Characterization of 35 novel microsatellite DNA markers from the duck (Anas platyrhynchos) genome and cross-amplification in other birds

Abstract

In order to study duck microsatellites, we constructed a library enriched for (CA)n, (CAG)n, (GCC)n and (TTTC)n. A total of 35 pairs of primers from these microsatellites were developed and used to detect polymorphisms in 31 unrelated Peking ducks. Twenty-eight loci were polymorphic and seven loci were monomorphic. A total of 117 alleles were observed from these polymorphic microsatellite markers, which ranged from 2 to 14 with an average of 4.18 per locus. The frequencies of the 117 alleles ranged from 0.02 to 0.98. The highest heterozygosity (0.97) was observed at the CAUD019 microsatellite locus and the lowest heterozygosity (0.04) at the CAUD008 locus, and 11 loci had heterozygosities greater than 0.50 (46.43%). The polymorphism information content (PIC) of 28 loci ranged from 0.04 to 0.88 with an average of 0.42. All the above markers were used to screen the polymorphism in other bird species. Two markers produced specific monomorphic products with the chicken DNA. Fourteen markers generated specific fragments with the goose DNA: 5 were polymorphic and 9 were monomorphic. But no specific product was detected with the peacock DNA. Based on sequence comparisons of the flanking sequence and repeat, we conclude that 2 chicken loci and 14 goose loci were true homologous loci of the duck loci. The microsatellite markers identified and characterized in the present study will contribute to the genetic map, quantitative traits mapping, and phylogenetic analysis in the duck and goose. duck / microsatellite marker / enriched library / polymorphism / cross-species amplification

A Genetic and Cytogenetic Map for the Duck (Anas platyrhynchos)

“…Sequencing of clones and designing of primers: A library enriched for (CA) n , (CAG) n , (GCC) n , and (TTTC) n was constructed from a female Peking duck (Huang et al 2005). Plasmids, extracted from clones of the microsatellite-enriched library, were sequenced with the BigDye kit on PRISM 377 DNA sequencers (ABI, Columbia, MD).…”

“…To isolate the specific microsatellite markers for duck, a total of 1025 plasmids, extracted from the microsatelliteenriched library (Huang et al 2005), were sequenced according to the procedures described in materials and methods; 753 (73.46%) were found to contain (CA) n , (CAG) n , (GCC) n , (TTTC) n , (TC) n , (TCC) n , (TTCC) n , (TTTTC) n , (TTGCC) n , (TTCCTC) n , (AAC) n , (AAAC) n , (TA) n , or (TTTA) n microsatellites with five or more repeats, and 5 contained (TCTCTTTC) n , (TTTCCCTCTTTC) n , or (CTTCTTTC) n with six or more repeats. Of the 758 sequences, 539 (71.11%) contained .12 bp of uninterrupted core repeats.…”

“…Up to now, most available molecular data concerning ducks have come from evolutionary studies based on the analysis of mitochondrial DNA sequence (Cooper et al 1996;Liu et al 1996;Sraml et al 1996;Sorenson 1998, 1999;Donne-Gousse et al 2002). However, information about genetic markers in the duck is limited (Buchholz et al 1998;Maak et al 2000Maak et al , 2003Paulus and Tiedemann 2003;Stai and Hughes 2003;Huang et al 2005). In addition, comparative mapping between the duck and chicken genome gains importance as the Sequence data from this article have been deposited with the GenBank Data Library under accession nos.…”

“…Up to now, most available comparative data between ducks and chickens have come from the analysis of chromosome painting (Guttenbach et al 2003). Herein, the preliminary genetic map was developed in an inbred Peking duck resource population (line VI cross with line V) on the basis of linkage analysis of 103 novel genetic markers from the microsatelliteenriched library (Huang et al 2005), together with 137 reported microsatellite loci (Cathey et al 1996;Fields and Scribner 1997;Buchholz et al 1998;Maak et al 2000;Genet et al 2003;Stai and Hughes 2003;Huang et al 2005). In addition, the preliminary genetic map was integrated with the cytogenetic map based on fluorescence in situ hybridization (FISH) using 28 chicken heterologous BAC clones.…”

“…To construct saturated genetic maps for more bird species, the isolation of many polymorphic genetic markers, particularly microsatellite markers, is a prerequisite. Although many chicken markers were available, it was difficult to screen the microsatellite marker for the duck by cross-species amplification from this species because of the poor conservation of the microsatellite sequences between the species (Huang et al 2005).…”