Ten polymorphic microsatellite loci in Tibetan chicken, Gallus gallus domesticus
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Through an improved enrichment protocol, a genomic library for (AC)12 repeats was constructed and 34 microsatellite loci were isolated and characterized in an endangered animal, Tibetan chicken, Gallus gallus domesticus. In the 34 loci, ten loci showed a distinct allelic variation ranging from 4 to 14 alleles in 54 individuals tested. Polymorphism information content (PIC) ranged from 0.590 to 0.869 with an average of 0.713. Average observed and expected heterozygosities were 0.7988 (ranged from 0.310 to 1.000) and 0.7495 (ranged from 0.609 to 0.897), respectively. These ten microsatellites loci would be the valuable genetic markers for further investigation of Tibetan chicken.
KeywordsTibetan chicken Microsatellite (AC)n
Tibetan chicken (Gallus gallus domesticus) is an endemic species to China and mainly distributed in Qinghai Province and Tibetan Plateau (Ji et al. 2001). It was estimated that the purebred Tibetan chicken was reduced from 750,000 to <100,000 individuals in the last 20 years, largely because of the introgression of other chicken species into purebred Tibetan chicken population. Moreover, the area of purebred Tibetan chicken decreased dramatically. Therefore, in order to protect this species, agriculture ministry of China listed Tibetan chicken in the first class “key” species of animals in 2000 (Ji et al. 2001). In addition, in order to protect this species, a study on genetic diversity of the population is clearly needed.
Microsatellite marker should be one of the most suitable DNA markers for this purpose (Zhang et al. 2006). Although microsatellites have been isolated in many chicken species (Wu et al. 2004), no report was found in the Tibetan chicken. In this research, we reported the isolation and characterization of ten polymorphic microsatellite loci in the Tibetan chicken.
A genomic library for (AC)12 repeats was constructed following the method of Bloor et al. (2001) and Zhang et al. (2008). The DNA of the genomic library was extracted from a male Tibetan chicken. Out of 63 recombinant clones screened by PCR, 47 (74.6%) positive clones were found and insured by sequencing.
Characterization of ten microsatellite loci in Tibetan chicken, including repeat motif, number of genotypes (Ng), number of alleles observed (Na), allele size range, annealing temperature (Ta), observed heterozygosity (Ho), expected heterozygosity (He), polymorphic information content (PIC), and GenBank accession numbers
Primer sequence (5′–3′)
GenBank accession number
About 10 loci of the 34 primers showed a distinct allelic variation ranging from 4 to 14 alleles in the individuals examined (Table 1). Their polymorphism information content (PIC) ranged from 0.590 to 0.869 with an average of 0.713. Average observed and expected heterozygosities were 0.7988 (range 0.310–1.000) and 0.7495 (range 0.609–0.897), respectively. No loci showed significant deviations from HWE (P > 0.01). Following Bonferroni correction, highly significant LD tests were not shown for any pair of loci (P > 0.01 for all comparisons). In addition, the remaining 24 primers were mono-morphism in the individuals tested.
The results indicated that these ten microsatellite markers would be useful in genetic diversity analyses and population management of Tibetan chicken population.
We thank Dr. Wenping Zhang and Xiuyue Zhang for giving us a lot of help in data analysis and advices in experiments. This research was funded by the Sichuan Youth Science and Technology Foundation (08ZQ026-027) and Southwest University for Nationalities Foundation of P. R. China.
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