The post-genomics era rice breeding: perspectives and practices

Rice, Oryza sativa L., is the staple food for half the world’s population. Future world food security requires continued and sustainable increase in rice production to mitigate the effects of climate change and loss of arable land. Much of this increase has to come from new high yielding cultivars with resistances to multiple stresses. To achieve this, accelerated genetic gains in rice improvement are expected through ‘breeding by design’ - the future knowledge and information based breeding strategy in the post-genomic era. As an important step to achieve this, the core collection of 3,024 rice accessions from 89 countries were re-sequenced through an international effort to establish a global, public rice genetic/genomic database and information platform for advancing rice breeding technology. The 3k sequenced rice genomes had an average sequencing depth of 14X, and average genome coverage and mapping rate of 94.0% and 92.5% when aligned on the reference Nipponbare genome. This effort produced 18.9 million SNPs and a total of `17 T raw sequence data, which is now deposited in GigaDB.org as a global public good, providing the foundation for large-scale discovery of novel alleles for important rice phenotypes using various bioinformatics and/or genetic approaches. However, great challenges remain in understanding the genetic/molecular systems underlying complex traits and linking the tremendous genetic diversity in the worldwide rice germplasm collections to phenotypic variation of complex traits. Tremendous efforts have been or are being taken to systematically phenotype the sequenced accessions, to use them as parental lines in large introgression breeding programs and to analyze the derived progenies for genetic/molecular dissection of important rice traits using high density SNPs and various omic tools. An example is given to show how the genomic information of the parents and their BC progenies is used for simultaneous improvement and genetic and molecular dissection of complex traits such as resistances to diseases and abiotic stresses. These efforts plus the continued progresses in the global rice functional genomics research are expected to generate enormous knowledge on rice traits and to establish the germplasm based genetic/molecular information platform that would enable breeders to more efficiently develop new rice varieties with high and stable yields in various ecosystems.