# Topics and Trends in Most Cited Genetic and phenotypic traits in livestock Papers, Class of 2026

*Canonical URL: https://pri.pepkio.com/top-papers/genetic-and-phenotypic-traits-in-livestock/2026*

## What topics and trends defined most-cited Genetic and phenotypic traits in livestock research in the Class of 2026?

The Class of 2026 is defined by a surge in high-resolution multi-omics and single-cell RNA sequencing, moving beyond traditional genomic selection. Research increasingly targets specific breeds like Hu and Tibetan sheep, emphasizing high-altitude adaptation and microbiome interactions to unravel complex phenotypic traits.

## At a glance

| Fact | Value |
| --- | --- |
| Field | Genetic and phenotypic traits in livestock |
| Cohort label | Class of 2026 (2024 publications) |
| Papers analyzed | 7,294 |
| Papers ranked | 20 |
| Top topics in ranked papers | Whole-genome sequencing, GWAS, and multi-omics integration |
| Publication window | Jan 1, 2024 – Dec 31, 2024 |
| Eligibility | Research articles; reviews excluded |
| Citation window | 18 months post-publication |
| 18m citation range | 18–118 |
| Data source | OpenAlex · Retrieved July 2026 |
| License | CC BY 4.0 |

## Rankings

| Rank | Title | Authors | Corresponding authors | Affiliation | Journal | 18m citations | DOI |
| ---: | --- | --- | --- | --- | --- | ---: | --- |
| 1 | A compendium of genetic regulatory effects across pig tissues | Jinyan Teng, Yahui Gao, Hongwei Yin, Zhonghao Bai, Shuli Liu, Haonan Zeng, PigGTEx Consortium, Lijing Bai, Zexi Cai, Bingru Zhao, Xiujin Li, Zhiting Xu, Qing Lin, Zhangyuan Pan, Wenjing Yang, Xiaoshan Yu, Dailu Guan, Yali Hou, Brittney N Keel, Gary A Rohrer, Amanda K Lindholm-Perry, William T Oliver, Maria Ballester, Daniel Crespo-Piazuelo, Raquel Quintanilla, Oriol Canela-Xandri, Konrad Rawlik, Charley Xia, Yuelin Yao, Qianyi Zhao, Wenye Yao, Liu Yang, Houcheng Li, Huicong Zhang, Wang Liao, Tianshuo Chen, Peter Karlskov-Mortensen, Merete Fredholm, Marcel Amills, Alex Clop, Elisabetta Giuffra, Jun Wu, Xiaodian Cai, Shuqi Diao, Xiangchun Pan, Chen Wei, Jinghui Li, Hao Cheng, Sheng Wang, Guosheng Su, Goutam Sahana, Mogens Sandø Lund, Jack C M Dekkers, Luke Kramer, Christopher K Tuggle, Ryan Corbett, Martien A M Groenen, Ole Madsen, Marta Gòdia, Dominique Rocha, Mathieu Charles, Cong-Jun Li, Hubert Pausch, Xiaoxiang Hu, Laurent Frantz, Yonglun Luo, Lin Lin, Zhongyin Zhou, Zhe Zhang, Zitao Chen, Leilei Cui, Ruidong Xiang, Xia Shen, Pinghua Li, Ruihua Huang, Guoqing Tang, Mingzhou Li, Yunxiang Zhao, Guoqiang Yi, Zhonglin Tang, Jicai Jiang, Fuping Zhao, Xiaolong Yuan, Xiaohong Liu, Yaosheng Chen, Xuewen Xu, Shuhong Zhao, Pengju Zhao, Chris Haley, Huaijun Zhou, Qishan Wang, Yuchun Pan, Xiangdong Ding, Li Ma, Jiaqi Li, Pau Navarro, Qin Zhang, Bingjie Li, Albert Tenesa, Kui Li, George E Liu, Zhe Zhang, Lingzhao Fang | Zhe Zhang, Albert Tenesa, Kui Li, George E. Liu | South China Agricultural University, China | Nature Genetics | 118 | 10.1038/s41588-023-01585-7 |
| 2 | Characterization of heterozygosity-rich regions in Italian and worldwide goat breeds | Giorgio Chessari, Andrea Criscione, Donata Marletta, Paola Crepaldi, Baldassare Portolano, Arianna Manunza, Alberto Cesarani, Filippo Biscarini, Salvatore Mastrangelo | Andrea Criscione | University of Catania, Italy | Scientific Reports | 51 | 10.1038/s41598-023-49125-x |
| 3 | Integrated multi-omics reveals the relationship between growth performance, rumen microbes and metabolic status of Hu sheep with different residual feed intakes | Yanzhen Zhang, Xiaowei Zhang, Dingren Cao, Jinyong Yang, Huiling Mao, Lingling Sun, Chong Wang | Lingling Sun, Chong Wang | Zhejiang A&F University, China | Animal nutrition | 39 | 10.1016/j.aninu.2024.04.021 |
| 4 | Genomic structural variation contributes to evolved changes in gene expression in high-altitude Tibetan sheep | Xiaolong Liang, Qijiao Duan, Bowen Li, Yinjia Wang, Yueting Bu, Yonglu Zhang, Zhuoran Kuang, Leyan Mao, Xuan An, Huihua Wang, Xiaojie Yang, Na Wan, Zhilong Feng, Wei Shen, Weilan Miao, Jiaqi Chen, Sanyuan Liu, Jay F Storz, Jianquan Liu, Eviatar Nevo, Kexin Li | Xiaolong Liang, Qijiao Duan, Bowen Li, Jianquan Liu, Eviatar Nevo, Kexin Li | Lanzhou University, China | Proceedings of the National Academy of Sciences | 30 | 10.1073/pnas.2322291121 |
| 5 | Genomic prediction using machine learning: a comparison of the performance of regularized regression, ensemble, instance-based and deep learning methods on synthetic and empirical data | Vanda M Lourenço, Joseph O Ogutu, Rui A P Rodrigues, Alexandra Posekany, Hans-Peter Piepho | Vanda M Lourenço | NOVA SST, Portugal | BMC Genomics | 25 | 10.1186/s12864-023-09933-x |
| 6 | Structural variant landscapes reveal convergent signatures of evolution in sheep and goats | Ji Yang, Dong-Feng Wang, Jia-Hui Huang, Qiang-Hui Zhu, Ling-Yun Luo, Ran Lu, Xing-Long Xie, Hosein Salehian-Dehkordi, Ali Esmailizadeh, George E Liu, Meng-Hua Li | Meng-Hua Li | China Agricultural University, China | Genome biology | 25 | 10.1186/s13059-024-03288-6 |
| 7 | Genome-wide variation study and inter-tissue communication analysis unveil regulatory mechanisms of egg-laying performance in chickens | Dandan Wang, Lizhi Tan, Yihao Zhi, Lina Bu, Yangyang Wang, Zhang Wang, Yulong Guo, Weihua Tian, Chunlin Xu, Donghua Li, Zhuanjian Li, Ruirui Jiang, Ruili Han, Guoxi Li, Yongqiang Wang, Dong Xia, Yadong Tian, Ian C Dunn, Xiaoxiang Hu, Hong Li, Yiqiang Zhao, Xiangtao Kang, Xiaojun Liu | Hong Li, Yiqiang Zhao, Xiangtao Kang, Xiaojun Liu | Henan Agricultural University, China | Nature Communications | 25 | 10.1038/s41467-024-50809-9 |
| 8 | The Population History of Domestic Sheep Revealed by Paleogenomes | Damla Kaptan, Gözde Atağ, Kıvılcım Başak Vural, Pedro Morell Miranda, Ali Akbaba, Eren Yüncü, Aleksey Buluktaev, Mohammad Foad Abazari, Sevgi Yorulmaz, Duygu Deniz Kazancı, Ayça Küçükakdağ Doğu, Yasin Gökhan Çakan, Rana Özbal, Fokke Gerritsen, Bea De Cupere, Refik Duru, Gülsün Umurtak, Benjamin S Arbuckle, Douglas Baird, Özlem Çevik, Erhan Bıçakçı, Can Yumni Gündem, Evangelia Pişkin, Lamys Hachem, Kayra Canpolat, Zohre Fakhari, Maria Ochir-Goryaeva, Viktoria Kukanova, Hamid Reza Valipour, Javad Hoseinzadeh, Fatma Küçük Baloğlu, Anders Götherström, Eleftherios Hadjisterkotis, Thierry Grange, Eva-Maria Geigl, İnci Z Togan, Torsten Günther, Mehmet Somel, Füsun Özer | Damla Kaptan | Middle East Technical University, Turkey | Molecular Biology and Evolution | 24 | 10.1093/molbev/msae158 |
| 9 | Insights into left-right asymmetric development of chicken ovary at the single-cell level | Tao Wang, Dong Leng, Zhongkun Cai, Binlong Chen, Jing Li, Hua Kui, Diyan Li, Zhuanjian Li | Diyan Li, Zhuanjian Li | Chengdu University, China | Journal of genetics and genomics/Journal of Genetics and Genomics | 23 | 10.1016/j.jgg.2024.08.002 |
| 10 | Transcriptome and Metabolome Insights into Key Genes Regulating Fat Deposition and Meat Quality in Pig Breeds | Suthar Teerath Kumar, Yunlong Zheng, Jing Xu, Ziyi Zhao, Qi Zhang, Yunpeng Zhang, Min Li, Hong Zou, Riaz Muhammad Azeem, Wu-Sheng Sun, Yuan Zhao, Shu-Min Zhang | Yuan Zhao, Shumin Zhang | Jilin Agricultural University, China | Animals | 23 | 10.3390/ani14243560 |
| 11 | Analysis of 206 whole‐genome resequencing reveals selection signatures associated with breed‐specific traits in Hu sheep | Fuping Zhao, Rui Xie, Lingzhao Fang, Ruidong Xiang, Zehu Yuan, Yang Liu, Lixian Wang | Yang Liu, Lixian Wang | Chinese Academy of Agricultural Sciences, China | Evolutionary Applications | 22 | 10.1111/eva.13697 |
| 12 | Comparative whole-genome resequencing to uncover selection signatures linked to litter size in Hu Sheep and five other breeds | Tao Zhong, Dunying Hou, Qianjun Zhao, Siyuan Zhan, Linjie Wang, Li Li, Hongping Zhang, Wei Zhao, Shizhong Yang, Lili Niu | Tao Zhong | Sichuan Agricultural University, China | BMC Genomics | 21 | 10.1186/s12864-024-10396-x |
| 13 | Integrating genome‐ and transcriptome‐wide association studies to uncover the host–microbiome interactions in bovine rumen methanogenesis | Wei Wang, Zhenyu Wei, Zhuohui Li, Jianrong Ren, Yanliang Song, Jingyi Xu, Anguo Liu, Xinmei Li, Manman Li, Huimei Fan, Liangliang Jin, Zhannur Niyazbekova, Wen Wang, Yuanpeng Gao, Yu Jiang, Junhu Yao, Fuyong Li, Shengru Wu, Yu Wang | Fuyong Li, Shengru Wu, Yu Wang | Northwest A&F University, China | iMeta | 20 | 10.1002/imt2.234 |
| 14 | Comprehensive Analysis of Transcriptome and Metabolome Reveals Regulatory Mechanism of Intramuscular Fat Content in Beef Cattle | Hengwei Yu, Shengchen Yu, Juntao Guo, Jianfang Wang, Chugang Mei, Sayed Haidar Abbas Raza, Gong Cheng, Linsen Zan | Gong Cheng, Linsen Zan | Northwest A&F University, China | Journal of Agricultural and Food Chemistry | 19 | 10.1021/acs.jafc.3c07844 |
| 15 | Decoding cow behavior patterns from accelerometer data using deep learning | Newlin Shebiah Russel, Arivazhagan Selvaraj | Newlin Shebiah Russel | Mepco Schlenk Engineering College, India | Journal of Veterinary Behavior | 19 | 10.1016/j.jveb.2024.06.005 |
| 16 | Integrative 3D genomics with multi-omics analysis and functional validation of genetic regulatory mechanisms of abdominal fat deposition in chickens | Linyong Shen, Xue Bai, Liru Zhao, Jiamei Zhou, Cheng Chang, Xinquan Li, Zhiping Cao, Yumao Li, Peng Luan, Hui Li, Hui Zhang | Hui Li, Hui Zhang | Northeast Agricultural University, China | Nature Communications | 19 | 10.1038/s41467-024-53692-6 |
| 17 | Single-cell transcriptomic and cross-species comparison analyses reveal distinct molecular changes of porcine testes during puberty | Xiaoyan Wang, Yang Wang, Yu Wang, Yifei Guo, Ruojun Zong, Shuaitao Hu, Jingwei Yue, Jing Yao, Chunsheng Han, Jingtao Guo, Jianguo Zhao | Chunsheng Han, Jingtao Guo, Jianguo Zhao | Institute of Zoology, China | Communications Biology | 19 | 10.1038/s42003-024-07163-9 |
| 18 | Pangenome-genotyped structural variation improves molecular phenotype mapping in cattle | Alexander S Leonard, Xena M Mapel, Hubert Pausch | Alexander S Leonard | ETH Zurich, Switzerland | Genome Research | 18 | 10.1101/gr.278267.123 |
| 19 | Multiomics Analyses Provide New Insight into Genetic Variation of Reproductive Adaptability in Tibetan Sheep | Buying Han, Dehong Tian, Xue Li, Sijia Liu, Fei Tian, Dehui Liu, Song Wang, Kai Zhao | Buying Han | Chinese Academy of Sciences, China | Molecular Biology and Evolution | 18 | 10.1093/molbev/msae058 |
| 20 | Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation | Meilin Jin, Huihua Wang, Gang Liu, Jian Lu, Zehu Yuan, Taotao Li, Engming Liu, Zengkui Lu, Lixin Du, Caihong Wei | Lixin Du, Caihong Wei | Chinese Academy of Agricultural Sciences, China | Genetics Selection Evolution | 18 | 10.1186/s12711-024-00880-z |

## Topic trends

### What Topics Define the Class of 2026?

The Class of 2026 for genetic and phenotypic traits in livestock is heavily anchored in the application of high-resolution genomics. Whole-genome sequencing and Genome-Wide Association Studies (GWAS) remain the dominant, foundational tools for uncovering novel trait-associated variants across populations. Crucially, however, the field is rapidly advancing into systems biology through a substantial and growing emphasis on multi-omics integration. Researchers are increasingly combining transcriptomic, metabolomic, and genomic datasets to map the complex molecular architecture underlying phenotypic traits.

Alongside these technological shifts, targeted studies on specialized and indigenous breeds are remarkably prevalent. Research focusing extensively on Hu sheep, Tibetan sheep, and Holstein-Friesian cattle forms a core component of this cohort's landscape. These breed-specific analyses are frequently coupled with targeted investigations into high-value functional attributes, such as fat deposition, body size traits, and unique adaptation mechanisms. Mechanistically, there is also an expanded focus on the rumen microbiome and its diverse metabolic outputs—such as volatile fatty acids—as critical drivers of host phenotype. This illustrates a broader paradigm shift toward understanding host-microbe interactions as an integral factor in modern livestock genetics.

*Leading research themes*

### How Did Topics Shift from the Class of 2025 to the Class of 2026?

A striking evolution in the Class of 2026 is the rapid ascent of single-cell RNA sequencing and targeted multi-omics approaches, which are actively displacing more conventional genetic mapping strategies. Traditional mainstays of the field, such as the analysis of selection signatures and the application of genomic selection, experienced nearly a 50% decline in relative frequency. This notable drop suggests that researchers are steadily moving past basic locus identification toward high-resolution functional validation and the exploration of complex molecular interactions.

Simultaneously, there is a pronounced and fascinating pivot toward the genetics of extreme adaptation and specialized breed traits. Research on Tibetan sheep and the associated EPAS1 gene emerged entirely in this cohort, driven by efforts to investigate the mechanisms of high-altitude adaptation. Similarly, studies centering on Hu sheep surged seven-fold, often intersecting with metabolic profiling (metabolomics) and the mapping of expression quantitative trait loci (eQTLs). The exponential rise of supporting topics like volatile fatty acids and body size traits further underscores this broader paradigm shift: modern livestock genetics is increasingly prioritizing systems-level mechanistic pathways—such as those mediated by the rumen microbiome—over isolated genomic breeding values.

*How topics shifted year over year*

## Cite this ranking

```
Pepkio Research Index (PRI). Topics and Trends in Most Cited Genetic and phenotypic traits in livestock Papers, Class of 2026. https://pri.pepkio.com/top-papers/genetic-and-phenotypic-traits-in-livestock/2026. Accessed 2026-07-15.

Zheng Su, Tinsley Li, Thematic Shifts in Early-High-Impact Cancer Genomics and Diagnostics Research: A Bibliometric and Semantic Analysis. bioRxiv 2026.07.04.736459; doi: https://doi.org/10.64898/2026.07.04.736459
```