Genomics of the Zygotic Transition in Rice

PI：Venkatesan Sundaresan（University of California-Davis）Co-PI：Scott D.罗素（俄克拉荷马大学诺曼分校）合作者：克拉伦斯·赫奇（兰斯顿大学）植物通过授粉和受精进行繁殖，导致卵细胞和精细胞融合产生一个被称为合子的单细胞。 受精卵分裂并在种子内生长形成胚，胚在发芽后产生整个成年植物。因此，合子是全能细胞，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被称为合子过渡。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被去除。因此，合子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和难以接近，目前对这种基本的转变知之甚少。 本项目将通过利用基因组学的最新进展来开发水稻植物的有利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合子是可行的。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，并深入了解这一转变背后的基因网络。 已知在种子发育期间许多基因的表达取决于亲本来源，即母系遗传和父系遗传基因的表达是不同的，这是由于DNA或其包装的修饰（称为表观遗传变化）。 该项目将评估两种不同水稻品系杂交中合子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，并将对表现出这种影响的基因进行表征，以确定其表观遗传修饰的性质。 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这一个细胞产生的新的二倍体世代时。 因此，该项目将解决植物繁殖理解方面的一个重大空白。了解胚胎中的合子转变在农业上可用于提高种子产量，从组织培养中再生植物，以及改进杂交育种方法。该项目的重点是水稻，这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，特别是谷物。 为此目的，该项目产生的数据将通过基因库和Gramene等公共数据库广泛提供，并通过加利福尼亚大学戴维斯分校的一个公众可访问的项目网站进行分析。 此外，该项目还将通过在俄克拉荷马州大学和加利福尼亚大学戴维斯分校的暑期实习，向来自历史上的非裔美国人机构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。该项目还将为俄克拉荷马州大学的本科生和研究生以及加利福尼亚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.