Revealing the genetic blueprint: A transcriptomic approach to deciphering blue iris color formation in Nili-Ravi buffalo

Dong Wang; Yixue Xu; Chaobin Qin; Xinhui Song; Hui Li; Xiaoxian Xu; Muhammad Farhan Khan; Kuiqing Cui; Zhipeng Li; Qingyou Liu

doi:10.1016/j.gene.2025.149878

Revealing the genetic blueprint: A transcriptomic approach to deciphering blue iris color formation in Nili-Ravi buffalo

Gene. 2025 Nov 6:978:149878. doi: 10.1016/j.gene.2025.149878. Online ahead of print.

Authors

Dong Wang¹, Yixue Xu¹, Chaobin Qin¹, Xinhui Song¹, Hui Li¹, Xiaoxian Xu¹, Muhammad Farhan Khan², Kuiqing Cui³, Zhipeng Li⁴, Qingyou Liu⁵

Affiliations

¹ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China.
² Department of Chemistry, Gomal University, Dera Ismail Khan 29050, Pakistan.
³ Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Animal Science and Technology, Foshan University, 528000 Foshan, China.
⁴ State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China. Electronic address: zp.li@gxu.edu.cn.
⁵ Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Animal Science and Technology, Foshan University, 528000 Foshan, China. Electronic address: qyliu-gene@fosu.edu.cn.

PMID: 41205780
DOI: 10.1016/j.gene.2025.149878

Abstract

Water buffalo are economically significant livestock worldwide, yet the genetic basis of the blue iris in Nili-Ravi buffalo remains elusive. We collected mixed iris-lens samples from two Murrah buffaloes (black iris) and two Nili-Ravi buffaloes (blue iris) and performed paired-end RNA-seq. After quality control, 64.53 Gb of high-quality data (Q30 ≥ 89.92 %) were obtained. Differential analysis (DESeq2,|log₂FoldChange| ≥ 2 and padj < 0.05) revealed 1,289 differentially expressed genes and 248 differentially expressed lncRNAs between blue and black irises. GO and KEGG enrichment highlighted melanogenesis, tyrosine metabolism, cysteine metabolism, and phototransduction pathways. Key differential genes related to eye development and melanin production-including the hub mRNAs KIT, MGST1, GNGT1, and TYRP1-were identified. Network analysis further showed that lncRNA MSTRG.14079.1 directly targets protein tyrosine phosphatase receptor T (PTPRT), and this interaction is significantly down-regulated in blue irises. Together, our study provides the first molecular network underlying the blue iris phenotype and establishes a theoretical basis for using this non-invasive marker to enhance breeding efficiency in buffalo.

Keywords: Blue iris color; Melanin; Transcriptome; Water Buffalo.