Rice revelations: nine new genome assemblies uncover key traits and evolutionary clues

Geographic ranges of wild Oryza species and the outgroup species L. perrieri sequenced in this study. Dashed red lines show the limits of rice cultivation. Mapped ranges are adapted from IRRI’s Knowledge Bank

Revered around the world, rice is a staple food for nearly half of the population. But as that population grows, rice breeders are faced with the challenge of producing crops that are high yielding, disease-resistant and nutritious, while at the same time being more sustainable.

The International Oryza Map Alignment Project (OMAP) was initiated in 2003 to develop a set of high-quality genomic resources for the wild relatives of rice that could be used as a resource to discover and utilize novel genes, traits and/or genomic regions for crop improvement and basic research.

Members of the consortium recently released new reference assemblies for six wild Oryza species (O. nivara, O. rufipogon, O. barthii, O. glumaepatula, O. meridionalis and O. punctata), two domesticates (O. sativa vg. indica (IR 8) and O. sativa vg. aus (N 22)) and the closely related outgroup species L. perrieri.

In a paper published in Nature Genetics, “Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza,” senior author Rod A. Wing, of the Arizona Genomics Institute at the University of Arizona, first author Joshua C. Stein, of Cold Spring Harbor, and colleagues from 17 other institutions, describe what they found when analyzing the new assemblies and comparing them to four previously published genomes.

Among the major findings were the identification of several disease resistance genes and haplotypes, which could support the breeding of new varieties for natural resistance to growing pathogen threats such as blast (Magnaporthe oryzae).

“Our sequencing of seven wild relatives of crop species opens a treasure trove of novel resistance haplotypes and loci to sustain this strategy,” the authors write.

“The practical utility of our resources is directly demonstrated by our identification of a strong candidate for the long-sought Pi-ta2 locus, which in combination with Pi-ta provides broad-specificity resistance to M. oryzae,” they add.

The study is also the first to contain a complete long-read assembly of IR 8 ‘Miracle Rice’, which relieved famine and drove the Green Revolution in Asia 50 years ago.

And it should prove valuable for the study of molecular evolution. As the authors note, the new dataset represents “a genome-wide vista of the results of ~15 million years of both natural and artificial selection on a single genus.”

Over this time period, the Oryzeae have maintained a base chromosome number of 12, despite their global distribution and bursts of transposable element diversification that, in some cases, led to doubling of genome sizes, the study found.

The reference genomes span the species tree, and were used to resolve several areas of the Oryza phylogeny. Their genome-based age estimates imply a “remarkably rapid diversification rate” (~0.50 net new species/million years), placing it on par with many rapidly diversifying taxa in island and continental hotspots, the authors state.

“Our phylogenomic work illustrates both the challenges of inferring species phylogenies in closely related plant taxa—incomplete lineage sorting, hybridization and introgression—and the power of whole-genome sequences to untangle the resulting phylogenetic discordance,” they write.

The amount and richness of data provided by long-read sequencing led to “a much more nuanced view… that reflects the mosaic history of different parts of the genome,” the author add.

To learn more about efforts by the Arizona Genomics Institute to sequence 23 species of rice using PacBio SMRT Sequencing, watch Rod Wing’s presentation at PAG or read this brief case study.