Czech J. Anim. Sci., 2024, 69(8):323-330 | DOI: 10.17221/91/2023-CJAS
Whole-genome sequencing revealed the population structure of Fujian chicken breedsOriginal Paper
- 1 Institute of Animal Husbandry and Veterinary Medicine, Fujian Academy of Agricultural Sciences, Fuzhou, P. R. China
- 2 Fujian Key Laboratory of Animal Genetics and Breeding, Fuzhou, P. R. China
Indigenous chicken breeds from Fujian Province, China, exhibit unique and distinctive phenotypic characteristics, including morphology, behaviour, integumentary pigmentation, feather colouration, and production performance. However, the underlying genetic basis governing these specific traits remains unclear. This study aimed to elucidate the population structure of six Fujian local chicken breeds [Bairong chickens (BRCs), Jinhu chickens (JHCs), Minqing chickens (MQCs), Dehua chickens (DHCs), Xiangdong chickens (XDCs), and Hetian chickens (HTCs)] in terms of their genetic resources within the province. The whole-genome resequencing revealed 8 678 612 single nucleotide polymorphisms (SNPs) in a cohort of 36 chickens. The results revealed a partial mismatch between the clustering patterns and geographic distributions of the six populations, with BRC displaying a noticeable genetic divergence from other chickens. Moreover, the genetic distance between XDC and HTC in Longyan County was relatively close and converged with JHC, MQC, and DHC into a subgroup. These findings provide a comprehensive understanding of the intrinsic characteristics and utilisation prospects of chicken germplasm resources in Fujian Province.
Keywords: indigenous chicken; genetic structure; genomic resequencing; germplasm resource
Received: June 29, 2023; Accepted: August 6, 2024; Prepublished online: August 16, 2024; Published: August 30, 2024 Show citation
References
- Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014 Aug 1;30(15):2114-20.
Go to original source...
Go to PubMed...
- Chen L, Wang X, Cheng D, Chen K, Fan Y, Wu G, You J, Liu S, Mao H, Ren J. Population genetic analyses of seven Chinese indigenous chicken breeds in a context of global breeds. Anim Genet. 2019 Feb;50(1):82-6.
Go to original source...
Go to PubMed...
- Dorshorst B, Harun-Or-Rashid M, Bagherpoor AJ, Rubin CJ, Ashwell C, Gourichon D, Tixier-Boichard M, Hallbook F, Andersson L. A genomic duplication is associated with ectopic eomesodermin expression in the embryonic chicken comb and two duplex-comb phenotypes. PLoS Genet. 2015 Mar 19;11(3):e1004947.
Go to original source...
Go to PubMed...
- Felsenstein J. PHYLIP: Phylogeny inference package. Version 3.5 c. Seattle, WA, USA: Univeristy of Washington; 1993.
- Aldana R, Freed D. Data processing and germline variant calling with the sentieon pipeline. Methods Mol Biol. 2022 Jun 26;2493:1-19.
Go to original source...
Go to PubMed...
- Gao CF, Xu GZ, Zhang XP, Li ZW, Chen E, Ying ZY. [Currect situation and development countermeasures of Hetian chicken industry in Changting county]. Fujian Agricultural Sci Technol. 2018 Aug 49;(8):35-8. Chinese.
- Gongora J, Rawlence NJ, Mobegi VA, Han JL, Alcalde JA, Matus JT, Hanotte O, Moran C, Austin JJ, Ulm S, Anderson AJ, Larson G, Cooper A. Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proc Natl Acad Sci USA. 2008 Jul 29;105(30):10308-13.
Go to original source...
Go to PubMed...
- Hua GY, Chen JF, Wang JK, Li JY, Deng XM. Genetic basis of chicken plumage color in artificial population of complex epistasis. Anim Genet. 2021 Sep 23;52(5):656-66.
Go to original source...
Go to PubMed...
- Huang XH, Otecko NO, Peng MS, Weng ZX, Li WN, Chen JB, Zhong M, Zhong FS, Jin SH, Geng ZY, Lou W, He DL, Ma C, Han JN, Ommeh SC, Zhang XQ, Du BW. Genome-wide genetic structure and selection signatures for color in 10 traditional Chinese yellow-feathered chicken breeds. BMC Genom. 2020 Apr 20;21(1):316.
Go to original source...
Go to PubMed...
- Letunic I, Bork P. Interactive tree of life (iTOL): An online tool for the display and annotation of phylogenetic and other trees. Version 3. Nucleic Acids Res. 2016 Jul 8;44(W1):W242-5.
Go to original source...
Go to PubMed...
- Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009 Jul 15; 25(14):1754-60.
Go to original source...
Go to PubMed...
- Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R. The sequence alignment/map format and SAMtools. Bioinformatics. 2009 Aug 15;25(16):2078-9.
Go to original source...
Go to PubMed...
- Malomane DK, Simianer H, Weigend A, Reimer C, Schmitt AO, Weigend S. The SYNBREED chicken diversity panel: A global resource to assess chicken diversity at high genomic resolution. BMC Genomics. 2019 May 7;20(1):345.
Go to original source...
Go to PubMed...
- McKenna A, Hanna M, Banks E, Sivachenko A, Kristian C, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA. The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010 Sep;20(9):1297-303.
Go to original source...
Go to PubMed...
- Miao YW, Peng MS, Wu GS, Quyang YN, Yang ZY, Yu N, Liang JP, Pianchou G, Beja-Pereira A, Mitra B, Palanichamy MG, Baig M, Chaudhuri TK, Shen YY, Kong QP, Murphy RW, Yao YG, Zhang YP. Chicken domestication: An updated perspective based on mitochondrial genomes. Heredity. 2013 Mar;3(110):277-82.
Go to original source...
Go to PubMed...
- Mwacharo JM, Bjornstad G, Han JL, Hanotte O. The history of African village chickens: An archaeological and molecular perspective. Afr Archaeolo Rev. 2013;30(1):97-114.
Go to original source...
Go to PubMed...
- Peter BM. Admixture, population structure, and F-statistics. Genetics. 2016 Apr;202(4):1485-501.
Go to original source...
Go to PubMed...
- Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, Bakker PIW, Daly MJ, Sham PC. PLINK: A tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet. 2007 Sep;81(3):559-75.
Go to original source...
Go to PubMed...
- Wang MS, Li Y, Peng MS, Zhong L, Wang ZJ, Li QY, Tu XL, Dong Y, Zhu CL,Wang L, Yang MM, Wu SF, Miao YW, Liu JP, Irwin DM, Wang W, Wu DD, Zhang YP. Genomic analyses reveal potential independent adaptation to high altitude in Tibetan chickens. Mol Biol Evol. 2015 Jul;32(7):1880-9.
Go to original source...
Go to PubMed...
- Wang MS, Thakur M, Pens MS, Jiang Y, Frantz L, Li M, Zhang JJ, Wang S, Peters J, Otecko NO, Suwannapoom C, Guo X, Zheng ZQ, Esmailizadeh A, Hirimuthugoda NY, Ashari H, Suladari S, Zein M, Kusza S, Sohrabi S, Kharrati-Koopaee H, Shen QK, Zeng L, Yang MM, Wu YJ, Yang XY, Lu XM, Jia XZ, Nie QH, Lamont SJ, Lasaqna E, Ceccobelli S, Gunwardana H, Senasige M, Feng SH, Si JF, Zhang H, Jin JQ, Li ML, Liu YH, Chen HM, Ma C, Dai SS, Bhuiyan A, Khan MS, Silva G, Le TT, Mai OA, Ibrahim M, Supple M, Shapiro B, Hanotte O, Zhang G, Larson G, Han JL, Wu DD, Zhang YP. 863 genomes reveal the origin and domestication of chicken. Cell Res. 2020 Aug;30(8):693-701.
Go to original source...
Go to PubMed...
- Wenne R. Microsatellites as molecular markers with applications in exploitation and conservation of aquatic animal populations. Genes. 2023 Mar 27;14(4):808.
Go to original source...
Go to PubMed...
- Xiang H, Gao JQ, Yu BQ, Zhou H, Cai D, Zhang YW, Chen XY, Wang X, Hofreiter M, Zhao XB. Early holocene chicken domestication in northern China. Proc Natl Acad Sci USA. 2014 Dec 9;111(49):17564-9.
Go to original source...
Go to PubMed...
- Yu SG, Wang G, Liao J, Liu QF. [Establishment of a general method for efficient extraction of avian genomic DNA]. Heilongjiang Anim Sci Vet Med. 2018 Jul 10;7(13):195-8. Chinese.
- Zhang T, Du W, Lu H, Wang L. Genetic diversity of mitochondrial DNA of Chinese black-bone chicken. Rev Bras Cienc Avic. 2018 Mar;20(3):565-72.
Go to original source...
- Zheng NZ, Dong XN, Zheng LZ. [Analysis of microsatellite of genetic diversity among native chicken breeds in Fujian and Taihe silky chicken in Jiangxi]. J Fujian Agric For Univ (Nat Sci Ed). 2008;(6):641-5. Chinese.
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