Genetic variation in the chloroplast genome suggests multiple domestication of cultivated Asian rice (Oryza sativa L.)

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Abstract:

Two hundred and seventy-five accessions of cultivated Asian rice and 44 accessions of AA genome Oryza species were classified into 8 chloroplast (cp) genome types (A–H) based on insertion–deletion events at 3 regions (8K, 57K, and 76K) of the cp genome. The ancestral cp genome type was determined according to the frequency of occurrence in Oryza species and the likely evolution of the variable 57K region of the cp genome. When 2 nucleotide substitutions (AA or TT) were taken into account, these 8 cp types were subdivided into 11 cp types. Most indica cultivars had 1 of 3 cp genome types that were also identified in the wild relatives of rice, O. nivara and O. rufipogon, suggesting that the 3 indica cp types had evolved from distinct gene pools of the O. rufipogonO. nivara complex. The majority of japonica cultivars had 1 of 3 different cp genome types. One of these 3 was identified in O. rufipogon, suggesting that at least 1 japonica type is derived from O. rufipogon with the same cp genome type. These results provide evidence to support a polyphyletic origin of cultivated Asian rice from at least 4 principal lineages in the O. rufipogonO. nivara complex.

Deux cent soixante-quinze accessions asiatiques du riz cultivé et 44 accessions d’espèces du genre Oryza à génome AA ont été classifiées en huit types (A à H) de génome chloroplastique (cp) sur la base d’insertions/délétions au sein de trois régions (8K, 57K et 76K) du génome cp. Le type ancestral du génome cp a été déterminé sur la base de la fréquence d’occurrence au sein des espèces d’Oryza et de la vraisemblable évolution de la région variable 57K au sein du génome cp. Lorsque deux substitutions nucléotidiques (AA ou TT) étaient prises en compte, ces huit types cp étaient subdivisés en 11 types cp. La majorité des cultivars indica possédait l’un de trois types de génome cp qui sont également présents chez les espèces sauvages apparentées au riz (O. nivara et O. rufipogon), ce qui suggère que les trois types de génome cp auraient évolué à partir de trois pools géniques distincts au sein du complexe O. rufipogon-O. nivara. La majorité des cultivars japonica possédait l’un de trois types de génome cp. Un de ces trois types a été identifié chez l’O. rufipogon, ce qui laisse croire que certains des cultivars de type japonica seraient dérivés de l’O. rufipogon ayant le même type de génome cp. Ces résultats supportent une origine polyphylétique pour le riz asiatique cultivé à partir d’au moins quatre principaux lignages au sein du complexe O. rufipogonO. nivara.

Document Type: Research Article

Publication date: February 1, 2007

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  • From its inception in 1957, this international cytogenetics journal has catered to the research areas of the members of the Genetics Society of Canada; traditionally, these have included agriculture, entomology, genetics/cytogenetics, and evolutionary mechanisms. The contents of the journal have evolved as contributors developed new technologies and interests. A 20-member Editorial Board is composed of scientists from around the world. Reviews and commentary from respected experts are often featured.
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