Genomics of the Zygotic Transition in Rice

Pi：Venkatesan Sundaresan(加州大学戴维斯分校)Co-Pi：Scott D.Russell(俄克拉荷马大学-诺曼分校)合作者：Clarence Hedge(兰斯顿大学)植物通过授粉和受精繁殖，导致卵细胞和精子细胞融合，产生称为受精卵的单一细胞。受精卵分裂并生长，在种子内形成胚胎，萌发后形成整个成年植株。因此，受精卵是一个全能细胞，具有再生植物所有组织和器官的能力。受精卵和早期胚胎的生长最初取决于卵细胞提供的母体因素。随着胚胎的发育，它后来变得独立于这些母体因素，只依赖于胚胎合成的RNA和蛋白质。从依赖母体基因产物的受精卵到由胚胎基因和基因产物控制的独立生长的转变称为合子转变。在这一转变过程中，合子基因组发生了广泛的变化：染色体中的DNA被重新包装，合子核中的基因被激活，母体提供的RNA被移除。因此，合子的转变是植物生命周期中的一个里程碑事件。由于植物受精卵的体积小且不易接近，目前对这一根本性转变知之甚少。这个项目将通过利用基因组学的最新进展来开发水稻植株的优势特征来解决这个问题。在水稻中，从授粉到受精的时间是所有开花植物中最短的，在精确定义的发育阶段解剖受精卵是可行的。该项目将在基因组规模上确定受精卵从受精卵到第一次胚胎分裂过程中基因表达的变化，并深入了解支撑这一转变的基因网络。众所周知，许多基因在种子发育过程中的表达取决于亲本，即母本遗传和父本遗传的基因表达不同，这是由于DNA或其包装的改变称为表观遗传变化。该项目将评估两个不同水稻品系之间杂交受精卵的父本和母本基因组的个体贡献，以确定亲本对合子转录的影响程度，并将根据表观遗传修改的性质来表征显示这种影响的基因。受精卵是植物生命周期中的一个关键过渡，此时基因组被重新编程，以启动从这个细胞产生的新的二倍体世代。因此，该项目将解决对植物繁殖的理解上的一个重大差距。了解胚胎的合子转换在提高种子产量、从组织培养中再生植物以及改进杂交育种方法方面具有农业应用。该项目将把重点放在大米上，大米是世界上最重要的粮食作物之一，也是美国许多州的主要作物。该项目的发现也应该适用于其他作物，特别是谷物。为此目的，该项目产生的数据将通过GenBank和Gramene等公共数据库广泛提供，并通过加州大学戴维斯分校可公开访问的项目网站进行分析。此外，该项目将通过在俄克拉何马大学和加州大学戴维斯分校的暑期实习，为兰斯顿大学的学生和教职员工提供植物基因组学方面的培训。兰斯顿大学历史上是一所非裔美国人的机构。该项目还将为俄克拉荷马大学的本科生和研究生以及加州大学戴维斯分校的本科生、研究生和博士后研究员提供培训。

PI: Venkatesan Sundaresan (University of California-Davis)Co-PI: Scott D. Russell (University of Oklahoma-Norman)Collaborator: Clarence Hedge (Langston University)Plants reproduce through pollination and fertilization, resulting in the fusion of an egg cell and a sperm cell to generate a single cell called a zygote. The zygote divides and grows to form an embryo inside the seed, which after germination gives rise to the entire adult plant. Thus, the zygote is a totipotent cell, with the capacity to regenerate all the tissues and organs of a plant. The growth of the zygote and the early embryo is initially dependent upon maternal factors provided by the egg cell. As the embryo develops, it later becomes independent of these maternal factors and relies only upon embryonically synthesized RNAs and proteins. The transition from the fertilized egg, reliant on maternal gene products, to independent growth controlled by embryonic genes and gene products, is called the Zygotic transition. During this transition, extensive changes occur to the zygotic genome: the DNA in the chromosomes is re-packaged, genes are activated in the zygotic nucleus, and the maternally-supplied RNA is removed. The Zygotic transition is therefore a landmark event in the life-cycle of a plant. Due to the small size and inaccessibility of the plant zygote, very little is currently known about this fundamental transition. This project will address the problem by utilizing recent advances in genomics to exploit advantageous features of rice plants. In rice, the time from pollination to fertilization is one of the shortest of all flowering plants, and dissection of zygotes at precisely defined stages of development is feasible. The project will determine on a genome scale the changes in gene expression as the zygote progresses from fertilized egg to the first embryonic division, and gain insights into gene networks that underlie this transition. It is known that expression of many genes during seed development depends upon the parent-of-origin, i.e. expression of maternally-inherited and paternally-inherited genes are different, due to modifications of the DNA or its packaging called epigenetic changes. The project will evaluate individual contributions of the paternal and maternal genomes of the zygote in crosses between two different rice strains, to determine the extent of parent-of-origin effects on zygotic transcription, and genes that show such effects will be characterized for the nature of their epigenetic modifications. The zygote is a critical transition in the plant life cycle, when the genome is reprogrammed for the initiation of a new diploid generation that arises from this one cell. This project will therefore be addressing a significant gap in the understanding of plant reproduction.Understanding of the zygotic transition in embryos has agricultural applications for increased seed yields, for regeneration of plants from tissue culture, and for improved methods of breeding hybrids. The project will focus on rice, one of the most important food crops in the world, and also a major crop in many states of the USA. The project findings should also be applicable to other crops, especially cereals. For this purpose, the data generated by the project will be made available for wide access through public databases such as GenBank and Gramene, and the analysis through a publicly-accessible project website at the University of California-Davis. Additionally, the project will provide training in plant genomics to students and faculty from Langston University, a historically African-American institution, through summer internships at the University of Oklahoma, and at the University of California-Davis. The project will also provide training for undergraduate students and graduate students at University of Oklahoma, and for undergraduate students, graduate students, and postdoctoral fellows at the University of California-Davis.