Morphological and molecular dissection of wild rices from eastern India suggests distinct speciation between O. rufipogon and O. nivara populations

Abstract

The inter relationships between the two progenitors is interesting as both wild relatives are known to be the great untapped gene reservoirs. The debate continues on granting a separate species status to Oryza nivara. The present study was conducted on populations of Oryza rufipogon and Oryza nivara from Eastern India employing morphological and molecular characteristics. The cluster analysis of the data on morphological traits could clearly classify the two wild forms into two separate discrete groups without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Amplification of hyper variable regions of the genome could reveal 144 alleles suggesting high genetic diversity values (average He = 0.566). Moreover, with 42.37% of uncommon alleles between the two wild relatives, the molecular variance analysis (AMOVA) could detect only 21% of total variation (p < 0.001) among them and rest 59% was within them. The population structure analysis clearly classified these two wild populations into two distinct sub-populations (K = 2) without any overlaps i.e. lack of intermediate forms, suggesting the non-sympatric existence of the wild forms. Clear differentiation into two distinct groups indicates that O. rufipogon and O. nivara could be treated as two different species.

Population genetics and evolutionary history of the wild rice species Oryza rufipogon and O. nivara in Sri Lanka

“…Microsatellites (SSRs) are featured as co‐dominant, highly polymorphic, abundant, and randomly distributed markers in the genomes and have been successfully used for a variety of studies in rice biology (Kuroda et al, ; McCouch et al, ; Pusadee et al, ; Samal et al, ; Wang et al, ; Zhou et al, ). As SSR markers have good cross‐species amplification to the close relatives, they provide a powerful tool for studying O. nivara and O. rufipogon given that thousands of SSR markers across rice genome have been well characterized (Cho et al, ; McCouch et al, ).…”

“…To date, many investigations on genetic diversity of O. rufipogon and O. nivara have been undertaken using SSR markers and relatively high genetic diversity has been detected at both population and species levels (Banaticla‐Hilario et al, ; Kuroda et al, ; Pusadee et al, ; Samal et al, ; Zhou et al, ;). In a study on the Chinese O. rufipogon populations, Zhou, Wang, Davy, and Liu () found a genetic diversity of 0.413 and 0.787, as measured by H E , at population and species levels, respectively.…”

“…To date, many efforts have been made to investigate their classification, population genetics, evolutionary history, and adaptation potential as well as agronomical traits of the two species (Barbier, 1989; Grillo et al, ; Huang et al, ; Huang et al., ; Liu, Zheng, Zhou, Zhou, & Ge, ; Morishima, Sano, & Oka, ; Zhu & Ge, ; Zhu, Zheng, Luo, Gaut, & Ge, ). Extensive studies on the population genetics of these two species have been carried out either in global scale (Banaticla‐Hilario, Berg, Hamilton, & McNally, ; Huang et al, ; Liu et al, ; Zhu & Ge, 2005; Zheng & Ge, ;) or local scale (Kuroda, Sato, Bounphanousay, Kono, & Tanaka, ; Pusadee, Schaal, Rerkasem, & Jamjod, ; Samal et al, ; Zhou, Xie, & Ge, ; Zhou et al, ). However, the genetic variability and population genetic structure of these two species in Sri Lanka are not well understood (Rajkumar, Weerasena, Fernando, Liyanage, & Silva, ).…”

Novel allelic variation in the Phospholipase D alpha1 gene (OsPLDα1) of wild Oryza species implies to its low expression in rice bran

“…Moreover, both O. rufipogon and O. nivara share a common geographical distribution in South and Southeast Asia therefore the probability of gene flow is higher between them. These species are cross compatible and exhibit little genetic differentiation and is supported by molecular phylogenetic analysis and population studies [48][49][50][51][52][53][54] .…”

Divergence in flowering time is a major component contributing to reproductive isolation between two wild rice species (Oryza rufipogon and O. nivara)

“…To date, many studies have been undertaken on O. nivara and O. rufipogon and have involved morphological variation and taxonomy, crossability and gene flow, and population genetic structure as well as population adaptation and speciation (Morishima et al, 1961;Chu et al, 1969;Morishima et al, 1984;Morishima, 1985;Barbier, 1989;Vaughan, 1989;Naredo et al, 1997;Lu et al, 1998;Cai et al, 2004;Kuroda et al, 2007;Zhou et al, 2008;Zheng and Ge, 2010;Huang and Schaal, 2012;Banaticla-Hilario et al, 2013;Liu et al, 2015;Samal et al, 2018;Cai et al, 2019). These studies clearly indicated that O. nivara was recently derived from O. rufipogon (about 0.16 million years ago) without apparent genetic differentiation between species, and supported the hypothesis that O. nivara originated from the adaptation of O. rufipogon to dry habitats during the last glaciations (Barbier, 1989;Zheng and Ge, 2010;Liu et al, 2015).…”