The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

Muhua Wang; Yeisoo Yu; Georg Haberer; Pradeep Reddy Marri; Chuanzhu Fan; Jose Luis Goicoechea; Andrea Zuccolo; Xiang Song; Dave Kudrna; Jetty S.S. Ammiraju; Rosa Maria Cossu; Carlos Maldonado; Jinfeng Chen; Seunghee Lee; Nick Sisneros; Kristi De Baynast; Wolfgang Golser; Marina Wissotski; Woojin Kim; Paul Sanchez; Marie Noelle Ndjiondjop; Kayode Sanni; Manyuan Long; Judith Carney; Olivier Panaud; Thomas Wicker; Carlos A. MacHado; Mingsheng Chen; Klaus F.X. Mayer; Steve Rounsley; Rod A. Wing

doi:10.1038/ng.3044

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

Muhua Wang, Yeisoo Yu, Georg Haberer, Pradeep Reddy Marri, Chuanzhu Fan, Jose Luis Goicoechea, Andrea Zuccolo, Xiang Song, Dave Kudrna, Jetty S.S. Ammiraju, Rosa Maria Cossu, Carlos Maldonado, Jinfeng Chen, Seunghee Lee, Nick Sisneros, Kristi De Baynast, Wolfgang Golser, Marina Wissotski, Woojin Kim, Paul SanchezMarie Noelle Ndjiondjop, Kayode Sanni, Manyuan Long, Judith Carney, Olivier Panaud, Thomas Wicker, Carlos A. MacHado, Mingsheng Chen, Klaus F.X. Mayer, Steve Rounsley, Rod A. Wing

Research output: Contribution to journal › Article › peer-review

300 Scopus citations

Abstract

The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.

Original language	English (US)
Journal	Nature Genetics
Volume	46
Issue number	9
DOIs	https://doi.org/10.1038/ng.3044
State	Published - Jan 1 2014
Externally published	Yes

Access to Document

10.1038/ng.3044

Cite this

Wang, M., Yu, Y., Haberer, G., Marri, P. R., Fan, C., Goicoechea, J. L., Zuccolo, A., Song, X., Kudrna, D., Ammiraju, J. S. S., Cossu, R. M., Maldonado, C., Chen, J., Lee, S., Sisneros, N., De Baynast, K., Golser, W., Wissotski, M., Kim, W., ... Wing, R. A. (2014). The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication. Nature Genetics, 46(9). https://doi.org/10.1038/ng.3044

@article{c27183873f794ab6bcb10a16c3a8dd49,

title = "The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication",

abstract = "The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.",

author = "Muhua Wang and Yeisoo Yu and Georg Haberer and Marri, {Pradeep Reddy} and Chuanzhu Fan and Goicoechea, {Jose Luis} and Andrea Zuccolo and Xiang Song and Dave Kudrna and Ammiraju, {Jetty S.S.} and Cossu, {Rosa Maria} and Carlos Maldonado and Jinfeng Chen and Seunghee Lee and Nick Sisneros and {De Baynast}, Kristi and Wolfgang Golser and Marina Wissotski and Woojin Kim and Paul Sanchez and Ndjiondjop, {Marie Noelle} and Kayode Sanni and Manyuan Long and Judith Carney and Olivier Panaud and Thomas Wicker and MacHado, {Carlos A.} and Mingsheng Chen and Mayer, {Klaus F.X.} and Steve Rounsley and Wing, {Rod A.}",

note = "Generated from Scopus record by KAUST IRTS on 2019-11-20",

year = "2014",

month = jan,

day = "1",

doi = "10.1038/ng.3044",

language = "English (US)",

volume = "46",

journal = "Nature Genetics",

issn = "1546-1718",

publisher = "Nature Research",

number = "9",

}

Wang, M, Yu, Y, Haberer, G, Marri, PR, Fan, C, Goicoechea, JL, Zuccolo, A, Song, X, Kudrna, D, Ammiraju, JSS, Cossu, RM, Maldonado, C, Chen, J, Lee, S, Sisneros, N, De Baynast, K, Golser, W, Wissotski, M, Kim, W, Sanchez, P, Ndjiondjop, MN, Sanni, K, Long, M, Carney, J, Panaud, O, Wicker, T, MacHado, CA, Chen, M, Mayer, KFX, Rounsley, S & Wing, RA 2014, 'The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication', Nature Genetics, vol. 46, no. 9. https://doi.org/10.1038/ng.3044

TY - JOUR

T1 - The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

AU - Wang, Muhua

AU - Yu, Yeisoo

AU - Haberer, Georg

AU - Marri, Pradeep Reddy

AU - Fan, Chuanzhu

AU - Goicoechea, Jose Luis

AU - Zuccolo, Andrea

AU - Song, Xiang

AU - Kudrna, Dave

AU - Ammiraju, Jetty S.S.

AU - Cossu, Rosa Maria

AU - Maldonado, Carlos

AU - Chen, Jinfeng

AU - Lee, Seunghee

AU - Sisneros, Nick

AU - De Baynast, Kristi

AU - Golser, Wolfgang

AU - Wissotski, Marina

AU - Kim, Woojin

AU - Sanchez, Paul

AU - Ndjiondjop, Marie Noelle

AU - Sanni, Kayode

AU - Long, Manyuan

AU - Carney, Judith

AU - Panaud, Olivier

AU - Wicker, Thomas

AU - MacHado, Carlos A.

AU - Chen, Mingsheng

AU - Mayer, Klaus F.X.

AU - Rounsley, Steve

AU - Wing, Rod A.

N1 - Generated from Scopus record by KAUST IRTS on 2019-11-20

PY - 2014/1/1

Y1 - 2014/1/1

N2 - The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.

AB - The cultivation of rice in Africa dates back more than 3,000 years. Interestingly, African rice is not of the same origin as Asian rice (Oryza sativa L.) but rather is an entirely different species (i.e., Oryza glaberrima Steud.). Here we present a high-quality assembly and annotation of the O. glaberrima genome and detailed analyses of its evolutionary history of domestication and selection. Population genomics analyses of 20 O. glaberrima and 94 Oryza barthii accessions support the hypothesis that O. glaberrima was domesticated in a single region along the Niger river as opposed to noncentric domestication events across Africa. We detected evidence for artificial selection at a genome-wide scale, as well as with a set of O. glaberrima genes orthologous to O. sativa genes that are known to be associated with domestication, thus indicating convergent yet independent selection of a common set of genes during two geographically and culturally distinct domestication processes.

UR - http://www.nature.com/articles/ng.3044

UR - http://www.scopus.com/inward/record.url?scp=84922395367&partnerID=8YFLogxK

U2 - 10.1038/ng.3044

DO - 10.1038/ng.3044

M3 - Article

SN - 1546-1718

VL - 46

JO - Nature Genetics

JF - Nature Genetics

IS - 9

ER -

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

Abstract

Access to Document

Other files and links

Fingerprint

Cite this