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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #329349
Title: Genomes of 11 rice relatives unveil genetic conservation, turnover and innovation across the genus Oryza

Author
item STEIN, JOSHUA - Cold Spring Harbor Laboratory
item YU, YEISOO - University Of Arizona
item COPETTI, DARIO - University Of Arizona
item ZWICKL, DERRICK - University Of Arizona
item ZHANG, LI - University Of Chicago
item ZHANG, CHENGJUN - University Of Chicago
item CHOUGULE, KAPEEL - Cold Spring Harbor Laboratory
item GAO, DONGYING - University Of Georgia
item IWATA, AIKO - University Of Georgia
item GOICOECHEA, JOSE - University Of Arizona
item WEI, SHARON - Cold Spring Harbor Laboratory
item WANG, JUN - Wayne State University
item LIAO, YI - Chinese Academy Of Sciences
item WANG, MUHUA - University Of Arizona
item JACQUEMIN, JULIE - University Of Hohenheim
item BECKER, CLAUDE - Max Planck Society
item KUDRNA, DAVE - University Of Arizona
item ZHANG, JIANWEI - University Of Arizona
item LONDONO, CARLOS - University Of Arizona
item SONG, XIANG - University Of Arizona
item LEE, SEUNGHEE - University Of Arizona
item SANCHEZ, PAUL - University Of Arizona
item ZUCCOLO, ANDREA - University Of Arizona
item JETTY, AMMIRAJU - University Of Arizona
item TALAG, JAYSON - University Of Arizona
item DANOWITZ, ANN - University Of Arizona
item RIVERA, LUIS - University Of Arizona
item GSCHWEND, ANDREA - University Of Chicago
item NOUTSOS, CHRISTOS - Cold Spring Harbor Laboratory
item WU, CHENG-CHIEH - National Taiwan University
item KAO, SHU-MIN - Ghent University
item ZENG, JHIH-WUN - Academia Sinica
item WEI, FU-JIN - National Taiwan University
item ZHAO, QIANG - Chinese Academy Of Sciences
item FENG, QI - Chinese Academy Of Sciences
item EL BAIDOURI, MOAINE - Universite De Perpignan
item CARPENTIER, MARIE-CHRISTIN - Universite De Perpignan
item LASSERRE, ERIC - Universite De Perpignan
item COOKE, RICHARD - Universite De Perpignan
item DA ROSA FARIAS, DANIEL - Universidade Federal De Pelotas
item CARLOS DA MAIA, LUCIANO - Universidade Federal De Pelotas
item DOS SANTOS, RAILSON - Universidade Federal De Pelotas
item BHATIA, DHARMINDER - Punjab Agricultural University
item NYBERG, KEVIN - University Of Maryland
item FAN, CHUANZHU - Wayne State University
item WEIGEL, DETLEF - Max Planck Institute Of Molecular Plant Physiology
item JENA, KSHIROD - International Rice Research Institute
item WICKER, THOMAS - University Of Zurich
item CHEN, MINGSHENG - Chinese Academy Of Sciences
item HAN, BIN - Chinese Academy Of Sciences
item HENRY, ROBERT - University Of Queensland
item HSING, YUE-IE - Academia Sinica
item KURATA, NORI - National Institute Of Genetics
item COSTA DE OLIVEIRA, ANTONIO - Universidade Federal De Pelotas
item PANAUD, OLIVIER - Universite De Perpignan
item JACKSON, SCOTT - University Of Georgia
item MACHADO, CARLOS - University Of Maryland
item SANDERSON, MICHAEL - University Of Arizona
item LONG, MANYUAN - University Of Chicago
item Ware, Doreen
item WING, ROD - University Of Arizona

Submitted to: Nature Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/18/2017
Publication Date: N/A
Citation: N/A

Interpretive Summary: Rice is the staple food for half the world’s population. As population increases by almost 3 billion over the next 35 years, rice breeders are tasked with the development of new and sustainable varieties with higher yields, healthier grains and reduced environmental footprints. The wild relatives of rice contain an untapped reservoir of genes/traits that can be exploited to improve rice. In this study, we generated genome sequences for seven wild species related to rice, and characterized and compared gene content in these, plus four additional species whose genomes were previously sequenced. We discovered many genes that are common between these species and in other plants, but also many genes that are new and arose through a variety of evolutionary processes. Among important findings, the wild relatives of rice have thousands of genes that function in disease immunity, which can be used to improve pest resistance in future varieties of cultivated rice.

Technical Abstract: The genus Oryza, with cultivated Asian and African rice and 22 wild species, is a model system for the study of molecular evolution over time-scales ranging from a few thousand to 15 million years. Over this period, species radiation, adaptation, and domestication all left their footprints in rice genomes. Using 11 complete reference genome assemblies that span the Oryza species tree, we show that despite few large-scale chromosomal rearrangements, rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and non-coding genes. Our study provides resolution in controversial areas of the species phylogeny of Oryza, reveals a complex history of introgression among different chromosomes in the young "AA" subclade containing the two domesticated species, and greatly expands our understanding of disease resistance genes, with many new integrated decoy genes. Finally, we identify new haplotype R-gene alleles and other loci that can potentially be used for future crop improvement.