Genomic Insights into Post‐Domestication Expansion and Selection of Body Size in Ponies
Source abstract
Abstract
Abstract Horse domestication revolutionizes human civilization by transforming transportation, agriculture, and warfare patterns. Despite extensive studies on modern domestic horse origins, the intricate demographic history and genetic signatures underlying pony size remain unexplored. Here, a high‐quality genome assembly of the Chinese Debao pony is presented, and 452 qualified individuals from 64 horse breeds worldwide are extensively analyzed. The authors’ results reveal the conservation of ancient components in East Asian horses and close relationships between Asian horses and Western pony lineages. Genetic analyses suggest an Asian paternal origin for European pony breeds. These pony‐sized horses share close genetic affinities, potentially attributed to their early expansion and adaptation to local environments. In addition, promising cis ‐regulatory elements influencing horse withers height by regulating genes such as RFLNA and FOXO1 are identified. Overall, this study provides insightful perspectives on the dispersal history and genetic determinants underlying body size in ponies, offering broader implications for horse population management and improvement.
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Research context
OpenAlex topics: Genetic and phenotypic traits in livestock · Genetic Mapping and Diversity in Plants and Animals · Silkworms and Sericulture Research
SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.
Affiliations
Shenzhen Branch Guangdong Laboratory of Lingnan Modern Agriculture Key Laboratory of Livestock and Poultry Multi‐omics of MARA Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Shenzhen 518124 China
Animal Husbandry Research Institute Guangxi Vocational University of Agriculture Nanning 530002 China
Nanning Capitano Equestrian Club Co., Ltd Nanning 530000 China
Anhui Provincial Key Laboratory of Livestock and Poultry Product Safety Institute of Animal Husbandry and Veterinary Medicine Anhui Academy of Agricultural Sciences Hefei 230031 China
Hainan Institute Zhejiang University Yongyou Industry Park, Yazhou Bay Sci‐Tech City Sanya 572000 China
Department of Animal Science North Carolina State University Raleigh NC 27695 USA
Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding School of Life Science and Engineering Foshan University Foshan 528225 China
Center for Quantitative Genetics and Genomics Aarhus University Aarhus 8000 Denmark
Kunpeng Institute of Modern Agriculture at Foshan Agricultural Genomics Institute at Shenzhen Chinese Academy of Agricultural Sciences Foshan 528226 China
Guangxi Veterinary Research Institute Nanning 530001 China
Bama Yao Autonomous County Rural Revitalization Research Institute Bama 547500 China
Funding
Guangxi Key Research and Development Program
References (100+)
Show source-provided references
1. 10.1038/s41586-021-04018-910.1038/s41586-021-04018-9 ↗
2. 10.1126/science.adc969110.1126/science.adc9691 ↗
3. 10.1007/s10963-021-09161-910.1007/s10963-021-09161-9 ↗
4. 10.1016/j.cell.2019.03.04910.1016/j.cell.2019.03.049 ↗
5. 10.1017/S175173111700139210.1017/S1751731117001392 ↗
6. Edwards E. H. · 2016
7. Chang H. · 2011
8. 10.1186/s12864-018-4877-510.1186/s12864-018-4877-5 ↗
9. 10.1371/journal.pone.021075110.1371/journal.pone.0210751 ↗
10. 10.1186/s12864-020-06887-210.1186/s12864-020-06887-2 ↗
11. 10.1016/j.cub.2021.11.05210.1016/j.cub.2021.11.052 ↗
12. 10.1371/journal.pone.003992910.1371/journal.pone.0039929 ↗
13. 10.1111/1755-0998.1381810.1111/1755-0998.13818 ↗
14. 10.1126/science.aao329710.1126/science.aao3297 ↗
15. 10.1073/pnas.111112210910.1073/pnas.1111122109 ↗
16. 10.1126/sciadv.abb003010.1126/sciadv.abb0030 ↗
17. 10.1038/s41586-024-07597-510.1038/s41586-024-07597-5 ↗
18. 10.1038/s42003-018-0199-z10.1038/s42003-018-0199-z ↗
19. 10.1186/s13059-022-02764-110.1186/s13059-022-02764-1 ↗
20. 10.1186/s40104-023-00860-110.1186/s40104-023-00860-1 ↗
21. Clutton‐Brock J. · 1992
22. Johns C. · 2006
23. 10.1038/nature1431710.1038/nature14317 ↗
24. 10.1186/s13293-015-0024-z10.1186/s13293-015-0024-z ↗
25. 10.3389/fgene.2020.0046710.3389/fgene.2020.00467 ↗
26. 10.1038/s41598-023-35539-010.1038/s41598-023-35539-0 ↗
27. 10.1126/sciadv.aap969110.1126/sciadv.aap9691 ↗
28. 10.1016/j.cub.2017.05.08610.1016/j.cub.2017.05.086 ↗
29. 10.1126/science.aam529810.1126/science.aam5298 ↗
30. 10.1073/pnas.151369611210.1073/pnas.1513696112 ↗
31. 10.4324/978020338992810.4324/9780203389928 ↗
32. 10.1038/s41586-021-03972-810.1038/s41586-021-03972-8 ↗
33. 10.3390/genes1003024110.3390/genes10030241 ↗
34. 10.1038/s10038-019-0581-910.1038/s10038-019-0581-9 ↗
35. 10.1038/nature1649810.1038/nature16498 ↗
36. 10.1016/j.ajhg.2017.04.01410.1016/j.ajhg.2017.04.014 ↗
37. 10.1038/s41586-021-03451-010.1038/s41586-021-03451-0 ↗
38. 10.1093/bioinformatics/btr01110.1093/bioinformatics/btr011 ↗
39. 10.1038/s41467-020-14998-310.1038/s41467-020-14998-3 ↗
40. 10.1038/nmeth.403510.1038/nmeth.4035 ↗
41. 10.1038/s41592-019-0669-310.1038/s41592-019-0669-3 ↗
42. 10.1101/gr.215087.11610.1101/gr.215087.116 ↗
43. 10.1093/bioinformatics/btaa02510.1093/bioinformatics/btaa025 ↗
44. 10.1126/science.aal332710.1126/science.aal3327 ↗
45. 10.1002/imt2.10710.1002/imt2.107 ↗
46. 10.1016/j.cels.2015.07.01210.1016/j.cels.2015.07.012 ↗
47. 10.1186/s13059-020-02154-510.1186/s13059-020-02154-5 ↗
48. 10.1371/journal.pone.011296310.1371/journal.pone.0112963 ↗
49. 10.1093/molbev/msab19910.1093/molbev/msab199 ↗
50. 10.1186/s13059-020-02134-910.1186/s13059-020-02134-9 ↗
51. 10.1371/journal.pcbi.100594410.1371/journal.pcbi.1005944 ↗
52. 10.1093/bioinformatics/btt08610.1093/bioinformatics/btt086 ↗
53. 10.1186/s13100-015-0041-910.1186/s13100-015-0041-9 ↗
54. 10.1073/pnas.192104611710.1073/pnas.1921046117 ↗
55. 10.1093/nar/27.2.57310.1093/nar/27.2.573 ↗
56. 10.1101/gr.8850210.1101/gr.88502 ↗
57. 10.1093/bioinformatics/bti101810.1093/bioinformatics/bti1018 ↗
58. 10.1104/pp.17.0131010.1104/pp.17.01310 ↗
59. 10.1093/nargab/lqaa10810.1093/nargab/lqaa108 ↗
60. 10.1002/0471250953.bi0411s4810.1002/0471250953.bi0411s48 ↗
61. 10.1038/s41587-019-0201-410.1038/s41587-019-0201-4 ↗
62. 10.1038/nbt.312210.1038/nbt.3122 ↗
63. 10.1093/bioinformatics/btab70510.1093/bioinformatics/btab705 ↗
64. 10.1101/gr.081612.10810.1101/gr.081612.108 ↗
65. 10.1186/1471-2105-5-5910.1186/1471-2105-5-59 ↗
66. 10.1093/bioinformatics/btn01310.1093/bioinformatics/btn013 ↗
67. 10.1093/bioinformatics/btu03110.1093/bioinformatics/btu031 ↗
68. 10.1371/journal.pcbi.100679010.1371/journal.pcbi.1006790 ↗
69. 10.1038/s41592-021-01101-x10.1038/s41592-021-01101-x ↗
70. 10.1093/nar/gkm16010.1093/nar/gkm160 ↗
71. 10.1093/nar/gkab68810.1093/nar/gkab688 ↗
72. 10.1093/bioinformatics/btt50910.1093/bioinformatics/btt509 ↗
73. 10.1186/s13059-019-1832-y10.1186/s13059-019-1832-y ↗
74. 10.1038/s41467-022-34630-w10.1038/s41467-022-34630-w ↗
75. 10.1093/bioinformatics/btu03310.1093/bioinformatics/btu033 ↗
76. 10.1093/molbev/msm08810.1093/molbev/msm088 ↗
77. 10.1093/bioinformatics/btaa102210.1093/bioinformatics/btaa1022 ↗
78. Wu T. · Innovation · 2021 · 2
79. 10.1186/1741-7007-4-4110.1186/1741-7007-4-41 ↗
80. 10.1093/molbev/msab29310.1093/molbev/msab293 ↗
81. H.Li Aligning sequence reads clone sequences and assembly contigs with BWA‐MEM arXiv preprint arXiv:1303.39972013.
82. 10.1093/gigascience/giab00810.1093/gigascience/giab008 ↗
83. 10.1007/978-1-0716-2293-3_1910.1007/978-1-0716-2293-3_19 ↗
84. 10.1186/s13742-015-0047-810.1186/s13742-015-0047-8 ↗
85. 10.1016/j.ajhg.2010.11.01110.1016/j.ajhg.2010.11.011 ↗
86. 10.1016/S0168-9525(00)02024-210.1016/S0168-9525(00)02024-2 ↗
87. 10.1002/imt2.5610.1002/imt2.56 ↗
88. 10.1101/gr.094052.10910.1101/gr.094052.109 ↗
89. 10.1534/g3.119.40083310.1534/g3.119.400833 ↗
90. 10.1371/journal.pone.016301910.1371/journal.pone.0163019 ↗
91. 10.1093/molbev/msx24810.1093/molbev/msx248 ↗
92. 10.1111/2041-210X.1241010.1111/2041-210X.12410 ↗
93. 10.1016/j.cub.2015.08.03210.1016/j.cub.2015.08.032 ↗
94. 10.1371/journal.pgen.100296710.1371/journal.pgen.1002967 ↗
95. 10.7554/eLife.8549210.7554/eLife.85492 ↗
96. 10.1093/bioinformatics/bty87510.1093/bioinformatics/bty875 ↗
97. 10.1038/s41587-019-0336-310.1038/s41587-019-0336-3 ↗
98. M.Milanesi S.Capomaccio E.Vajana L.Bomba J. F.Garcia P.Ajmone‐Marsan L.Colli BITE: an R package for biodiversity analyses bioRxiv2017 181610.10.1101/181610 ↗
99. 10.1093/bioinformatics/btr33010.1093/bioinformatics/btr330 ↗
100. 10.1016/j.ajhg.2021.08.00510.1016/j.ajhg.2021.08.005 ↗