Genetic variation for domestication related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) x ancestral rice, O. nivara, mapping population

Authors: Eizenga, Georgia; SANCHEZ, PAUL - University Of Arizona; Jackson, Aaron; Edwards, Jeremy; HURWITZ, BONNIE - University Of Arizona; WING, ROD - University Of Arizona; KUDRNA, DAVID - University Of Arizona

Submitted to: Molecular Breeding
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/25/2017
Publication Date: 10/18/2017
Citation: Eizenga, G.C., Sanchez, P., Jackson, A.K., Edwards, J., Hurwitz, B.L., Wing, R.A., Kudrna, D. 2017. Genetic variation for domestication related traits revealed in a cultivated rice, Nipponbare (Oryza sativa ssp. japonica) x ancestral rice, O. nivara, mapping population. Molecular Breeding. https://doi.org:10.1007/s11032-017-0734-5.
DOI: https://doi.org/10.1007/s11032-017-0734-5

Interpretive Summary: Cultivated rice, which is grown worldwide, was domesticated thousands of years ago from the wild progenitor species, Oryza rufipogon which is often referred to as Oryza nivara when growing as an annual plant. During the course of rice domestication, man selected for desirable traits including erect and shorter plants, non-shattering seed, increased panicle size, seed size, and seed quantity, as well as specific cooking and sensory qualities. Still today, rice breeders select for these traits to improve rice yield and rice quality after incorporating other desirable traits like resistance to diseases and insects, as well as, tolerance to stresses like salt, acid soils and reduced water use. With the molecular tools currently available, it is theoretically possible to reconstruct the changes that occurred during domestication and the evolution of the genes controlling traits related to yield and domestication. To better understand the changes that took place in these genes and reintroduce variation from the wild progenitor species, O. nivara, for yield improvement, pest resistance and stress tolerance, we compared the DNA of the cultivated rice variety Nipponbare, with the DNA from the wild ancestor, O. nivara. Based on differences in the DNA, we selected DNA markers that could be used to identify important yield and domestication traits, and ultimately the genes controlling these traits. The utility of these DNA markers was evaluated in the progeny from a cross between Nipponbare and O. nivara evaluated for 18 traits related to erect plants, shorter plants, non-shattering seed, increased panicle size, larger seed and brown rice. We discovered 32 potential genes controlling these 18 traits, of which 26 potential genes were related to genes previously discovered as important to rice yield improvement and/or domestication. Knowing where these extremely important genes are located in the wild progenitor, O. nivara, will facilitate incorporation of desirable traits from wild species into cultivated rice for improving not only yield but also resistance to diseases like rice blast and sheath blight, as well as, tolerance to various stresses like salt, acid soil and reduced water use.

Technical Abstract: Oryza nivara is an annual plant that is the ancestral species of cultivated rice (Oryza sativa). It has been the source of novel alleles for resistance to biotic and abiotic stresses, as well as yield improvement, which have been lost during the course of domestication. To determine the molecular changes that may have occurred during domestication, the O. sativa ssp. japonica cultivar, Nipponbare, from which a reference sequence (RefSeq) was developed, was crossed with the O. nivara accession (IRGC100897), from which BAC-end sequences (BES) were derived. The mapping population composed of 279 F2 progeny lines derived from this cross was phenotyped for 18 traits important to domestication and yield improvement, including basal sheath and culm color, culm angle, days to heading, plant height, seed shattering, flag leaf length and width, panicle type and length, awn length and color, pericarp color, and seed color, length, width, length to width ratio, and volume. The population was genotyped using 95 SSR markers and 114 single nucleotide variation (SNV) markers, selected by comparing the Nipponbare RefSeq and O. nivara BES. At least one major QTL was identified for each trait evaluated, and for 26 of the 32 QTL, the trait increase was attributed to the allele contributed by the O. nivara parent. Candidate genes were identified in 26 of the QTL regions. This study validated SNV markers can be used for mapping in populations with a wild species parent and for marker-assisted selection to incorporate desirable, novel alleles for stress resistance and yield improvement, identified in rice wild species like O. nivara, into elite cultivars that are adapted to the local environment.