All roads lead to weediness: Patterns of genomic divergence reveal extensive recurrent weedy rice origins from South Asian Oryza

被引:52
作者
Huang, Zhongyun [1 ]
Young, Nelson D. [1 ]
Reagon, Michael [2 ]
Hyma, Katie E. [1 ]
Olsen, Kenneth M. [3 ]
Jia, Yulin [4 ]
Caicedo, Ana L. [1 ]
机构
[1] Univ Massachusetts, Dept Biol, Amherst, MA 01003 USA
[2] Ohio State Univ, Dept Biol, Lima, OH 45804 USA
[3] Washington Univ, Dept Biol, Campus Box 1137, St Louis, MO 63130 USA
[4] USDA ARS, Dale Bumpers Natl Rice Res Ctr, Stuttgart, AR USA
基金
美国国家科学基金会;
关键词
adaptation; agricultural weeds; Oryza; parallel evolution; recurrent evolution; weedy traits; MULTILOCUS GENOTYPE DATA; POPULATION-STRUCTURE; CULTIVATED RICE; RED RICE; GENETIC DIVERSITY; SATIVA L; PHYLOGENETIC ANALYSIS; ADAPTIVE EVOLUTION; SORGHUM-HALEPENSE; HELIANTHUS-ANNUUS;
D O I
10.1111/mec.14120
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
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 USA, 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. Genomewide divergence scans between weed groups from the USA 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 among 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.
引用
收藏
页码:3151 / 3167
页数:17
相关论文
共 91 条
[1]   Histological and genetic characteristics associated with the seed-shattering habit of weedy rice (Oryza sativa L.) from Okayama, Japan [J].
Akasaka, Maiko ;
Konishi, Saeko ;
Izawa, Takeshi ;
Ushiki, Jun .
BREEDING SCIENCE, 2011, 61 (02) :168-173
[2]   Mechanism of primisulfuron resistance in a shattercane (Sorghum bicolor) biotype [J].
Anderson, DD ;
Nissen, SJ ;
Mattin, AR ;
Roeth, FW .
WEED SCIENCE, 1998, 46 (02) :158-162
[3]   LOSITAN:: A workbench to detect molecular adaptation based on a Fst-outlier method [J].
Antao, Tiago ;
Lopes, Ana ;
Lopes, Ricardo J. ;
Beja-Pereira, Albano ;
Luikart, Gordon .
BMC BIOINFORMATICS, 2008, 9 (1)
[4]   Convergence and parallelism reconsidered: what have we learned about the genetics of adaptation? [J].
Arendt, Jeff ;
Reznick, David .
TRENDS IN ECOLOGY & EVOLUTION, 2008, 23 (01) :26-32
[5]   Crop-to-weed gene flow in the genus Sorghum (Poaceae): Spontaneous interspecific hybridization between johnsongrass, Sorghum halepense, and crop sorghum, S-bicolor [J].
Arriola, PE ;
Ellstrand, NC .
AMERICAN JOURNAL OF BOTANY, 1996, 83 (09) :1153-1159
[6]  
Baker H. G., 1965, The genetics of colonizing species., P147
[7]   Rapid evolution in plant chitinases: Molecular targets of selection in plant-pathogen coevolution [J].
Bishop, JG ;
Dean, AM ;
Mitchell-Olds, T .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (10) :5322-5327
[8]   TASSEL: software for association mapping of complex traits in diverse samples [J].
Bradbury, Peter J. ;
Zhang, Zhiwu ;
Kroon, Dallas E. ;
Casstevens, Terry M. ;
Ramdoss, Yogesh ;
Buckler, Edward S. .
BIOINFORMATICS, 2007, 23 (19) :2633-2635
[9]   The Impact of Herbicide-Resistant Rice Technology on Phenotypic Diversity and Population Structure of United States Weedy Rice [J].
Burgos, Nilda Roma ;
Singh, Vijay ;
Tseng, Te Ming ;
Black, Howard ;
Young, Nelson D. ;
Huang, Zhongyun ;
Hyma, Katie E. ;
Gealy, David R. ;
Caicedo, Ana L. .
PLANT PHYSIOLOGY, 2014, 166 (03) :1208-1220
[10]   Genome-wide patterns of nucleotide polymorphism in domesticated rice [J].
Caicedo, Ana L. ;
Williamson, Scott H. ;
Hernandez, Ryan D. ;
Boyko, Adam ;
Fledel-Alon, Adi ;
York, Thomas L. ;
Polato, Nicholas R. ;
Olsen, Kenneth M. ;
Nielsen, Rasmus ;
McCouch, Susan R. ;
Bustamante, Carlos D. ;
Purugganan, Michael D. .
PLOS GENETICS, 2007, 3 (09) :1745-1756