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Article: Development and characterization of microsatellite markers in Rosy-faced and other lovebirds (Agapornis spp.) using next-generation sequencing

TitleDevelopment and characterization of microsatellite markers in Rosy-faced and other lovebirds (Agapornis spp.) using next-generation sequencing
Authors
KeywordsAgapornis roseicollis
High throughput sequencing
Kinship inference
Parentage analysis
Peach-faced lovebirds
Polymorphic microsatellite loci
Issue Date2020
PublisherSpringer Verlag Dordrecht. The Journal's web site is located at http://springerlink.metapress.com/openurl.asp?genre=journal&issn=0301-4851
Citation
Molecular Biology Reports, 2020, v. 47 n. 8, p. 6417-6427 How to Cite?
AbstractAgapornis 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.
Persistent Identifierhttp://hdl.handle.net/10722/286504
ISSN
2023 Impact Factor: 2.6
2023 SCImago Journal Rankings: 0.649
ISI Accession Number ID

 

DC FieldValueLanguage
dc.contributor.authorLam, DK-
dc.contributor.authorSin, SYW-
dc.date.accessioned2020-08-31T07:04:47Z-
dc.date.available2020-08-31T07:04:47Z-
dc.date.issued2020-
dc.identifier.citationMolecular Biology Reports, 2020, v. 47 n. 8, p. 6417-6427-
dc.identifier.issn0301-4851-
dc.identifier.urihttp://hdl.handle.net/10722/286504-
dc.description.abstractAgapornis 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.-
dc.languageeng-
dc.publisherSpringer Verlag Dordrecht. The Journal's web site is located at http://springerlink.metapress.com/openurl.asp?genre=journal&issn=0301-4851-
dc.relation.ispartofMolecular Biology Reports-
dc.subjectAgapornis roseicollis-
dc.subjectHigh throughput sequencing-
dc.subjectKinship inference-
dc.subjectParentage analysis-
dc.subjectPeach-faced lovebirds-
dc.subjectPolymorphic microsatellite loci-
dc.titleDevelopment and characterization of microsatellite markers in Rosy-faced and other lovebirds (Agapornis spp.) using next-generation sequencing-
dc.typeArticle-
dc.identifier.emailSin, SYW: sinyw@hku.hk-
dc.identifier.authoritySin, SYW=rp02377-
dc.description.naturelink_to_subscribed_fulltext-
dc.identifier.doi10.1007/s11033-020-05623-z-
dc.identifier.pmid32607954-
dc.identifier.scopuseid_2-s2.0-85087384540-
dc.identifier.hkuros313466-
dc.identifier.volume47-
dc.identifier.issue8-
dc.identifier.spage6417-
dc.identifier.epage6427-
dc.identifier.isiWOS:000545835700003-
dc.publisher.placeNetherlands-
dc.identifier.issnl0301-4851-

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