Development of new tetranucleotide microsatellite loci and assessment of genetic variation of giant panda in two largest giant panda captive breeding populations

Abstract

The giant panda Ailuropoda melanoleuca is a critically endangered species endemic to China. In order to carry out effective genetic management for the giant panda population, sufficient and reliable polymorphic genetic markers are required to provide essential information on the genetic diversity survey of this species. Seven new tetranucleotide microsatellite loci were isolated and characterized in this study and presented here as a tool for evaluating the genetic variation of giant pandas in the world's two largest captive populations (Chengdu Research Base of Giant Panda Breeding, Sichuan Province and the China Research and Conservation Center for the Giant Panda in Wolong, Sichuan Province). A total of 45 alleles were identified from these seven new microsatellite loci on the basis of 48 giant panda individuals, including 19 private alleles (six from the Chengdu population, 13 from the Wolong population) and 26 shared alleles. The average number of alleles, the average allelic richness the and mean observed heterozygosity were 4.6, 4.367 and 0.649, respectively in the Chengdu population and 5.6, 5.697 and 0.675 in the Wolong population, suggesting that the Chengdu population has a much lower allelic diversity than the Wolong population. Thus, we proposed a better strategy for the captive breeding of giant pandas.

Genome-wide survey and analysis of microsatellites in giant panda (Ailuropoda melanoleuca), with a focus on the applications of a novel microsatellite marker system

“…It demonstrated that these markers developed in this study were effective in genetic diversity analyses. Moreover, the mean allelic richness of the Chengdu captive population in our study was much higher than Li et al [ 8 ] and Shen et al [ 7 ]. However, the level of heterozygosity was similar, which means that the loci developed in this study with a higher number of alleles.…”

“…In addition, the design of conservation strategies for the wild panda population is also limited by the lack of information on the population’s genetics. Although microsatellite loci analyses [ 3 - 8 ] have been used to assess the genetic variability and evaluate the population size for giant pandas, the genetic status of the giant panda is still matters of significant controversy. For example, some researchers assumed that wild populations might have low genetic variability [ 9 - 11 ], while Lu et al [ 3 ] and Zhang et al [ 5 ] concluded that wild populations might maintain high genetic variation.…”

“…Therefore, a universal genetic marker system, which is powerful and repeatability, will be convenient for different researchers to make comparison. Although nearly 100 microsatellite markers have already been developed for the giant panda [ 3 , 8 , 12 - 16 ], most of them are dinucleotide repeats. Dinucleotide microsatellite is easily subject to mistyping due to polymerase slippage during polymerase chain reaction (PCR) [ 17 , 18 ].…”

Genome-wide distribution and organization of microsatellites in six species of birds

“…During the past several years, SSRs have been widely employed in genome mapping, forensics, population structure, phylogenetics, linkage, and kinship relationships (Dib et al, 1996;Selkoe and Toonen, 2006;Li et al, 2010). In addition, SSRs have been found in recent studies to serve a functional role affecting gene regulation, transcription, protein function, and genome organization (Kashi and King, 2006;Lawson and Zhang, 2006).…”

Large‐scale genetic surveys for main extant population of wild giant panda (Ailuropoda melanoleuca) reveals an urgent need of human management

“…Microsatellite markers have become an important genetic markers in the field of molecular biology (Selkoe & Toonen, 2010 ) and have been widely used in population surveys (Creel et al, 2003 ; Piggott et al, 2006 ; Wang et al, 2016 ), genetic diversity assessments (Du et al, 2016 ; Li et al, 2010 ; Shen et al, 2010 ; Vanhala et al, 1998 ; Zhang et al, 2007 ), and genetic management of populations (Shan et al, 2014 ). The combined application of microsatellite markers, mitochondrial markers and noninvasive genetic sampling has contributed greatly to giant pandas conservation in the past 20 years, allowing giant panda population studies without the risk of capture stress, injury or death.…”