Publications · Chao Ning

In review

Chao Ning, Xiang Zhou^*. fastGxE: powering genome-wide detection of genotype–environment interactions in biobank studies

Under review, Nature Genetics. Project page →

2026 5 papers

Integrative analysis of GWAS, Bayesian fine-mapping, Mendelian randomization and colocalization reveals genetic determinants underlying milk-related traits in dairy cattle

Jun Teng, Xiuxin Zhao, Qingxia Yan, Jian Yang, Fen Pei, Xinyi Zhang, Chongwei Duan, Zhujun Chen, Qianwen Xu, Yan Liu, Guanghui Xue, Shuwen Xia, Huili Wang, Yao Gu, Lingzhao Fang, Huiming Liu, Hongding Gao, Jing An, Li Jiang, Chao Ning, Rongling Li, Yundong Gao, Xiao Wang, Jianbin Li, Qin Zhang. Genetics Selection Evolution, 2026.
Genome-wide variation landscape reveals temperature adaptation in Chinese indigenous cattle

Changheng Zhao, Jun Teng, Yan Chen, Cheng Yang, Xinyi Zhang, Chao Ning, Huili Wang, QiEn Yang, Wenfa Lv, Dan Wang, Qin Zhang. Journal of Animal Science and Biotechnology, 2026.
Insights into Nuclear Mitochondrial Sequence Distribution in the Pig Genome Based on the Latest Reference Assembly

Hongtao Li, Cheng Yang, Guiming Zhu, Qin Zhang, Chao Ning, Dan Wang. Animals, 2026.
Comparative Accuracy of Machine Learning and GBLUP for Predicting Genomic Estimated Breeding Values in Chickens

Haoxiang Chai, Yuqi Yang, Dan Wang, Chao Ning, Xiaohui Zhang, Wenwen Wang, Qin Zhang, Haigang Bao, Hui Tang. Genes, 2026.
Meta‐GWAS of Pig Semen Quality Traits Reveals Conserved Genes Regulating Mammalian Fertility

Qing Lin, Xiaodian Cai, Zhanming Zhong, Tingting Li, Xinyou Chen, Wondossen Ayalew, Zhiting Xu, Chen Wei, Xiaoke Zhang, Hong Cheng, Zhenyang Zhang, Xuehua Li, Yongjie Tang, Siqian Chen, Jun Zhou, Jinglei Si, Xibo Wu, Chao Ning, Qishan Wang, Yuchun Pan, Yahui Gao, Jiaqi Li, Ying Yu, Zhe Zhang, Yunxiang Zhao, Lingzhao Fang, Zhe Zhang. Advanced Science, 2026.

2025 5 papers

Bayesian fine-mapping and Mendelian randomization leveraging expression quantitative trait loci reveal novel candidate causal genes for body conformation traits in cattle

Jun Teng, Chongwei Duan, Xinyi Zhang, Zhujun Chen, Chao Ning, Rongling Li, Yundong Gao, Hongding Gao, Huiming Liu, Jianbin Li, Xiao Wang, Qin Zhang. Journal of Dairy Science, 2025.
Identification of key LncRNAs and mRNAs associated with intramuscular fat in pig via WGCNA

Wenqiang Li, Suozhou Yang, Huixin Liu, Zhi Cao, Fei Xu, Chao Ning, Qin Zhang, Dan Wang, Hui Tang. BMC genomics, 2025.
Improving multi-trait genomic prediction by incorporating local genetic correlations

Jun Teng, Tingting Zhai, Xinyi Zhang, Changheng Zhao, Wenwen Wang, Hui Tang, Chao Ning, Yingli Shang, Dan Wang, Qin Zhang. Communications Biology, 2025.
Integrating proteomics and metabolomics to elucidate the regulatory mechanisms of pimpled egg production in chickens: Multi-omics analysis of the mechanism of pimpled egg formation

Wenqiang Li, Xueying Ma, Xiaomin Li, Xuguang Zhang, Yifei Sun, Chao Ning, Qin Zhang, Dan Wang, Hui Tang. Poultry Science, 2025.
Genomic selection based on random regression test-day model in dairy cattle with respect to different reference populations

Xianming Wei, Jun Teng, Shixi Zhang, Pengju Zhao, Guilin Chen, Zhi Cao, Yan Chen, Jianbin Li, Chao Ning, Qin Zhang. Animal – Open Space, 2025.

2024 9 papers

Integrating single-cell RNA-seq and ATAC-seq analysis reveals uterine cell heterogeneity and regulatory networks linked to pimpled eggs in chickens

Wenqiang Li, Xueying Ma, Xiaomin Li, Xuguang Zhang, Yifei Sun, Chao Ning, Qin Zhang, Dan Wang, Hui Tang. International Journal of Molecular Sciences, 2024.
Genome-wide association study of insertions and deletions identified novel loci associated with milk production traits in dairy cattle

Lu Zhao, Jun Teng, Chao Ning, Qin Zhang. Animals, 2024.
Population structure and breed identification of Chinese indigenous sheep breeds using whole genome SNPs and InDels

Chang-heng Zhao, Dan Wang, Cheng Yang, Yan Chen, Jun Teng, Xin-yi Zhang, Zhi Cao, Xian-ming Wei, Chao Ning, Qi-en Yang, Wen-fa Lv, Qin Zhang. Genetics Selection Evolution, 2024.
Improving multi-population genomic prediction accuracy using multi-trait GBLUP models which incorporate global or local genetic correlation information

Jun Teng, Tingting Zhai, Xinyi Zhang, Changheng Zhao, Wenwen Wang, Hui Tang, Dan Wang, Yingli Shang, Chao Ning^*, Qin Zhang^*. Briefings in Bioinformatics, 2024.
Whole transcriptome sequencing reveals key genes and ceRNA regulatory networks associated with pimpled eggs in hens

Wenqiang Li, Zhi Cao, Fei Xu, Xuguang Zhang, Yifei Sun, Zhongbiao Xie, Chao Ning, Qin Zhang, Dan Wang, Hui Tang. Poultry Science, 2024.
Marker density and models to improve the accuracy of genomic selection for growth and slaughter traits in meat rabbits

Wenjie Li, Wenqiang Li, Zichen Song, Zihao Gao, Kerui Xie, Yubing Wang, Bo Wang, Jiaqing Hu, Qin Zhang, Chao Ning, Dan Wang, Xinzhong Fan. Genes, 2024.
Resequencing analyses revealed genetic diversity and selection signatures during rabbit breeding and improvement

Kerui Xie, Chao Ning, Aiguo Yang, Qin Zhang, Dan Wang, Xinzhong Fan. Genes, 2024.
Identify candidate genes associated with the weight and egg quality traits in Wenshui green shell-laying chickens by the copy number variation-based genome-wide association study

Suozhou Yang, Chao Ning, Cheng Yang, Wenqiang Li, Qin Zhang, Dan Wang, Hui Tang. Veterinary Sciences, 2024.
Whole-genome resequencing revealed the origin and domestication of Chinese domestic rabbits

Kerui Xie, Zichen Song, Yanyan Wang, Di Yan, Wenqiang Li, Yubin Wang, Aiguo Yang, Xibo Qiao, Bo Wang, Mingyong Li, Xiping Xie, Xiaohong Xie, Lie Liu, Chao Ning, Hui Tang, Xianyao Li, Xinsheng Wu, Qin Zhang, Dan Wang, Xinzhong Fan. bioRxiv, 2024.

2023 4 papers

Mitogenome-wide association study on body measurement traits of Wenshang Barred chickens

Dan Wang, Jun Teng, Chao Ning, Wenwen Wang, Shuai Liu, Qin Zhang, Hui Tang. Animal Biotechnology, 2023.
Genome-wide association study for numbers of vertebrae in Dezhou donkey population reveals new candidate genes

SUN Yan, TENG Jun, WANG Yong-hui, WANG Tian-qi, SHI Xiao-yuan, LIU Zi-wen, LI Hai-jing, WANG Ji-jing, WANG Wen-wen, NING Chao, WANG Chang-fa. Journal of Integrative Agriculture, 2023.
Longitudinal genome-wide association studies of milk production traits in Holstein cattle using whole-genome sequence data imputed from medium-density chip data

Jun Teng^†, Dan Wang^†, Changheng Zhao, Xinyi Zhang, Zhi Chen, Jianfeng Liu, Dongxiao Sun, Hui Tang, Wenwen Wang, Jianbin Li, Cheng Mei, Zhangping Yang, Chao Ning^*, Qin Zhang^*. Journal of Dairy Science, 2023.
Identification of key lncRNAs and mRNAs related to intramuscular fat in pigs by WGCNA

Wenqiang Li, Suozhou Yang, Huixin Liu, Zhi Cao, Fei Xu, Chao Ning, Qin Zhang, Dan Wang, Hui Tang. Research Square (preprint), 2023.

2022 6 papers

Cost-effectively dissecting the genetic architecture of complex wool traits in rabbits by low-coverage sequencing

Dan Wang, Kerui Xie, Yanyan Wang, Jiaqing Hu, Wenqiang Li, Aiguo Yang, Qin Zhang, Chao Ning, Xinzhong Fan. Genetics Selection Evolution, 2022.
Marker density and statistical model designs to increase accuracy of genomic selection for wool traits in Angora rabbits

Chao Ning, Kerui Xie, Juanjuan Huang, Yan Di, Yanyan Wang, Aiguo Yang, Jiaqing Hu, Qin Zhang, Dan Wang^*, Xinzhong Fan^*. Frontiers in Genetics, 2022.
Estimate of inbreeding depression on growth and reproductive traits in a Large White pig population

Yu Zhang, Yue Zhuo, Chao Ning, Lei Zhou, Jian-Feng Liu. G3, 2022.
Assessment of the performance of different imputation methods for low-coverage sequencing in Holstein cattle

Jun Teng, Changheng Zhao, Dan Wang, Zhi Chen, Hui Tang, Jianbin Li, Cheng Mei, Zhangping Yang, Chao Ning^*, Qin Zhang^*. Journal of Dairy Science, 2022.
Transcriptional regulation of the chicken ASMT gene – a preliminary analysis

Jun Teng, Dan Wang, Wenwen Wang, Chao Ning, Qin Zhang, Hui Tang. British Poultry Science, 2022.
Effects of growth-related genes on body measurement traits in Wenshang barred chickens

Cheng Yang, Jun Teng, Chao Ning, Wenwen Wang, Shuai Liu, Qin Zhang, Dan Wang, Hui Tang. The journal of poultry science, 2022.

2021 4 papers

Towards a cost-effective implementation of genomic prediction based on low coverage whole genome sequencing in Dezhou donkey

Changheng Zhao, Jun Teng, Xinhao Zhang, Dan Wang, Xinyi Zhang, Shiyin Li, Xin Jiang, Haijing Li, Chao Ning^*, Qin Zhang^*. Frontiers in Genetics, 2021.
Breed-specific reference sequence optimized mapping accuracy of NGS analyses for pigs

Dan Wang, Liu Yang, Chao Ning, Jian-Feng Liu, Xingbo Zhao. BMC genomics, 2021.
Mining Unknown Porcine Protein Isoforms by Tissue-based Map of Proteome Enhances Pig Genome Annotation

Pengju Zhao, Xianrui Zheng, Ying Yu, Zhuocheng Hou, Chenguang Diao, Haifei Wang, Huimin Kang, Chao Ning, Junhui Li, Wen Feng, Wen Wang, George E Liu, Bugao Li, Jacqueline Smith, Yangzom Chamba, Jian-Feng Liu. Genomics, Proteomics & Bioinformatics, 2021.
Integrative analysis of genome‐wide DNA methylation and gene expression profiles reveals important epigenetic genes related to milk production traits in dairy cattle

Wanting Dong, Jie Yang, Yu Zhang, Shuli Liu, Chao Ning, Xiangdong Ding, Wenwen Wang, Yi Zhang, Qin Zhang, Li Jiang. Journal of Animal Breeding and Genetics, 2021.

2020 6 papers

Cybrid model supports mitochondrial genetic effect on pig litter size

Hao Liu, Jikun Wang, Dan Wang, Minghua Kong, Chao Ning, Xing Zhang, Jinlong Xiao, Xin Zhang, Jianfeng Liu, Xingbo Zhao. Frontiers in Genetics, 2020.
Rapid epistatic mixed-model association studies by controlling multiple polygenic effects

Dan Wang, Hui Tang, Jian-Feng Liu, Shizhong Xu, Qin Zhang^*, Chao Ning^*. Bioinformatics, 2020.
Mitochondrial DNA enrichment reduced NUMT contamination in porcine NGS analyses

Dan Wang, Hai Xiang, Chao Ning, Hao Liu, Jian-Feng Liu, Xingbo Zhao. Briefings in bioinformatics, 2020.
CNV analysis of Meishan pig by next-generation sequencing and effects of AHR gene CNV on pig reproductive traits

Xianrui Zheng, Pengju Zhao, Kaijie Yang, Chao Ning, Haifei Wang, Lei Zhou, Jianfeng Liu. Journal of animal science and biotechnology, 2020.
Identification of whole-genome significant single nucleotide polymorphisms in candidate genes associated with serum biochemical traits in Chinese Holstein cattle

Kerong Shi, Fugui Niu, Qin Zhang, Chao Ning, Shujian Yue, Chengzhang Hu, Zhongjin Xu, Shengxuan Wang, Ranran Li, Qiuling Hou, Zhonghua Wang. Frontiers in Genetics, 2020.
Relationship between mitochondrial DNA haplogroup and litter size in the pig

Dan Wang, Chao Ning, Jian-Feng Liu, Xingbo Zhao. Reproduction, Fertility and Development, 2020.

2019 5 papers

Efficient multivariate analysis algorithms for longitudinal genome-wide association studies

Chao Ning, Dan Wang, Lei Zhou, Julong Wei, Yuanxin Liu, Huimin Kang, Shengli Zhang, Xiang Zhou, Shizhong Xu, Jian-Feng Liu. Bioinformatics, 2019.
A novel mutation in the promoter region of RPL8 regulates milk fat traits in dairy cattle by binding transcription factor Pax6

Xian-Rui Zheng, Li Jiang, Chao Ning, Zheng-Zheng Hu, Lei Zhou, Ying Yu, Sheng-Li Zhang, Jian-Feng Liu. Biochimica et Biophysica Acta (BBA)-Molecular and Cell Biology of Lipids, 2019.
A novel lncRNA regulates the toll-like receptor signaling pathway and related immune function by stabilizing FOS mRNA as a competitive endogenous RNA

Hao Fan, Zengpeng Lv, Liping Gan, Chao Ning, Zhui Li, Minghui Yang, Beibei Zhang, Bochen Song, Guang Li, Dazhi Tang, Jinxin Gao, Shaojia Yan, Youli Wang, Jianfeng Liu, Yuming Guo. Frontiers in Immunology, 2019.
Replication of genome-wide association studies for milk production traits in Chinese Holstein by an efficient rotated linear mixed model

Dan Wang^†, Chao Ning^†, Jian-Feng Liu, Qin Zhang, Li Jiang. Journal of dairy science, 2019.
RNA Expression Profile and Alternative Splicing Signatures of Genistein‐Treated Breeder Hens Revealed by Hepatic Transcriptomic Analysis

Zengpeng Lv, Jingle Jiang, Chao Ning, Hongjian Dai, Song Jin, Xihui Wei, Debing Yu, Fangxiong Shi. Oxidative Medicine and Cellular Longevity, 2019.

2018 10 papers

Single-step genomic evaluation of milk production traits using multiple-trait random regression model in Chinese Holsteins

H Kang, C Ning, L Zhou, S Zhang, Q Yan, J-F Liu. Journal of dairy science, 2018.
Integrated analysis of long noncoding RNA and mRNA expression profiles reveals the potential role of long noncoding RNA in different bovine lactation stages

X Zheng^†, C Ning^†, P Zhao, W Feng, Y Jin, L Zhou, Y Yu, J Liu. Journal of dairy science, 2018.
Polymorphism of mitochondrial tRNA genes associated with the number of pigs born alive

Dan Wang^†, Chao Ning^†, Hai Xiang, Xianrui Zheng, Minghua Kong, Tao Yin, Jianfeng Liu, Xingbo Zhao. Journal of animal science and biotechnology, 2018.
Genome-wide association study for intramuscular fat content in Chinese Lulai black pigs

Yanping Wang^†, Chao Ning^†, Cheng Wang, Jianfeng Guo, Jiying Wang, Ying Wu. Asian-Australasian journal of animal sciences, 2018.
Piblup: high-performance software for large-scale genetic evaluation of animals and plants

Huimin Kang, Chao Ning, Lei Zhou, Shengli Zhang, Ning Yang, Jian-Feng Liu. Frontiers in Genetics, 2018.
Dietary genistein supplementation in laying broiler breeder hens alters the development and metabolism of offspring embryos as revealed by hepatic transcriptome analysis

Zengpeng Lv, Hao Fan, Beibei Zhang, Chao Ning, Kun Xing, Yuming Guo. The FASEB Journal, 2018.
A rapid epistatic mixed-model association analysis by linear retransformations of genomic estimated values

Chao Ning, Dan Wang, Huimin Kang, Raphael Mrode, Lei Zhou, Shizhong Xu, Jian-Feng Liu. Bioinformatics, 2018.
Eigen decomposition expedites longitudinal genome-wide association studies for milk production traits in Chinese Holstein

Chao Ning^†, Dan Wang^†, Xianrui Zheng^†, Qin Zhang, Shengli Zhang, Raphael Mrode, Jian-Feng Liu. Genetics Selection Evolution, 2018.
Profiling long noncoding RNA of multi-tissue transcriptome enhances porcine noncoding genome annotation

Pengju Zhao, Xianrui Zheng, Wen Feng, Haifei Wang, Huimin Kang, Chao Ning, Heng Du, Ying Yu, Bugao Li, Yi Zhao, Jian-Feng Liu. Epigenomics, 2018.
Transcriptome of porcine PBMCs over two generations reveals key genes and pathways associated with variable antibody responses post PRRSV vaccination

Ting Yang, Fengxia Zhang, Liwei Zhai, Weiyong He, Zhen Tan, Yangyang Sun, Yuan Wang, Lei Liu, Chao Ning, Weiliang Zhou, Hong Ao, Chuduan Wang, Ying Yu. Scientific reports, 2018.

2017 6 papers

Quantitative proteome analysis of bovine mammary gland reveals protein dynamic changes involved in peak and late lactation stages

Xianrui Zheng^†, Chao Ning^†, Yichun Dong, Pengju Zhao, Junhui Li, Ziyao Fan, Jiang Li, Ying Yu, Raphael Mrode, Jian-feng Liu. Biochemical and biophysical research communications, 2017.
Genome-wide association study of piglet uniformity and farrowing interval

Yuan Wang, Xiangdong Ding, Zhen Tan, Chao Ning, Kai Xing, Ting Yang, Yongjie Pan, Dongxiao Sun, Chuduan Wang. Frontiers in genetics, 2017.
Genome-wide DNA methylation and transcriptome analyses reveal genes involved in immune responses of pig peripheral blood mononuclear cells to poly I: C

Haifei Wang^†, Jiying Wang^†, Chao Ning^†, Xianrui Zheng, Jinlian Fu, Aiguo Wang, Qin Zhang, Jian-Feng Liu. Scientific reports, 2017.
Functional validation of GPIHBP1 and identification of a functional mutation in GPIHBP1 for milk fat traits in dairy cattle

Jie Yang, Xuan Liu, Dan Wang, Chao Ning, Haifei Wang, Qin Zhang, Li Jiang. Scientific reports, 2017.
Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals

Xiaotian Feng, Jicai Jiang, Abinash Padhi, Chao Ning, Jinluan Fu, Aiguo Wang, Raphael Mrode, Jian-Feng Liu. BMC genomics, 2017.
Performance gains in genome-wide association studies for longitudinal traits via modeling time-varied effects

Chao Ning^†, Huimin Kang^†, Lei Zhou, Dan Wang, Haifei Wang, Aiguo Wang, Jinluan Fu, Shengli Zhang, Jianfeng Liu. Scientific reports, 2017.