Format

Send to

Choose Destination
See comment in PubMed Commons below
Mol Cells. 2016 Dec;39(12):862-868. doi: 10.14348/molcells.2016.0219. Epub 2016 Dec 13.

Detecting Positive Selection of Korean Native Goat Populations Using Next-Generation Sequencing.

Author information

  • 1Department of Agricultural Biotechnology, Animal Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea.
  • 2Department of Natural Science, Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 08826, Korea.
  • 3Bahir Dar University, college of Agriculture and Environmental Sciences, POBox 79, Bahir Dar, Ethiopia.
  • 4C&K genomics, Seoul National University Research Park, Seoul 08826, Korea.
  • 5Division of Animal Genomics and Bioinformatics, National Institute of Animal science, Rural Development Administration, Suwon 16637, Korea.
  • 6Institute for Biomedical Sciences, Shinshu University, Nagano, Japan.

Abstract

Goats (Capra hircus) are one of the oldest species of domesticated animals. Native Korean goats are a particularly interesting group, as they are indigenous to the area and were raised in the Korean peninsula almost 2,000 years ago. Although they have a small body size and produce low volumes of milk and meat, they are quite resistant to lumbar paralysis. Our study aimed to reveal the distinct genetic features and patterns of selection in native Korean goats by comparing the genomes of native Korean goat and crossbred goat populations. We sequenced the whole genome of 15 native Korean goats and 11 crossbred goats using next-generation sequencing (Illumina platform) to compare the genomes of the two populations. We found decreased nucleotide diversity in the native Korean goats compared to the crossbred goats. Genetic structural analysis demonstrated that the native Korean goat and crossbred goat populations shared a common ancestry, but were clearly distinct. Finally, to reveal the native Korean goat's selective sweep region, selective sweep signals were identified in the native Korean goat genome using cross-population extended haplotype homozygosity (XP-EHH) and a cross-population composite likelihood ratio test (XP-CLR). As a result, we were able to identify candidate genes for recent selection, such as the CCR3 gene, which is related to lumbar paralysis resistance. Combined with future studies and recent goat genome information, this study will contribute to a thorough understanding of the native Korean goat genome.

KEYWORDS:

NGS; XP-CLR; XP-EHH; genomic comparison; native Korean goat; population analysis

PMID:
27989103
PMCID:
PMC5223103
DOI:
10.14348/molcells.2016.0219
[PubMed - in process]
Free PMC Article
PubMed Commons home

PubMed Commons

0 comments
How to join PubMed Commons

    Supplemental Content

    Full text links

    Icon for Publishing M2Community Icon for PubMed Central
    Loading ...
    Support Center