Distribution, genetic diversity and potential spatiotemporal scale of alien gene flow in crop wild relatives of rice (Oryza spp.) in Colombia

Abstract

BackgroundCrop wild relatives (CWRs) of rice hold important traits that can contribute to enhancing the ability of cultivated rice (Oryza sativa and O. glaberrima) to produce higher yields, cope with the effects of climate change, and resist attacks of pests and diseases, among others. However, the genetic resources of these species remain dramatically understudied, putting at risk their future availability from in situ and ex situ sources. Here we assess the distribution of genetic diversity of the four rice CWRs known to occur in Colombia (O. glumaepatula, O. alta, O. grandiglumis, and O. latifolia). Furthermore, we estimated the degree of overlap between areas with suitable habitat for cultivated and wild rice, both under current and predicted future climate conditions to assess the potential spatiotemporal scale of potential gene flow from GM rice to its CWRs.ResultsOur findings suggest that part of the observed genetic diversity and structure, at least of the most exhaustively sampled species, may be explained by their glacial and post-glacial range dynamics. Furthermore, in assessing the expected impact of climate change and the potential spatiotemporal scale of gene flow between populations of CWRs and GM rice we find significant overlap between present and future suitable areas for cultivated rice and its four CWRs. Climate change is expected to have relatively limited negative effects on the rice CWRs, with three species showing opportunities to expand their distribution ranges in the future.ConclusionsGiven (i) the sparse presence of CWR populations in protected areas (ii) the strong suitability overlap between cultivated rice and its four CWRs; and (iii) the complexity of managing and regulating areas to prevent alien gene flow, the first priority should be to establish representative ex situ collections for all CWR species, which currently do not exist. In the absence of studies under field conditions on the scale and extent of gene flow between cultivated rice and its Colombian CWRs, effective in situ conservation might best be achieved through tailor-made management plans and exclusion of GM rice cultivation in areas holding the most genetically diverse CWR populations. This may be combined with assisted migration of populations to suitable areas where rice is unlikely to be cultivated under current and future climate conditions.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-017-0150-9) contains supplementary material, which is available to authorized users.

Draft Genome Sequence and intraspecific diversification of the wild crop relativeBrassica creticaLam. using demographic model selection

“…14 On the other hand, analysis of the sequence can reveal genetic variation and important genetic 15 characters that have been lost during domestication, and that could be transfer into crop 16 species to support food security, climate adaptation and nutritional improvement (Brozynska 17 et al 2016). The ready availability of low-cost and high-throughput re-sequencing technologies 18 enable the survey of CWR genomes for genetic variation and novel genes and allelels. 19 Recent decades have seen some remarkable examples of introducing favored traits from CWRs 20 into their respective domesticated crop plants.…”

“…A total of 45,758 protein-coding genes 15 were predicted, with mean transcript length of 1,761 bp and 3,756 non-coding RNAs (miRNA, 16 tRNA, rRNA and snRNA). It is observed that there is a greater number of transposable elements 17 (TEs) in B. oleracea than in B. rapa as a consequence of continuous amplification over the last 18 4 million years (MY), the time that the two species were diverged from a common ancestor, 19 whereas in B. rapa the amplification is made mostly in the recent 0.2 MY (Liu et al 2014). 20 Moreover, there has been observed massive gene loss and frequent reshuffling of triplicated 21 genomic blocks, which favored over-retention of genes for metabolic pathways.…”

“…Grant 1994). However, the rates of migration among B. cretica populations have 17 not been properly quantified, which makes unclear whether the low gene flow alone could 18 explain the population divergence, or if the local adaptation (divergent selection) must be 19 invoked. Widen and colleagues, (Widén et al 2002) reported that the high levels of 20 differentiation observed at allozyme loci and quantitative traits among Cretan B. cretica 21 populations, were in agreement with the idea of non-adaptive differentiation combined with 22 limited gene flow.…”

“…9 cretica populations taking into consideration their genomic and subspecies variation. one from the third mainland population (C) and the other from Crete, the island population (D), 18 have been used for the genome assembly ( Figure 1). 19 20 Total DNA extraction and Library preparation for NGS 21 Genomic DNA was extracted from the young emerging leaves using two previously published 22 protocols.…”

“…Another issue arises when 16 multiple populations are free to interact through migration (either symmetric or asymmetric) 17 resulting in an increase of the parameters and, therefore, the required complex calculations. 18 These complexities hinder any effort to thorough explain the statistical properties of the 19 summary statistics produced during the walks. To avoid these problems we based our 20 demographic model inference on the multi-population allele frequency spectrum (AFS) 21 ( 22 the fact that demographic history of a population is reflected in the allele frequency spectrum.…”