Reticulate Evolution in AA-Genome Wild Rice in Australia.

Sharmin Hasan,Agnelo Furtado,Robert Henry

doi:10.3389/fpls.2022.767635

Sharmin Hasan, Agnelo Furtado + Show 1 more

Open Access

https://doi.org/10.3389/fpls.2022.767635

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Abstract

The wild rice gene pool, i.e., AA-genome, in Australia is geographically and genetically distinct from that in Asia. Two distinct taxa are found growing together in northern Australia, Oryza meridionalis (including annual and perennial forms) and an Oryza rufipogon like taxa that have been shown to have a chloroplast genome sequence that is closer to that of O. meridionalis than to O. rufipogon from Asia. Rare plants of intermediate morphology have been observed in the wild despite a reported reproductive barrier between these two species. We now report the resequencing of plants from 26 populations including both taxa and putative hybrids. A comparison of chloroplast and nuclear genome sequences indicated re-combinations that demonstrated hybridisation in both directions. Individuals with intermediate morphology had high nuclear genome heterozygosity consistent with a hybrid origin. An examination of specific genes (e.g., starch biosynthesis genes) revealed the presence of heterozygotes with alleles from both parents suggesting that some wild plants were early generation hybrids. These plants may have low cross-fertility preserving the continuation of the two distinct species. Repeated backcrossing of these rare hybrids to one parent would explain the plants exhibiting chloroplast capture. These observations suggest that reticulate evolution is continuing in wild Oryza populations and may have been a key process in rice evolution and domestication.

Highlights

Hybridisation and introgression undoubtedly play a crucial role in evolution allowing gene exchange between species resulting in genomic diversification and novel genetic combinations (Stebbins, 1959)
Chloroplast capture can be the consequence of lineage sorting, convergent evolution, and recurrent hybridisation (Tsitrone et al, 2003)
Chloroplast capture can occur in species through one single hybridisation event and species with the freshly obtained chloroplast genome can be inherited by descendant lineages over time (Nge et al, 2021)

Summary

Introduction

Hybridisation and introgression undoubtedly play a crucial role in evolution allowing gene exchange between species resulting in genomic diversification and novel genetic combinations (Stebbins, 1959). Chloroplast capture has been used to infer reticulate evolution in many plant species such as Pisum (Palmer et al, 1985), Australian cotton (Wendel et al, 1991), sunflower (Rieseberg, 1991), peonies (Sang et al, 1995), Opuntia (Griffith, 2003), soybeans (Doyle et al, 2003); kiwifruit (Chat et al, 2004), the wheat tribe (Elymus) (Mason-Gamer, 2004); baobabs (Karimi et al, 2019); and Adenanthos (Nge et al, 2021). Genetic evidence can be derived through implying an additivity of molecular markers (Wendel et al, 1991; Griffith, 2003), polymorphic nucleotide additivity at a single position, i.e., ITS additivity (Sang et al, 1995), and incongruence between gene trees (Mason-Gamer, 2004). Next-generation sequencing (NGS) approaches appear to be increasingly effective in addressing the causes of cytonuclear incongruence (Lemmon et al, 2012; Weitemier et al, 2014)

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