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

• Published in: Molecular biology reports Vol. 47; no. 8; pp. 6417 - 6427
• Main Authors: Lam, Derek Kong, Sin, Simon Yung Wa
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer Netherlands 01-08-2020; Springer Nature B.V
• 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; Polymorphic microsatellite loci; Peach-faced lovebirds; High throughput sequencing; Kinship inference; Parentage analysis; Agapornis roseicollis
• ISSN: 0301-4851; 1573-4978
• DOI: 10.1007/s11033-020-05623-z

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.