Animal Science and Zoology; Food Animals; General Medicine
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Evelyne, Moyse ✱; Biostatistics & Bioinformatics, FARAH‐PAD, Faculty of Veterinary Medicine University of Liege Liège Belgium
Nguyen Van Duy ✱; Université de Liège - ULiège > Fundamental and Applied Research for Animals and Health (FARAH) ; Faculty of Animal Science Vietnam National University of Agriculture Hanoi Vietnam
Amelyne, Dor ✱; Biostatistics & Bioinformatics, FARAH‐PAD, Faculty of Veterinary Medicine University of Liege Liège Belgium
Nguyen Hoang, Thinh ✱; Faculty of Animal Science Vietnam National University of Agriculture Hanoi Vietnam
Duc, Luc Do ✱; Faculty of Animal Science Vietnam National University of Agriculture Hanoi Vietnam
Nassim, Moula ✱; Biostatistics & Bioinformatics, FARAH‐PAD, Faculty of Veterinary Medicine University of Liege Liège Belgium
Dinh, Ton Vu ✱; Faculty of Animal Science Vietnam National University of Agriculture Hanoi Vietnam
Frédéric, Farnir ✱; Biostatistics & Bioinformatics, FARAH‐PAD, Faculty of Veterinary Medicine University of Liege Liège Belgium
✱ These authors have contributed equally to this work.
Language :
English
Title :
High‐resolution genomic analysis of four local Vietnamese chicken breeds
Benjamini, Y., & Hochberg, Y. (1995). Controlling the false discovery rate: A practical and powerful approach to multiple testing. J. Royal Statistical Society (Series B), 57, 289–300.
Berthouly, C., Leroy, G., Nhu Van, T., Hoang Thanh, H., Bed'Hom, B., Trong Nguyen, B., Vu Chi, C., Monicat, F., Tixier-Boichard, M., Verrier, E., Maillard, J. C., & Rognon, X. (2009). Genetic analysis of local Vietnamese chickens provides evidence of gene flow from wild to domestic populations. BMC Genetics, 10(1), 1–8. https://doi.org/10.1186/1471-2156-10-1
Bertrand, A. R., Kadri, N. K., Flori, L., Gautier, M., & Druet, T. (2019). RZooRoH: An R package to characterize individual genomic autozygosity and identify homozygous-by-descent segments. Methods in Ecology and Evolution, 10(6), 860–866. https://doi.org/10.1111/2041-210X.13167
Besbes, B. (2009). Genotype evaluation and breeding of poultry for performance under sub-optimal village conditions. World's Poultry Science Journal, 65(2), 260–271. https://doi.org/10.1017/S0043933909000221
Burgos, S., Hong Hanh, P. T., Roland-Holst, D., & Burgos, S. A. (2007). Characterization of poultry production systems in Vietnam. International Journal of Poultry Science, 6(10), 709–712.
Ceballos, F. C., Joshi, P. K., Clark, D. W., Ramsay, M., & Wilson, J. F. (2018). Runs of homozygosity: Windows into population history and trait architecture. Nature Reviews Genetics, 19(4), 220–234. https://doi.org/10.1038/nrg.2017.109
Cuc, N. T., Dinh, N. C., Hien, L. T., Thien, V. C., Thong, T. T., Cuong, N. H., & Thieu, P. C. (2016). Selection of Mia chicken breed. Journal of Animal Science and Technology, 11(61), 33–44.
Cuc, N. T., Simianer, H., Eding, H., Tieu, H. V., Cuong, V. C., Wollny, C. B. A., Groeneveld, L. F., & Weigend, S. (2010). Assessing genetic diversity of Vietnamese local chicken breeds using microsatellites. Animal Genetics, 41(5), 545–547. https://doi.org/10.1111/j.1365-2052.2010.02039.x
Cuc, N. T., Tien, P. D., Cuong, N. H., Dinh, N. C., Thieu, P. C., Thien, V. C., Huong, P. T. B., Thong, T. T. T., & Tuyen, N. T. (2016). Selection of Mong chicken breed. Journal of Animal Husbandry Sciences and Technics, 18(132), 22–32.
Cuc, N. T., Weigend, S., Tieu, H. V., & Simianer, H. (2011). Conservation priorities and optimum allocation of conservation funds for Vietnamese local chicken breeds. Journal of Animal Breeding and Genetics, 128(4), 284–294.
Curik, I., Ferenčaković, M., & Sölkner, J. (2014). Inbreeding and runs of homozygosity: A possible solution to an old problem. Livestock Science, 166, 26–34. https://doi.org/10.1016/j.livsci.2014.05.034
Desvaux, S, Vu Dinh, T, Phan Dang, T, & Pham Thi, T. (2008). A general review and description of the poultry production in Vietnam: 38.
Dray, S., & Dufour, A. B. (2007). The ade4 package: Implementing the duality diagram for ecologists. Journal of Statistical Software, 22(4), 1–20.
Druet, T., & Gautier, M. (2017). A model-based approach to characterize individual inbreeding at both global and local genomic scales. Molecular Ecology, 26(20), 5820–5841. https://doi.org/10.1111/mec.14324
Falconer, D., & Mackay, T. (1996). Introduction to quantitative genetics (4th ed.). Addison-Wesley Longman.
FAO. (2008). Poultry systems in Vietnam Prepared by Duc. N.V, Long. T,. GCP/RAS/228/GER working paper N0.4.Rome.
Fleming, D. S., Koltes, J. E., Markey, A. D., Schmidt, C. J., Ashwell, C. M., Rothschild, M. F., Persia, M. E., Reecy, J. M., & Lamont, S. J. (2016). Genomic analysis of Ugandan and Rwandan chicken ecotypes using a 600 k genotyping array. BMC Genomics, 17(1), 1–16. https://doi.org/10.1186/s12864-016-2711-5
Fu, W., Dekkers, J. C. M., Lee, W. R., & Abasht, B. (2015). Linkage disequilibrium in crossbred and pure line chickens. Genetics Selection Evolution, 47(1), 1–12. https://doi.org/10.1186/s12711-015-0098-4
Gandini, G., Stella, A., Del Corvo, M., & Jansen, G. B. (2014). Selection with inbreeding control in simulated young bull schemes for local dairy cattle breeds. Journal of Dairy Science, 97(3), 1790–1798.
Groenen, M., Wahlberg, O., Foglio, M., Megens, H. J., Crooijmans, R., Besnier, F., Lathrop, A., Muir, W., Wong, G., Gut, I., & Andersson, L. (2009). A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genome Research, 19(3), 510–519. https://doi.org/10.1101/gr.086538.108
Hayes, B. J., Visscher, P. M., McPartlan, H. C., & Goddard, M. E. (2003). Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research, 13(4), 635–643. https://doi.org/10.1101/gr.387103
Johansson, A. M., & Nelson, R. M. (2015). Characterization of genetic diversity and gene mapping in two Swedish local chicken breeds. Frontiers in Genetics, 6, 44. https://doi.org/10.3389/fgene.2015.00044
Khanyile, K. S., Dzomba, E. F., & Muchadeyi, F. C. (2015). Population genetic structure, linkage disequilibrium and effective population size of conserved and extensively raised village chicken populations of southern Africa. Frontiers in Genetics, 6, 13. https://doi.org/10.3389/fgene.2015.00013
Lan Phuong, T. N., Dong Xuan, K. D. T., & Szalay, I. (2015). Traditions and local use of native Vietnamese chicken breeds in sustainable rural farming. World's Poultry Science Journal, 71(2), 385–396. https://doi.org/10.1017/S0043933915000380
Mekchay, S., Supakankul, P., Assawamakin, A., Wilantho, A., Chareanchim, W., & Tongsima, S. (2014). Population structure of four Thai indigenous chicken breeds. BMC Genetics, 15(1), 1–9.
Muir, W. M., Wong, G. K. S., Zhang, Y., Wang, J., Groenen, M. A. M., Crooijmans, R. P. M. A., Megens, H. J., Zhang, H., Okimoto, R., Vereijken, A., Jungerius, A., Albers, G. A. A., Lawley, C. T., Delany, M. E., Mac Eachern, S., & Cheng, H. H. (2008). Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proceedings of the National Academy of Sciences of the United States of America, 105(45), 17312–17317. https://doi.org/10.1073/pnas.0806569105
Ngoc, H. (2020). Livestock statistics. Vietnam Association of Agriculture and Rural Development. http://nhachannuoi.vn/binh-phuoc-89-trang-trai-chan-nuoi-gia-cam/
Nguyen Van, D., Moula, N., Pham Kim, D., Dao Thi, H., Bui Huu, D., Vu Dinh, T., & Farnir, F. (2015). Ho chicken in Bac Ninh Province (Vietnam): From an indigenous chicken to local poultry breed. International Journal of Poultry Science, 14(9), 521–528.
Nguyen Van, G., Nguyen Thi, L., Tran Thi, U. L., Do Manh, H., & Dang, D. (2015). The Vietnamese livestock market has changed structure to improve competitiveness. Hong Duc Publishing House.
Paradis, E., & Schliep, K. (2019). Ape 5.0: An environment for modern phylogenetics and evolutionary analyses in R. Bioinformatics, 35(3), 526–528. https://doi.org/10.1111/age.12526
Peripolli, E., Munari, D. P., Silva, M. V. G. B., Lima, A. L. F., Irgang, R., & Baldi, F. (2017). Runs of homozygosity: Current knowledge and applications in livestock. Animal Genetics, 48(3), 255–271.
Pham Cong, T. (2016). Result in conservation, exploitation and development of livestock gene sources. Journal of Animal Husbandry Sciences and Technics, 24(208), 19–25.
Pham, M. H., Berthouly-Salazar, C., Tran, X. H., Chang, W. H., Crooijmans, R. P., Lin, D. Y., Hoang, V. T., Lee, Y. P., Tixier-Boichard, M., & Chen, C. F. (2013). Genetic diversity of Vietnamese domestic chicken populations as decision-making support for conservation strategies. Animal Genetics, 44(5), 509–521. https://doi.org/10.1111/age.12045
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A., Bender, D., Maller, J., Sklar, P., De Bakker, P. I., & Daly, M. J. (2007). PLINK: A tool set for whole-genome association and population-based linkage analyses. The American Journal of Human Genetics, 81(3), 559–575. https://doi.org/10.1086/519795
Qanbari, S., Hansen, M., Weigend, S., Preisinger, R., & Simianer, H. (2010). Linkage disequilibrium reveals different demographic history in egg laying chickens. BMC Genetics, 11(1), 1–10.
R Core Team. (2016). R: A language and environment for statistical computing [internet] (p. 2016). R Foundation for Statistical Computing.
Rabiner, L. R. (1989). A tutorial on hidden Markov models and selected applications in speech recognition. Proceedings of the IEEE, 77(2), 257–286. https://doi.org/10.1109/5.18626
Raj, A., Stephens, M., & Pritchard, J. K. (2014). fastSTRUCTURE: Variational inference of population structure in large SNP data sets. Genetics, 197(2), 573–589. https://doi.org/10.1534/genetics.114.164350
Rischkowsky, B., & Pilling, D. (2007). The state of the world's animal genetic resources for food and agriculture. Food & Agriculture Organization.
Sambrook, J., & Russell, D. W. (2001). Molecular cloning: A laboratory manual (3rd ed., pp. 620–621). Cold Spring Harbor Laboratory Press.
Sargolzaei, M., Schenkel, F. S., Jansen, G. B., & Schaeffer, L. R. (2008). Extent of linkage disequilibrium in Holstein cattle in North America. Journal of Dairy Science, 91(5), 2106–2117. https://doi.org/10.3168/jds.2007-0553
Seo, D. W., Oh, J. D., Jin, S., Song, K. D., Park, H. B., Heo, K. N., Shin, Y., Jung, M., Park, J., Jo, C., Lee, H. K., & Lee, J. H. (2014). Single nucleotide polymorphism analysis of Korean native chickens using next generation sequencing data. Molecular Biology Reports, 42(4), 471–477. https://doi.org/10.1007/s11033-014-3790-5
Slatkin, M., & Excoffier, L. (1996). Testing for linkage disequilibrium in genotypic data using the expectation-maximization algorithm. Heredity, 76(4), 377–383.
Solé, M., Gori, A.-S., Faux, P., Bertrand, A., Farnir, F., Gautier, M., & Druet, T. (2017). Age-based partitioning of individual genomic inbreeding levels in Belgian blue cattle. Genetics Selection Evolution, 49(1), 1–18. https://doi.org/10.1186/s12711-017-0370-x
Strillacci, M. G., Cozzi, M. C., Gorla, E., Mosca, F., Schiavini, F., Román-Ponce, S. I., López, F. J., Schiavone, A., Marzoni, M., & Cerolini, S. (2017). Genomic and genetic variability of six chicken populations using single nucleotide polymorphism and copy number variants as markers. Animal, 11(5), 737–745. https://doi.org/10.1017/S1751731116002135
Tenesa, A., Navarro, P., Hayes, B. J., Duffy, D. L., Clarke, G. M., Goddard, M. E., & Visscher, P. M. (2007). Recent human effective population size estimated from linkage disequilibrium. Genome Research, 17(4), 520–526. https://doi.org/10.1101/gr.6023607
Vu Dinh, T., Bui Huu, D., Dao Thi, H., & Nguyen Van, D. (2014). Project report: Selection local chicken breed of ho for sustainable conservation in Vietnam. Vietnam National University of Agriculture.
Vu Dinh, T., Dao Thi, H., & Nguyen Van, D. (2013). Project report: The solutions for conservation, sustainable use and development of local chicken breed of Dong Tao in hung Yen Province. Vietnam National University of Agriculture.
Weir, B. S., & Cockerham, C. C. (1984). Estimating F-statistics for the analysis of population structure. Evolution, 38(6), 1358–1370. https://doi.org/10.1111/j.1558-5646.1984.tb05657.x
Wigginton, J. E., Cutler, D. J., & Abecasis, G. R. (2005). A note on exact tests of hardy-Weinberg equilibrium. The American Journal of Human Genetics, 76(5), 887–893. https://doi.org/10.1086/429864
Zanetti, E., De Marchi, M., Dalvit, C., & Cassandro, M. (2010). Genetic characterization of local Italian breeds of chickens undergoing in situ conservation. Poultry Science, 89(3), 420–427. https://doi.org/10.3382/ps.2009-00324
Zhang, M., Han, W., Tang, H., Li, G., Zhang, M., Xu, R., Liu, Y., Yang, T., Li, W., & Zou, J. (2018). Genomic diversity dynamics in conserved chicken populations are revealed by genome-wide SNPs. BMC Genomics, 19(1), 1–12. https://doi.org/10.1186/s12864-018-4973-6
Zhao, Q.-B., Liao, R.-R., Sun, H., Zhang, Z., Wang, Q.-S., Yang, C.-S., Zhang, X., & Pan, Y.-C. (2018). Identifying genetic differences between dongxiang blue-shelled and white leghorn chickens using sequencing data. G3: Genes, Genomes Genetics, 8(2), 469–476. https://doi.org/10.1534/g3.117.300382
