Development and characterization of 260 microsatellite loci in the domestic goat, <i>Capra hircus</i>

Seki, Yuta; Yokohama, Michinari; Ishikawa, D.; Ikehara, Norikatsu; Wada, Kenta; Nomura, Kenta; Amano, Takashi; Kikkawa, Yoshiaki

doi:10.1111/j.1365-2052.2011.02262.x

Cited by 5 publications

(5 citation statements)

References 9 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A large number of these hypervariable markers is available in goat (Seki et al, 2012), however, their genotyping and scoring are labour intensive, and allele size calling is difficult to be calibrated across apparata and laboratories, in the absence of a substantial number of shared samples.…”

Section: Development Of High-throughput Snp Assays For the Analysis Omentioning

confidence: 99%

The characterization of goat genetic diversity: Towards a genomic approach

Ajmone‐Marsan

Colli

Han

et al. 2014

Small Ruminant Research

View full text Add to dashboard Cite

a b s t r a c tThe investigation of genetic diversity at molecular level has been proposed as a valuable complement and sometimes proxy to phenotypic diversity of local breeds and is presently considered as one of the FAO priorities for breed characterization. By recommending a set of selected molecular markers for each of the main livestock species, FAO has promoted the meta-analysis of local datasets, to achieve a global view of molecular genetic diversity. Analysis within the EU Globaldiv project of two large goat microsatellite datasets produced by the Econogene Consortium and the IAEA CRP-Asia Consortium, respectively, has generated a picture of goat diversity across continents. This indicates a gradient of decreasing diversity from the domestication centre towards Europe and Asia, a clear phylogeographic structure at the continental and regional levels, and in Asia a limited genetic differentiation among local breeds. The development of SNP panels that assay thousands of markers and the whole genome sequencing of livestock permit an affordable use of genomic technologies in all livestock species, goats included. Preliminary data from the Italian Goat Consortium indicate that the SNP panel developed for this species is highly informative. The existing panel can be improved by integrating additional SNPs identified from the whole genome sequence alignment of goats adapted to extreme climates. Part of this effort is being achieved

show abstract

Section: Development Of High-throughput Snp Assays For the Analysis Omentioning

confidence: 99%

The characterization of goat genetic diversity: Towards a genomic approach

Ajmone‐Marsan

Colli

Han

et al. 2014

Small Ruminant Research

View full text Add to dashboard Cite

show abstract

“…We extracted DNA from 214 fecal samples, and confirmed the PCR amplification of the Cytb gene in 192 feces-derived DNA samples. Microsatellite regions were isolated using a standard procedure (Glenn and Schable, 2005;Seki et al, 2012). Approximately 5 µg genomic DNA was digested with XmnI and RsaI restriction enzymes (New England Biolabs Japan Inc., Sumida-ku, Tokyo, Japan).…”

Section: Methodsmentioning

confidence: 99%

“…The purified PCR-products were ligated to the pT7Blue T-vector (Novagen, Madison, WI, USA), and transformed into ECOS-competent Escherichia coli JM109 (Nippon Gene, Chiyoda-ku, Tokyo, Japan). The cloned inserts were amplified and sequenced using the universal M13 primers, P7 and P8 (Seki et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

Characterization and application of newly developed polymorphic microsatellite markers in the Ezo red fox (Vulpes vulpes schrencki)

et al. 2016

Self Cite

View full text Add to dashboard Cite

The Ezo red fox (Vulpes vulpes schrencki), a subspecies endemic to Hokkaido island, Japan, is a known host species for the tapeworm Echinococcus multilocularis. To develop tools for molecular ecological studies, we isolated 28 microsatellite regions from the genome of Ezo red fox, and developed 18 polymorphic microsatellite markers. These markers were characterized using 7 individuals and 22 fecal samples of the Ezo red fox. The number of alleles for these markers ranged from 1 to 7, and the observed heterozygosity, estimated on the basis of the genotypes of 7 individuals, ranged from 0.29 to 1.00. All markers, except DvNok5, were in Hardy-Weinberg equilibrium (P> 0.05), and no linkage disequilibrium was detected among these loci, except between DvNok14 and DvNok28 (P = 0.01). Moreover, six microsatellite loci were successfully genotyped using feces-derived DNA from the Ezo red fox. The markers developed in our study might serve as a useful tool for molecular ecological studies of the Ezo red fox.

show abstract

“…The amplification of DNA using the SuperSNX linker primer is biased against producing small PCR products, and PCR products obtained after enrichment can be cloned directly without contaminating a large proportion of the small DNA fragments [19]. We succeeded in developing 260 novel microsatellite loci using hybridization with biotinylated microsatellite oligonucleotide (TG) 12 or (AG) 12 probes [11]. These developed markers were composed of two types of repeat motifs containing interrupted DNA sequences: 15 markers contained compound repeats such as (CA) n and (AT) n , and 243 were composed of simple repeats such as dinucleotide motifs (239 markers), trinucleotide motifs (two markers), tetranucleotide motifs (one marker), and heptanucleotide motifs (one marker).…”

Section: Development Of Microsatellite Markers In Goatsmentioning

confidence: 99%

“…In particular, information regarding the number and chromosomal location of goat genetic markers is limited. Although in a previous study we developed a large number of new microsatellite markers [11], these were insufficient for linkage analyses of phenotypic traits. Recently published studies have reported on whole-genome mapping technologies [12] and on the sequencing data of the goat genome obtained by integrating next-generation sequencing [10].…”

Section: Introductionmentioning

confidence: 99%

Practical Applications of Microsatellite Markers in Goat Breeding

Seki¹,

Wada²,

Kikkawa³

2016

Microsatellite Markers

View full text Add to dashboard Cite

To date, the genetic loci associated with disease and economic traits have been identified in livestock based on linkage analysis or genome-wide association studies. These analyses require the use of numerous genetic markers, of which microsatellites have been utilized most extensively because they allow for the easy genotyping of allelic variation at each locus using PCR. In the domestic goat (Capra hircus), microsatellite markers are powerful tools for various genetic studies, such as the estimation of intraand interpopulation genetic diversity, linkage analyses of phenotypic traits, and markerassisted selection of favorable phenotypes; however, the studies on goats are less extensive than those on other major livestock. The aim of this chapter is to summarize the currently available information on goat breeding using microsatellite markers. In particular, we use various studies, including our own recent work, to illustrate how these markers may be used to identify phenotypic traits.

show abstract

Development and characterization of 260 microsatellite loci in the domestic goat, Capra hircus

Cited by 5 publications

References 9 publications

The characterization of goat genetic diversity: Towards a genomic approach

The characterization of goat genetic diversity: Towards a genomic approach

Characterization and application of newly developed polymorphic microsatellite markers in the Ezo red fox (Vulpes vulpes schrencki)

Practical Applications of Microsatellite Markers in Goat Breeding

Contact Info

Product

Resources

About