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.

Racing pigeon identification using STR and chromo‐helicase DNA binding gene markers

“…Microsatellites have been studied in a number of avian species, including a high level of kinship and mixed paternity in a population of Australian magpies (Gymnorhina tibicen) [7], microsatellite variation in Red-Winged Blackbirds (Agelaius phoeniceus) [8], and mutation rates of microsatellite loci of barn swallows [9]. Characterization of 35 novel microsatellite DNA markers from the duck (Anasplatyrhynchos) genome and cross-amplification in other birds, such as chickens, geese, and peacocks, were reported by Huang et al [10]. Seven polymorphic STR markers have been isolated from the domestic pigeon (Columba livia, var.…”

Genome Mapping and Genomics in Domestic Animals

“…Molecular markers and tools have been generated for the Japanese quail (e.g., Pang et al 1999;Kayang et al 2002), duck and goose (Maak et al 2003;Huang et al 2005Huang et al , 2006b, pheasant , peafowl (Hanotte et al 1991;Hale et al 2004), pigeon (Traxler et al 2000), ostrich (Tang et al 2003), emu (Taylor et al 1999), budgerigar (Kamara et al 2007, and other avian species. These tools should facilitate linkage map construction, which has lately become reality for the duck (Huang et al 2006b).…”

Genomic research and applications in the duck (Anas platyrhynchos)

“…High-density genetic linkage maps are now available for many livestock species, such as pigs, cattle, sheep, goats, and chicken (Archibald et al, 1995;Groenen et al, 2000;Ihara et al, 2004;Maddox et al, 2001;Vaiman et al, 1996). Although many chicken genetic markers are available, it is difficult to use these in the duck or other waterfowl because of poor sequence conservation between species (Huang et al, 2005). To construct saturated genetic maps the isolation of many polymorphic genetic markers, particularly microsatellite markers and single nucleotide polymorphisms, is a prerequisite.…”

“…To construct saturated genetic maps the isolation of many polymorphic genetic markers, particularly microsatellite markers and single nucleotide polymorphisms, is a prerequisite. Following that, seven papers were published on the isolation of microsatellite loci in waterfowl (Buchholz et al, 1998;Huang et al, 2005;2006;Maak et al, 2000;Maak et al, 2003;Paulus and Tiedemann, 2003;Stai and Hughes, 2003). Therefore waterfowl-specific genomic libraries need to be constructed.…”

“…The first attempt to make cross-species comparative genetic maps was to map duck genetic markers on the chicken genetic map (Huang et al, 2005). Thirty-five duckspecific primers were used to screen for homologous loci in the chicken.…”