Origin of the Aromatic Group of Cultivated Rice (Oryza sativa L.) Traced to the Indian Subcontinent.

Domestication Genetic Variation Genome, Plant India Oryza / genetics Phylogeography
chloroplast genome domestication local ancestry inference population genomics

Journal

Genome biology and evolution
ISSN: 1759-6653
Titre abrégé: Genome Biol Evol
Pays: England
ID NLM: 101509707

Informations de publication

Date de publication:
01 03 2019
Historique:
accepted: 19 02 2019
pubmed: 23 2 2019
medline: 19 6 2019
entrez: 23 2 2019
Statut: ppublish

Résumé

The aromatic group of Asian cultivated rice is a distinct population with considerable genetic diversity on the Indian subcontinent and includes the popular Basmati types characterized by pleasant fragrance. Genetic and phenotypic associations with other cultivated groups are ambiguous, obscuring the origin of the aromatic population. From analysis of genome-wide diversity among over 1,000 wild and cultivated rice accessions, we show that aromatic rice originated in the Indian subcontinent from hybridization between a local wild population and examples of domesticated japonica that had spread to the region from their own center of origin in East Asia. Most present-day aromatic accessions have inherited their cytoplasm along with 29-47% of their nuclear genome from the local Indian rice. We infer that the admixture occurred 4,000-2,400 years ago, soon after japonica rice reached the region. We identify aus as the original crop of the Indian subcontinent, indica and japonica as later arrivals, and aromatic a specific product of local agriculture. These results prompt a reappraisal of our understanding of the emergence and development of rice agriculture in the Indian subcontinent.

Identifiants

DOI: 10.1093/gbe/evz039 PMID: 30793171 PMC: PMC6427689
pubmed: 30793171
pii: 5355065
doi: 10.1093/gbe/evz039
pmc: PMC6427689
doi:

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

832-843

Subventions

Organisme : European Research Council
ID : 339941
Pays : International

Informations de copyright

© The Author(s) 2019. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Références

Mol Biol Evol. 1999 Jan;16(1):37-48
pubmed: 10331250
Gigascience. 2015 Feb 25;4:7
pubmed: 25722852
Theor Appl Genet. 1987 May;74(1):21-30
pubmed: 24241451
ScientificWorldJournal. 2016;2016:2796720
pubmed: 27127800
Gigascience. 2014 May 28;3:7
pubmed: 24872877
Genome Biol. 2020 Feb 5;21(1):21
pubmed: 32019604
Plant Cell. 2006 Feb;18(2):283-94
pubmed: 16399804
Mol Biol Evol. 2004 Feb;21(2):255-65
pubmed: 14660700
J Archaeol Sci. 2017 Feb;78:193-201
pubmed: 33414573
Mol Biol Evol. 2018 Sep 1;35(9):2318-2326
pubmed: 29931083
Genome. 2007 Feb;50(2):180-7
pubmed: 17546083
Bioinformatics. 2009 Jul 15;25(14):1754-60
pubmed: 19451168
Nat Commun. 2011 Sep 13;2:467
pubmed: 21915109
Science. 2006 Mar 31;311(5769):1936-9
pubmed: 16527928
Am J Hum Genet. 2007 Nov;81(5):1084-97
pubmed: 17924348
Genetics. 2011 Dec;189(4):1515-24
pubmed: 21954164
Rice (N Y). 2016 Dec;9(1):57
pubmed: 27757948
Proc Natl Acad Sci U S A. 2008 Aug 12;105(32):11436-41
pubmed: 18678896
Plant Cell. 2008 Jul;20(7):1850-61
pubmed: 18599581
Genome Res. 2010 Sep;20(9):1297-303
pubmed: 20644199
Nat Genet. 2008 Nov;40(11):1360-4
pubmed: 18820699
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nature. 2018 May;557(7703):43-49
pubmed: 29695866
Mol Biol Evol. 2017 Apr 1;34(4):969-979
pubmed: 28087768
Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14444-9
pubmed: 19706531
Curr Opin Genet Dev. 2007 Dec;17(6):533-8
pubmed: 17988855
Bioinformatics. 2011 Aug 1;27(15):2156-8
pubmed: 21653522
Genetics. 2005 Mar;169(3):1631-8
pubmed: 15654106
PLoS Genet. 2009 Jun;5(6):e1000519
pubmed: 19543370
Plant Cell Environ. 2015 Nov;38(11):2327-39
pubmed: 25854544
Mol Biol Evol. 2016 Oct;33(10):2496-505
pubmed: 27461246
Plant Mol Biol. 2008 Nov;68(4-5):439-49
pubmed: 18704694
Nature. 2012 Oct 25;490(7421):497-501
pubmed: 23034647
PLoS Genet. 2006 Dec;2(12):e190
pubmed: 17194218
BMC Bioinformatics. 2015 Nov 09;16:374
pubmed: 26552596
BMC Evol Biol. 2018 Apr 23;18(1):57
pubmed: 29688851
Genet Resour Crop Evol. 2017;64(6):1125-1132
pubmed: 28736485
Nat Plants. 2015 Nov 02;1:15164
pubmed: 27251535
Nat Genet. 2013 Apr;45(4):462-5, 465e1-2
pubmed: 23435087
Plant Cell. 2015 Jul;27(7):1875-88
pubmed: 26082172

Auteurs

Peter Civáň (P)

Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, United Kingdom.
INRA-Université Clermont-Auvergne, UMR 1095 GDEC, Clermont-Ferrand, France.

Sajid Ali (S)

Institute of Biotechnology & Genetic Engineering, The University of Agriculture, Peshawar, Pakistan.

Riza Batista-Navarro (R)

School of Computer Science, University of Manchester, United Kingdom.

Konstantina Drosou (K)

Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, United Kingdom.

Chioma Ihejieto (C)

Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, United Kingdom.

Debarati Chakraborty (D)

Department of Molecular Biology and Biotechnology, University of Kalyani, India.

Avik Ray (A)

Center for Studies in Ethnobiology, Biodiversity, and Sustainability (CEiBa), Malda, West Bengal, India.

Pierre Gladieux (P)

BGPI, Université de Montpellier, INRA, CIRAD, Montpellier SupAgro, Montpellier, France.

Terence A Brown (TA)

Manchester Institute of Biotechnology, School of Earth and Environmental Sciences, University of Manchester, United Kingdom.

Articles similaires

Exploring the complexity of genome size reduction in angiosperms.

Akihiro Ezoe, Motoaki Seki
1.00
Genome Size Genome, Plant Magnoliopsida Evolution, Molecular Arabidopsis

Exploring transcriptomic mechanisms underlying pulmonary adaptation to diverse environments in Indian rams.

Ritika Gera, Reena Arora, Pooja Chhabra et al.
1.00
Animals Lung India Sheep Transcriptome

Environmental impact assessment of Flora and its role in offsetting carbon along National Highway-16, India.

H Ramamohan, S Raminaidu, I Sudhakara Rao et al.
1.00
India Carbon Sequestration Environmental Monitoring Carbon Biomass

Insights into genomic sequence diversity of the SAG surface antigen superfamily in geographically diverse Eimeria tenella isolates.

Alice Li-Wen Kiang, Shu-San Loo, Mohd-Noor Mat-Isa et al.
1.00
Eimeria tenella Animals Antigens, Protozoan Chickens Genetic Variation

Classifications MeSH

Recherchemedicale.com › Technologie, industrie et agriculture › Agriculture › Domestication › Origin of the Aromatic Group of Cultivated...
Recherchemedicale.com › Phénomènes génétiques › Variation génétique › Origin of the Aromatic Group of Cultivated...
Recherchemedicale.com › Phénomènes génétiques › Structures génétiques › Génome › Génome végétal › Origin of the Aromatic Group of Cultivated...
Recherchemedicale.com › Régions géographiques › Asie › Asie de l'Ouest › Asie du Sud › Inde › Origin of the Aromatic Group of Cultivated...
Recherchemedicale.com › Eucaryotes › Viridiplantae › Streptophyta › Embryophyta › Tracheobionta › Magnoliopsida › Poaceae › Oryza › Origin of the Aromatic Group of Cultivated...
Recherchemedicale.com › Disciplines des sciences naturelles › Sciences de la Terre › Géographie › Phylogéographie › Origin of the Aromatic Group of Cultivated...