Origin of rice (Oryza sativa L.) domestication genes

Abstract

A number of genes that contribute to the domestication traits of cultivated rice have been identified. These include Sh4, Rc, PROG1 and LABA1, which are associated with non-shattering rachis, white pericarp, erect growth and barbless awns, respectively. The mutations giving rise to the “domestication alleles” of these genes are either invariable in cultivated rice, or have variability that is strictly associated with the phenotypic trait. This observation forms the basis to those current rice domestication models that envisage a single origin for the domesticated phenotype. Such models assume that the domestication alleles are absent or rare in wild rice, emerged under cultivation and spread across all rice groups by introgressive hybridization. We examined whole-genome sequencing datasets for wild and cultivated rice to test the former two assumptions. We found that the rc and laba1 alleles occur in wild rice with broad geographical distribution, and reach frequencies as high as 13 and 15%, respectively. These results are in agreement with previous observations of the prog1 and sh4 domestication alleles in wild populations. We also show that the diversity of the genomic regions surrounding the rc, laba1, prog1 and sh4 alleles in wild accessions is greater than that in cultivated rice, suggesting that these alleles emerged prior to domestication. Our findings indicate that the possibility that independent rice groups obtained identical domestication alleles directly from the wild population needs to be considered.Electronic supplementary materialThe online version of this article (doi:10.1007/s10722-017-0518-0) contains supplementary material, which is available to authorized users.

Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL

“…Furthermore, the amplitude of selection was stronger within japonica than indica population in contrast to aus population and thought to be created historically long time ago. This observation is also in accordance with the recent studies suggesting that aus rice group might have originated from distinct wild progenitor (Civán et al, 2015;Choi et al, 2017;Civáň and Brown, 2017). We suggest that chromosome 5 desert region is very crucial genomic region that might be harbouring important trait loci created by targeted selection, more specifically in japonica and indica genotypes owing to their phylogeographical isolation from aus group during the course of domestication.…”

Comment on ‘Multiple Origin but Single Domestication Led to Oryza sativa’

“…This could have occurred during a single domestication, but equally could have occurred during multiple domestication processes. In agreement with the latter interpretation, we have recently documented multiple genealogical lineages of the Sh4 and Prog1 regions in cultivated rice (Civáň and Brown 2017).…”

“…We agree with this possibility, but excluding the Sh4 upstream region leads again to a paraphyletic tree with similar haplotypes present in indica, japonica and wild rice. Presence of the sh4 'domestication' allele in wild rice (without phenotypic effect) has been confirmed by Sanger sequencing (Zhu et al 2012) and we have shown that the causative SNP pre-dates domestication (Civáň and Brown 2017). It is therefore impossible to infer whether indica obtained the sh4 allele from japonica or its wild progenitor, and the paraphyletic trees in Choi and Purugganan (2018) are inconclusive.…”

The Impact of Genetic Changes during Crop Domestication

“…Finally, domesticated rice (Oryza sativa L.) has the strongest evidence for polyphyletic origins, with independent, spatially separate domestication in China (japonica gene pool), Indochina to Brahmaputra valley (indica gene pool), and central India to Bangladesh (aus gene pool) [31,32]. Subsequently, there was geneflow between each of these genepools, which may [32] or may not [33] be responsible for the introgression of domestication syndrome traits from the japonica to the indica pool.…”

“…Domestication applies selective sweeps on standing genetic variation [81] and on new genetic variation introduced via mutation or introgression. Selection on standing genetic variation might cause the repeated involvement of the same locus in independent domestication events [33] because the selection of favorable alleles that are already present in a wild population usually proceeds faster than new mutations can arise [68,82,83]. On the other hand, new mutations not found in natural populations, possibly detrimental to plant survival, have been identified [39].…”