基于转录组和蛋白质组分析筛选绒山羊绒毛脱落相关候选基因

doi:10.16431/j.cnki.1671-7236.2025.08.001

摘要/Abstract

摘要： 【目的】通过转录组和蛋白质组联合分析筛选绒山羊绒毛脱落相关候选基因，为研究绒毛脱落遗传机制和分子标记辅助育种提供理论基础。【方法】选取6只2周岁雌性半同胞罕山白绒山羊，随机分为对照组和埋植组，每组3个生物学重复。采集自然脱绒的5月(D5)、外源褪黑素(melatonin,MT)诱导提前脱绒的4月(M4)和二次脱绒的8月(M8)绒山羊皮肤组织，提取RNA和蛋白质，分别通过转录组测序(RNA-Seq)和Label-free DIA蛋白组定量分析筛选差异表达基因(DEGs)和差异表达蛋白(DEPs)，并对其进行功能富集分析和蛋白互作(PPI)网络构建。【结果】在M4 vs D5组中共鉴定到332个DEGs和47个DEPs，其中P4HA2和DLX3为重叠基因；富集分析显示，DEGs和DEPs显著富集到皮肤发育、毛囊发育、毛发周期、PPAR信号通路和PI3K-Akt信号通路等通路，并筛选出DLX3、FOXN1、COL1A1等9个关键基因。在M8 vs D5组中共鉴定到345个DEGs和120个DEPs，重叠基因有CNDP1、KRTAP11-1和OAT，这些基因或蛋白显著富集到皮肤发育、毛囊发育、毛发周期、PPAR和钙信号通路等，并筛选出KRTAP11-1、OAT和FOXN1等6个关键基因。在M8 vs M4组中共鉴定到193个DEGs和51个DEPs，主要富集在细胞投射组织的调控、PI3K-Akt和黏着斑等通路，并筛选出COL1A1、COL1A2和S100A4共3个关键基因。其中，半胱氨酸和蛋氨酸代谢通路在脱绒组中持续激活，COL1A1和FOXN1基因在多个比较组中反复出现，提示其可能作为核心调控因子参与毛囊周期异常。【结论】本研究在MT诱导提前脱绒的4月份绒山羊皮肤组织中鉴定出2个重叠基因(P4HA2、DLX3)和2个特有基因(KRT32、DKK1)；在MT诱导提前脱绒的8月份绒山羊皮肤组织中鉴定出3个重叠基因(KRTAP11-1、OAT、CNDP1)和1个特有基因(S100A4)，并发现半胱氨酸和蛋氨酸代谢在不同脱绒组中持续激活。研究结果为解析绒山羊绒毛脱绒性能的分子调控机制提供了关键线索，为精准调控绒毛生长周期、优化MT诱导脱绒和长绒技术奠定了靶标基础。

关键词: 罕山白绒山羊; 转录组; 蛋白质组; 褪黑素; 候选基因

Abstract: 【Objective】 This study integrated transcriptomic and proteomic profiling to identify candidate genes associated with cashmere fiber shedding in cashmere goats,elucidating genetic regulatory mechanisms and establishing a theoretical framework for molecular marker-assisted breeding. 【Method】 Six 2-year-old female half-sib Hanshan White cashmere goats were randomly divided into control and melatonin (MT)-implanted groups,with three biological replicates per group.Skin tissues were collected during natural shedding in May (D5),MT-induced premature shedding in April (M4),and secondary shedding in August (M8).RNA and proteins were extracted for transcriptomic sequencing (RNA-Seq) and Label-free DIA-based proteomic quantification to identify differentially expressed genes (DEGs) and proteins (DEPs),followed by functional enrichment analysis and protein-protein interaction (PPI) network construction. 【Result】 In M4 vs D5 comparison group,332 DEGs and 47 DEPs were identified,including overlapping genes P4HA2 and DLX3,with DEGs and DEPs significantly enriched in pathways related to skin development,hair follicle cycling,PPAR signaling pathway,and PI3K-Akt signaling pathway,leading to the identification of nine key genes such as DLX3,FOXN1,and COL1A1.In M8 vs D5 comparison group,345 DEGs and 120 DEPs were identified,with overlapping genes CNDP1,KRTAP11-1,and OAT,enriched in skin development,hair follicle development,hair cycle,PPAR,and calcium signaling pathway,highlighting six key genes including KRTAP11-1,OAT,FOXN1,etc.The M8 vs M4 comparison group showed 193 DEGs and 51 DEPs primarily involved in cell projection regulation,PI3K-Akt signaling,focal adhesion,etc.with three key genes (COL1A1,COL1A2,and S100A4) identified.Among them,cysteine and methionine metabolic pathways in shedding groups were continuously activated,while the COL1A1 and FOXN1 genes repeatedly appeared in multiple comparison groups,suggesting that they might be involved as core regulatory factors in abnormal hair follicle cycles. 【Conclusion】 This study revealed distinct genetic regulatory patterns during MT-induced cashmere shedding in April and August.In the April shedding group,two overlapping genes (P4HA2 and DLX3) and two unique genes (KRT32 and DKK1) were identified,while the August secondary shedding group exhibited three overlapping genes (KRTAP11-1,OAT,and CNDP1) and one unique gene (S100A4).Persistent activation of cysteine and methionine metabolism pathways was observed across shedding groups.The results provided critical insights into the molecular mechanisms governing cashmere shedding characteristics in cashmere goats,establishing a theoretical foundation for precisely regulating hair follicle cycle and optimizing MT-induced shedding techniques alongside cashmere elongation strategies.

Key words: Hanshan White cashmere goat; transcriptome; proteome; melatonin; candidate genes

中图分类号:

S813.3

田进东, 塔拉, 李巍巍, 徐惠娟, 吴江鸿, 勿都巴拉, 胡斯乐, 曹文雅, 宋泓利, 付绍印, 丽春. 基于转录组和蛋白质组分析筛选绒山羊绒毛脱落相关候选基因[J]. 中国畜牧兽医, 2025, 52(8): 3497-3514.

TIAN Jindong, TA La, LI Weiwei, XU Huijuan, WU Jianghong, WUDUBALA, HU Sile, CAO Wenya, SONG Hongli, FU Shaoyin, LI Chun. Screening of Candidate Genes Related to Cashmere Shedding in Cashmere Goats Based on Transcriptome and Proteome Analysis[J]. China Animal Husbandry & Veterinary Medicine, 2025, 52(8): 3497-3514.

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