基于自然群体随机交配的单个印迹QTL定位的初步研究

郑珂晖; 黎哲镇; 叶景山; 周富杰; 温永仙

doi:10.19303/j.issn.1008-0384.2019.12.002

基于自然群体随机交配的单个印迹QTL定位的初步研究

doi: 10.19303/j.issn.1008-0384.2019.12.002

郑珂晖^{1, 2,},
黎哲镇²,
叶景山²,
周富杰²,
温永仙^{1, 2, ,}

1.
福建农林大学生命科学学院，福建　福州　350002
2.
福建农林大学计算机与信息学院，福建　福州　350002

基金项目: 国家自然科学基金项目（31571558）；福建省自然科学基金项目（2017J01606）；福建农林大学科技创新专项基金（KFA17028A）

详细信息

作者简介:
郑珂晖（1979−），男，博士，讲师，研究方向：生物信息学（E-mail：38193754@qq.com）

通讯作者:
温永仙（1966−），女，博士，教授，研究方向：生物信息学（E-mail：wenyx9681@fafu.edu.cn）

中图分类号: Q 348
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出版历程
- 收稿日期: 2019-09-25
- 修回日期: 2019-10-27
- 刊出日期: 2019-12-01

A Preliminary Study on Single Imprinted QTL Mapping Based on Random Mating of Natural Populations

1.
College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian　350002, China
2.
College of Computer and Information Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian　350002, China

摘要

摘要: 目的探索基于自然群体随机交配的单个印迹QTL的定位方法，分析影响定位准确性的关键因素。方法若印迹QTL决定的某一性状为数量性状，假设该性状与标记之间的关系存在线性关系，可以采用最小二乘法进行印迹QTL定位和遗传参数的估计。利用计算机模拟单点模拟标记、水稻真实自然群体标记进行印迹QTL定位，比较在不同最小等位基因频率(Minor allele frequency, MAF)、不同遗传率、不同随机交配轮数下的统计功效与参数估计精度，印迹QTL的显著性采用F检验和t检验。结果通过模拟研究，证明该试验设计对于检测单个印迹QTL是有效的，在MAF大于5%时，印迹遗传率大于10%时，定位与遗传参数估计趋于无偏。结论采用自然群体随机交配产生作图群体，可以用来进行单个印迹QTL的定位，定位的结果较好，是一种有效的试验设计，为下一步进行多个印迹QTL奠定了基础。
- 自然群体 /
- 关联分析 /
- F 检验 /
- 印迹QTL /
- 随机交配
Abstract: Objective To explore the application of single imprinted QTL mapping based on random mating of natural populations and analyze key factors affecting the mapping accuracy. Method Assuming the trait determined by the imprinted QTL to be quantitative and a linear relationship between the trait and the markers existed, then the least squares method could be used to estimate the QTL mapping and genetic parameters. The imprinted QTL mapping was generated by computer simulating the single-point markers as well as a real data set of natural population markers. The statistical power and parameter estimation accuracy of different genotype frequencies, heritability rates, and random mating rounds were compared. The significance of imprinted QTLs was determined by using F- and t-tests. Result Through a simulation study, it was proven that the experimental design was effective in detecting a single imprinted QTL. When the MAF was greater than 5% and the imprinted heritability greater than 10%, the iQTLs positions and genetic parameters were presumably unbiased Conclusion Using random mating in the nature to generate mapping populations could conceivably be used to locate single-imprinted QTLs with acceptable results of localization. It seemed to be an effective design for the next step for QTL mapping.
- Natural population /
- association analysis /
- F-test /
- imprinted QTL /
- random mating

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图 1 自然群体随机交配示意图

Figure 1. Schematic diagram of random mating in natural populations

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图 2 水稻自然群体随机交配产生的群体SNP等位基因频率（p）示例（包含254个不同株系）

Figure 2. Examples of SNP allele frequencies (p) in populations from random mating of natural populations of rice (including 254 different lines)

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表 1 自然群体中基因型的频率与哑变量取值

Table 1. Frequency of genotypes and value of dummy variables in natural populations

基因型 Genotype	频率 Frequency	x	z	t
基因型 Genotype	频率 Frequency	a	d	h
A/A	p²	1	0	0
A/a	pq	0	1	1
a/A	pq	0	1	−1
A/A	q²	−1	0	0

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表 2 印迹类型与参数设置与缩写

Table 2. Imprint types, parameter settings, and abbreviations

印迹类型 Imprinting type	简写 abbreviation	参数 parameter
来源于父本的表达 Parental expression, Paternal	PEP	d=0且a=h
来源于母本的表达 Parental expression, Maternal	PEM	d=0且a=−h
显性印迹(双相） Dominance imprinting, Bipolar	DIB	a=0且d=0
显性印迹（单相）超显性 Dominance imprinting, Polar, Over-dominance	DIPOD	a=0且d=h
显性印迹（单相）低于显性 Dominance imprinting, Polar, Under dominance	DIPUD	a=0且d=−h

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表 3 单点模拟5种类型的iQTL定位结果

Table 3. Single-point simulation of 5 types of iQTL mapping results

MAF/%	H/%	DIPOD				DIPUD				DIB				PEM				PEP
MAF/%	H/%	a	d	h	P/%	a	d	h	P/%	a	d	h	P/%	a	d	h	P/%	a	d	h	P/%
RV		0	2.35	2.35		0	2.35	−2.35		0	0	2.35		2.35	0	−2.35		2.35	0	2.35
5	5	0.18	2.2	2.4	85	0.07	2.25	−2.4	93	0.12	−0.1	2.35	88	2.41	−0.06	−2.35	91	2.16	0.24	2.35	87
5	5	(1.17)	(1.22)	(0.31)	85	(1.22)	(1.23)	(0.33)	93	(1.19)	(1.24)	(0.37)	88	(1.16)	(1.22)	(0.31)	91	(1.04)	(1.13)	(0.29)	87
RV		0	3.42	3.42		0	3.42	−3.42		0	0	3.42		3.42	0	−3.42		3.42	0	3.42
5	10	0.09	3.31	3.45	83	0	3.47	−3.38	82	−0.02	−0.02	3.43	86	3.46	0.03	−3.45	92	3.37	0.1	3.38	86
5	10	(1.19)	(1.21)	(0.35)	83	(1.01)	(1.06)	(0.31)	82	(1.19)	(1.25)	(0.35)	86	(1.34)	(1.35)	(0.35)	92	(1.03)	(1.05)	(0.29)	86
RV		0	4.31	4.31		0	4.31	−4.31		0	0	4.31		4.31	0	−4.31		4.31	0	4.31
5	15	0.07	4.28	4.34	90	−0.01	4.31	−4.35	90	0.03	−0.05	4.25	90	4.36	−0.05	−4.31	88	4.42	−0.08	4.33	85
5	15	(1.2)	(1.25)	(0.27)	90	(1.18)	(1.26)	(0.29)	90	(1.24)	(1.24)	(0.33)	90	(1.03)	(1.03)	(0.3)	88	(1.03)	(1.08)	(0.32)	85
RV		0	1.71	1.71		0	1.71	−1.71		0	0	1.71		1.71	0	−1.71		1.71	0	1.71
10	5	−0.02	1.75	1.72	100	−0.04	1.75	−1.73	100	−0.04	0.06	1.72	100	1.64	0.06	−1.67	100	1.69	−0.02	1.69	100
10	5	(0.53)	(0.6)	(0.21)	100	(0.53)	(0.55)	(0.21)	100	(0.57)	(0.63)	(0.23)	100	(0.47)	(0.58)	(0.24)	100	(0.57)	(0.63)	(0.22)	100
RV		0	2.48	2.48		0	2.48	−2.48		0	0	2.48		2.48	0	−2.48		2.48	0	2.48
10	10	−0.05	2.52	2.5	100	−0.05	2.53	−2.51	100	−0.02	0.03	2.51	100	2.54	−0.04	−2.51	100	2.59	−0.06	2.52	100
10	10	(0.55)	(0.61)	(0.23)	100	(0.57)	(0.63)	(0.25)	100	(0.61)	(0.7)	(0.26)	100	(0.51)	(0.56)	(0.2)	100	(0.6)	(0.62)	(0.23)	100
RV		0	3.13	3.13		0	3.13	−3.13		0	0	3.13		3.13	0	−3.13		3.13	0	3.13
10	15	−0.04	3.18	3.12	100	−0.08	3.22	−3.13	100	−0.08	0.06	3.13	100	3.24	−0.05	−3.12	100	3.18	0.01	3.12	100
10	15	(0.49)	(0.57)	(0.23)	100	(0.52)	(0.57)	(0.23)	100	(0.62)	(0.65)	(0.26)	100	(0.47)	(0.53)	(0.22)	100	(0.55)	(0.59)	(0.24)	100
注：表中括号内为标准差，此处列出的为C=10，交配轮数为20的结果，表中H代表遗传率（Heritability），RV代表真值（Real value），P代表统计功效(Power) Note: The number in parentheses in the table is the standard deviation，C=10 and cross rounds is 20, H represents heritability, RV means real value and p means statistical power.

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表 4 不同C值下5种印迹类型的iQTL定位结果

Table 4. iQTL mapping results of 5 imprint types under varied C values

H	C	DIPOD				DIPUD				DIB				PEM				PEP
H	C	POS/kbp	a	d	h	POS/kbp	a	d	h	POS/kbp	a	d	h	POS/Kbp	a	d	h	POS/kbp	a	d	h	P/%
RV		470	0	0.73	0.73	470	0	0.73	−0.73	470	0	0	0.73	470	0.73	0	−0.73	470	0.73	0	0.73
10	2	470	−0.01	0.74	0.73	470	0.01	0.74	−0.72	470	0	0	0.74	470	0.73	0	−0.73	470	−0.01	0.74	0.73	100
10	2	0	(0.1)	(0.13)	(0.07)	0	(0.09)	(0.13)	(0.07)	0	(0.1)	(0.14)	(0.08)	0	(0.1)	(0.12)	(0.08)	0	(0.1)	(0.1)	(0.1)
RV		470	0	1.26	1.26	470	0	1.26	−1.26	470	0	0	1.26	470	1.26	0	−1.26	470	1.26	0	1.26
10	6	470	0.02	1.25	1.28	470	−0.04	1.25	−1.28	470.02	0.01	0.01	1.26	470	1.27	0	−1.25	470	0.02	1.25	1.28	100
10	6	0	(0.18)	(0.23)	(0.11)	0	(0.16)	(0.18)	(0.13)	(0.2)	(0.16)	(0.22)	(0.15)	0	(0.17)	(0.21)	(0.12)	0	(0.18)	(0.2)	(0.1)
RV		470	0	0.93	0.93	470	0	0.93	−0.93	470	0	0	0.93	470	0.93	0	−0.93	470	0.93	0	0.93
15	2	470	−0.01	0.92	0.93	470	0	0.9	−0.93	470	−0.01	0	0.92	470	0.95	0	−0.92	470	−0.01	0.92	0.93	100
15	2	0	(0.1)	(0.12)	(0.07)	0	(0.1)	(0.13)	(0.07)	0	(0.11)	(0.13)	(0.09)	0	(0.1)	(0.14)	(0.07)	0	(0.1)	(0.1)	(0.1)
RV		470	0	1.6	1.6	470	0	1.6	−1.6	470	0	0	1.6	470	1.6	0	−1.6	470	1.3	0	1.6
15	6	470	0	1.59	1.59	470	0	1.62	−1.63	470	0.01	0.01	1.6	470	1.59	−0.03	−1.62	470	0	1.59	1.59	100
15	6	0	(0.17)	(0.2)	(0.13)	0	(0.18)	(0.22)	(0.13)	0	(0.16)	(0.19)	(0.12)	0	(0.17)	(0.2)	(0.12)	0	(0.17)	(0.2)	(0.1)
注：表中括号内为标准差，此处列出C=2、6，交配轮数为7次的结果，表中H代表遗传率，H代表遗传率（Heritability），C代表C值（C value），RV代表真值（Real value），P代表统计功效(Power)，POS代表iQTL在染色体上的位置(iQTL position)。 Note: The number in parentheses in the table is the standard deviation，the results listed here are the C values are 2 and 4,the number of mating rounds is 7, C represents C-value, RV represents real value, P represents statistical power and POS means the iQTL’s position on chromosome.

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