Local differentiation amidst extensive allele sharing in Oryza nivara and O. rufipogon.

Maria Celeste N Banaticla-Hilario,Ronald G Van Den Berg,Kenneth L Mcnally,Nigel Ruaraidh Sackville Hamilton

doi:10.1002/ece3.689

Maria Celeste N Banaticla-Hilario, Ronald G Van Den Berg + Show 2 more

Open Access

https://doi.org/10.1002/ece3.689

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Abstract

Genetic variation patterns within and between species may change along geographic gradients and at different spatial scales. This was revealed by microsatellite data at 29 loci obtained from 119 accessions of three Oryza series Sativae species in Asia Pacific: Oryza nivara Sharma and Shastry, O. rufipogon Griff., and O. meridionalis Ng. Genetic similarities between O. nivara and O. rufipogon across their distribution are evident in the clustering and ordination results and in the large proportion of shared alleles between these taxa. However, local-level species separation is recognized by Bayesian clustering and neighbor-joining analyses. At the regional scale, the two species seem more differentiated in South Asia than in Southeast Asia as revealed by FST analysis. The presence of strong gene flow barriers in smaller spatial units is also suggested in the analysis of molecular variance (AMOVA) results where 64% of the genetic variation is contained among populations (as compared to 26% within populations and 10% among species). Oryza nivara (HE = 0.67) exhibits slightly lower diversity and greater population differentiation than O. rufipogon (HE = 0.70). Bayesian inference identified four, and at a finer structural level eight, genetically distinct population groups that correspond to geographic populations within the three taxa. Oryza meridionalis and the Nepalese O. nivara seemed diverged from all the population groups of the series, whereas the Australasian O. rufipogon appeared distinct from the rest of the species.

Highlights

The unwavering pursuit to fully understand the rice gene pool is reflected in the growing number of publications on Oryza rufipogon and O. nivara
One hundred nineteen accessions from the International Rice Genebank (IRG) at the International Rice Research Institute (IRRI) in the Philippines were selected to represent sympatric populations of O. nivara and O. rufipogon and of O. meridionalis and O. rufipogon across their distribution range, as well as O. rufipogon populations that are nonsympatric to both annual species (Table S1)
The recognition of local differentiation in the midst of global similarities reconciles the conflicting results of prior studies (Second 1985; Barbier 1989; Aggarwal et al 1999; Iwamoto et al 1999; Park et al 2003; Ren et al 2003; Cai et al 2004; Zhu and Ge 2005; Duan et al 2007; Kuroda et al 2007; Takahashi et al 2008; Zhou et al 2008; Zheng and Ge 2010; Xu et al 2012; Singh et al 2013)

Summary

Introduction

The unwavering pursuit to fully understand the rice gene pool is reflected in the growing number of publications on Oryza rufipogon and O. nivara These two closest relatives of Asian cultivated rice (O. sativa L.) are morphologically distinct (Ng et al 1981; Uga et al 2003; Banaticla-Hilario 2012), whereas genetic isolation is effected by differences in habitat, mating system, and flowering time. Oryza nivara is variously treated as a distinct species (Sharma and Shastry 1965; Ng et al 1981; Lu 1999; Lu et al 2001) or as an ecotype of O. rufipogon (Tateoka 1963; Oka 1988; Vaughan et al 2003). The annual taxon is tentatively considered as a distinct species

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