【作者】 汤在祥；

【导师】 徐辰武；

【作者基本信息】 扬州大学 ， 作物遗传育种， 2009， 博士

【摘要】 通过建立各种新的研究方法和手段,开展杂种优势以及复杂性状基因的功能研究已经成为当今遗传学领域的主要研究内容。随着生物学技术的进步,特别是近十年来人类以及其他模式生物基因组计划的开展,对于复杂性状的遗传研究越来越深入。然而,要彻底了解杂种优势以及复杂性状表型变异的遗传基础,仍具有相当大的挑战,需要从控制表型建成的各个遗传系统全局考虑。各个遗传系统,包括核基因组、线粒体基因组以及叶绿体基因组在复杂性状的遗传表达以及杂种优势形成中均可能发挥重要的作用。细胞质提供了基因表达的环境,细胞质中的线粒体更是生物进行生化活动的重要能量来源,基因功能的实现是核内基因与细胞质遗传物质共同作用的结果。细胞质效应在动植物中广泛存在,在模式生物果蝇、小鼠和酵母上的研究表明,细胞质与细胞核间的上位性互作效应对后代有明显的影响。遗传物质间上位性是物种分化和适应的重要遗传学动力,也是复杂性状和杂种优势形成的重要遗传组分。然而,由于技术发展的限制和相关统计分析方法的缺乏,上位性,特别是核质互作上位性在复杂性状遗传中的重要性常常被研究人员忽视。因此,发展出合适的统计分析方法在分子层次上剖析细胞质与细胞核基因间的上位性作用是揭开核质互作遗传机理的核心问题。本研究结合遗传交配设计,在常规QTL分析方法的基础上,提出一种剖析核质互作QTL的统计模型和分析方法,即核质互作QTL分析方法(Cytonuclear interacting QTL mapping,CNQM),以定位存在核质上位性的QTL。玉米是我国最重要的三大粮食作物之一,同时也是重要的饲料和经济作物,在国民经济中占有重要地位。玉米杂种优势的利用是玉米生产发展的重要动力,广泛开展玉米复杂性状以及杂种优势遗传基础的研究和探讨具有十分重要的理论价值和现实意义。本研究在提出核质互作QTL分析方法的基础上,同时采用强优势玉米杂交种苏玉16(JB×Y53)的两个亲本自交系,配置具有不同细胞质背景的混合作图群体,构建分子标记连锁图谱,并采用本研究提出的核质互作QTL分析方法(CNQM)定位玉米重要农艺和产量性状相关的核质互作QTL。研究结果概述如下:(1)建立了一套剖分核质互作遗传机制的统计遗传模型和分析方法本文提出利用遗传设计获得具有不同细胞质背景的混合分离群体,并以此为基础建立了一种剖分核质互作遗传机制的统计分析方法。该方法既可无偏估计核质互作QTL在核基因组中的位置与效应,又可对有关QTL与细胞质遗传物质间的重要互作效应作出测验和估计。方法的有效性和可行性通过染色体水平和基因组水平两套模拟方案得到验证。模拟结果表明:低遗传力和小样本容量下,QTL的统计功效低,参数估计值有偏,随着遗传力的提高,QTL的统计功效不断提高,各参数的估计值也接近真值,这与一般期望相符。在遗传力达到15%以上时,正反交各100的样本容量即可获得100%的统计功效。染色体水平的模拟试验表明,无论对于主效QTL,还是对具有不同核质互作方式的QTL,本文方法均具有很好的分析能力。(2)基于核质互作QTL分析方法解析强优势玉米杂交种苏玉16号的遗传组成本研究在上述遗传交配设计的基础上,利用玉米强优势杂交组合的两个亲本材料,即自交系JB和Y53组配正反交F2和F2:3群体,利用105个SSR标记构建连锁图谱,覆盖全基因组1214.6cM,各标记间平均图距为11.7cM。同时考察F2和F2:3群体的株高,穗位高等12个重要农艺性状和产量性状。采用本文提出的核质互作QTL定位方法定位有关的QTL,分析其相对贡献的大小,深入解析具有强优势玉米杂交种苏玉16号重要农艺性状的各遗传组分,包括细胞质效应,核内QTL效应,核内QTL与细胞质的互作效应以及它们对表型的贡献。为了便于比较,本文同时采用QTL Network 2.0和Windows QTL Cartographer 2.5软件在不考虑细胞质背景的情况下进行有关QTL的重演性验证。分析结果显示:采用CNQM方法共检测到99个QTL,其中53个能够被重复检测到。抽穗期、株高、雄穗一级分支数、雄穗长、穗位高和茎粗检测到的QTL达到了10个以上,且平均一半以上的QTL能够被重复检测到,被重复检测到的QTL的平均贡献率在10%以上。在第7染色体上检测到的QTL最多,达到24个,核质互作QTL有8个,24个QTL中11个能够被重复检测到。在第10染色体上仅检测到1个QTL。99个QTL中34个具有显著的加性×细胞质或显性×细胞质互作效应,可被认为是具有核质互作效应的QTL。平均每个性状有3个核质互作QTL。这些结果表明,本研究调查的12个农艺性状不同程度地受到核质上位性的影响。此外,许多QTL定位在同一标记区间内,这可能是控制不同性状基因间存在紧密连锁,也可能是同一QTL影响不同的性状。更多还原

【Abstract】 Functional research of the genes underlying heterosis and complex traits is the main objective of modern genetics, through new technology and method. With the development of biological technology, especially the development of genome project of human and other model organism, the research on the genetic basis of complex traits is more intensive. However, understanding the genetic basis of complex traits and heterosis is still a great challenge, which should be considered from the overall genetic systems. Each genetic system, including nuclear genome, mitochondrial genome and chloroplast genome, plays an important role in the genetic expression of complex traits and heterosis. Cytoplasm is the environment of gene expression, and mitochondrion provides the energy to support the biochemical reaction. It can be said that the realization of gene function is the result of cooperation between the nuclear gene and maternal cytoplasmic environment. Cytoplasmic effect exists widely in plants and animals. Researches on drosophila, mice and yeast also suggested that epistasis between nuclear and mitochondria affected significantly the phenotype of offspring. Furthermore, it was indicated that epistasis was the main genetic dynamics of speciation and adaption and the primary genetic component of heterosis and complex traits. However, because of the limitation of technology and the lack of flexible statistical method, epistasis, especially the cytonuclear epistasis was neglected too often in complex trait studies. Therefore, developing the proper methodology for dissecting the interaction between nuclear and cytoplasmic background was the core to understand the genetic basis of the cytonuclear epistasis. In this paper, we proposed a special genetic design to dissect cytonuclear epistasis. We called it cytonuclear interacting QTL mapping method, abbreviated to CNQM.Maize is one of the most important food crops in China. It plays a vital role in agricultural economy of China. The utilization of heterosis promotes the maize production greatly. So, understanding the genetic basis of heterosis and complex traits highlights the theoretical value and practical significance in maize. Based on the proposed genetic design, the maize inbreed lines JB and Y53, which are the parental lines of maize hybrid suyu 16 with strong heterosis, were used to create the mixed mapping population with two different cytoplasm backgrounds. The proposed method for mapping cytonuclear epistatic QTL were used to identify the cytonuclear QTL underlying maize agricultural and yield traits. The results are as follows.(1) Statictical model and method for dissecting cytonuclear epistasisThe mixed segregating population with the different cytoplasm backgrounds was created by using the reciprocal mating design. And the corresponding statistical method was proposed for dissecting cytonuclear epistatic interaction. The method can unbiasedly estimate positions and effects of cytonuclear epistatic QTL as well as simultaneously detect the important epistatic interaction between QTL and inherited cytoplasmic genomes. The validation of the statistical procedure was verified through two sets of simulation studies which are implemented via chromosome level and genome level, respectively.Simulation results showed that, higher QTL heritability and larger sample sizes tend to produce more accurate and precise estimates and higher statistical power, whereas lower heritability, especially with smaller sample sizes, produce less accurate estimates with large estimation errors and lower statistical power, which is in accordance with our general expectations. When the QTL heritability was above 15%, the statistical power of QTL can reach almost 100% when only 200 individuals were collected. Genome level simulation results suggested that, no matter which interaction model was adopted, the proposed method would perform very well.(2) The genetic dissection of maize hybrid Suyu 16 with strong heterosisBased on the proposed genetic design, JB and Y53, the parental lines of maize hybrid Suyu 16 with strong heterosis, were used to create reciprocal F2 and F2:3 populations. The genetic linkage map was constructed containing 105 SSR markers, which covered 1214.6cM of maize genome. The average distance of the flanking markers was 11.7cM. The phenotypic value of 12 traits were investigated in reciprocal F2 and F2:3 populations. The proposed method was used to identify the QTL with cytonuclear epistatic effect and to evaluate the contribution of QTL to the phenotypic variation. This will help us to understand the genetic components of maize hybrid Suyu 16, including cytoplasmic effect, nuclear gene effect, cytonuclear epistatic effect. For comparison, two QTL mapping softwares, QTL Network 2.0 and Windows QTL Cartographer 2.5, were used to verify the QTL mapping result without considering the cytoplasmic effect and cytonuclear epistasis.The results showed that 99 QTL controlling 12 traits were detected by CNQM method, and 53 of them were verified by different segregating populations or by different mapping methods. More than 10 QTL were detected in heading date, plant height, tassel branch number, tassel length, ear height and stem diameter, respectively. On average, half of them can be verified. The contribution of these QTL was over 10% of the phenotypic variation. Twenty four QTL were detected on Chromosome 7, in which eight of them had cytonuclear epistatic effects and eleven of them were verified by different mapping methods. However, only one QTL was detected on Chromosome 10. Thirty four of total 99 QTL showed significant cytonuclear epistatic effects. The size of cytonuclear epistasis had different altitudes in different traits. In addition, many QTL were found locating at the same marker interval. This implied the existence of pleiotropic QTL or tightly linked QTL.更多还原