The hidden mystery under Oryza genome revealed through nine new reference genomes in combination with four existing genomes analysis

Dhaka, February 4, 2018: Oryza has a vital role in developing human civilization and food security. As the world population approaches 10 billion by 2050, rice breeders are confronted with the challenge of producing crops that are high yielding as well as stress tolerant. Because the wild relatives of rice are adapted to different biogeographic ranges and can tolerate many biotic and abiotic stresses, they contain an important reservoir for crop improvement. Strategies to introduce such traits for crop improvement show clear potential, as illustrated by the introgression of bacterial blight resistance (Xa21) from the wild species Oryza longistaminata. The basis of the International Oryza Map Alignment Project (IOMAP), started in 2003, was to establish a set of high-quality genomic resources for the genus Oryza that could be used as a fundamental resource to discover and utilize new genes, traits and/or genomic regions for crop improvement and basic research. Recently the generation of 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 has been published. Grouping with four previously published Oryza genome it has been found that a single locus is maintained by both natural and artificial selection for about ~15 million years and also Oryzeae have retained a base chromosome number of 12.  From extensive phylogenomic work it has been found that this genome-based estimation of the age of the AA genome clade implies a remarkably rapid diversification rate of ~0.50 net new species/million years. This rapid species diversification among Oryza species in the AA clade likely provided special opportunities for cultivation and development by humans, resulting in two independent (Oryza sativa and Oryza glaberrima) domestication events in this group. Rice Transposable Elements (TEs) has had a key role in Oryza genome and chromosome evolution. This process results from both recent lineage-specific TE amplifications and a high deletion rate of TE-related sequences. So TE polymorphisms in wild Oryza species could thus be subjugated for breeding. Comparative analysis of gene annotations across the Oryzeae revealed many surprising features like shorter coding sequences, low expression, rapid evolution rates and family instability. Oryzeae have specific genes that contain conserved domains which are enriched for defense and stress response functions, representing that their rapid evolution was driven by adaptation to varied environmental stress. Already some putative de novo–originated genes have been functionally characterized in plants, the rice OsDR10 gene, conserved only in the Oryzeae having function in the regulation of pathogen defense responses. It has also been found that lincRNA gene activity may contribute to the origination of new genes. Sequencing of these seven wild relatives of crop species unlocks a treasure of novel stress resistant genes in such haplotypes. The utility of this resource is directly demonstrated by identification of a resilient candidate for the long-sought Pi-ta2 locus, which in combination with Pi-ta provides broad-specificity resistance to M. oryzae. The availability of 13 high-quality reference genome assemblies now permits exploration of the majority of orthologous loci and genomic regions for the AA, BB and FF genome types and L. perrieri. As more wild and cultivated Oryza genomes become available, this resource will become even more useful.


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Compiled by
Tasmia Islam
Department of Biochemistry and Molecular Biology
Jagannath University

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