Data from: All roads lead to weediness: patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza
Huang, Zhongyun, University of Massachusetts Amherst
Young, Nelson D., University of Massachusetts Amherst
Reagon, Michael, University of Massachusetts Amherst
Hyma, Katie E., University of Massachusetts Amherst
Olsen, Kenneth M., Washington University in St. Louis
Jia, Yulin, United States Department of Agriculture
Caicedo, Ana L., University of Massachusetts Amherst
Published Apr 07, 2017 on Dryad.
Cite this dataset
Huang, Zhongyun et al. (2017). Data from: All roads lead to weediness: patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza [Dataset]. Dryad. https://doi.org/10.5061/dryad.8p9j6
Weedy rice (Oryza spp.), a weedy relative of cultivated rice (O. sativa), infests and persists in cultivated rice fields worldwide. Many weedy rice populations have evolved similar adaptive traits, considered part of the “agricultural weed syndrome,” making this an ideal model to study the genetic basis of parallel evolution. Understanding parallel evolution hinges on accurate knowledge of the genetic background and origins of existing weedy rice groups. Using population structure analyses of South Asian and US weedy rice, we show that weeds in South Asia have highly heterogeneous genetic backgrounds, with ancestry contributions both from cultivated varieties (aus and indica) and wild rice. Moreover, the two main groups of weedy rice in the US, which are also related to aus and indica cultivars, constitute a separate origin from that of Asian weeds. Weedy rice populations in South Asia largely converge on presence of red pericarps and awns and on ease of shattering. Genome-wide divergence scans between weed groups from the US and South Asia and their crop relatives are enriched for loci involved in metabolic processes. Some candidate genes related to iconic weedy traits and competitiveness are highly divergent between some weed-crop pairs, but are not shared amongst all weed-crop comparisons. Our results show that weedy rice is an extreme example of recurrent evolution, and suggest that most populations are evolving their weedy traits through different genetic mechanisms.
SNP polymorphisms among the Oryza population
This hapmap file is generated from Genotyping-by-Sequencing, a Next-Generation-Sequencing method. Single nucleotide polymorphisms recorded in this file are called from the sequencing data with the standard Tassel pipeline. Each of the 51934 rows is for one SNP locus, with the first 11 columns describing the ID, alleles, chromosome positions and other features of the locus, and the rest columns recording the SNP alleles of the panel of Oryza samples included.