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. This award was co-funded by the Plant Genome Research Program in the Division of Integrative Organismal Systems, and the Infrastructure Capacity for Biology Program in the Division of Biological Infrastructure.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
