基因渗入的检测和表征方法

doi:10.16288/j.yczz.22-394

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Hereditas(Beijing) ›› 2023, Vol. 45 ›› Issue (2): 128-143.doi: 10.16288/j.yczz.22-394

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Methods to detect and characterize introgression

Zexuan Liu(), Yiqiang Zhao()

College of Biological Sciences, China Agricultural University, Beijing 100193, China

Received:2022-12-01 Revised:2023-01-04 Online:2023-02-20 Published:2023-01-26
Contact: Zhao Yiqiang E-mail:liuzexuan@cau.edu.cn;yiqiangz@cau.edu.cn

Abstract

Abstract:

Introgression, also known as introgressive hybridization, refers to the process that genetic components from the gene pool of one population transfer to the other via constant backcrossing. Introgression is widespread in nature, which plays important roles in increasing genetic diversity and improving adaptability to the environment, and in turn, influences the evolutionary progress of animals, plants and humans. Being as an important evolutionary event, researchers pay great attention to the detection of introgression, the introgression direction, the introgression timing, the pattern of introgression and so on. With the rapid development of high-throughput sequencing technologies, methods to detect and characterize introgression based on genome-wide data are continuously developed. In this review, we summarize a series of methods for introgression detection, and introduce the design principles and applications of these methods. We also discuss the maintenance and selection of gene segments after introgression. This review provides a relatively comprehensive reference for the studies on introgression.

Key words: introgression, introgression detection, introgression direction, introgression timing, adaptive introgression

Zexuan Liu, Yiqiang Zhao. Methods to detect and characterize introgression[J]. Hereditas(Beijing), 2023, 45(2): 128-143.

Figures/Tables 6

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统计量	检测策略	功能	计算原理
rIBD	遗传相似性	个体间的定性分析	个体间IBD相似性
χ²	遗传相似性	群体间的定性分析	群体间单倍型相似性
D	频率差异及拓扑结构分析	个体或群体间的定性分析	ABBA与BABA频率差异
f₄/f₄-ratio	频率差异及拓扑结构分析	群体间定性/定量分析	群体间等位基因频率差异的平均相关性
f_d	频率差异及拓扑结构分析	个体或群体间的滑窗定量分析	基于D统计量分子构建完全渗入模型
f_dM	频率差异及拓扑结构分析	个体或群体间的滑窗定量分析	在f_d基础上同等量化H₁、H₃和H₂、H₃之间的基因流
D_p	频率差异及拓扑结构分析	个体或群体间的定量分析	扩展D统计量分母包含全部位点模式

渗入方向	统计量
渗入方向	D_FO	D_IL	D_FI	D_OL
无	0	0	0	0
H₁→H₃	+	+	+	+
H₃→H₁	+	0	+	+
H₁→H₄	-	-	0	+
H₄→H₁	-	0	+	+
H₂→H₃	+	+	-	0
H₃→H₂	0	+	-	-
H₂→H₄	-	-	0	-
H₄→H₂	0	-	-	-
H₁₂→H₃	+	+	0	0
H₃→H₁₂	+	+	0	0
H₁₂→H₄	-	-	0	0
H₄→H₁₂	-	-	0	0
H_{1$\rightleftarrows $}H₂	0	0	0	0
H_{2$\rightleftarrows $}H₄	0	0	0	0

供体	受体	渗入位点	适应性特征	参考文献
丹尼索瓦人	藏族人	EPAS1	适应高原缺氧环境	[82]
丹尼索瓦人尼安德特人	现代人类	TLR10	先天免疫	[52]
黑尾兔	雪兔	ASIP	多态性季节伪装	[16]
阿尔及利亚小鼠	家鼠	Vkorc1	华法林杀鼠剂抗性	[86]
野山羊	现代山羊	MUC6	肠道病原体免疫	[5]
冈比亚按蚊群	-	常染色体中大量渗入	杀虫剂抗性	[87]
慈鲷鱼群	-	RH2B	深水适应性	[88]
Heliconius蝴蝶群	-	RAY	翅膀颜色图案	[22]
毛果杨	黑杨	PRR5 CMOT1	调节转录叶片氮含量	[6]
北美向日葵	向日葵	多个QTL	种子和花粉数量	[89]

Methods to detect and characterize introgression

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