Whole genome analyses revealed genomic difference between European taurine and East Asian taurine.
East Asian taurine
European taurine
genomic difference
whole genome analysis
Journal
Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie
ISSN: 1439-0388
Titre abrégé: J Anim Breed Genet
Pays: Germany
ID NLM: 100955807
Informations de publication
Date de publication:
Jan 2021
Jan 2021
Historique:
received:
03
02
2020
revised:
29
06
2020
accepted:
10
07
2020
pubmed:
10
8
2020
medline:
18
9
2021
entrez:
10
8
2020
Statut:
ppublish
Résumé
European taurine and East Asian taurine are two main clades in Bos taurus, but their genomic differences are not clearly elucidated. Here, we sequenced 16 Mongolian cattle genomes and compared them to the 92 genomes of 10 representative breeds worldwide. We found the highest LD level in Mishima cattle and the fastest LD decay in European taurine. Phylogenetic analysis revealed that Mongolian, Hanwoo and Mishima cattle were clustered into East Asian taurine. From selective sweep, gene annotation, functional enrichment and differential expression analysis, we identified selective signals including genes and/or pathways related to rapid growth and large body size in European taurine, and superior meat quality in East Asian taurine. Our findings will help us understand the evolutionary history and formation process of the breeds and provide theoretical materials regarding the genetic mechanism underlying breed characteristics and molecular breeding programmes of the taurine clades in the future.
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
56-68Subventions
Organisme : National Natural Science Foundation of China
ID : 31872317
Organisme : Program of National Beef Cattle and Yak Industrial Technology system
ID : CARS-37
Informations de copyright
© 2020 Wiley-VCH GmbH.
Références
Albrecht, E., Komolka, K., Ponsuksili, S., Gotoh, T., Wimmers, K., & Maak, S. (2016). Transcriptome profiling of Musculus longissimus dorsi in two cattle breeds with different intramuscular fat deposition. Genomics Data, 7, 109-111. https://doi.org/10.1016/j.gdata.2015.12.014
Alexander, D. H., & Lange, K. (2011). Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC Bioinformatics, 12(1), 246. https://doi.org/10.1186/1471-2105-12-246
Barrett, J. C., Fry, B., Maller, J., & Daly, M. J. (2005). Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics, 21(2), 263-265. https://doi.org/10.1093/bioinformatics/bth457
Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
Bouwman, A. C., Daetwyler, H. D., Chamberlain, A. J., Ponce, C. H., Sargolzaei, M., Schenkel, F. S., … Hayes, B. J. (2018). Meta-analysis of genome-wide association studies for cattle stature identifies common genes that regulate body size in mammals. Nature Genetics, 50(3), 362. https://doi.org/10.1038/s41588-018-0056-5
Castro Bulle, F., Paulino, P., Sanches, A., & Sainz, R. (2007). Growth, carcass quality, and protein and energy metabolism in beef cattle with different growth potentials and residual feed intakes. Journal of Animal Science, 85(4), 928-936.
Chen, N., Cai, Y., Chen, Q., Li, R., Wang, K., Huang, Y., … Lei, C. (2018). Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia. Nature Communications, 9(1), 2337. https://doi.org/10.1038/s41467-018-04737-0
Chen, Q., Zhan, J., Shen, J., Qu, K., Hanif, Q., Liu, J., … Lei, C. (2020). Whole-genome resequencing reveals diversity, global and local ancestry proportions in Yunling cattle. Journal of Animal Breeding and Genetics, https://doi.org/10.1111/jbg.12479
Choi, J.-W., Choi, B.-H., Lee, S.-H., Lee, S.-S., Kim, H.-C., Yu, D., … Lim, D. (2015). Whole-genome resequencing analysis of Hanwoo and Yanbian cattle to identify genome-wide SNPs and signatures of selection. Molecules and Cells, 38(5), 466. https://doi.org/10.14348/molcells.2015.0019
Danecek, P., Auton, A., Abecasis, G., Albers, C. A., Banks, E., DePristo, M. A., … Durbin, R. (2011). The variant call format and VCFtools. Bioinformatics, 27(15), 2156-2158. https://doi.org/10.1093/bioinformatics/btr330
Decker, J. E., McKay, S. D., Rolf, M. M., Kim, J. W., Molina Alcalá, A., Sonstegard, T. S., … Taylor, J. F. (2014). Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics, 10(3), e1004254. https://doi.org/10.1371/journal.pgen.1004254
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., … Gingeras, T. R. (2013). STAR: Ultrafast universal RNA-seq aligner. Bioinformatics, 29(1), 15-21. https://doi.org/10.1093/bioinformatics/bts635
Elsik, C. G., Tellam, R. L., & Worley, K. C. (2009). The genome sequence of taurine cattle: A window to ruminant biology and evolution. Science, 324(5926), 522-528.
Frazee, A. C., Pertea, G., Jaffe, A. E., Langmead, B., Salzberg, S. L., & Leek, J. T. (2015). Ballgown bridges the gap between transcriptome assembly and expression analysis. Nature Biotechnology, 33(3), 243. https://doi.org/10.1038/nbt.3172
Gotoh, T., & Joo, S.-T. (2016). Characteristics and health benefit of highly marbled Wagyu and Hanwoo beef. Korean Journal for Food Science of Animal Resources, 36(6), 709. https://doi.org/10.5851/kosfa.2016.36.6.709
Green, M. R., & Sambrook, J. (2012). Molecular cloning. A laboratory manual (4th ed.). Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.
Herrmann, J. P., & Enders, E. (2000). Effect of body size on the standard metabolism of horse mackerel. Journal of Fish Biology, 57(3), 746-760. https://doi.org/10.1111/j.1095-8649.2000.tb00272.x
Huang, W., Guo, Y., Du, W., Zhang, X., Li, A., & Miao, X. (2017). Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle. Scientific Reports, 7(1), 5278. https://doi.org/10.1038/s41598-017-05702-5
Joo, S.-T., Hwang, Y.-H., & Frank, D. (2017). Characteristics of Hanwoo cattle and health implications of consuming highly marbled Hanwoo beef. Meat Science, 132, 45-51. https://doi.org/10.1016/j.meatsci.2017.04.262
Kantanen, J. (2010). The origin and genetic diversity of native Yakutian cattle as revealed by DNA-marker analysis. Good to Eat, Good to Live with: Nomads and Animals in Northern Eurasia and Africa, 195-201.
Kantanen, J., Edwards, C. J., Bradley, D. G., Viinalass, H., Thessler, S., Ivanova, Z., … Vilkki, J. (2009). Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus). Heredity, 103(5), 404-415. https://doi.org/10.1038/hdy.2009.68
Kessler, J., Morel, I., Dufey, P.-A., Gutzwiller, A., Stern, A., & Geyer, H. (2003). Effect of organic zinc sources on performance, zinc status and carcass, meat and claw quality in fattening bulls. Livestock Production Science, 81(2-3), 161-171. https://doi.org/10.1016/S0301-6226(02)00262-2
Kim, D., Langmead, B., & Salzberg, S. L. (2015). HISAT: A fast spliced aligner with low memory requirements. Nature Methods, 12(4), 357. https://doi.org/10.1038/nmeth.3317
Kim, J., Hanotte, O., Mwai, O. A., Dessie, T., Bashir, S., Diallo, B., … Kim, H. (2017). The genome landscape of indigenous African cattle. Genome Biology, 18(1), 34. https://doi.org/10.1186/s13059-017-1153-y
Kim, S.-J., Ka, S., Ha, J.-W., Kim, J., Yoo, D. A., Kim, K., … Kim, H. (2017). Cattle genome-wide analysis reveals genetic signatures in trypanotolerant N’Dama. BMC Genomics, 18(1), 371. https://doi.org/10.1186/s12864-017-3742-2
Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870-1874. https://doi.org/10.1093/molbev/msw054
Larson, G., Piperno, D. R., Allaby, R. G., Purugganan, M. D., Andersson, L., Arroyo-Kalin, M., … Fuller, D. Q. (2014). Current perspectives and the future of domestication studies. Proceedings of the National Academy of Sciences, 111(17), 6139-6146. https://doi.org/10.1073/pnas.1323964111
Lee, S.-H., Park, B.-H., Sharma, A., Dang, C.-G., Lee, S.-S., Choi, T.-J., … Kang, H.-S. (2014). Hanwoo cattle: Origin, domestication, breeding strategies and genomic selection. Journal of Animal Science and Technology, 56(1), 2. https://doi.org/10.1186/2055-0391-56-2
Letunic, I., & Bork, P. (2016). Interactive tree of life (iTOL) v3: An online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Research, 44(W1), W242-W245. https://doi.org/10.1093/nar/gkw290
Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754-1760. https://doi.org/10.1093/bioinformatics/btp324
Loftus, R. T., MacHugh, D. E., Bradley, D. G., Sharp, P. M., & Cunningham, P. (1994). Evidence for two independent domestications of cattle. Proceedings of the National Academy of Sciences, 91(7), 2757-2761. https://doi.org/10.1073/pnas.91.7.2757
McTavish, E. J., Decker, J. E., Schnabel, R. D., Taylor, J. F., & Hillis, D. M. (2013). New World cattle show ancestry from multiple independent domestication events. Proceedings of the National Academy of Sciences, 110(15), E1398-E1406. https://doi.org/10.1073/pnas.1303367110
Nagamine, Y., Nirasawa, K., Takahashi, H., Sasaki, O., Ishii, K., Minezawa, M., … Furukawa, T. (2008). Estimation of the time of divergence between Japanese Mishima Island cattle and other cattle populations using microsatellite DNA markers. Journal of Heredity, 99(2), 202-207. https://doi.org/10.1093/jhered/esm129
Nekrutenko, A., & Taylor, J. (2012). Next-generation sequencing data interpretation: Enhancing reproducibility and accessibility. Nature Reviews Genetics, 13(9), 667. https://doi.org/10.1038/nrg3305
Nolte, W., Weikard, R., Brunner, R. M., Albrecht, E., Hammon, H. M., Reverter, A., & Kuehn, C. (2019). Biological network approach for the identification of regulatory long non-coding RNAs associated with metabolic efficiency in cattle. Frontiers in Genetics, 10, 1130. https://doi.org/10.3389/fgene.2019.01130
Okoye, C., & Ugwu, J. (2010). Impact of environmental cadmium, lead, copper and zinc on quality of goat meat in Nigeria. Bulletin of the Chemical Society of Ethiopia, 24(1).
Paradis, E. (2010). pegas: An R package for population genetics with an integrated-modular approach. Bioinformatics, 26(3), 419-420. https://doi.org/10.1093/bioinformatics/btp696
Patterson, N., Price, A. L., & Reich, D. (2006). Population structure and eigenanalysis. PLoS Genetics, 2(12), e190. https://doi.org/10.1371/journal.pgen.0020190
Pegolo, S., Cecchinato, A., Savoia, S., Di Stasio, L., Pauciullo, A., Brugiapaglia, A., … Albera, A. (2019). Genome-wide association and pathway analysis of carcass and meat quality traits in Piemontese Young Bulls. Animal, 14, 243-252.
Pertea, M., Pertea, G. M., Antonescu, C. M., Chang, T.-C., Mendell, J. T., & Salzberg, S. L. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology, 33(3), 290. https://doi.org/10.1038/nbt.3122
Porto-Neto, L. R., Kijas, J. W., & Reverter, A. (2014). The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes. Genetics Selection Evolution, 46(1), 22. https://doi.org/10.1186/1297-9686-46-22
Purcell, S., Neale, B., Todd-Brown, K., Thomas, L., Ferreira, M. A. R., Bender, D., … Sham, P. C. (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., Pausch, H., Jansen, S., Somel, M., Strom, T. M., Fries, R., … Simianer, H. (2014). Classic selective sweeps revealed by massive sequencing in cattle. PLoS Genetics, 10(2), e1004148. https://doi.org/10.1371/journal.pgen.1004148
Seidel, G. E. Jr (2014). Beef cattle in the year 2050. In G. Lamb & N. DiLorenzo (Eds.), Current and Future Reproductive Technologies and World Food Production (pp. 239-244). New York, NY: Springer.
Seo, M., Caetano-Anolles, K., Rodriguez-Zas, S., Ka, S., Jeong, J. Y., Park, S., … Lee, H.-J. (2016). Comprehensive identification of sexually dimorphic genes in diverse cattle tissues using RNA-seq. BMC Genomics, 17(1), 81. https://doi.org/10.1186/s12864-016-2400-4
Siddiq, A., Aminova, L. R., & Ratan, R. R. (2007). Hypoxia inducible factor prolyl 4-hydroxylase enzymes: Center stage in the battle against hypoxia, metabolic compromise and oxidative stress. Neurochemical Research, 32(4-5), 931-946. https://doi.org/10.1007/s11064-006-9268-7
Szpiech, Z. A., & Hernandez, R. D. (2014). selscan: An efficient multithreaded program to perform EHH-based scans for positive selection. Molecular Biology and Evolution, 31(10), 2824-2827. https://doi.org/10.1093/molbev/msu211
Tan, S. C., Gomes, R. S. M., Yeoh, K. K., Perbellini, F., Malandraki-Miller, S., Ambrose, L., … Carr, C. A. (2016). Preconditioning of cardiosphere-derived cells with hypoxia or prolyl-4-hydroxylase inhibitors increases stemness and decreases reliance on oxidative metabolism. Cell Transplantation, 25(1), 35-53. https://doi.org/10.3727/096368915X687697
Tizioto, P. C., Meirelles, S. L., Veneroni, G. B., Tullio, R. R., Rosa, A. N., Alencar, M. M., … Regitano, L. (2012). A SNP in ASAP1 gene is associated with meat quality and production traits in Nelore breed. Meat Science, 92(4), 855-857. https://doi.org/10.1016/j.meatsci.2012.05.018
Wang, K., Li, M., & Hakonarson, H. (2010). ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38(16), e164. https://doi.org/10.1093/nar/gkq603
Xie, C., Mao, X., Huang, J., Ding, Y., Wu, J., Dong, S., … Wei, L. (2011). KOBAS 2.0: A web server for annotation and identification of enriched pathways and diseases. Nucleic Acids Research, 39(suppl_2), W316-W322.
Zhang, C., Dong, S., Xu, J., He, W., & Yang, T. (2019). PopLDdecay: A fast and effective tool for linkage disequilibrium decay analysis based on variant call format files. Bioinformatics, 35(10), 1786-1788. https://doi.org/10.1093/bioinformatics/bty875