Integrating genome-wide association study and haplotype-resolved epigenomes reveals complex parent-of-origin…

Abstract

Background: Parent-of-origin effects (POEs) violate the assumption of additive genetic models by allowing allelic effects to depend on parental origin, yet their mechanistic basis remains incompletely understood.

Results: Here, we combine genome-wide POE mapping in an F2 Eurasian pig population with haplotype-resolved transcriptomes and epigenomes from reciprocal crosses. We uncover widespread POEs affecting growth traits, many outside canonical imprinted regions, indicating that canonical imprinting explains only a subset of parent-of-origin-dependent variation. We recapitulate known imprinting effects at loci such as IGF2 and KCNQ1 , and link distal POE loci for rib length to IGF2 by long-range chromatin interactions. Strikingly, some POEs emerge from parent-specific 3D chromatin architecture, independent of allele-specific expression or histone marks. Cross-species comparisons nominate additional candidate imprinted genes.

Conclusions: Together, our results reveal POEs as pervasive and mechanistically diverse, and show chromatin topology as a plausible candidate mechanism of parental-origin regulation, reshaping our understanding of complex trait inheritance.

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BibTeX RIS

BibTeX

@article{tao2026integrating,
  title = {{Integrating genome-wide association study and haplotype-resolved epigenomes reveals complex parent-of-origin effects in pigs}},
  author = {Lin Tao and Li-Gang Wang and Jian-Bo Li and Shu-Run Zhang and Long-Chao Zhang and Jia-Kun Deng and Jiang-Wei Lin and Mei Hu and Adeniyi C. Adeola and Xin-Yao Feng and Dao-Ji Cen and Zi-Qin Huang and Qing-Long Li and Chen-Yan Liao and Shu-Shu Yan and Li-Xian Wang and Hai-Bing Xie and Ya-Ping Zhang},
  journal = {BMC Genomics},
  year = {2026},
  month = oct,
  doi = {10.1186/s12864-026-13396-1},
  url = {https://link.springer.com/article/10.1186/s12864-026-13396-1},
  note = {CC BY 4.0},
}

RIS

TY  - JOUR
TI  - Integrating genome-wide association study and haplotype-resolved epigenomes reveals complex parent-of-origin effects in pigs
AU  - Lin Tao
AU  - Li-Gang Wang
AU  - Jian-Bo Li
AU  - Shu-Run Zhang
AU  - Long-Chao Zhang
AU  - Jia-Kun Deng
AU  - Jiang-Wei Lin
AU  - Mei Hu
AU  - Adeniyi C. Adeola
AU  - Xin-Yao Feng
AU  - Dao-Ji Cen
AU  - Zi-Qin Huang
AU  - Qing-Long Li
AU  - Chen-Yan Liao
AU  - Shu-Shu Yan
AU  - Li-Xian Wang
AU  - Hai-Bing Xie
AU  - Ya-Ping Zhang
PY  - 2026
DA  - 2026/10/21
JO  - BMC Genomics
DO  - 10.1186/s12864-026-13396-1
UR  - https://link.springer.com/article/10.1186/s12864-026-13396-1
AB  - Background: Parent-of-origin effects (POEs) violate the assumption of additive genetic models by allowing allelic effects to depend on parental origin, yet their mechanistic basis remains incompletely understood.  Results: Here, we combine genome-wide POE mapping in an F2 Eurasian pig population with haplotype-resolved transcriptomes and epigenomes from reciprocal crosses. We uncover widespread POEs affecting growth traits, many outside canonical imprinted regions, indicating that canonical imprinting explains only a subset of parent-of-origin-dependent variation. We recapitulate known imprinting effects at loci such as IGF2 and KCNQ1 , and link distal POE loci for rib length to IGF2 by long-range chromatin interactions. Strikingly, some POEs emerge from parent-specific 3D chromatin architecture, independent of allele-specific expression or histone marks. Cross-species comparisons nominate additional candidate imprinted genes.  Conclusions: Together, our results reveal POEs as pervasive and mechanistically diverse, and show chromatin topology as a plausible candidate mechanism of parental-origin regulation, reshaping our understanding of complex trait inheritance.
SN  - 1471-2164
ER  -

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