Key Roles of De-Domestication and Novel Mutation in Origin and Diversification of Global Weedy Rice

Agricultural weeds pose great challenges to sustainable crop production, owing to their complex origins and abundant genetic diversity. Weedy rice (WD) infests rice fields worldwide causing tremendous losses of rice yield/quality. To explore WD origins and evolution, we analyzed DNA sequence polymorphisms of the seed shattering genes (sh4 and qsh1) in weedy, wild, and cultivated rice from a worldwide distribution. We also used microsatellite and insertion/deletion molecular fingerprinting to determine their genetic relationship and structure. Results indicate multiple origins of WD with most samples having evolved from their cultivated progenitors and a few samples from wild rice. WD that evolved from de-domestication showed distinct genetic structures associated with indica and japonica rice differentiation. In addition, the weed-unique haplotypes that were only identified in the WD samples suggest their novel mutations. Findings in this study demonstrate the key role of de-domestication in WD origins, in which indica and japonica cultivars stimulated further evolution and divergence of WD in various agroecosystems. Furthermore, novel mutations promote continued evolution and genetic diversity of WD adapting to different environments. Knowledge generated from this study provides deep insights into the origin and evolution of conspecific weeds, in addition to the design of effective measures to control these weeds.

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Extraordinarily polymorphic ribosomal DNA in wild and cultivated rice

Genome ◽

10.1139/g96-139 ◽

1996 ◽

Vol 39 (6) ◽

pp. 1109-1116 ◽

Cited By ~ 16

Author(s):

K. D. Liu ◽

Qifa Zhang ◽

G. P. Yang ◽

M. A. Saghai Maroof ◽

S. H. Zhu ◽

...

Keyword(s):

Oryza Sativa ◽

Ribosomal Dna ◽

Wild Rice ◽

Indica Rice ◽

Intergenic Spacer ◽

Oryza Rufipogon ◽

Japonica Rice ◽

Cultivated Rice ◽

Spacer Length ◽

Origin And Evolution

A collection of 481 rice accessions was surveyed for ribosomal DNA (rDNA) intergenic spacer length polymorphism to assess the extent of genetic diversity in Chinese and Asian rice germplasm. The materials included 83 accessions of common wild rice, Oryza rufipogon, 75 of which were from China; 348 entries of cultivated rice (Oryza sativa), representing almost all the rice growing areas in China; and 50 cultivars from South and East Asia. A total of 42 spacer length variants (SLVs) were detected. The size differences between adjacent SLVs in the series were very heterogeneous, ranging from ca. 21 to 311 bp. The 42 SLVs formed 80 different rDNA phenotypic combinations. Wild rice displayed a much greater number of rDNA SLVs than cultivated rice, while cultivated rice showed a larger number of rDNA phenotypes. Indica and japonica groups of O. sativa contained about equal numbers of SLVs, but the SLV distribution was significantly differentiated: indica rice was preferentially associated with longer SLVs and japonica rice with shorter ones. The results may have significant implications regarding the origin and evolution of cultivated rice, as well as the inheritance and molecular evolution of rDNA intergenic spacers in rice. Key words : rDNA, Oryza rufipogon, Oryza sativa, germplasm diversity, evolution.

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Dormancy-linked Population Structure of Weedy Rice (Oryza sp.)

Weed Science ◽

10.1017/wsc.2017.86 ◽

2018 ◽

Vol 66 (3) ◽

pp. 331-339 ◽

Cited By ~ 3

Author(s):

Te-Ming Tseng ◽

Vinod K. Shivrain ◽

Amy Lawton-Rauh ◽

Nilda R. Burgos

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Seed Dormancy ◽

Weed Management ◽

Production Systems ◽

Gene Diversity ◽

Weedy Rice ◽

Cultivated Rice ◽

Simple Sequence

AbstractSeed dormancy allows weedy rice (Oryza sp.) to persist in rice production systems. Weedy and wild relatives of rice (Oryza sativa L.) exhibit different levels of dormancy, which allows them to escape weed management tactics, increasing the potential for flowering synchronization, and therefore gene flow, between weedy Oryza sp. and cultivated rice. In this study, we determined the genetic diversity and divergence of representative dormant and nondormant weedy Oryza sp. groups from Arkansas. Twenty-five simple sequence repeat markers closely associated with seed dormancy were used. Four populations were included: dormant blackhull, dormant strawhull, nondormant blackhull, and nondormant strawhull. The overall gene diversity was 0.355, indicating considerable genetic variation among populations in these dormancy-related loci. Gene diversity among blackhull populations (0.398) was higher than among strawhull populations (0.245). Higher genetic diversity was also observed within and among dormant populations than in nondormant populations. Cluster analysis of 16 accessions, based on Nei’s genetic distance, showed four clusters. Clusters I, III, and IV consisted of only blackhull accessions, whereas Cluster II comprised only strawhull accessions. These four clusters did not separate cleanly into dormant and nondormant populations, indicating that not all markers were tightly linked to dormancy. The strawhull groups were most distant from blackhull weedy Oryza sp. groups. These data indicate complex genetic control of the dormancy trait, as dormant individuals exhibited higher genetic diversity than nondormant individuals. Seed-dormancy trait contributes to population structure of weedy Oryza sp., but this influence is less than that of hull color. Markers unique to the dormant populations are good candidates for follow-up studies on the control of seed dormancy in weedy Oryza sp.

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Geographic pattern of variation among Asian native rice cultivars (Oryza sativa L.) based on fifteen isozyme loci

Genome ◽

10.1139/g88-126 ◽

1988 ◽

Vol 30 (5) ◽

pp. 782-792 ◽

Cited By ~ 19

Author(s):

J. C. Glaszmann

Keyword(s):

Genetic Diversity ◽

Oryza Sativa ◽

Oryza Sativa L ◽

Indian Subcontinent ◽

Indica Rice ◽

Japonica Rice ◽

Geographic Pattern ◽

Cultivated Rice ◽

Rice Varieties ◽

Himalayan Foothills

The geographic pattern of isozyme variation among rice varieties (Oryza sativa L.) in Asia is described based on an electrophoretic survey of 1688 accessions for 15 loci. The distribution patterns are strongly determined by the existence of several varietal groups that are characterized by contrasting multilocus types with dissimilar environmental and macrogeographic distributions. The two main groups correspond to the indica and japonica subspecies. Other types are frequently found in the Indian subcontinent, especially along the Himalayan foothills. These types are predominant in the Indus River basin. They are differentiated into four groups in the eastern part of the Himalayan foothills. There is variation within the groups. Non-random allele distributions are observed, such as regional clines and narrow localization of alleles. Diversity among indica rice is evenly distributed in whole tropical Asia. Variation among japonica rice shows the hilly part of continental Southeast Asia to be the region of highest genetic diversity and its probable area of origin. All this information provides a guide for further analysis aimed at elucidating the history of cultivated rice in Asia and, subsequently, in other continents.Key words: Asian rice, genetic diversity, isozymes, geographic distributions.

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Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution

Communications Biology ◽

10.1038/s42003-021-02484-5 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Toshiyuki Imaizumi ◽

Kaworu Ebana ◽

Yoshihiro Kawahara ◽

Chiaki Muto ◽

Hiroyuki Kobayashi ◽

...

Keyword(s):

Crop Production ◽

Genetic Basis ◽

Whole Genome Sequence ◽

Weedy Rice ◽

Cultivated Rice ◽

Tropical Japonica ◽

Adaptive Introgression ◽

Genomic Signatures ◽

Genomic Divergence ◽

Genetic Mechanisms

AbstractAgricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin from tropical japonica crop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolved temperate japonica- and tropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice.

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A large-scale analysis of seed natural aging revealed stronger aging resistance in weedy rice than coexisting cultivated rice for continuous 4 years across China

10.21203/rs.2.17773/v1 ◽

2019 ◽

Author(s):

weimin dai ◽

Yuan Wang ◽

Yu-Jie Zhang ◽

Xi-Xi Sun ◽

Jin-Ling Yang ◽

...

Keyword(s):

Oryza Sativa ◽

Large Scale ◽

Oryza Sativa L ◽

Germination Rate ◽

Weedy Rice ◽

Japonica Rice ◽

Rice Cultivars ◽

Cultivated Rice ◽

Rice Varieties ◽

Aging Resistance

Abstract Increasing resistance to aging is conducive to seed storage and germination rate of crop. Meanwhile, the resistance to aging is one of the important adaptive mechanisms of weed to thrive in farmland. Weedy rice (Oryza sativa f. spontanea) and cultivated rice (Oryza sativa L.) provide a unique pair demonstrating a weed and conspecific model crop that can be used to study the aging resistance of plants across a diverse geographical range. Chinese weedy rice derived from de-domestication of cultivated rice has rapidly risen to malignant weeds, though the hazard has only been reported for about 20 years. Whether weedy rice rapidly evolves higher seed aging resistance than cultivated rice during the process of dedomestication, which is conducive to its persistence in rice fields, is still unclear. In this experiment, the seeds of weed rice populations and their co-existing rice varieties were collected from 61 regions of China and germinated under normal and high temperatures for consecutive four years (2013–2016). Our study found that the aging resistance of weedy rice was higher than that of the co-existing rice cultivars, and weedy rice may have evolved a different aging resistance mechanism than rice cultivars and could be used as a germplasm resource to cultivate aging-resistant rice. The indica-type has strong aging resistance and no dormancy, while the japonica type has weak aging resistance and a little weak dormancy. Thus, by introducing indica-type aging-resistant alleles into japonica rice, cultivation of aging-resistant japonica rice could be possible.

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The New Is Old: Novel Germination Strategy Evolved From Standing Genetic Variation in Weedy Rice

Frontiers in Plant Science ◽

10.3389/fpls.2021.699464 ◽

2021 ◽

Vol 12 ◽

Author(s):

Chengchuan Zhou ◽

Yang Feng ◽

Gengyun Li ◽

Mengli Wang ◽

Jinjing Jian ◽

...

Keyword(s):

Crop Production ◽

Rapid Evolution ◽

Weedy Rice ◽

Specific Gene ◽

Cultivated Rice ◽

Transcriptomic Data ◽

Yield And Quality ◽

Novel Traits ◽

Allele Specific

Feralization of crop plants has aroused an increasing interest in recent years, not only for the reduced yield and quality of crop production caused by feral plants but also for the rapid evolution of novel traits that facilitate the evolution and persistence of weedy forms. Weedy rice (Oryza sativa f. spontanea) is a conspecific weed of cultivated rice, with separate and independent origins. The weedy rice distributed in eastern and northeastern China did not diverge from their cultivated ancestors by reverting to the pre-domestication trait of seed dormancy during feralization. Instead, they developed a temperature-sensing mechanism to control the timing of seed germination. Subsequent divergence in the minimum critical temperature for germination has been detected between northeastern and eastern populations. An integrative analysis was conducted using combinations of phenotypic, genomic and transcriptomic data to investigate the genetic mechanism underlying local adaptation and feralization. A dozen genes were identified, which showed extreme allele frequency differences between eastern and northeastern populations, and high correlations between allele-specific gene expression and feral phenotypes. Trancing the origin of potential adaptive alleles based on genomic sequences revealed the presence of most selected alleles in wild and cultivated rice genomes, indicating that weedy rice drew upon pre-existing, “conditionally neutral” alleles to respond to the feral selection regimes. The cryptic phenotype was exposed by activating formerly silent alleles to facilitate the transition from cultivation to wild existence, promoting the evolution and persistence of weedy forms.

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Multiple streams of genetic diversity in Japonica rice

10.1101/2020.01.23.915918 ◽

2020 ◽

Cited By ~ 1

Author(s):

João D. Santos ◽

Claire Billot ◽

Dmytro Chebotarov ◽

Gaëtan Droc ◽

Mathias Lorieux ◽

...

Keyword(s):

Genetic Diversity ◽

Japonica Rice ◽

Multiple Streams ◽

Cultivated Rice ◽

Data Set ◽

Geographic Ranges ◽

Cultivar Groups ◽

Domestication Process ◽

Wide Population ◽

Traditional Representation

AbstractIn-depth studies on the genetic diversity of crops indicate that domestication is likely a drawn-out process that differs from the traditional representation of a simple rapid bottleneck. Asian cultivated rice provides a clear picture of multiple foundations of crop diversity. Among them, Japonica rice is likely the group derived from the first human manipulations of this species. We make use of the 3,000 Rice Genomes (3K RG) data set, first described in 2018, to explore the genetic diversity of traditional Japonica rice. After delineating introgressions from the Indica and cAus cultivar groups, we mask these traces to analyse Japonica diversity in more depth. We find differentiation between the established “temperate”, “subtropical” and “tropical” subgroups, and identify stream-like traces of highly divergent sources from broad geographic ranges and subgroups. We characterize five such streams, most visible respectively in: 1) Indonesia, 2) continental Southeast Asia, 3) China, 4) uplands of Japan, and 5) Bhutan. These streams likely consist of ancient alien introgressions propagated through geneflow to different degrees. They currently appear as long genome segments conserved among specific germplasm groups, as well as shorter segments more broadly distributed across diverse germplasm along what could be adaptive corridors. They are all represented in the Japonica component of cBasmati varieties, thought to have emerged over two millennia ago. We thus provide strong evidence that Japonica, the group posited as being the most direct product of a simple domestication process in China, is an aggregate derived from multiple waves of admixture and represents a composite gene pool with ancient Asia-wide population dynamics.

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Exploring the Genetic Diversity among Weedy Rice Accessions Differing in Herbicide Tolerance and Allelopathic Potential

Diversity ◽

10.3390/d14010044 ◽

2022 ◽

Vol 14 (1) ◽

pp. 44

Author(s):

Swati Shrestha ◽

Gourav Sharma ◽

Shandrea Stallworth ◽

Edilberto D. Redona ◽

Te Ming Tseng

Keyword(s):

Genetic Diversity ◽

Crop Improvement ◽

Herbicide Tolerance ◽

Weedy Rice ◽

Cultivated Rice ◽

Allelopathic Potential ◽

Improvement Programs ◽

Rice Improvement ◽

Genetic Diversity Study ◽

Diversity Study

Increasing agricultural productivity is indispensable to meet future food demand. Crop improvement programs rely heavily on genetic diversity. The success of weeds in the ecosystem can be attributed to genetic diversity and plasticity. Weedy rice, a major weed of rice, has diverse morphology and phenology, implying wide genetic diversity. Study was conducted to genotype weedy rice accessions (n = 54) previously phenotyped for herbicide tolerance and allelopathic potential using 30 SSR markers. Cultivated rice (CL163, REX) and allelopathic rice (RONDO, PI312777, PI338047) were also included in the study. Nei’s genetic diversity among weedy rice (0.45) was found to be higher than cultivated rice (0.24) but less than allelopathic rice (0.56). The genetic relationship and population structure based on herbicide tolerance and allelopathic potential were evaluated. Herbicide-tolerant and susceptible accessions formed distinct clusters in the dendrogram, indicating their genetic variation, whereas no distinction was observed between allelopathic and non-allelopathic weedy rice accessions. Weedy rice accession B2, which was previously reported to have high allelopathy and herbicide tolerance, was genetically distinct from other weedy rice. Results from the study will help leverage weedy rice for rice improvement programs as both rice and weedy rice are closely related, thus having a low breeding barrier.

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Origin and evolution of aus type fragrant rice (Oryza sativa L.) : A review

ORYZA- An International Journal on Rice ◽

10.35709/ory.2020.57.3.1 ◽

2020 ◽

Vol 57 (3) ◽

pp. 169-180

Author(s):

S Das ◽

CM Khanda

Keyword(s):

Wild Rice ◽

Oryza Sativa L ◽

Abiotic Stress Tolerance ◽

Japonica Rice ◽

Biotic And Abiotic Stress ◽

Cultivated Rice ◽

Significant Group ◽

Origin And Evolution ◽

Fragrant Rice ◽

Wild Rice Species

Diversity in wild forms and landraces of a crop in a region is an indicator and the core tenet of determining its centre of origin. Jeypore tract of Odisha with diverse rice forms is considered as the earliest, independent rice domestication region of aus ecotype. The aus group of Asian cultivated rice is a distinct population with unique alleles for biotic and abiotic stress tolerance and high genetic diversity even in its fragrant accessions, detected at the molecular level. Annual wild rice Oryza nivara is considered as the progenitor of aus rice. The aus type fragrant rice is the original crop of Indian sub-continent, domesticated in hill areas by primitive tribes, around 4500 years ago. The Chinese japonica rice which came to India later, inherited chloroplast and nuclear genome from wild aus rice and the resulting hybrids formed the aromatic group. Loss or gain of phenotypic characters is the common feature of evolution. The aus landraces possessing characters such as black hull, red pericarp, poor panicle features, low grain yield, associated with wild rice species have evolved into cultivated forms from the intermediate stages of domestication. Considering the archeological evidences, genetic inferences and correlations of different investigations relating to aus type fragrant rice, Jeypore tract is regarded as the place of origin and evolution of this small but significant group of fragrant rice.

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Exploring the Genetic Diversity Among Weedy Rice Accessions Differing in Herbicide Tolerance and Allelopathic Potential

10.20944/preprints202112.0157.v1 ◽

2021 ◽

Author(s):

Swati Shrestha ◽

Gourav Sharma ◽

Shandrea Stallworth ◽

E. D. Redoña ◽

Te Ming Tseng

Keyword(s):

Genetic Diversity ◽

Herbicide Tolerance ◽

Weedy Rice ◽

Rice Accession ◽

Cultivated Rice ◽

Allelopathic Potential ◽

Improvement Programs ◽

Rice Improvement ◽

Genetic Diversity Study ◽

Diversity Study

Increasing agricultural productivity is indispensable to meet future food demand. Crop im-provement programs rely heavily on genetic diversity. The success of weeds in the ecosystem can be attributed to genetic diversity and plasticity. Weedy rice, a major weed of rice, has diverse morphology and phenology, implying wide genetic diversity. Study was conducted to genotype weedy rice accessions (n =54) previously phenotyped for herbicide tolerance and allelopathic potential using 30 SSR markers. Cultivated rice (CL163, REX) and allelopathic rice (RONDO, PI312777, PI338047) were also included in the study. Nei’s genetic diversity among weedy rice (0.45) was found to be higher than cultivated rice (0.24) but less than allelopathic rice (0.56). The genetic relationship and population structure based on herbicide tolerance and allelopathic po-tential were evaluated. Herbicide-tolerant and susceptible accessions formed distinct clusters in the dendrogram, indicating their genetic variation, whereas no distinction was observed between allelopathic and non-allelopathic weedy rice accessions. Weedy rice accession B2, which was previously reported to have high allelopathy and herbicide tolerance, was genetically distinct from other weedy rice. Results from the study will help leverage weedy rice for rice improvement programs as both rice and weedy rice are closely related, thus having a low breeding barrier.

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