RT Journal
A1 Xi, Yang
A1 Qi, Jingjing
A1 Yang, Zhao
A1 Zeng, Yutian
A1 Zhang, Huicong
A1 Tao, Qiuyu
A1 Xu, Mengru
A1 Huang, Anqi
A1 Hu, Shenqiang
A1 Han, Chunchun
A1 Bai, Lili
A1 Hu, Jiwei
A1 Wang, Jiwen
A1 Li, Liang
A1 Fang, Lingzhao
A1 Liu, Hehe
T1 Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
JF Genome Research 
JO Genome Research 
YR 2025 
FD October 01 
VO 35 
IS 10 
SP 2211 
OP 2225 
DO 10.1101/gr.280345.124 
UL http://genome.cshlp.org/content/35/10/2211.abstract 
AB Poultry egg production is shaped by the intertwined action of multiple physiological systems, greatly magnifying the complexity of its underlying genetic regulation. Although multitissue mapping of regulatory variants offers a powerful route to untangle this complexity, comprehensive data sets in ducks remain scarce. Meanwhile, the contributions of peripheral systems beyond neuroendocrine regulation on poultry egg production are still largely unexplored. Here, we generate 979 RNA-seq samples from the liver, ovary, oviduct shell gland, and spleen, along with matched whole-genome sequencing data from 307 egg-laying ducks. We map cis-regulatory variants associated with gene expression (eQTL), alternative splicing (sQTL), and 3′ alternative polyadenylation (apaQTL), yielding 14,074, 6267, and 4994 genes with at least one significant eQTL, sQTL, and apaQTL, respectively. By integrating this resource and GWAS results, we confirm that ABCG2 expression in the shell gland specifically regulates eggshell color, with additional involvement of ENOPH1’s 3′APA sites in both the shell gland and liver. In addition, expression of LOC101800576 and LOC101790890 in the shell gland, of LOC119713219 in the ovary, and of GLP2R in the spleen is causally linked to declining egg production at peak laying. Last, we delineate a cross-tissue regulatory landscape underlying duck egg production and identify liver-derived modules, particularly Liver_ME1, which is mainly involved in cell cycle regulation, as central hubs coordinating with peripheral tissues affecting duck egg production. This work delivers a key resource and fresh perspectives for the genetic mechanism dissection of duck egg production and for future studies on cross-tissue regulation of reproduction.