双列杂交分析与QTL定位分析之间关系的研究
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摘要
双列杂交分析是经典数量遗传学中应用最为广泛的一种重要的遗传分析方法,推动了遗传研究与育种实践的发展。QTL定位分析则属于分子数量遗传学范畴,是数量遗传学与分子遗传学相结合的产物,是当今遗传学研究中的一个热点。这两种分析方法都属于数量遗传学的研究范畴,都是用来研究数量性状遗传规律的遗传分析方法,在遗传分析中都起着举足轻重的作用,它们有着许多相似之处;但是双列杂交分析是将控制性状的所有基因作为一个整体来研究的,而QTL定位分析则是将控制性状的多个基因单个剖析开来加以研究的,因此二者又有许多不同之处。双列杂交分析与QTL定位分析之间究竟存在什么样的关系以及二者结合起来能否提供更多的遗传信息,是一个令人感兴趣的课题。但是目前没有看到相关研究的报道。
本文就是针对双列杂交分析与QTL定位分析之间的关系进行了探讨。主要运用了Monte Carlo模拟方法对双列杂交分析与QTL定位分析之间的关系进行了模拟研究,同时用水稻珍汕97B×明恢63所衍生的重组自交系(RIL)群体和永久F_2(IF_2)群体的性状数据与分子标记信息,进行了实例分析。本文研究的主要内容分为两大部分:一是模拟研究部分;二是实例分析部分。
在模拟研究部分,运用Monte Carlo模拟的方法,主要研究了影响双列杂交分析与QTL定位分析之间关系的多种因素。在研究中,引入了相关系数来衡量双列杂交分析与QTL定位分析之间的关系。模拟研究的主要内容与部分结论如下:
(1) 双列杂交分析与QTL定位分析分别采用不同遗传效应的定义,这会影响二者之间的相关性;当遗传方差比例相同或遗传效应相同时,一般加性效应的相关性最大,其次为显性效应的相关性,而加加上位性效应的相关性最小;(2) 随着某遗传方差在总方差中所占比例的增加,它的相关性就明显增大;但当该遗传效应在总方差中所占的比例大到一定程度时,该遗传效应的相关性增大的幅度就变的越来越小,甚至不再增加,最后进入“平台期”;(3) 各遗传效应相互之间对彼此相关性存在一定的影响,但残差对二者之间遗传效应相关性的影响最为明显;(4) 当各遗传方差所占比例不变时,QTL连锁与QTL数目不会影响相关性;(5) 在一定的范围内,DH群体与IF_2群体样本容量之间的比例越大,相关性就越小;(6) 在QTL定位分析中,QTL效应值与位置的偏差程度越大,二者的相关性就越低;(7)QTL定位时选择不同的概率Threshold对二者之间的相关性有一定的影响。(8) 多基因遗传体系的差异对双列杂交分析与QTL定位分析之间的相关性有很大的影响;微效多基因的存在,会使双列杂交分析与QTL定位分析之间的相关性降低;微效基因的遗传方差所占的比例越大,相关性就越低;反之,根据双列杂交分析与QTL定位分析之间的相关性大小也可以判断控制性状的基因遗传体系的类型,结合遗传方差分析,也可以粗略地判断微效基因与主效基因之间的方差比例。(9) 如果有微效多基因存在时,双列杂交分析的结果比QTL定位分析结果更接近于真值。
在实例分析部分,对水稻的株高、千粒重和产量等三个性状进行了双列杂交与QTL定位进行了分析与比较;并根据模拟研究中得到的结果,对水稻三个性状进行了双列杂交与QTL定位之间的相关性分析,推断出了控制它们的遗传体系的特点,得到了一些对遗传研究与育种实践有指导意义的结论。
Diallel analysis has been broadly used as an important tool of genetic analysis in classical quantitative genetics, which advanced the development of genetics studies and breeding practices. Being a hotspot in genetic studies, QTL mapping is a powerful tool in molecular quantitative genetics, which is an inter-discipline between quantitative genetics and molecular genetics. Both tools serve as the key methods of genetic analysis for investigating the genetic natures of quantitative traits, and play important roles in the studies of quantitative genetics. Therefore, there were many similarities between the two methods. In diallel analysis, those genes controlling a quantitative trait were analyzed as a whole. However, those genes controlling a quantitative trait could be dissected into single genes and be studied individually using the method of QTL mapping. Therefore, there also were many differences between the two methods. What's the relationship between diallel analysis and QTL mapping? Could more interesting informations be provided if diallel analysis and QTL mapping were jointly applied to analyzing the same set of data. This was an interesting problem. Up to now, no reports on this was seen.The present studies were conducted to investigate the relationship between diallel analysis and QTL mapping. Monte Carlo simulations were employed for this purpose. Both tools were used to analyze a real set of data including quantitative trait and molecular marker information of an immortalized F2 (IF2) population of rice, which was constructed by random mating among RIL hues derived from Zhenshan97B x Minghui63. The dissertation consists of two sections: simulation studies and a worked example.In the section of simulation studies, Monte Carlo simulations were conducted to study the relationship between diallel analysis and QTL mapping. The section was mainly involved in studying the factors influencing the relationship between diallel analysis and QTL mapping. The correlation coefficient was introduced into present studies for measuring the relationship between diallel analysis and QTL mapping. The main contents and conclusions of the simulation studies are as follows:(1) Diallel analysis and QTL mapping adopted different definations of genetic effect respectively. This had an influence on the correlation between diallel analysis and QTL mapping. When genetic variance or genetic effect was equal, the ranking of the correlation from large to small was additive, dominance and additive by additive in turn.(2) When genetic variance increased relative to total variance, its correlation between diallel analysis and QTL mapping also obviously aggrandized; But when the genetic effect increased to certain level, the speed of aggrandizement of its correlation changed more and more slow, and the correlation curse entered into a platform stage finally.(3) The correlation of each genetic effect was influenced by other genetic effects. Among the genetic components, residual variance had the most remarkable influence on the correlation between diallel analysis and QTL mapping.(4) The linkage of QTLs and number of QTLs showed no effects on the correlation
between diallel analysis and QTL mapping when genetic variances were not changed.(5) The sample proportion of DH to IF2 was bigger; the correlation between diallel analysis and QTL mapping was lower.(6) In the results of QTL mapping, either biased effects or biased positions were capable of affecting the correlation between diallel analysis and QTL mapping. The bias was larger, the correlation was lower.(7) Selecting different thresholds in QTL mapping had certain influence to the correlation between diallel analysis and QTL mapping.(8) The different of polygenic system was the main factor influencing the correlation between diallel analysis and QTL mapping. Because of the existence of polygenes, the correlation between diallel analysis and QTL mapping was lower. The variance proportion of polygenes to major genes was larger, the correlation was lower. On the contrary, according to
本文就是针对双列杂交分析与QTL定位分析之间的关系进行了探讨。主要运用了Monte Carlo模拟方法对双列杂交分析与QTL定位分析之间的关系进行了模拟研究,同时用水稻珍汕97B×明恢63所衍生的重组自交系(RIL)群体和永久F_2(IF_2)群体的性状数据与分子标记信息,进行了实例分析。本文研究的主要内容分为两大部分:一是模拟研究部分;二是实例分析部分。
在模拟研究部分,运用Monte Carlo模拟的方法,主要研究了影响双列杂交分析与QTL定位分析之间关系的多种因素。在研究中,引入了相关系数来衡量双列杂交分析与QTL定位分析之间的关系。模拟研究的主要内容与部分结论如下:
(1) 双列杂交分析与QTL定位分析分别采用不同遗传效应的定义,这会影响二者之间的相关性;当遗传方差比例相同或遗传效应相同时,一般加性效应的相关性最大,其次为显性效应的相关性,而加加上位性效应的相关性最小;(2) 随着某遗传方差在总方差中所占比例的增加,它的相关性就明显增大;但当该遗传效应在总方差中所占的比例大到一定程度时,该遗传效应的相关性增大的幅度就变的越来越小,甚至不再增加,最后进入“平台期”;(3) 各遗传效应相互之间对彼此相关性存在一定的影响,但残差对二者之间遗传效应相关性的影响最为明显;(4) 当各遗传方差所占比例不变时,QTL连锁与QTL数目不会影响相关性;(5) 在一定的范围内,DH群体与IF_2群体样本容量之间的比例越大,相关性就越小;(6) 在QTL定位分析中,QTL效应值与位置的偏差程度越大,二者的相关性就越低;(7)QTL定位时选择不同的概率Threshold对二者之间的相关性有一定的影响。(8) 多基因遗传体系的差异对双列杂交分析与QTL定位分析之间的相关性有很大的影响;微效多基因的存在,会使双列杂交分析与QTL定位分析之间的相关性降低;微效基因的遗传方差所占的比例越大,相关性就越低;反之,根据双列杂交分析与QTL定位分析之间的相关性大小也可以判断控制性状的基因遗传体系的类型,结合遗传方差分析,也可以粗略地判断微效基因与主效基因之间的方差比例。(9) 如果有微效多基因存在时,双列杂交分析的结果比QTL定位分析结果更接近于真值。
在实例分析部分,对水稻的株高、千粒重和产量等三个性状进行了双列杂交与QTL定位进行了分析与比较;并根据模拟研究中得到的结果,对水稻三个性状进行了双列杂交与QTL定位之间的相关性分析,推断出了控制它们的遗传体系的特点,得到了一些对遗传研究与育种实践有指导意义的结论。
Diallel analysis has been broadly used as an important tool of genetic analysis in classical quantitative genetics, which advanced the development of genetics studies and breeding practices. Being a hotspot in genetic studies, QTL mapping is a powerful tool in molecular quantitative genetics, which is an inter-discipline between quantitative genetics and molecular genetics. Both tools serve as the key methods of genetic analysis for investigating the genetic natures of quantitative traits, and play important roles in the studies of quantitative genetics. Therefore, there were many similarities between the two methods. In diallel analysis, those genes controlling a quantitative trait were analyzed as a whole. However, those genes controlling a quantitative trait could be dissected into single genes and be studied individually using the method of QTL mapping. Therefore, there also were many differences between the two methods. What's the relationship between diallel analysis and QTL mapping? Could more interesting informations be provided if diallel analysis and QTL mapping were jointly applied to analyzing the same set of data. This was an interesting problem. Up to now, no reports on this was seen.The present studies were conducted to investigate the relationship between diallel analysis and QTL mapping. Monte Carlo simulations were employed for this purpose. Both tools were used to analyze a real set of data including quantitative trait and molecular marker information of an immortalized F2 (IF2) population of rice, which was constructed by random mating among RIL hues derived from Zhenshan97B x Minghui63. The dissertation consists of two sections: simulation studies and a worked example.In the section of simulation studies, Monte Carlo simulations were conducted to study the relationship between diallel analysis and QTL mapping. The section was mainly involved in studying the factors influencing the relationship between diallel analysis and QTL mapping. The correlation coefficient was introduced into present studies for measuring the relationship between diallel analysis and QTL mapping. The main contents and conclusions of the simulation studies are as follows:(1) Diallel analysis and QTL mapping adopted different definations of genetic effect respectively. This had an influence on the correlation between diallel analysis and QTL mapping. When genetic variance or genetic effect was equal, the ranking of the correlation from large to small was additive, dominance and additive by additive in turn.(2) When genetic variance increased relative to total variance, its correlation between diallel analysis and QTL mapping also obviously aggrandized; But when the genetic effect increased to certain level, the speed of aggrandizement of its correlation changed more and more slow, and the correlation curse entered into a platform stage finally.(3) The correlation of each genetic effect was influenced by other genetic effects. Among the genetic components, residual variance had the most remarkable influence on the correlation between diallel analysis and QTL mapping.(4) The linkage of QTLs and number of QTLs showed no effects on the correlation
between diallel analysis and QTL mapping when genetic variances were not changed.(5) The sample proportion of DH to IF2 was bigger; the correlation between diallel analysis and QTL mapping was lower.(6) In the results of QTL mapping, either biased effects or biased positions were capable of affecting the correlation between diallel analysis and QTL mapping. The bias was larger, the correlation was lower.(7) Selecting different thresholds in QTL mapping had certain influence to the correlation between diallel analysis and QTL mapping.(8) The different of polygenic system was the main factor influencing the correlation between diallel analysis and QTL mapping. Because of the existence of polygenes, the correlation between diallel analysis and QTL mapping was lower. The variance proportion of polygenes to major genes was larger, the correlation was lower. On the contrary, according to
引文
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