Population Dynamics Among six Major Groups of the Oryza rufipogon Species Complex, Wild Relative of Cultivated Asian Rice

Abstract

BackgroundUnderstanding population structure of the wild progenitor of Asian cultivated rice (O. sativa), the Oryza rufipogon species complex (ORSC), is of interest to plant breeders and contributes to our understanding of rice domestication. A collection of 286 diverse ORSC accessions was evaluated for nuclear variation using genotyping-by-sequencing (113,739 SNPs) and for chloroplast variation using Sanger sequencing (25 polymorphic sites).ResultsSix wild subpopulations were identified, with 25 % of accessions classified as admixed. Three of the wild groups were genetically and geographically closely related to the O. sativa subpopulations, indica, aus and japonica, and carried O. sativa introgressions; the other three wild groups were genetically divergent, had unique chloroplast haplotypes, and were located at the geographical extremes of the species range. The genetic subpopulations were significantly correlated (r 2 = 0.562) with traditional species designations, O. rufipogon (perennial) and O. nivara (annual), differentiated based on morphology and life history. A wild diversity panel of 95 purified (inbred) accessions was developed for future genetic studies.ConclusionsOur results suggest that the cultivated aus subpopulation is most closely related to an annual wild relative, japonica to a perennial wild relative, and indica to an admixed population of diverse annual and perennial wild ancestors. Gene flow between ORSC and O. sativa is common in regions where rice is cultivated, threatening the identity and diversity of wild ORSC populations. The three geographically isolated ORSC populations harbor variation rarely seen in cultivated rice and provide a unique window into the genetic composition of ancient rice subpopulations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0119-0) contains supplementary material, which is available to authorized users.

The buffering capacity of stems: genetic architecture of nonstructural carbohydrates in cultivated Asian rice, Oryza sativa

“…We next performed QTL mapping in a CSSL population derived from an interspecific cross between cv Curinga, an upland tropical japonica variety from Brazil that served as the recurrent parent, and a wild aus ‐like O. rufipogon donor accession (Arbelaez et al ., ; Kim et al ., ). Here we were interested to determine whether QTL associated with stem NSC traits in the CSSLs co‐localized with any regions identified from GWAS in the US‐TRJ and/or GLOBAL‐TRJ.…”

“…1d); zoomed-in view is not shown here because its msSNP is identical to US-TRJ sucrose-at-heading. (Arbelaez et al, 2015;Kim et al, 2016). Here we were interested to determine whether QTL associated with stem NSC traits in the CSSLs co-localized with any regions identified from GWAS in the US-TRJ and/or GLOBAL-TRJ.…”

Evolutionary Insights Based on SNP Haplotypes of Red Pericarp, Grain Size and Starch Synthase Genes in Wild and Cultivated Rice

“…(ii) Independent domestication at more than one location (polyphyletic) model suggesting that the major groups of rice cultivars were domesticated separately in different parts of Asia from separate wild rice ancestors (Vitte et al, 2004; Londo et al, 2006; Civan et al, 2015; Singh et al, 2015). Most recent study on 286 diverse O. rufipogon accessions originating from 15 countries using 113,739 nuclear single nucleotide polymorphisms (SNPs) and 25 polymorphic sites in chloroplast sequence has confirmed that three separate wild rice sub-populations were genetically and geographically closely related to Indica, Aus, and Japonica cultivar groups of O. sativa (Kim et al, 2016). …”

Genetic diversity of Australian wild rice

“…aus rice has the oldest one. This agrees with the theory of three independent origins of the domesticated rice (Civáň et al, 2015;Kim et al, 2016;Singh et al, 2015;Singh et al, 2017). GBSSI gene variation was found to be less in the wild than in cultivated rice, which demonstrates that selection pressure has been applied it to meet the demands of different consumers during domestication (Cheng et al, 2012;Singh et al, 2017;Vaughan et al, 2008).…”