Identification and characterization of polymorphic microsatellite loci in the red-crowned crane

Abstract

ABSTRACT. We isolated and characterized microsatellite loci for the redcrowned crane (Grus japonensis) from a microsatellite-enriched database, which was obtained using high-throughput sequencing technology. We designed primer sets for 445 microsatellite loci and after initial screening, 34 loci were genotyped in 31 red-crowned cranes. The number of observed alleles ranged from 3 to 10. Observed and expected heterozygosities ranged from 0.197 to 0.935 and 0.453 to 0.887, respectively; the mean polymorphic information content was 0.663. Loci Lia10943, Lia60455, Lia48514, Lia62171, Lia1059, and Lia5286 deviated from expectation of the Hardy-Weinberg equilibrium; however, significant linkage disequilibrium was not observed among the 34 loci. Using these 34 markers, we successfully completed parental identification for 19 cranes. The probability of exclusion for 7 selected loci (Lia271333, Lia3745, Lia11091, Lia45761, Lia16468, Lia21909, and Lia22355) was >0.9977 and analyses with more loci increased the combination efficiency. These 34 markers were also proven to be efficient for individual identification. We recommend that this 15169-15176 (2015) marker system be used in the systematic control of pedigree management and future genetic variation studies of red-crowned cranes.

Characterization of novel microsatellite markers of the Emei Shan Liocichla using restriction site-associated DNA sequencing

“…According to the criteria of Botstein et al (1980), 21 of these 24 microsatellite loci characterized by RAD sequencing showed a high level of polymorphism (PIC > 0.5). Other researchers like Huang et al (2015) and Zhang et al (2015) who have used other NGS methods to identify microsatellites within threatened bird species have observed similar polymorphism levels. Therefore, the use of RAD sequencing strategy to identify microsatellite is economically appealing and effective (Barchi et al 2011).…”

Comprehensive transcriptome characterization of Grus japonensis using PacBio SMRT and Illumina sequencing

“…To protect red-crowned crane, many studies about its population dynamics, feeding habits, habitat protection, disease control, overwintering ecology and reproductive behavior have been conducted 7 , 12 – 16 , including molecular studies mainly focused on marker development and genetic diversity analysis. Several markers were identified and characterized, such as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) 11 , 17 , 18 and genetic diversity and population structure of the red-crowned crane populations were estimated using various markers, such as major histocompatibility complex (MHC), SSRs, and mitochondrial genes 19 – 25 . However, only two studies involving transcriptome and genome of the red-crowned crane have been performed, which included the analysis of the expression profiles of cytochrome P450 (CYP) 1–3 genes in red-crowned crane tissues by Illumina HiSeq 2500 and analysis of the genomic relationships between the crane and other birds by Illumina HiSeq 2000 26 , 27 .…”

Comparative analysis of microsatellite and SNP markers for parentage testing in the golden snub-nosed monkey (Rhinopithecus roxellana)

“…Microsatellite markers have been used in the animal husbandry industry, initially for horses, since the 1990s because of their high rate of polymorphism and low required marker numbers. Since then, they have been successfully used in many threatened animals such as Ailuropoda melanoleuca (Zhang et al 2003), Panthera tigris amoyensis (Zhang et al 2006), and Grus japonensis (Zhang et al 2015). Single Nucleotide Polymorphisms (SNPs), a third-generation genetic marker, has the advantages of good genetic stability, rapid detection, high multi-density, and wide distribution, and has been applied to the animal kingdom, and especially the animal husbandry industry, for parentage testing (Heaton et al 2002;Werner et al 2004).…”