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 chicken such as auditory sense, growth rate and egg traits. In addition, we assembled unaligned reads that could not be mapped to the reference genome. By assembling the unaligned reads, we were able to present genomic sequences characteristic to the KNC. Based on this, we also identified genes related to the olfactory receptors and antigen that are common to all 5 strains. Finally, through the reconstructed mitochondrial genome sequences, we performed phylogenomic analysis and elucidated the maternal origin of the artificially restored KNC. Our results revealed that the KNC has multiple maternal origins which are in agreement with Korea's history of chicken breed imports. The results presented here provide a valuable basis for future research on genomic features of KNC and further understanding of KNC's origin.
Highlights
While Korean Native Chicken (KNC) have a relatively slow growth rate compared to commercial broiler breeds, the breed is preferred in Korea for consumption due to its low-fat and high-protein meat content and taste[1]
The proportion of strain specific single nucleotide variants (SNVs) made up 28% of all identified SNVs and 21% of the total identified SNVs were common to all strains (Figure S5 in S1 File)
Genetic variants and specific genome sequences of KNC. This is the first whole genome sequencing study on KNC. 4.6million SNVs (42.37%) were novel variants based on the Ensembl database
Summary
While Korean Native Chicken (KNC) have a relatively slow growth rate compared to commercial broiler breeds, the breed is preferred in Korea for consumption due to its low-fat and high-protein meat content and taste[1]. In early 20th century, South Korea was blighted with several wars like Second World War and Korean War. The genetic resource of KNC was greatly reduced during this time period. During the Japanese occupation and post-war recovery period, a number of foreign breeds were imported, further pushing KNC to extinction. To remedy the loss of endemic genetic resources, the National Institute of Animal Science, Rural Development Administration of Korea, implemented a project to restore KNC in the late 1970s. Researchers collected KNCs remained in the countryside farms and increased its population size. In addition to the effort of research institute, general farm showed interest in KNC and many KNCs were raised in the private sector. In 1992, research team of national institute, university and industry researchers developed and restored the standard KNC at the end of 8th generation. The restored KNC breed is composed of five strains defined by its plumage color: red, yellow, black, grey, and white
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