• Revealing the genetic blueprin...

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

Title:
Revealing the genetic blueprint: A transcriptomic approach to deciphering blue iris color formation in Nili-Ravi buffalo.
Authors:
Wang D; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China., Xu Y; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China., Qin C; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China., Song X; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China., Li H; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China., Xu X; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China., Khan MF; Department of Chemistry, Gomal University, Dera Ismail Khan 29050, Pakistan., Cui K; Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Animal Science and Technology, Foshan University, 528000 Foshan, China., Li Z; 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., Liu Q; 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.
Source:
Gene [Gene] 2026 Feb 05; Vol. 978, pp. 149878. Date of Electronic Publication: 2025 Nov 06.
Publication Type:
Journal Article
Language:
English
Journal Info:
Publisher: Elsevier/North-Holland Country of Publication: Netherlands NLM ID: 7706761 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1879-0038 (Electronic) Linking ISSN: 03781119 NLM ISO Abbreviation: Gene Subsets: MEDLINE
Imprint Name(s):
Original Publication: Amsterdam, Elsevier/North-Holland, 1976-
MeSH Terms:
Buffaloes*/genetics , Iris*/metabolism , Transcriptome*/genetics , Eye Color*/genetics , Pigmentation*/genetics, Animals ; RNA, Long Noncoding/genetics ; Gene Expression Profiling/methods ; Gene Regulatory Networks ; Phenotype
Contributed Indexing:
Keywords: Blue iris color; Melanin; Transcriptome; Water Buffalo
Substance Nomenclature:
0 (RNA, Long Noncoding)
Entry Date(s):
Date Created: 20251108 Date Completed: 20251211 Latest Revision: 20251211
Update Code:
20260130
DOI:
10.1016/j.gene.2025.149878
PMID:
41205780
Database:
MEDLINE

*Further Information*

*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,|log <subscript>2</subscript> FoldChange| ≥ 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.
(Copyright © 2025. Published by Elsevier B.V.)*

*Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Qingyou Liu reports financial support was provided by Guangxi Science and Technology Major Project. Qingyou Liu reports financial support was provided by the National Key R&D Program of China. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.*