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，产生一个称为受精卵的单细胞。合子分裂并生长在种子内形成胚胎，胚萌发后产生整个成虫。因此，受精卵是一种全能细胞，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依赖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过渡称为合子过渡。在这个转变过程中，受精卵基因组发生了广泛的变化：染色体中的DNA被重新包装，基因在受精卵核中被激活，母体提供的RNA被移除。因此，合子的转变是植物生命周期中具有里程碑意义的事件。由于植物受精卵的体积小，难以接近，目前对这种基本转变知之甚少。该项目将利用基因组学的最新进展来利用水稻植物的优势特征来解决这个问题。在水稻中，从传粉到受精的时间是所有开花植物中最短的，在精确确定的发育阶段解剖受精卵是可行的。该项目将在基因组尺度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，并深入了解这种转变背后的基因网络。众所周知，在种子发育过程中，许多基因的表达取决于亲本，即由于DNA的修饰或其包装称为表观遗传变化，母本遗传基因和父本遗传基因的表达是不同的。该项目将评估两种不同水稻品种杂交中父本和母本合子基因组的个别贡献，以确定亲本起源对合子转录的影响程度，并将根据其表观遗传修饰的性质对显示这种影响的基因进行表征。受精卵是植物生命周期中的一个关键转变，当基因组被重新编程以开始从一个细胞产生新的二倍体一代时。因此，该项目将解决对植物繁殖的理解上的一个重大差距。了解胚胎的合子转变在提高种子产量、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价值。该项目将以水稻为重点，水稻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。该项目的研究结果也应适用于其他作物，特别是谷类作物。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的一个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（Langston University）的学生和教师提供植物基因组学方面的培训。兰斯顿大学是一所历史上的非裔美国人大学。该项目还将为俄克拉何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.