2014
DOI: 10.1371/journal.pone.0114763 View full text |Buy / Rent full text
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Abstract: The Korean Native Chicken (KNC) is an important endemic biological resource in Korea. While numerous studies have been conducted exploring this breed, none have used next-generation sequencing to identify its specific genomic features. We sequenced five strains of KNC and identified 10.9 million SNVs and 1.3 million InDels. Through the analysis, we found that the highly variable region common to all 5 strains had genes like PCHD15, CISD1, PIK3C2A, and NUCB2 that might be related to the phenotypic traits of the… Show more

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“…The haplotype frequency results revealed that all lines had from 2 to 4 haplotypes at a frequency of more than 0.10 ( Table 2 ), with additional haplotypes at lower frequencies (< 0.10). The 5 KNC lines are being maintained as restored breeds after successful regeneration and establishment project ( Kwak et al., 2014 ; Jin et al, 2017 ). Initial diverse population sampling in KNC and large population size maintained through advanced breeding practices such as artificial insemination, within-line selection, and within-line breeding may be the possible reasons for having considerable unique genetic diversity at the MHC-B region in 5 KNC lines.…”
Section: Resultsmentioning
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“…The haplotype frequency results revealed that all lines had from 2 to 4 haplotypes at a frequency of more than 0.10 ( Table 2 ), with additional haplotypes at lower frequencies (< 0.10). The 5 KNC lines are being maintained as restored breeds after successful regeneration and establishment project ( Kwak et al., 2014 ; Jin et al, 2017 ). Initial diverse population sampling in KNC and large population size maintained through advanced breeding practices such as artificial insemination, within-line selection, and within-line breeding may be the possible reasons for having considerable unique genetic diversity at the MHC-B region in 5 KNC lines.…”
Section: Resultsmentioning
“…To improve these remaining KNC and to supply the rising demand for quality native chicken meat, a nationwide native chicken breed restoration and establishment project was developed from 1992 to 2007, mainly by the National Institute of Animal Science ( NIAS ) in South Korea. Fifteen years later, 5 distinct KNC lines with distinctive feather color (white [ KNCW ], black [ KNCL ], gray–brown [ KNCG ], red–brown [ KNCR ], and yellow–brown [ KNCY ]) were established ( Kwak et al., 2014 ; Seo et al., 2018 ). Previous genetic analyses using microsatellite markers have shown that these lines are genetically distinct ( Suh et al., 2014 ).…”
Section: Introductionmentioning
“…The mitochondrion contains hundreds of mitochondrial genome copies [2], which are, in contrast to the biparentally inherited nuclear genome, strictly maternally inherited. With NGS data, complete mitogenomes have been obtained for many vertebrate species, including pigs [3][4][5][6], chickens [7][8][9] and cattle [10][11][12]. It has been reported that the reference sequences used affect the accuracy of genome mapping [13][14][15].…”
Section: Introductionmentioning
“…The mitochondrion contains hundreds of innate DNAs [2], which permits high read depths and makes mitogenome alignment from NGS data indeed feasible. With NGS data, the complete mitogenomes of many mammals have been obtained, including pigs [3][4][5][6], chickens [7][8][9] and cattle [10][11][12][13]. It is reported that reference sequences affected the accuracy in genome mapping [14][15][16].…”
Section: Introductionmentioning