太行鸡与坝上长尾鸡品种区分的分子标记筛选与鉴定

doi:10.11843/j.issn.0366-6964.2025.08.018

摘要/Abstract

摘要：

旨在通过筛选和挖掘太行鸡与坝上长尾鸡的特征SNPs分子标记，实现利用少量SNPs区分两个品种的目标。本研究通过61只太行鸡和56只坝上长尾鸡品种的全基因组重测序数据，采用连锁不平衡和群体分化指数分析筛选重要的SNPs；采用6种机器学习分类模型对个体类别进行预测并评估模型性能；利用随机森林模型评估SNPs重要性，根据准确率、召回率和AUC值筛选出最少数量的SNPs；最后通过主成分分析、系统进化树和基因组关系矩阵验证其区分效果。结果，筛选出28个SNPs标记能够有效区分太行鸡和坝上长尾鸡，这些SNPs位点主要分布于基因间区或内含子区，显著富集在免疫、组蛋白乙酰化、代谢等相关的GO生物学过程以及碱基切除修复的KEGG信号通路，并发现免疫(BCL11B、AvBD13、KAT7)、脂质代谢(URI1、RREB1、ZBTB20)和适应性(ZNF536)相关基因。利用群体遗传学和机器学习方法筛选出能够区分太行鸡和坝上长尾鸡品种的分子标记组合，为地方品种“分子身份证”的构建以及种质资源的保护和鉴定工作提供重要参考。

关键词: 太行鸡, 坝上长尾鸡, 分子标记, 机器学习

Abstract:

The aim was to distinguish between Taihang chickens and Bashang long-tailed chickens using a small number of SNPs by screening characteristic SNPs molecular markers. The whole genome resequencing data from 61 Taihang and 56 Bashang long-tailed chickens were used to extract important SNPs through linkage disequilibrium and population differentiation index analyses. Six machine learning classification models were adopted to predict individual categories and evaluate the model performance. The random forest model was used to evaluate the importance of SNPs, and the minimum number of SNPs were selected according to the accuracy, recall rate and AUC value. The effect was validated using principal component analysis, phylogenetic tree, and a genomic relationship matrix. A total of 28 SNPs were identified that effectively discriminate between Taihang and Bashang long-tailed chickens. The SNPs were primarily located in intergenic and intronic regions and were significantly enriched in the GO biological processes related to immunity, histone acetylation, metabolism as well as in the KEGG signaling pathway for base excision repair. Additionally, we identified genes associated with immunity (BCL11B, AvBD13, KAT7), lipid metabolism (URI1, RREB1, ZBTB20), and adaptability (ZNF536). The identified molecular marker combinations with integration of population genetics and machine learning techniques could distinguish Taihang and Bashang long-tailed chicken breeds. This study provides valuable insights for the development of "molecular identity cards" for local breeds, contributing to the conservation and identification of germplasm resources.

Key words: Taihang chicken, Bashang long-tailed chicken, molecular marker, machine learning

中图分类号:

S831.2

付伟, 张冉, 丁虹, 臧素敏, 李祥龙, 褚素乔, 刘华格, 周荣艳. 太行鸡与坝上长尾鸡品种区分的分子标记筛选与鉴定[J]. 畜牧兽医学报, 2025, 56(8): 3761-3772.

FU Wei, ZHANG Ran, DING Hong, ZANG Sumin, LI Xianglong, CHU Suqiao, LIU Huage, ZHOU Rongyan. Screening and Identification of Molecular Markers for Differentiating Taihang Chickens and Bashang Long-tailed Chickens[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(8): 3761-3772.

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性状 Trait	鸡种 Breed	周龄 Weeks of age
性状 Trait	鸡种 Breed	1	2	4	6	8	10	12	14	16	18	20
周末体重/g Weekend weight	太行鸡 Taihang chicken	58	84	159	328	473	647	786	914	1 058	1 184	1 239
周末体重/g Weekend weight	坝上长尾鸡 Bashang long-tailed chicken	62	125	212	336	453	596	756	924	1 150	1 264	1 409

模型 Model	AUC	MCC 值 MCC value	准确率 Accuracy
随机森林 Random forest	1.00	1.00	1.00
逻辑回归 Logistic regression	1.00	1.00	1.00
支持向量机 Support vector machine	1.00	1.00	1.00
极致梯度提升树 eXtreme gradient boosting	1.00	1.00	1.00
K 近邻算法 K-nearest neighbor classification	1.00	1.00	1.00
决策树 Decision tree	0.82	0.63	0.79

染色体 Chromosome	位置 Position	等位基因 Allele	基因 Gene	等位基因频率 Allele frequency
染色体 Chromosome	位置 Position	等位基因 Allele	基因 Gene	太行鸡 Taihang chicken	坝上长尾鸡 Bashang long-tailed chicken
1	83424842	G/A	ZBTB20	0.67/0.33	0.94/0.06
1	84642349	T/G	CD200R1、CCDC80	0.38/0.62	0.71/0.29
1	124613919	G/A	EGFL6	0.34/0.66	0.71/0.29
1	188821891	G/A	CHORDC1	0.69/0.31	0.29/0.71
2	21199573	C/T	ZNF804B	0.73/0.27	0.26/0.74
2	64783482	C/T	RREB1	0.52/0.48	0.86/0.14
3	52482379	C/T	PHACTR2	0.66/0.34	0.35/0.65
3	107385968	C/A	gga-mir-6702、AvBD13	0.65/0.35	0.34/0.66
4	83205244	G/A	-	0.71/0.29	0.31/0.69
4	89928184	A/G	EXOC6B	0.41/0.59	0.76/0.24
4	90119859	G/A	EXOC6B	0.50/0.50	0.83/0.17
5	48014977	C/A	BCL11B	0.51/0.49	0.81/0.19
6	3512624	A/G	PARG	0.34/0.66	0.65/0.35
6	23346870	G/A	SLIT1	0.74/0.26	0.22/0.78
8	4957820	A/G	DNM3	0.35/0.65	0.74/0.26
8	22102533	G/C	-	0.66/0.34	0.90/0.10
9	3411829	C/T	-	0.74/0.26	0.39/0.61
11	8491921	T/C	-	0.70/0.30	0.95/0.05
11	8532637	A/G	URI1	0.69/0.31	0.30/0.70
11	8851889	C/T	ZNF536	0.74/0.26	0.96/0.04
24	671698	T/C	KIRREL3	0.45/0.55	0.78/0.22
24	5374821	C/T	DSCAML1	0.32/0.68	0.74/0.26
25	3692518	A/G	MCL1	0.36/0.64	0.71/0.29
26	3849905	G/T	TRIM33	0.71/0.29	0.95/0.05
26	4170859	T/C	SCUBE3	0.32/0.68	0.70/0.30
27	5676121	A/C	KAT7	0.80/0.20	0.39/0.61
28	2536492	G/A	MBD3	0.67/0.33	0.33/0.67
33	5235050	G/A	-	0.66/0.34	0.93/0.07

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