Isolation and characterization of ten novel microsatellite loci in the red-winged tinamou (Rhynchotus rufescens, Tinamiformes, Aves) and crossamplification in other tinamous Dimas O. Santos, Lucas R. Moreira, Humberto Tonhati & Renato Caparroz
Molecular Biology Reports An International Journal on Molecular and Cellular Biology ISSN 0301-4851 Mol Biol Rep DOI 10.1007/s11033-011-1277-1
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Author's personal copy Mol Biol Rep DOI 10.1007/s11033-011-1277-1
Isolation and characterization of ten novel microsatellite loci in the red-winged tinamou (Rhynchotus rufescens, Tinamiformes, Aves) and cross-amplification in other tinamous Dimas O. Santos • Lucas R. Moreira • Humberto Tonhati • Renato Caparroz
Received: 16 August 2011 / Accepted: 15 September 2011 Ó Springer Science+Business Media B.V. 2011
Abstract We describe the isolation and characterization of ten microsatellite loci from the red-winged tinamou (Rhynchotus rufescens) and also evaluated the crossamplification of these loci and other ten loci previously developed for the great tinamou (Tinamus major) in other tinamous. Genetic variability was assessed using 24 individuals. Six loci were polymorphic with moderate to high number of alleles per locus (2–12 alleles) and showed expected heterozygosity (HE) ranging from 0.267 to 0.860. All loci conformed to the Hardy–Weinberg expectation and linkage disequilibrium was not significant for any pair of loci. This battery of polymorphic loci showed high paternity exclusion probability (0.986) and low genetic identity probability (4.95 9 10-5), proving to be helpful for parentage tests and population analyses in the red-winged tinamou. The cross-amplification was moderate where of the 160 locus/taxon combinations, 46 (28.75%) successfully amplified. Keywords Microsatellite Neotropical Rhyncothus rufescens Tinamiformes Tinamous
D. O. Santos H. Tonhati Faculdade de Cieˆncias Agra´rias e Veterina´rias de Jaboticabal, UNESP, Sa˜o Paulo, Brazil L. R. Moreira R. Caparroz Laborato´rio de Gene´tica e Biodiversidade, Instituto de Cieˆncias Biolo´gicas, Universidade Federal de Goia´s, Goiaˆnia, Brazil R. Caparroz (&) ´ rea Faculdade UnB Planaltina, Universidade de Brası´lia, A Universita´ria 1, Vila Nossa Senhora de Fa´tima, Planaltina, Distrito Federal CEP 73340-710, Brazil e-mail:
[email protected]
Introduction The order Tinamiformes comprises 47 species grouped in 9 genera, distributed in the Neotropical region from Northwest Mexico to southern South America [1]. These birds are terrestrial with limited flight capabilities and occur in a wide range of habitats. Tinamiformes is the only order of birds where exclusive male parental care is found in all known species, while mating systems are varied [2]. Around 6% of tinamous are considered near threatened and 11% vulnerable by the World Conservation Union [3]. However, little is known about their natural history and few long-term studies have been conducted on these species (for review see [1]). The red-winged tinamou (Rhynchotus rufescens) is a medium-sized (38–42 cm) ground-living species and has an extremely large range from central and eastern South America [1]. The population size of this species has not been quantified, but the population trend appears to be decreasing [3], indicating that population studies are required to evaluate the conservation status of this species. Furthermore, due to its broad geographic dispersion, omnivorous feeding habit, and the taste of its meat, this species has become attractive for economic purposes [4]. However, the reproductive performance of this species in captivity is still a problem that needs to be solved. Thus, several biological aspects related to breeding behavior and population genetic structured need to be clarified in tinamous and microsatellite markers could be really helpful for this purpose. However, at the present time, only eighteen microsatellite loci have been developed in tinamous [5]. Here, we described ten novel microsatellite in the redwinged tinamou and tested these markers on the other eight species of tinamous. We also tested cross-amplification of previously described tinamou microsatellite primers (Tinamus major [5]) in all tinamou species studied.
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Materials and methods The enrichment of a microsatellite library was undertaken using the methodology described by Billotte et al. [6]. High quality genomic DNA was fragmented using a restriction enzyme Rsa I. The fragmented DNAs were ligated to specific adapters (Rsa21 50 CTCTTGCTTACGCGTGGACTA30 and Rsa25 50 TAGTCCACGCGTAAGCAAGAGCACA30 ). The polymerase chain reaction (PCR) products were size-selected to preferentially obtain small fragments (300–1,200 bp), which were hybridized to two streptavidin-biotinylated oligo simple sequence repeats: (CT) and (GT). The enriched DNAs were ligated into pGEM-T easy vector (Promega) and used to transform XL1-Blue MRF super competent cells (Stratagene). The recombinant clones were directly sequenced and flanking regions were recovered to design primers for the amplification of each microsatellite sequence using websat [7] and Primer3 [8] programs. In total, 96 positive clones were obtained through the enrichment method, but only 59 sequences were confirmed to carry microsatellite sequences. Among these, only 34 distinct microsatellite loci were identified, and 10 were selected and used to evaluate genetic variation in the redwinged tinamou. We selected the loci which showed perfect or uninterrupted motifs and more than five repeat units long. Genomic DNAs from 24 adult red-winged tinamou samples
were used for PCR amplification of ten microsatellite loci shown in Table 1. PCR reactions were carried out on a Perkin Elmer Gene Amp PCR System 9,700 in 10 ll volumes containing 50 ng of genomic DNA, 20 mM Tris–HCl (pH 8.4), 50 mM KCl, 1.5 mM MgCl2, 0.2 mM of each dNTP, 0.8 lM of each primer and 0.5 unit of Taq DNA polymerase (Phoneutria). Details of the thermal profile for all loci consisted of an initial denaturation at 96°C for 7 min, followed by 35 cycles of 96°C for 1 min, 53–61°C for 45 s depending on the locus and 72°C for 45 s and a final extension at 72°C for 20 min. The PCR products were subsequently separated on 6% denaturing polyacrylamide gel and visualized by silverstaining, as described by Creste et al.[9]. The alleles were sized based on the 10-bp DNA ladder standard (Invitrogen). The Hardy–Weinberg expectation (HWE) and gametic disequilibrium were tested using Genepop 4.1 [10]. Sequential Bonferroni corrections were applied using a nominal P value of 0.05 [11]. We also estimated the genetic identity (I) [12] and paternity exclusion probabilities (Q) [13] for each polymorphic locus and overall loci using Identity 1.0 [14]. Microchecker version 2.2.3 [15] was used to identify possible null alleles, large allele dropout, scoring errors, and typographic errors. To evaluate cross-species amplification, we tested the 10 primer pairs described here and ten previously described for the great tinamou (T. major [5]) in eight tinamou
Table 1 Characterization of the ten microsatellite loci developed for Rhynchotus rufencens Locus ID (GenBank)
Anneal (°C)
Repeat motif
Primer sequences (50 –30 )
A
Size–range (bp)
HE
HO
P-EHW
Q
I
RruGT12A (JN391512)
58
(GT)7
F: GGTTCTTCTTGAGGTTCCTG
5
190–200
0.791
0.579
0.0152
0.582
0.077
5
196–204
0.605
0.700
0.8496
0.350
0.214
12
222–260
0.860
0.696
0.0279
0.730
0.032
2
282–288
0.496
0.273
0.0340
0.186
0.377
11
270–292
0.857
0.818
0.2528
0.717
0.036
2
196–204
0.267
0.318
1.0000
0.116
0.572
1
192
1
204
1
258
1
258
R: TTTTCCTTCCCCCAGTT RruGT12B (JN391513)
50
(GT)8
F: ACTGCACTTTTGCAGTTAGC R: GCTGCAGATACAAGGCTACA
RruGT10D (JN391516)
60
(GT)24
F: GTGACACATTCCAGATTTGC R: CATGCTCAGGATGAAGACAC
RruGT06G (JN391519)
54
(AT)5(GT)7(AT)4
F: CCTGTGCCCCTCTGCGGGTC R: GGCAGCTTTCAGGAGCTTAG
RruGT04F (JN391517)
54
(AT)3(AC)8(AT)3
F: CCTCCTCTCCTCAACACTTC R: CCAATGGAGTCTTTTCCTTC
RruGT12F (JN391518)
60
(GT)25
F: GCACGTGGATACACCACAGG R: ACAGCCCCTGCAATGTCCGC
RruGT08A (JN391511)
54
(GT)16
F: GGGTAGCTGTGACCCTTTGC R: GATGCAAAGATGATGGTGAG
RruGT09C (JN391514)
58
(GT)7
F: AAGATGACAGTGGGACTGAA R: AGAGGGAGCTGTATCCTTTG
RruGT09D (JN391515)
56
(GT)7
F: CCACCTCCCTTCATCTCAAT R: TGCCTCATTCCACCTCTTCT
RruGT11G (JN391520)
54
(GT)8
F: RGTGTGCCTGTGATTTTCTGC R: CACACACGCATGTATGTAGC
F forward primer; R reverse primer; A number of alleles; HE expected heterozygosities; HO observed heterozygosities; P-HWE P-values for the Hardy–Wienberg Expectation test; Q paternity exclusion probability; I genetic identity
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–
Rhynchotus rufescens Solitary Tinamou
–
–
–
–
–
–
–
–
–
–
–
58
–
–
58
12A
50
50
50
50
50
50
50
50
50
12B
–
–
–
–
–
–
–
–
58
09C
The annealing temperature in Celsius degree was shown
Crypturellus noctivagus
Yellow-legged Tinamou
Crypturellus undulatus
Undulated Tinamou
Crypturellus variegatus
Variegated Tinamou
Crypturellus tataupa
Tataupa Tinamou
Crypturellus parvirostris
Small-billed Tinamou
Crypturellus obsoletus
Brown Tinamou
Tinamus tao
Gray Tinamou
–
54
Red-winged tinamou
Tinamus solitarius
08A
Species
RruGT
56
56
56
56
56
56
56
56
56
09D
–
–
–
–
–
–
–
–
60
10D
–
–
–
–
52
–
–
54
04F
–
–
–
–
–
–
–
–
60
12F
–
–
–
–
–
–
–
–
54
06G
–
–
–
–
56
56
–
–
54
11G
–
–
–
53
55
–
53
51
–
A01
51
–
–
–
–
–
–
51
–
A11
53
–
–
53
53
53
53
53
–
A104
–
–
–
53
–
–
53
51
–
A106
Loci developed for T. major [5]
–
–
–
–
–
–
–
53
–
A108
51
–
51
–
–
–
51
51
53
E101
53
–
53
53
53
53
53
53
–
E105
–
–
–
–
–
–
51
53
53
E111
Table 2 Cross-species amplification for the ten microsatellite loci developed for Rhynchotus rufescens (RruGT) and ten for Tinamous major in eight tinamous species
51
–
–
51
51
–
51
53
–
E118
51
–
–
51
53
–
51
53
–
E119
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Mol Biol Rep
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species of two genera: Tinamus solitarius, T. tao, Crypturellus notivagus, C. tataupa, C. parvirostris, C. variegatus, C. obsoletus and C. undulatus. Two individuals of each species were analyzed. Three annealing temperatures (50, 53, and 56°C) were used with the same PCR conditions described above. Amplification products were visualized in 1.5% agarose gels, and fragments were sized by comparison with a 1 kb Plus DNA ladder (Invitrogen). Primer pairs that amplified fragments with similar sizes than those observed in source species were considered as successful cross-species amplification. For most of positive amplifications, one individual was sequenced and the presence of microsatellites was confirmed.
Results and discussion In total, 41 alleles were obtained from all loci. The number of alleles per locus ranged from 2 to 12 (Table 1). No evidence of significant linkage disequilibrium was found among the tests for each pair of loci. Of these 10 microsatellite loci, four displayed no polymorphism and only two polymorphic loci had two alleles (RruGT06G and RruGT12F). Among polymorphic loci, the observed heterozygosity (HO) ranged from 0.273 to 0.818, whereas the expected heterozygosity (HE) ranged from 0.267 to 0.860 (Table 1). All loci conformed to HWE after sequential Bonferroni correction (P [ 0.006). However, Microchecker detected two loci (RruGT12A and RruGT10D) which scoring errors or null alleles may be present. On considering all the loci, the potential of paternity/maternity exclusion was greater than 98% and probability of identity was lightly low (4.95 9 10-5), indicating the suitability of these loci for parentage testing and genetic population studied in the red-winged tinamou. Overall, a moderate level of cross-species amplication was observed across the eight tinamou species tested (Table 2). Of the 160 locus/taxon combinations, 46 (28.75%) successfully amplified. The best cross-amplification results were observed in the T. solitarius and T. tao using T. major primers pairs (Table 2). These results are not surprising considering that those species belong to the same genus. Before developing R. rufencens primers, we tested ten primer pairs CAU1, CAU7, CAU14, CAU17, CAU40, CAU83, CAU85 [16], OSM4, OSM5 and OSM6 [17] previously developed from ostrich (Struthio camelus), one of the sister species of the red-winged tinamou. Although some primers amplified R. rufencens DNA, multiple undefined and unwanted products were obtained and the optimization of PCRs was not possible. Some ostrich primers have been previously tested to amplify in great tinamou and optimization of PCRs was also not possible [5].
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Acknowledgments The authors are very grateful to researchers and technicians of the Centro de Biologia Molecular e Engenharia Gene´tica (CBMEG -Unicamp) for assistance to build a tinamou library, Gislaine Aparecida Fernandes of the Laborato´rio de Gene´tica e Biodiversidade da UFG for technical assistance in bird genotypings, and two anonymous reviewers for helpful suggestions and comments on a previous version of this paper. We thank Dr. Mariana Pires de Campos Telles for technical suggestions.
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