BBSRC-NSF/BIO PanOryza: Globally coordinated genomes, proteomes and pathways for rice

全球人口面临的最严重问题是100亿人的问题。在气候变化将使肥沃的土地更加稀缺，天气更加难以预测（干旱、洪水、温度飙升）的背景下，世界能否支持生产足够高质量、有营养的粮食，以养活预计到2050年将达到100亿的人口？可以肯定的是，大米将在养活全球大部分地区方面发挥核心作用。目前，大米为50%的人口提供了主要的每日热量需求。该属作为一个整体，包括驯化水稻的两个主要分支（Oryza sativa Japonica和Indica），以及各种各样的野生近缘种，具有在异常广泛的环境下生长的能力。世界各地的研究团队一直在与育种者密切合作，以帮助确定当地地方品种（即当地适应品种）及其野生亲缘品种中存在的理想性状，例如对周期性干旱、洪水或高温的抗性，并进行杂交，将这些基因/性状转移到高产和广泛分布的品种中。基因组科学现在是研发工作的核心。一个粳稻参考品种和一个籼稻参考品种的基因组大约在15年前测序完成。然而，基因组序列只是一个起点。为了使数据对研究有用，需要一个称为基因组注释的过程。注释包括发现和定义基因组中的基因，并计算出这些基因编码的功能角色。注释通常涉及几个不同的软件包，错误率很高，随后需要多年的人工修复错误和改进基因。遗憾的是，水稻基因注释工作一直缺乏国际协调，导致使用不同方法对水稻基因进行了几种不同的独立注释工作，这些工作至今仍存在于不同的数据库中。代表更广泛的地方品种和野生水稻品种的新基因组刚刚上线，因此，如果没有国际协调的重大努力，这个问题将迅速恶化。植物科学家和育种家将发现，解释和比较从不同水稻品种收集的信息非常具有挑战性。该项目旨在解决这一问题，它将六个国际合作伙伴聚集在一起，共同实现在所有品种的水稻基因集中建立一致性的目标。我们将建立新的软件和协议来共享数据，这将使我们能够定义在所有水稻类型的基因组中存在的基因（以及它们编码的蛋白质），称为泛基因组或泛基因集。我们的项目成果将“面向未来”的水稻基因组资源，使研究人员能够集中精力了解水稻的生物学，并寻找跨越亚洲栽培水稻遗传多样性的理想性状。

The most serious issue facing the global human population is the 10 billion person question. Can the world support production of enough high-quality, nutritious food to feed a projected 10 billion people by 2050, against a backdrop of climate change that will make fertile land more scarce and weather more unpredictable (droughts, floods, temperature spikes). It is certain that rice will play a central role in feeding much of the globe. At present, rice provides the major daily caloric need for 50% of the human population. The genus as a whole, including the two main branches of domesticated rice (Oryza sativa Japonica and Indica), and a huge variety of wild relatives, has the capacity to grow under an exceptionally wide range of environments. Research teams around the world have been working closely with breeders to help identify desirable traits present in local landraces (i.e. locally adapted varieties) and their wild relatives, such as resistance to periodic droughts, flooding or high temperatures, and perform crosses to transfer such genes/traits into high yielding, and widely distributed varieties. Genomic science is now central to research and development efforts. The genome of one reference variety of Japonica and one of Indica were sequenced around 15 years ago. However, the genome sequence is just the starting point. For the data to be useful for research, requires a process called genome annotation. Annotation involves finding and defining the genes within the genome, and working out what functional roles those genes code for. Annotation usually involves several different software packages, which high error rates, followed by manual work to fix errors and improve genes over many years. Rice gene annotation efforts have unfortunately suffered from a lack of international coordination, leading to several different independent efforts to annotate rice genes using different methods, which persist in different databases today. New genomes for varieties representing a wider pool of landraces and wild rice species are just coming online, and thus without a major effort in international coordination, this problem will get rapidly worse. Plant scientists and breeders will find it very challenging to interpret and compare information collected from different rice varieties. This project aims to solve this issue, bringing together six international partners with a shared goal of creating consistency in the rice gene set across all varieties. We will build new software and protocols for sharing data, which will enable us to define what genes are present (and the proteins they encode) in the genomes of all rice types, called a pan-genome or pan gene set. The outcomes of our project will "future-proof" rice genomic resources, so that researchers can focus their efforts on understanding the biology of rice, and searching for desirable traits that span the genetic diversity of cultivated Asian rice.