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

IF 2.7 3区生物学 Q2 GENETICS & HEREDITY

Gene Pub Date : 2026-02-05 Epub Date: 2025-11-06 DOI:10.1016/j.gene.2025.149878

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

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引用次数: 0

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.

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揭示遗传蓝图：一种转录组学方法来破译Nili-Ravi水牛蓝色虹膜颜色的形成。

水牛是世界范围内具有重要经济意义的牲畜，但尼利-拉维水牛蓝虹膜的遗传基础仍然难以捉摸。我们采集了两只Murrah水牛（黑色虹膜）和两只Nili-Ravi水牛（蓝色虹膜）的混合虹膜透镜样本，并进行了对端rna测序。经质量控制，获得高质量数据64.53 Gb （Q30 ≥ 89.92 %）。差异分析(DESeq2， | log2FoldChange |≥2和padj

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来源期刊

Gene 生物-遗传学

CiteScore

6.10

自引率

2.90%

发文量

718

审稿时长

42 days

期刊介绍： Gene publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses.