Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens
Introduction: Domestic chickens primarily descended from the wild red junglefowl, play a crucial role in global egg and meat production. China hosts diverse indigenous chicken populations that have adapted to various environmental conditions, including high-altitude with hypoxic and ultraviolet radi...
| Autores principales: | , , , , , , , , , , , , , , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Elsevier
2026
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/179247 |
| _version_ | 1855516186320568320 |
|---|---|
| author | Bello, S.F. Terefe, E. Ye, H. Adeola, A.C. Zhou, Z. Jebessa, E. Qi, L. Ahmed, R.O. Aloryi, K.D. Ositanwosu, O.E. Eludodun, S.J. Zhang, Z. Tiamiyu, B.B. Ladejobi, A.K. Ahbara, A.M. Salim, B. Rothenberg, D.O. Adigun, O.A. Zhang, X. Cai, B. Hanotte, Olivier H. Nie, Q. |
| author_browse | Adeola, A.C. Adigun, O.A. Ahbara, A.M. Ahmed, R.O. Aloryi, K.D. Bello, S.F. Cai, B. Eludodun, S.J. Hanotte, Olivier H. Jebessa, E. Ladejobi, A.K. Nie, Q. Ositanwosu, O.E. Qi, L. Rothenberg, D.O. Salim, B. Terefe, E. Tiamiyu, B.B. Ye, H. Zhang, X. Zhang, Z. Zhou, Z. |
| author_facet | Bello, S.F. Terefe, E. Ye, H. Adeola, A.C. Zhou, Z. Jebessa, E. Qi, L. Ahmed, R.O. Aloryi, K.D. Ositanwosu, O.E. Eludodun, S.J. Zhang, Z. Tiamiyu, B.B. Ladejobi, A.K. Ahbara, A.M. Salim, B. Rothenberg, D.O. Adigun, O.A. Zhang, X. Cai, B. Hanotte, Olivier H. Nie, Q. |
| author_sort | Bello, S.F. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Introduction: Domestic chickens primarily descended from the wild red junglefowl, play a crucial role in global egg and meat production. China hosts diverse indigenous chicken populations that have adapted to various environmental conditions, including high-altitude with hypoxic and ultraviolet radiation stress.
Method: We analyzed whole-genome sequences of 118 birds from five Indigenous Chinese chicken populations and 295 chicken genomes from publicly available databases to identify genomic diversity, admixture, and selection signatures of chickens adapted to high-altitude environments. Selection signatures were identified using nucleotide diversity (π), Tajima’s D, XPEHH, and XP-CLR, selection scan methods.
Results: We observed a reduction in genetic diversity and historical declines in effective population size in high-altitude chicken, suggesting ongoing selection pressures shaping these populations. Selection scans identified nine genomic regions under strong positive selection, enriched for genes associated with hypoxia and ultraviolet radiation. Notably, five genes (TPK1, BAZ2B, MARCHF7, LLGL2, and RCAN3) were repeatedly detected across multiple selection signature analyses. RNA-seq analysis further confirmed the differential expression of these genes in the lung and heart tissues of chickens adapted to high and low altitudes, reinforcing their role in physiological adaptation to hypoxic environments. Altitude adaptation is driven by the selection of genes involved in oxygen metabolism, cellular stress response, and energy regulation.
Conclusion: Our study provides compelling genetic evidence for differentiation between high and low and high-altitude Chinese chicken populations. These findings also ensure our understanding of local adaptation in poultry and establish a genomic framework for breeding strategies to improve environmental resilience to altitude-related stressors. |
| format | Journal Article |
| id | CGSpace179247 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2026 |
| publishDateRange | 2026 |
| publishDateSort | 2026 |
| publisher | Elsevier |
| publisherStr | Elsevier |
| record_format | dspace |
| spelling | CGSpace1792472026-01-19T10:04:15Z Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens Bello, S.F. Terefe, E. Ye, H. Adeola, A.C. Zhou, Z. Jebessa, E. Qi, L. Ahmed, R.O. Aloryi, K.D. Ositanwosu, O.E. Eludodun, S.J. Zhang, Z. Tiamiyu, B.B. Ladejobi, A.K. Ahbara, A.M. Salim, B. Rothenberg, D.O. Adigun, O.A. Zhang, X. Cai, B. Hanotte, Olivier H. Nie, Q. chickens genomics poultry Introduction: Domestic chickens primarily descended from the wild red junglefowl, play a crucial role in global egg and meat production. China hosts diverse indigenous chicken populations that have adapted to various environmental conditions, including high-altitude with hypoxic and ultraviolet radiation stress. Method: We analyzed whole-genome sequences of 118 birds from five Indigenous Chinese chicken populations and 295 chicken genomes from publicly available databases to identify genomic diversity, admixture, and selection signatures of chickens adapted to high-altitude environments. Selection signatures were identified using nucleotide diversity (π), Tajima’s D, XPEHH, and XP-CLR, selection scan methods. Results: We observed a reduction in genetic diversity and historical declines in effective population size in high-altitude chicken, suggesting ongoing selection pressures shaping these populations. Selection scans identified nine genomic regions under strong positive selection, enriched for genes associated with hypoxia and ultraviolet radiation. Notably, five genes (TPK1, BAZ2B, MARCHF7, LLGL2, and RCAN3) were repeatedly detected across multiple selection signature analyses. RNA-seq analysis further confirmed the differential expression of these genes in the lung and heart tissues of chickens adapted to high and low altitudes, reinforcing their role in physiological adaptation to hypoxic environments. Altitude adaptation is driven by the selection of genes involved in oxygen metabolism, cellular stress response, and energy regulation. Conclusion: Our study provides compelling genetic evidence for differentiation between high and low and high-altitude Chinese chicken populations. These findings also ensure our understanding of local adaptation in poultry and establish a genomic framework for breeding strategies to improve environmental resilience to altitude-related stressors. 2026 2025-12-23T17:31:40Z 2025-12-23T17:31:40Z Journal Article https://hdl.handle.net/10568/179247 en Open Access Elsevier Bello, S.F., Terefe, E., Ye, H., Adeola, A.C., Zhou, Z., Jebessa, E., Qi, L., Ahmed, R.O., Aloryi, K.D., Ositanwosu, O.E., Eludodun, S.J., Zhang, Z., Tiamiyu, B.B., Ladejobi, A.K., Ahbara, A.M., Salim, B., Rothenberg, D.O., Adigun, O.A., Zhang, X., Cai, B., Hanotte, O. and Nie, Q. 2026. Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens. Journal of Advanced Research. |
| spellingShingle | chickens genomics poultry Bello, S.F. Terefe, E. Ye, H. Adeola, A.C. Zhou, Z. Jebessa, E. Qi, L. Ahmed, R.O. Aloryi, K.D. Ositanwosu, O.E. Eludodun, S.J. Zhang, Z. Tiamiyu, B.B. Ladejobi, A.K. Ahbara, A.M. Salim, B. Rothenberg, D.O. Adigun, O.A. Zhang, X. Cai, B. Hanotte, Olivier H. Nie, Q. Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens |
| title | Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens |
| title_full | Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens |
| title_fullStr | Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens |
| title_full_unstemmed | Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens |
| title_short | Whole-genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in Chinese chickens |
| title_sort | whole genome sequencing identifies genetic diversity and adaptive signatures of hypoxia and ultraviolet radiation in chinese chickens |
| topic | chickens genomics poultry |
| url | https://hdl.handle.net/10568/179247 |
| work_keys_str_mv | AT bellosf wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT terefee wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT yeh wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT adeolaac wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT zhouz wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT jebessae wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT qil wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT ahmedro wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT aloryikd wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT ositanwosuoe wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT eludodunsj wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT zhangz wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT tiamiyubb wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT ladejobiak wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT ahbaraam wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT salimb wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT rothenbergdo wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT adigunoa wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT zhangx wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT caib wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT hanotteolivierh wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens AT nieq wholegenomesequencingidentifiesgeneticdiversityandadaptivesignaturesofhypoxiaandultravioletradiationinchinesechickens |