May, 2011 based on these regressions, the ct required for weedy rice seed germination was 23c higher than the ht, indicating that ht in every location immediately after rice harvesting was too cold to allow germination of the local weedy rice population. Sep 21, 2007 however, weedy red rice can often be found outside the range of o. The name weedy rice is used for all types and variations of rice which show some characteristic features of cultivated rice and grow as weeds in commercial rice fields. Diverse genetic mechanisms underlie worldwide convergent rice. Population genetics is the basis of evolutionary studies, and has been widely used in several researches. The main group includes weedy rice varity type with awnless seeds and. Dormancylinked population structure of weedy rice oryza. The us ranks third among rice exporting nations childs 2005 and us rice production is among the most efficient in the world moldenhauer et al. Forinstance,riceandwildoatseedsaftermapping population. Gene flow from cultivated rice oryza sativa to its weedy.
Morphological characterization of weedy rice populations. In fact, the determined average gene flow migrants level for a particular weedy rice population is significantly positively correlated with the level of its expected heterozygosity h e, indicating the importance of gene flow to create and accumulate within population genetic diversity in sri lankan weedy rice populations. Genetic diversity of seed dormancy and molecular evolution of. Recent studies have characterized the range of morphological and genetic diversity in weedy rice from different locations and have revealed that there is often great morphological diversity within growing regions. The us ranks third among riceexporting nations childs 2005 and us rice production is among the most efficient in the world moldenhauer et al. Although multiple origins for weedy rice have been proposed, currently dedomestication from cultivated varieties has been acknowledged as one of the main routes for. Genomic variation associated with local adaptation of. In order to generate a representative population of chinese weedy rice isolates, 155 samples were collected from multiple fields in four heavily. In this study, we attempt to identify the origin and population structure of weedy red rice sampled from the usa using both dna sequence data from a neutral nuclear locus as well as microsatellite genotype data. These characteristics or their components differed in average degree of dominance from.
Population genomics identifies the origin and signatures of. Phenotypic selection for dormancy introduced a set. Jun 01, 20 an f2 population from the cross between a cultivated em931 and a u. An earlier us weedy rice population genetics study by londo and schaal included microsatellite data for a single california weedy rice genotype, rr28, collected in california. Signatures of adaptation in the weedy rice genome, nature genetics. Seedmediated gene flow promotes genetic diversity of weedy. May 24, 2017 phenotypes and genome resequencing of weedy rice. Based on a sampling of rice production areas in colombia and evaluation of 27 phenotypic traits, a twostep cluster analysis identified four morphological groups for weedy rice in colombia. Quantitative trait locus and haplotype analyses of wild.
This recent field of science has important applications for the management of populations natural and domesticated, as well as for evolutionary studies of the various factors that affect gene frequencies over time and spatial distribution. Rapid evolutionary divergence and ecotypic diversification of. Sep 01, 2019 for the sabah weeds characterized by the purple population component in the structure analysis, h3 was the most common haplotype 79% of accessions. Mar 26, 2020 weedy rice samples were sequenced to an average 19. The authors report here a case of hybrid sterility between an indica cultivar, ir36 and a weedy strain, ludao, which naturally grows in and around farms in jiangsu province, china.
Jun 15, 2010 weedy rice red rice, a conspecific weed of cultivated rice oryza sativa l. Origins and population genetics of weedy rice in the usa. Tseng, te ming, genetic diversity of seed dormancy and molecular evolution of weedy red rice 20. Ss182 and many other species respond best to cool, moist is a wildlike, indica type of weedy rice originating from thai. Origins and population genetics of weedy red rice in the usa.
Genetic analysis of adaptive syndromes interrelated with. Seeddormancy trait contributes to population structure of weedy oryza sp. The weedy rice parents are representatives of the sh and bha populations of u. Furthermore, we detected many adaptive loci in the weedy rice population that may be valuable resources for control and utilization of weedy rice in the future. Mar 23, 2020 rice sheath blight shb disease, caused by the pathogenic fungus rhizoctonia solani, causes significant yield losses globally. Free fulltext pdf articles from hundreds of disciplines, all in one place a chromosome segment substitution library of weedy rice for genetic dissection of complex agronomic and domestication traits pdf paperity. Genomic patterns of nucleotide diversity in divergent. In the usa, weedy red rice was first documented as early as 1846 and has continued to affect rice production areas. As an evolutionary evil twin of cultivated rice, weedy rice oryza sativa f. Us weedy rice populations, which are dedomesticated forms of indica and aus cultivated rice, appear to be more resistant to shb than local japonica cultivated rice. The origin of weedy rice ludao in china deduced by genome. The use of herbicideresistant hr1 clearfield rice oryza sativa to control weedy rice has increased in the past 12 years to constitute about 60% of rice acreage in arkansas, where most u. A cross between the weedy strain ss182 and the breeding line em931 was developed to investigate the genetic basis and adaptive significance of these interrelationships.
Quantitative trait locus and haplotype analyses of wild and. Weedy rice, which differs genetically from wild and crop rice, is adapted for undercover life in agricultural fields 3 april 2017 weedy rice the taller plants is outgrowing and. Genetic analysis of adaptive syndromes interrelated with seed. Weedy rice produces a low number of grains per plant and is considered undesirable in cultivated rice fields. Genetic diversity of seed dormancy and molecular evolution. Weedy strains of rice with hullimposed seed dormancy will be crosspollinated with nondormant rice varieties to produce f1, f2, and other generations segregating for dormancy. Project methods weedy rice oryza sativa is being developed as a genetic system to clone dormancy genes from grasses. Our discussion of weedy rice in the present paper focuses on the latter situation, and specifically on the weedy rice found in us rice fields. Methods experiments were conducted at two sites in korea and china to determine gene flow from cultivated rice oryza sativa l. For the sabah weeds characterized by the purple population component in the structure analysis, h3 was the most common haplotype 79% of accessions. Population genomics identifies the origin and signatures of selection of korean weedy rice.
An f2 population from the cross between a cultivated em931 and a u. Using population genetics analyses of south asian and us weedy. In this study, we attempt to identify the origin and population structure of. Caicedo2 and yulin jia3 1department of biology, washington university, st louis, mo 63, usa.
Weeds, especially close relatives of crops, pose severe threats to agricultural production worldwide. However, weedy red rice can often be found outside the range of o. Introgression and selection shaping the genome and adaptive loci of weedy rice in northern china jian sun key laboratory of northeast rice biology and breeding, ministry of agriculture, and key laboratory of northern japonica rice genetics and breeding, ministry of education, rice research institute, shenyang agricultural university, dongling. Apr 03, 2017 weedy rice, which differs genetically from wild and crop rice, is adapted for undercover life in agricultural fields.
Genetic diversity of seed dormancy and molecular evolution of weedy red rice a dissertation submitted in partial fulfillment of the requirements for the degree of. Signatures of adaptation in the weedy rice genome nature. Most previous population genetics studies of weedy rice used. Rice sheath blight shb disease, caused by the pathogenic fungus rhizoctonia solani, causes significant yield losses globally. It spreads rapidly because of its high phenotypic plasticity and seed shattering. Weedy rice samples were sequenced to an average 19.
Weedy rice exerts a severe impact on rice production by competing for sunlight, water and nutrients. The objectives of this study were to evaluate the level of morphological and agronomical variation and the level and pattern of genetic diversity and population structure of weedy rice populations in thailand. A genomewide analysis was performed with a backcross population of ir36ludaoir36 using a total of 151 simple sequence repeat ssr markers covering the entire rice linkage map. We used the rid14 marker to identify the genotypes governing red and white pericarp color in weedy rice. Seed dormancy in rice interrelates to the weedy characteristics shattering, awn, black hull color, and red pericarp color. An earlier us weedy rice population genetics study by londo and schaal 22 included microsatellite data for a single california weedy rice genotype, rr28, collected in california. 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. Sequence analysis of the pvatpase region of this genotype indicated that it was a unique, private haplotype genetically most similar to o.
H3 is also the highestfrequency haplotype in peninsular malaysia weedy rice with the purple population component present at 41% frequency, whereas it was not detected in any other rice group. The term weedy rice generally includes all the species of genus oryza which behave as rice and which crop in rotation with rice weeds. Origins and population genetics of weedy red rice in the. A genomewide analysis was performed with a backcross population of ir36ludaoir36 using a total of 151 simple sequence repeat ssr markers covering the entire.
Markers unique to the dormant populations are good candidates for followup studies on the control of seed dormancy in weedy oryza sp. Despite belonging to the same species complex as domesticated rice and its wild relatives, the evolutionary origins of weedy rice remain unclear. We have also utilized genomewide gene coding markers and divergence population genetics to determine the origin of weedy rice in california ca. Weedy rice populations have been reported in many rice growing areas in the world where the crop is directly seeded parker and dean, 1976. The abundant within population genetic diversity coupled with limited population genetic structure and differentiation is likely caused by the considerable seedmediated gene flow of weedy rice along with the longdistance exchange of farmersaved rice seeds between weedy rice contaminated regions in sri lanka. Population genomics identifies the origin and signatures. In order to generate a representative population of chinese weedy rice isolates, 155 samples were collected from multiple fields in. The reference genome published herein will benefit rice molecular breeding by accelerating. In fact, the determined average gene flow migrants level for a particular weedy rice population is significantly positively correlated with the level of its expected heterozygosity h e, indicating the importance of gene flow to create and accumulate withinpopulation genetic diversity in sri lankan weedy rice populations. Here, we examined the population genetics of weedy rice in malaysia, where wild rice o.
A paddy field devoid of weedy rice was used for the polleninflow experiment, and weedy rice was only present in adjacent fields. A backcross was made to develop the ripen under warm, dry conditions, while arabidopsis mapping population em931em931ss182 bc 1. To assess the impact of hr1 cultivated rice on the herbicide resistance and population structure of weedy rice, weedy samples were collected from commercial fields with a. Weedy rice, which differs genetically from wild and crop rice, is adapted for undercover life in agricultural fields. Weedy rice red rice, a conspecific weed of cultivated rice oryza sativa l.
Diverse genetic mechanisms underlie worldwide convergent. Genetic diversity and origin of weedy rice oryza sativa f. Phenotypic characterization of weedy rice in california. The objectives of this study are to determine the genetic diversity and differentiation of weedy rice populations from liaoning province in northeastern china and to explore the possible origin of these weedy populations by comparing their genetic. We mapped quantitative trait loci qtl associated with shb resistance using two f8 recombinant inbred. What rice farmers say about weeds weeds is rank as 1st or 2nd problem in rice weed management in rice is challenging, complex, expensive, and regulated herbicide is the preferred method of controlling weed and it is the first and probably the last line of defense farmers are not quit sure if herbicides are working well. Dormancylinked population structure of weedy rice oryza sp. For genomic comparison, public genomic sequence data were retrieved for a worldwide sample of 426 locally cultivated rice varieties and 53 wild rice accessions 3, 9, 10. Association of seed dormancy with shattering, awn, and black hull and red pericarp colors enhances survival of wild and weedy species, but challenges the use of dormancy genes in breeding varieties resistant to preharvest sprouting.
These groupings had some limited association with geography and the genetic ancestries of weedy rice. Plant characteristics of weedy rice ecotypes and cultivated rice varieties carv. Introgression and selection shaping the genome and. Weedy rice, which differs genetically from wild and crop rice. Multiple lines of evidence suggest that differentiation between weedy rice at asian high latitudes wrah and cultivated rice was initiated by the genetic improvement of cultivated rice.
Population structure of weedy rice ecotypes based on 14 morphological and physiological traits by canonical discriminant analysis. A chromosome segment substitution library of weedy rice. The list of 183 accessions of wild, cultivated, and weedy rice. This study assayed the population structure, genetic diversity and origin of northeast asia weedy rice by using 48 simple sequence repeat markers.
Feral rice from introgression of weedy rice genes into. Mar 22, 2005 seed dormancy in rice interrelates to the weedy characteristics shattering, awn, black hull color, and red pericarp color. Oct 01, 2005 association of seed dormancy with shattering, awn, and black hull and red pericarp colors enhances survival of wild and weedy species, but challenges the use of dormancy genes in breeding varieties resistant to preharvest sprouting. The abundant withinpopulation genetic diversity coupled with limited population genetic structure and differentiation is likely caused by the considerable seedmediated gene flow of weedy rice along with the longdistance exchange of farmersaved rice seeds between. Multiple loci and epistases control genetic variation for. The dynamics of spatial and temporal population genetic. Ecological genetics genomics of weedy rice by muhamad. Weedy strains of rice with hullimposed seed dormancy will be crosspollinated with nondormant rice varieties to produce f1. Weedy rice, which differs genetically from wild and crop. Characterization of the phenotypic variability in colombian.
Seedmediated gene flow promotes genetic diversity of. Evaluation of population structure, genetic diversity and. Genomic variation associated with local adaptation of weedy. Wild and weedy rice accessions the morphological and molecular analysis of the colombian weedy rice samples allowed the discrimination of three main groups within the weedy rice population. Identification of novel qtl conferring sheath blight. Although multiple origins for weedy rice have been proposed, currently dedomestication from cultivated varieties has been acknowledged as one of the main routes for the origin of weedy rice all over the world814. Even if the glufosinate is used to eliminate the weedy rice population in a paddy field planted with glufosinateresistant rice, some weedy rice plants are likely to escape treatment busconi et al. Evolutionary genomics of weedy rice in the usa kenneth m. A phenotypic selection and recurrent backcrossing technique was used to introduce dormancy genes from a wildlike weedy rice to a breeding line to determine their.
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