birds are very limited. Therefore, we developed polymorphic microsatellite markers in
A. roseicollis
and tested the transferability on 5 lovebird species including
A. personatus
,
A. nigrigenis
,
A. fischeri
,
A. pullarius
, and
A. canus
, and two closely related outgroups (i.e.
Bolbopsittacus lunulatus
and
Loriculus galgulus
). We first performed whole-genome re-sequencing on five individuals of
A. roseicollis
to identify potential polymorphic loci. Out of 37 loci tested in 11
A. roseicollis
, 27 loci were demonstrated to be polymorphic, with the number of the alleles ranging from 2 to 7 (mean = 3.963). The observed heterozygosity ranged from 0 to 0.875 (mean = 0.481) and expected heterozygosity ranged from 0.233 to 0.842 (mean = 0.642). Five loci (
Agro-A13
,
p
< 0.01;
Agro-A15
,
p <
0.05;
Agro-A43
,
p <
0.05,
Agro-A65
,
p
< 0.05;
Agro-A67
,
p
< 0.05) were detected to deviate from Hardy-Weinberg equilibrium, with the presence of null alleles suggested in locus
Agro-A13
and
Agro-A77
. The exclusion powers for PE1 and PE2 are 0.997 and 0.999, respectively. The 27 novel polymorphic markers developed here will be useful for parentage and kinship assignment and population genetics study in
Agapornis
, and provide a tool for scientific research, captive breeding industry, and invasion and conservation management of these species.</description><identifier>ISSN: 0301-4851</identifier><identifier>EISSN: 1573-4978</identifier><identifier>DOI: 10.1007/s11033-020-05623-z</identifier><identifier>PMID: 32607954</identifier><language>eng</language><publisher>Dordrecht: Springer Netherlands</publisher><subject>Agapornis ; Agapornis - genetics ; Alleles ; Animal Anatomy ; Animal Biochemistry ; Animals ; Binding sites ; Biomedical and Life Sciences ; Breeding ; Captive breeding ; Conservation ; Endangered Species ; Genetic diversity ; Genetic markers ; Genomes ; Heterozygosity ; Heterozygote ; High-Throughput Nucleotide Sequencing ; Histology ; Internet resources ; Introduced species ; Invasive species ; Life Sciences ; Microsatellite Repeats ; Microsatellites ; Molecular biology ; Morphology ; Museums ; Next-generation sequencing ; Polymorphism, Genetic ; Population genetics ; Population structure ; Population studies ; Short Communication ; Whole Genome Sequencing</subject><ispartof>Molecular biology reports, 2020-08, Vol.47 (8), p.6417-6427</ispartof><rights>Springer Nature B.V. 2020</rights><rights>Springer Nature B.V. 2020.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c375t-114b5de8b29f405c7a4fac22cdd2871a4b1a2399f727fddd687d994cbe20f1953</citedby><cites>FETCH-LOGICAL-c375t-114b5de8b29f405c7a4fac22cdd2871a4b1a2399f727fddd687d994cbe20f1953</cites><orcidid>0000-0002-5570-5011 ; 0000-0003-2484-2897</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s11033-020-05623-z$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s11033-020-05623-z$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27923,27924,41487,42556,51318</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/32607954$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Lam, Derek Kong</creatorcontrib><creatorcontrib>Sin, Simon Yung Wa</creatorcontrib><title>Development and characterization of microsatellite markers in Rosy-faced and other lovebirds (Agapornis spp.) using next-generation sequencing</title><title>Molecular biology reports</title><addtitle>Mol Biol Rep</addtitle><addtitle>Mol Biol Rep</addtitle><description>Agapornis
are a group of small African parrots that are heavily traded around the world. They are invasive species in many places, but some of them are listed as Vulnerable or Near Threatened. However, the genetic tools for assessing inter-individual relationships, population structure, and genetic diversity of these birds are very limited. Therefore, we developed polymorphic microsatellite markers in
A. roseicollis
and tested the transferability on 5 lovebird species including
A. personatus
,
A. nigrigenis
,
A. fischeri
,
A. pullarius
, and
A. canus
, and two closely related outgroups (i.e.
Bolbopsittacus lunulatus
and
Loriculus galgulus
). We first performed whole-genome re-sequencing on five individuals of
A. roseicollis
to identify potential polymorphic loci. Out of 37 loci tested in 11
A. roseicollis
, 27 loci were demonstrated to be polymorphic, with the number of the alleles ranging from 2 to 7 (mean = 3.963). The observed heterozygosity ranged from 0 to 0.875 (mean = 0.481) and expected heterozygosity ranged from 0.233 to 0.842 (mean = 0.642). Five loci (
Agro-A13
,
p
< 0.01;
Agro-A15
,
p <
0.05;
Agro-A43
,
p <
0.05,
Agro-A65
,
p
< 0.05;
Agro-A67
,
p
< 0.05) were detected to deviate from Hardy-Weinberg equilibrium, with the presence of null alleles suggested in locus
Agro-A13
and
Agro-A77
. The exclusion powers for PE1 and PE2 are 0.997 and 0.999, respectively. The 27 novel polymorphic markers developed here will be useful for parentage and kinship assignment and population genetics study in
Agapornis
, and provide a tool for scientific research, captive breeding industry, and invasion and conservation management of these species.</description><subject>Agapornis</subject><subject>Agapornis - genetics</subject><subject>Alleles</subject><subject>Animal Anatomy</subject><subject>Animal Biochemistry</subject><subject>Animals</subject><subject>Binding sites</subject><subject>Biomedical and Life Sciences</subject><subject>Breeding</subject><subject>Captive breeding</subject><subject>Conservation</subject><subject>Endangered Species</subject><subject>Genetic diversity</subject><subject>Genetic markers</subject><subject>Genomes</subject><subject>Heterozygosity</subject><subject>Heterozygote</subject><subject>High-Throughput Nucleotide Sequencing</subject><subject>Histology</subject><subject>Internet resources</subject><subject>Introduced species</subject><subject>Invasive species</subject><subject>Life Sciences</subject><subject>Microsatellite Repeats</subject><subject>Microsatellites</subject><subject>Molecular biology</subject><subject>Morphology</subject><subject>Museums</subject><subject>Next-generation sequencing</subject><subject>Polymorphism, Genetic</subject><subject>Population genetics</subject><subject>Population structure</subject><subject>Population studies</subject><subject>Short Communication</subject><subject>Whole Genome Sequencing</subject><issn>0301-4851</issn><issn>1573-4978</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNp9kc1uFDEQhC0EIkvgBTggS1zCwcG_6_UxCr9SJCQEZ8tj92wcZuzBnonIPgTPjJMJIHHg5EN_VdXuQug5o6eMUv26MkaFIJRTQtWWC3J4gDZMaUGk0buHaEMFZUTuFDtCT2q9opRKptVjdCT4lmqj5Ab9fAPXMORphDRjlwL2l644P0OJBzfHnHDu8Rh9ydXNMAxxBjy68g1KxTHhz7nekN55CHfiPF9CwUO-hi6WUPHJ2d5NuaRYcZ2m01d4qTHtcYIfM9lDgrJGVPi-QPJt9BQ96t1Q4dn9e4y-vnv75fwDufj0_uP52QXxQquZMCY7FWDXcdNLqrx2si3BuQ-B7zRzsmOOC2N6zXUfQtjudDBG-g447ZlR4hidrL5TyS27znaM1bf_uQR5qZZLZiRXim4b-vIf9CovJbXtLFdaaym5EY3iK3V7qVqgt1OJ7VA3llF725Zd27KtLXvXlj000Yt766UbIfyR_K6nAWIFahulPZS_2f-x_QUFRKMa</recordid><startdate>20200801</startdate><enddate>20200801</enddate><creator>Lam, Derek Kong</creator><creator>Sin, Simon Yung Wa</creator><general>Springer Netherlands</general><general>Springer Nature B.V</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7TK</scope><scope>7TM</scope><scope>7X7</scope><scope>7XB</scope><scope>88A</scope><scope>88E</scope><scope>88I</scope><scope>8AO</scope><scope>8FD</scope><scope>8FE</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABUWG</scope><scope>AFKRA</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BHPHI</scope><scope>CCPQU</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>LK8</scope><scope>M0S</scope><scope>M1P</scope><scope>M2P</scope><scope>M7P</scope><scope>P64</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>Q9U</scope><scope>RC3</scope><scope>7X8</scope><orcidid>https://orcid.org/0000-0002-5570-5011</orcidid><orcidid>https://orcid.org/0000-0003-2484-2897</orcidid></search><sort><creationdate>20200801</creationdate><title>Development and characterization of microsatellite markers in Rosy-faced and other lovebirds (Agapornis spp.) using next-generation sequencing</title><author>Lam, Derek Kong ; Sin, Simon Yung Wa</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c375t-114b5de8b29f405c7a4fac22cdd2871a4b1a2399f727fddd687d994cbe20f1953</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Agapornis</topic><topic>Agapornis - genetics</topic><topic>Alleles</topic><topic>Animal Anatomy</topic><topic>Animal Biochemistry</topic><topic>Animals</topic><topic>Binding sites</topic><topic>Biomedical and Life Sciences</topic><topic>Breeding</topic><topic>Captive breeding</topic><topic>Conservation</topic><topic>Endangered Species</topic><topic>Genetic diversity</topic><topic>Genetic markers</topic><topic>Genomes</topic><topic>Heterozygosity</topic><topic>Heterozygote</topic><topic>High-Throughput Nucleotide Sequencing</topic><topic>Histology</topic><topic>Internet resources</topic><topic>Introduced species</topic><topic>Invasive species</topic><topic>Life Sciences</topic><topic>Microsatellite Repeats</topic><topic>Microsatellites</topic><topic>Molecular biology</topic><topic>Morphology</topic><topic>Museums</topic><topic>Next-generation sequencing</topic><topic>Polymorphism, Genetic</topic><topic>Population genetics</topic><topic>Population structure</topic><topic>Population studies</topic><topic>Short Communication</topic><topic>Whole Genome Sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Lam, Derek Kong</creatorcontrib><creatorcontrib>Sin, Simon Yung Wa</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>Biology Database (Alumni Edition)</collection><collection>Medical Database (Alumni Edition)</collection><collection>Science Database (Alumni Edition)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest Central UK/Ireland</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Medical Database</collection><collection>Science Database</collection><collection>Biological Science Database</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>ProQuest Central Basic</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><jtitle>Molecular biology reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Lam, Derek Kong</au><au>Sin, Simon Yung Wa</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Development and characterization of microsatellite markers in Rosy-faced and other lovebirds (Agapornis spp.) using next-generation sequencing</atitle><jtitle>Molecular biology reports</jtitle><stitle>Mol Biol Rep</stitle><addtitle>Mol Biol Rep</addtitle><date>2020-08-01</date><risdate>2020</risdate><volume>47</volume><issue>8</issue><spage>6417</spage><epage>6427</epage><pages>6417-6427</pages><issn>0301-4851</issn><eissn>1573-4978</eissn><abstract>Agapornis
are a group of small African parrots that are heavily traded around the world. They are invasive species in many places, but some of them are listed as Vulnerable or Near Threatened. However, the genetic tools for assessing inter-individual relationships, population structure, and genetic diversity of these birds are very limited. Therefore, we developed polymorphic microsatellite markers in
A. roseicollis
and tested the transferability on 5 lovebird species including
A. personatus
,
A. nigrigenis
,
A. fischeri
,
A. pullarius
, and
A. canus
, and two closely related outgroups (i.e.
Bolbopsittacus lunulatus
and
Loriculus galgulus
). We first performed whole-genome re-sequencing on five individuals of
A. roseicollis
to identify potential polymorphic loci. Out of 37 loci tested in 11
A. roseicollis
, 27 loci were demonstrated to be polymorphic, with the number of the alleles ranging from 2 to 7 (mean = 3.963). The observed heterozygosity ranged from 0 to 0.875 (mean = 0.481) and expected heterozygosity ranged from 0.233 to 0.842 (mean = 0.642). Five loci (
Agro-A13
,
p
< 0.01;
Agro-A15
,
p <
0.05;
Agro-A43
,
p <
0.05,
Agro-A65
,
p
< 0.05;
Agro-A67
,
p
< 0.05) were detected to deviate from Hardy-Weinberg equilibrium, with the presence of null alleles suggested in locus
Agro-A13
and
Agro-A77
. The exclusion powers for PE1 and PE2 are 0.997 and 0.999, respectively. The 27 novel polymorphic markers developed here will be useful for parentage and kinship assignment and population genetics study in
Agapornis
, and provide a tool for scientific research, captive breeding industry, and invasion and conservation management of these species.</abstract><cop>Dordrecht</cop><pub>Springer Netherlands</pub><pmid>32607954</pmid><doi>10.1007/s11033-020-05623-z</doi><tpages>11</tpages><orcidid>https://orcid.org/0000-0002-5570-5011</orcidid><orcidid>https://orcid.org/0000-0003-2484-2897</orcidid></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0301-4851 |
| ispartof | Molecular biology reports, 2020-08, Vol.47 (8), p.6417-6427 |
| issn | 0301-4851 1573-4978 |
| language | eng |
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| source | MEDLINE; SpringerLink Journals - AutoHoldings |
| subjects | Agapornis Agapornis - genetics Alleles Animal Anatomy Animal Biochemistry Animals Binding sites Biomedical and Life Sciences Breeding Captive breeding Conservation Endangered Species Genetic diversity Genetic markers Genomes Heterozygosity Heterozygote High-Throughput Nucleotide Sequencing Histology Internet resources Introduced species Invasive species Life Sciences Microsatellite Repeats Microsatellites Molecular biology Morphology Museums Next-generation sequencing Polymorphism, Genetic Population genetics Population structure Population studies Short Communication Whole Genome Sequencing |
| title | Development and characterization of microsatellite markers in Rosy-faced and other lovebirds (Agapornis spp.) using next-generation sequencing |
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