High-throughput microsatellite markers discovery for the Sichuan Hill Partridge (Arborophila rufipectus) and assessment of genetic diversity in the Laojunshan population

Abstract

Sichuan Hill Partridge (Arborophila rufipectus) is a globally endangered species endemic to China. However, the genetic diversity of this species was poorly studied due to lack of molecular markers. We used 454 pyrosequencing to discover microsatellites from the A. rufipectus genome in this study. A total of 6280 di-nucleotides, 8139 tri-nucleotides, and 11,987 tetra-nucleotides with sufficient flanking region for primer design were screened with in silico mining. Ultimately, 18 tetra-nucleotide polymorphic loci were first identified and used to examine the genetic diversity in the Laojunshan population. The number of alleles per locus ranged from 5 to 13, observed and expected heterozygosity varied from 0.292 to 0.917 and 0.722 to 0.909, respectively. These results revealed that this endangered species' genetic diversity as not as low as expected. However, a heterozygote deficit was found in the Laojunshan population. We proposed that the management should focus on increasing the connectivity of remnant patches and fragments to increase the opportunity of greater gene flow among fragmented populations of A. rufipectus. This is the first time that polymorphic microsatellite markers were reported for A. rufipectus. These markers provide a valuable resource for future population genetics studies and for the management and conservation of this species.