Compensation of Wild Plants Weakens the Effects of Crop-Wild Gene Flow on Wild Rice Populations

Crop-wild gene flow may alter the fitness of the recipient i.e., crop-wild hybrids, then potentially impact wild populations, especially for the gene flow carrying selective advantageous crop alleles, such as transgenes conferring insect resistance. Given the continuous crop-wild gene flow since crop domestication and the occasionally stressful environments, the extant wild populations of most crops are still “wild.” One interpretation for this phenomenon is that wild populations have the mechanism buffered for the effects of crop alleles. However, solid evidence for this has been scarce. We used wild rice (Oryza rufipogon) and transgenic (Bt/CpTI) rice (O. sativa) as a crop-wild gene flow model and established cultivated, wild, and F7 hybrid rice populations under four levels of insect (Chilo suppressalis) pressure. Then, we measured the trait performance of the plants and estimated fitness to test the compensatory response of relatively high fitness compared to the level of insect damage. The performance of all plants varied with the insect pressure level; wild plants had higher insect-tolerance that was expressed as over- or equal-compensatory responses to insect damage, whereas crop and hybrids exhibited under-compensatory responses. The higher compensation resulted in a better performance of wild rice under insect pressure where transgenes conferring insect resistance had a somewhat beneficial effect. Remarkable hybrid vigour and the benefit effect of transgenes increased the fitness of hybrids together, but this joint effect was weakened by the compensation of wild plants. These results suggest that compensation to environmental stress may reduce the potential impacts of crop alleles on wild plants, thereby it is a mechanism maintaining the “wild” characteristics of wild populations under the scenario of continuous crop-wild gene flow.

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Diversity of Domestication Loci in Wild Rice Populations

Proceedings ◽

10.3390/proceedings2019036014 ◽

2019 ◽

Vol 36 (1) ◽

pp. 14

Author(s):

Hasan ◽

Furtado ◽

Henry

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

Wild Rice ◽

Genetic Manipulation ◽

Starch Synthesis ◽

Oryza Rufipogon ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Wild Populations ◽

Cultivated Rice

Domestication syndrome, i.e. seed shattering, seed dormancy and plant architecture have been selected during the domestication of wild rice around 10,000 years ago. These traits evolved through a series of genomic modifications, including selection of nucleotide polymorphisms resulting from spontaneous mutations, recombination, and fixation of alleles and were incorporated into cultivated rice by hybridization or introgression. The Australian wild rice populations are geographically and genetically distinct and free from genetic exchange with cultivated rice unlike the wild populations in Asia. Furthermore, recent studies reveal they have numerous traits of value and unique alleles. Therefore, these populations seem to be suitable to use to investigate the genetic basis of domestication traits as well as other important traits. In this study, we aim to determine the origin and role of domestication loci using two Australian wild populations: Taxa A (like Oryza rufipogon) and Taxa B (like Oryza meridionalis) endemic near Cairns, Northern Queensland. To do so, firstly, we will analyse the variation of domestication loci in these two wild populations by the comparison with cultivated rice (Oryza sativa spp. japonica cv. Nipponbare) using the whole genome sequencing. Secondly, we will look at the gene expression of the domestication loci at different seed development stages using transcriptomics. Thirdly, we will determine the variation of starch synthesis related genes using whole genome sequencing. Next generation sequencing along with a set of bioinformatics tools will be applied. This research may enlighten our understanding about the domestication process as well as provide insights into how to domesticate these species through genetic manipulation for commercial purpose.

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Diversity and plant growth promoting activities of the cultivable rhizo-bacteria of Dongxiang wild rice (Oryza rufipogon)

Biodiversity Science ◽

10.3724/sp.j.1003.2011.09002 ◽

2011 ◽

Vol 19 (4) ◽

pp. 476-484 ◽

Cited By ~ 6

Author(s):

Luo Fei ◽

Wang Ya ◽

Zeng Qinggui ◽

Yan Riming ◽

Zhang Zhibin ◽

...

Keyword(s):

Plant Growth ◽

Wild Rice ◽

Oryza Rufipogon ◽

Plant Growth Promoting Activities ◽

Plant Growth Promoting ◽

Growth Promoting ◽

Dongxiang Wild Rice

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Genetic Analysis of Cold Tolerance at the Seedling Stage in Dongxiang Wild Rice (Oryza rufipogon)

CHINESE BULLETIN OF BOTANY ◽

10.3724/sp.j.1259.2011.00021 ◽

2011 ◽

Vol 46 (1) ◽

pp. 21-27

Author(s):

Jian Shuirong ◽

Wan Yong ◽

Luo Xiangdong ◽

Fang Jun ◽

Chu Chengcai ◽

...

Keyword(s):

Genetic Analysis ◽

Cold Tolerance ◽

Wild Rice ◽

Oryza Rufipogon ◽

Seedling Stage ◽

Dongxiang Wild Rice

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Identification of novel insertion–deletion markers for Dongxiang wild rice (Oryza rufipogon Griff.) using high-throughput sequencing technology

Journal of Genetics ◽

10.1007/s12041-015-0556-3 ◽

2015 ◽

Vol 94 (S2) ◽

pp. 51-55 ◽

Cited By ~ 3

Author(s):

FANTAO ZHANG ◽

LIANGXING ZHANG ◽

FENGLEI CUI ◽

XIANGDONG LUO ◽

YI ZHOU ◽

...

Keyword(s):

High Throughput ◽

Wild Rice ◽

High Throughput Sequencing ◽

Oryza Rufipogon ◽

Sequencing Technology ◽

Oryza Rufipogon Griff ◽

Dongxiang Wild Rice

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Rapid, ultra-local adaptation facilitated by phenotypic plasticity

10.1101/598292 ◽

2019 ◽

Author(s):

Syuan-Jyun Sun ◽

Andrew M. Catherall ◽

Sonia Pascoal ◽

Benjamin J. M. Jarrett ◽

Sara E. Miller ◽

...

Keyword(s):

Gene Flow ◽

Rapid Evolution ◽

Reaction Norm ◽

Ancestral Population ◽

Adaptive Divergence ◽

Wild Populations ◽

Rapid Adaptation ◽

Burying Beetles ◽

Genetic Accommodation ◽

Nicrophorus Vespilloides

AbstractModels of ‘plasticity-first’ evolution are attractive because they explain the rapid evolution of new complex adaptations. Nevertheless, it is unclear whether plasticity can still facilitate rapid evolution when diverging populations are connected by gene flow. Here we show how plasticity has generated adaptive divergence in fecundity in wild populations of burying beetlesNicrophorus vespilloides, which are still connected by gene flow, which occupy distinct Cambridgeshire woodlands that are just 2.5km apart and which diverged from a common ancestral population c. 1000-4000 years ago. We show that adaptive divergence is duetothe coupling of an evolved increase in the elevation of the reaction norm linking clutch size to carrion size (i.e. genetic accommodation) with plastic secondary elimination of surplus offspring. Working in combination, these two processes have facilitated rapid adaptation to fine-scale environmental differences, despite ongoing gene flow.

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Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

10.21203/rs.3.rs-280217/v1 ◽

2021 ◽

Author(s):

Yong-Chao Xu ◽

Jie Zhang ◽

Dong-Yan Zhang ◽

Ying-Hui Nan ◽

Song Ge ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Wild Rice ◽

Oryza Rufipogon ◽

Cultivated Rice ◽

Antisense Transcripts ◽

High Genetic Diversity ◽

Natural Antisense Transcripts ◽

Form Complex ◽

Oryza Nivara

Abstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa L.), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although many rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa ssp. japonica) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1,246 lncRNAs were identified, including 1,091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1,091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes previously demonstrated to be involved in stress response; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

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Modeling gene flow from genetically modified plants.

10.1079/9781789247480.0007 ◽

2021 ◽

pp. 103-117

Author(s):

Wei Wei ◽

Jun-Ming Wang ◽

Xiang-Cheng Mi ◽

Yan-Da Li ◽

Yan-Ming Zhu

Keyword(s):

Gene Flow ◽

Genetically Modified ◽

Predictive Ability ◽

Crop Wild Relatives ◽

Gm Crops ◽

Wild Plants ◽

Experimental Conditions ◽

Flow Models ◽

Herbicide Resistant ◽

Gm Plants

Abstract Gene flow from genetically modified (GM) plants is concerning because of its ecological risks. In modeling studies, these risks may be reduced by altering crop management while taking environmental conditions into account. Gene flow modeling should consider many field aspects, both biological and physical. For example, empirical statistical models deduced from experimental data simulate gene flow well only under limited conditions (similar to experimental conditions). Mechanistic models, however, offer a potentially greater predictive ability. Gene flow models from GM crops to non-GM crops are used to simulate field conditions and minimize the adventitious presence of transgenes to meet certain threshold levels. These models can be adapted to simulate gene flow from GM crops to crop wild relatives using parameters of sexual compatibility and growth characteristics of the wild plants. Currently, modeling gene flow from herbicide-resistant weeds has become very important in light of the increased application of herbicides and widely evolved resistance in weeds.

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Competition among wild rice, landrace, improved cultivar and F1 hybrid rice

Journal of Agriculture and Environment ◽

10.3126/aej.v18i0.19887 ◽

2018 ◽

Vol 18 ◽

pp. 29-40

Author(s):

Bal Krishna Joshi ◽

Sanjaya Gyawali ◽

Surya Narayan Sah ◽

Rewati Raman Chaudhary

Keyword(s):

Grain Yield ◽

Wild Rice ◽

Growth Period ◽

Oryza Rufipogon ◽

Panicle Length ◽

F1 Hybrid ◽

Panicle Number ◽

Growing Environment ◽

Different Response ◽

Competition Environment

Four genotypes, namely Oryza rufipogon, F1 of IR68888A/Chaite-6, Chaite-6 and Ratodhan were grown in crop and competition environment at Rampur, Nepal to study the effect of genotypes mixture on the characters. Univariate, multivariate and correlation methods of analysis were applied. Seven characters namely panicle length, panicle number, grain yield, harvest index, internode length and leaf width showed significantly different response in crop and competition environment. The performance of cultivar was poor in competition environment than hybrid and wild rice. Hybrid and wild rice showed longer panicle length in competition environment. Significant reduction in panicle number was found in cultivars. The pattern of tiller number over the growth period showed that the competition started after 50 days of seeding. Grain yield of cultivars was significantly reduced in competition environment. Considering the most important characters, hybrid was best competitor and local landrace (Ratodhan) was poorest competitor. Significant variations in culm characters were not found between two environments but leaf characters varied significantly. Highest increment in plant height was found in F1 grown in competition than crop environment. Relationship between characters was affected by growing environment. Among 162 pairs of characters r-value of six and 36 pairs were highly significant different from zero in crop and competition environment respectively. Multivariate analysis indicates that growing environment does not suppress the genetic characters. Competition among the tested genotypes exists even in the recommended spacing. Competition should be studied in detail planting at different spacing.

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