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Selection signature analysis using whole genome resequencing data reveals candidate genes for white plumage color in Korean native ducks |
Jaewon Kim1 
, Jaegwon Kim2
, Eunjin Cho3
, Sunghyun Cho4
, Minjun Kim1
, Won-Hyong Chung2
, Jungwoo Choi2
, Hyo Jun Choo5,*
, Jun Heon Lee1,*
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1Division of Animal and Dairy Science, Chungnam National University, Daejeon, Korea
2Department of Animal Science, College of Animal Life Sciences, Kangwon National University, Chuncheon , Korea
3Department of Bio-AI Convergence, Chungnam National University, Daejeon , Korea
4Research and Development Center, Insilicogen Inc., Yongin , Korea
5Poultry Research Institute, National Institute of Animal Science, Rural Development Administration, Pyeongchang , Korea |
Correspondence:
Hyo Jun Choo,Email: hyojy@korea.kr
Jun Heon Lee, Tel: +82-42-821-5779, Fax: +82-42-825-9754, Email: junheon@cnu.ac.kr
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Received: 14 October 2024 • Revised: 19 December 2024 • Accepted: 14 January 2025 |
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| Abstract |
Objective
Domestication alters the phenotypes of wild animals to meet human demands and leaves characteristic patterns in their genomes. Various selection signature analysis methods have been developed to identify these characteristic patterns left in the genome. The Korean native duck (KND) is one of the domesticated species in Korea. KND is categorized into two populations based on plumage color; colored KND (KNDC) and white KND (KNDW). To enhance the competitiveness of native ducks, it is necessary to establish a KNDW line. In this study, we conducted selection signature analysis to identify candidate genes associated with white plumage color in KNDs.
Methods
We generated whole genome resequencing data from 22 KNDCs, 22KNDWs, and 10 Pekin ducks (PKDs). To detect distinct genomic regions between KND populations with different plumage colors, we analyzed three types of selection signature analysis: the fixation index (Fst), nucleotide diversity(π), and cross-population extended haplotype heterozygosity (XP-EHH).
Results
Population structure analysis showed that although KNDC and KNDW are distinct from PKD, they form a single group sharing a common ancestor. The results of Fst and π analyses revealed that compared to KNDC, there were strong selection signals in the MITF gene in KNDW, with a 6,641 bp insertion in the intron 2 region. This variant is a transposable element insertion that causes white plumage in PKD. In addition, XP-EHH analysis identified DCT, KIT, TYR, and ADCY9 as major candidate genes associated with pigmentation in the KND population.
Conclusion
White plumage in KNDW is caused by a transposable element insertion in the MITF gene. This finding improves our understanding of plumage color in KND and supports the establishment of KNDW breeding programs.
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| Keywords:
Korean native duck; Plumage color; Population analysis; Selection signature analysis; Transposable element; Whole genome resequencing |
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