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

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.

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

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.

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

Biology ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 828
Author(s):  
Yong-Qing Zhu ◽  
Jia Fang ◽  
Ying Wang ◽  
Li-Hao Pang ◽  
Bao-Rong Lu
Keyword(s):  
Genetic Diversity ◽  
Crop Production ◽  
Novel Mutation ◽  
Weedy Rice ◽  
Japonica Rice ◽  
Molecular Fingerprinting ◽  
Cultivated Rice ◽  
Novel Mutations ◽  
Origin And Evolution ◽  
Worldwide Distribution

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.

scholarly journals Assessing Physiological and Genetic Evidence for Evolution of Shared Weedy Rice Traits at the Vegetative Growth Stage

2021 ◽  
Vol 3 ◽  
Author(s):  
Zhongyun Huang ◽  
Jorge Andres Rodriguez ◽  
Rika Matsuo ◽  
Ana L. Caicedo
Keyword(s):  
Vegetative Growth ◽  
Physiological Traits ◽  
Weedy Rice ◽  
Growth Stages ◽  
Cultivated Rice ◽  
Seed Shattering ◽  
Common Path ◽  
Crop Fields ◽  
Vegetative Traits ◽  
Genetic Mechanisms

Weedy rice (Oryza spp.) has successfully adapted to invasion of cultivated rice (O. sativa L.) fields by being a strong competitor from the early vegetative growth stages to crop harvest. While seed shattering and seed dormancy have been shown to contribute to competitiveness at the reproductive stage, much less is known about the traits that could contribute to weedy rice adaptation at the vegetative stage. We examined several growth and physiological traits in five different weedy rice lineages with different ancestral origins, and found that no single vegetative phenotype characterizes all weedy rice. Divergence in growth and physiological traits between weedy rice groups and their putative cultivated ancestors has been limited, suggesting that altered vegetative traits have not been a common path to weed adaptation. There is a lack of convergence in patterns of gene expression in two independent weedy rice lineages, suggesting that there are few shared genetic mechanisms in the evolution of vegetative traits. We conclude that it must not be assumed that all weedy rice groups necessarily have altered vegetative growth or physiological mechanisms compared to their ancestors, that facilitate their invasion of crop fields.

scholarly journals Improving Drought Tolerance in Mungbean (Vigna radiata L. Wilczek): Morpho-Physiological, Biochemical and Molecular Perspectives

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1534
Author(s):  
Chandra Mohan Singh ◽  
Poornima Singh ◽  
Chandrakant Tiwari ◽  
Shalini Purwar ◽  
Mukul Kumar ◽  
...  
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Crop Production ◽  
Mitigation Strategies ◽  
Theoretical Research ◽  
Whole Genome Sequence ◽  
Complex Nature ◽  
Drought Tolerant ◽  
Breeding Programmes ◽  
The Impact

Drought stress is considered a severe threat to crop production. It adversely affects the morpho-physiological, biochemical and molecular functions of the plants, especially in short duration crops like mungbean. In the past few decades, significant progress has been made towards enhancing climate resilience in legumes through classical and next-generation breeding coupled with omics approaches. Various defence mechanisms have been reported as key players in crop adaptation to drought stress. Many researchers have identified potential donors, QTLs/genes and candidate genes associated to drought tolerance-related traits. However, cloning and exploitation of these loci/gene(s) in breeding programmes are still limited. To bridge the gap between theoretical research and practical breeding, we need to reveal the omics-assisted genetic variations associated with drought tolerance in mungbean to tackle this stress. Furthermore, the use of wild relatives in breeding programmes for drought tolerance is also limited and needs to be focused. Even after six years of decoding the whole genome sequence of mungbean, the genome-wide characterization and expression of various gene families and transcriptional factors are still lacking. Due to the complex nature of drought tolerance, it also requires integrating high throughput multi-omics approaches to increase breeding efficiency and genomic selection for rapid genetic gains to develop drought-tolerant mungbean cultivars. This review highlights the impact of drought stress on mungbean and mitigation strategies for breeding high-yielding drought-tolerant mungbean varieties through classical and modern omics technologies.

scholarly journals Shifts in morphology, gene expression, and selection underlie web loss in Hawaiian Tetragnatha spiders

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Cory A. Berger ◽  
Michael S. Brewer ◽  
Nobuaki Kono ◽  
Hiroyuki Nakamura ◽  
Kazuharu Arakawa ◽  
...  
Keyword(s):  
Genetic Basis ◽  
Adaptive Traits ◽  
Deep Time ◽  
Selective Pressures ◽  
Silk Production ◽  
Silk Glands ◽  
Genetic Mechanisms ◽  
Orb Web ◽  
Short Time ◽  
Web Building

Abstract Background A striking aspect of evolution is that it often converges on similar trajectories. Evolutionary convergence can occur in deep time or over short time scales, and is associated with the imposition of similar selective pressures. Repeated convergent events provide a framework to infer the genetic basis of adaptive traits. The current study examines the genetic basis of secondary web loss within web-building spiders (Araneoidea). Specifically, we use a lineage of spiders in the genus Tetragnatha (Tetragnathidae) that has diverged into two clades associated with the relatively recent (5 mya) colonization of, and subsequent adaptive radiation within, the Hawaiian Islands. One clade has adopted a cursorial lifestyle, and the other has retained the ancestral behavior of capturing prey with sticky orb webs. We explore how these behavioral phenotypes are reflected in the morphology of the spinning apparatus and internal silk glands, and the expression of silk genes. Several sister families to the Tetragnathidae have undergone similar web loss, so we also ask whether convergent patterns of selection can be detected in these lineages. Results The cursorial clade has lost spigots associated with the sticky spiral of the orb web. This appears to have been accompanied by loss of silk glands themselves. We generated phylogenies of silk proteins (spidroins), which showed that the transcriptomes of cursorial Tetragnatha contain all major spidroins except for flagelliform. We also found an uncharacterized spidroin that has higher expression in cursorial species. We found evidence for convergent selection acting on this spidroin, as well as genes involved in protein metabolism, in the cursorial Tetragnatha and divergent cursorial lineages in the families Malkaridae and Mimetidae. Conclusions Our results provide strong evidence that independent web loss events and the associated adoption of a cursorial lifestyle are based on similar genetic mechanisms. Many genes we identified as having evolved convergently are associated with protein synthesis, degradation, and processing, which are processes that play important roles in silk production. This study demonstrates, in the case of independent evolution of web loss, that similar selective pressures act on many of the same genes to produce the same phenotypes and behaviors.

scholarly journals Comparative transcriptomic and physiological analyses of weedy rice and cultivated rice to identify vital differentially expressed genes and pathways regulating the ABA response

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hong Lang ◽  
Yuting He ◽  
Faliang Zeng ◽  
Fan Xu ◽  
Minghui Zhao ◽  
...  
Keyword(s):  
Differentially Expressed Genes ◽  
Differentially Expressed ◽  
Weedy Rice ◽  
Cultivated Rice ◽  
Biotic Stresses ◽  
Aba Sensitivity ◽  
Aba Catabolism ◽  
Physiological Analysis ◽  
Response To Stress ◽  
Aba Response

AbstractWeedy rice is a valuable germplasm resource characterized by its high tolerance to both abiotic and biotic stresses. Abscisic acid (ABA) serves as a regulatory signal in plant cells as part of their adaptive response to stress. However, a global understanding of the response of weedy rice to ABA remains to be elucidated. In the present study, the sensitivity to ABA of weedy rice (WR04-6) was compared with that of temperate japonica Shennong9816 (SN9816) in terms of seed germination and post-germination growth via the application of exogenous ABA and diniconazole, an inhibitor of ABA catabolism. Physiological analysis and a transcriptomic comparison allowed elucidation of the molecular and physiological mechanisms associated with continuous ABA and diniconazole treatment. WR04-6 was found to display higher ABA sensitivity than SN9816, resulting in the rapid promotion of antioxidant enzyme activity. Comparative transcriptomic analyses indicated that the number of differentially expressed genes (DEGs) in WR04-6 seedlings treated with 2 μM ABA or 10 μM diniconazole was greater than that in SN9816 seedlings. Genes involved in stress defense, hormone signal transduction, and glycolytic and citrate cycle pathways were highly expressed in WR04-6 in response to ABA and diniconazole. These findings provide new insight into key processes mediating the ABA response between weedy and cultivated rice.

Weedy Rice Diversity in Southern Brazil

Weed Science ◽  
2021 ◽  
pp. 1-37
Author(s):  
Leonard Bonilla Piveta ◽  
José Alberto Noldin ◽  
Nilda Roma-Burgos ◽  
Vívian Ebeling Viana ◽  
Lariza Benedetti ◽  
...  
Keyword(s):  
Oryza Sativa ◽  
Flowering Time ◽  
Weed Management ◽  
Phenotypic Diversity ◽  
Weedy Rice ◽  
Phenotypic Traits ◽  
Southern Brazil ◽  
Variable Response ◽  
Cultivated Rice ◽  
Flowering Synchrony

Abstract Weedy rice (Oryza sativa L.) is one of the most troublesome weeds affecting rice (Oryza sativa L.) production in many countries. Weedy rice control is difficult in rice fields because the weed and crop are phenotypically and morphologically similar. Weedy rice can be a source of genetic diversity to cultivated rice. Thus, this study aimed to characterize the morphological diversity of weedy rice in Southern Brazil. Qualitative and quantitative traits of 249 accessions from eight rice growing mesoregions in Rio Grande do Sul (RS) and Santa Catarina (SC) states were analyzed. For each accession, 24 morphological descriptors (14 qualitative and 10 quantitative) were evaluated. All the 249 accessions from RS and SC are of indica lineage. Considering all the phenotypic traits evaluated, the accessions separated into 14 distinct groups. One of the largest groups consisted of plants that were predominantly tall and with green leaves, intermediate shattering, and variable in flowering time. Distinct subgroups exist within larger clusters, showing discernable phenotypic diversity within the main clusters. The variability in flowering time was high (77 to 110 d after emergence), indicating high potential for flowering synchrony with rice cultivars and, consequently, gene flow. This indicates the need to remove escapes when planting herbicide-resistant rice. Thus, weedy rice populations in Southern Brazil are highly diverse and this diversity could result in variable response to weed management.

scholarly journals Explore the genetics of weedy traits using rice 3K database

2021 ◽  
Vol 62 (1) ◽  
Author(s):  
Yu-Lan Lin ◽  
Dong-Hong Wu ◽  
Cheng-Chieh Wu ◽  
Yung-Fen Huang
Keyword(s):  
Seed Coat ◽  
Coat Color ◽  
Rice Genome ◽  
Genome Project ◽  
Weedy Rice ◽  
Seed Coat Color ◽  
Allele Mining ◽  
Cultivated Rice ◽  
Population Structure Analysis ◽  
Public Data

Abstract Background Weedy rice, a conspecific weedy counterpart of the cultivated rice (Oryza sativa L.), has been problematic in rice-production area worldwide. Although we started to know about the origin of some weedy traits for some rice-growing regions, an overall assessment of weedy trait-related loci was not yet available. On the other hand, the advances in sequencing technologies, together with community efforts, have made publicly available a large amount of genomic data. Given the availability of public data and the need of “weedy” allele mining for a better management of weedy rice, the objective of the present study was to explore the genetic architecture of weedy traits based on publicly available data, mainly from the 3000 Rice Genome Project (3K-RGP). Results Based on the results of population structure analysis, we have selected 1378 individuals from four sub-populations (aus, indica, temperate japonica, tropical japonica) without admixed genomic composition for genome-wide association analysis (GWAS). Five traits were investigated: awn color, seed shattering, seed threshability, seed coat color, and seedling height. GWAS was conducted for each sub-population × trait combination and we have identified 66 population-specific trait-associated SNPs. Eleven significant SNPs fell into an annotated gene and four other SNPs were close to a putative candidate gene (± 25 kb). SNPs located in or close to Rc were particularly predictive of the occurrence of seed coat color and our results showed that different sub-populations required different SNPs for a better seed coat color prediction. We compared the data of 3K-RGP to a publicly available weedy rice dataset. The profile of allele frequency, phenotype-genotype segregation of target SNP, as well as GWAS results for the presence and absence of awns diverged between the two sets of data. Conclusions The genotype of trait-associated SNPs identified in this study, especially those located in or close to Rc, can be developed to diagnostic SNPs to trace the origin of weedy trait occurred in the field. The difference of results from the two publicly available datasets used in this study emphasized the importance of laboratory experiments to confirm the allele mining results based on publicly available data.

scholarly journals Elucidating the genetic basis of an oligogenic birth defect using whole genome sequence data in a non-model organism, Bubalus bubalis

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Lynsey K. Whitacre ◽  
Jesse L. Hoff ◽  
Robert D. Schnabel ◽  
Sara Albarella ◽  
Francesca Ciotola ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Birth Defect ◽  
Genetic Basis ◽  
Sequence Data ◽  
Model Organism ◽  
Bubalus Bubalis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data

scholarly journals The Genetic Basis of High Resistance to Rice Yellow Mottle Virus (RYMV) in Cultivars of Two Cultivated Rice Species

Plant Disease ◽  
1999 ◽  
Vol 83 (10) ◽  
pp. 931-935 ◽  
Author(s):  
M. N. Ndjiondjop ◽  
L. Albar ◽  
D. Fargette ◽  
C. Fauquet ◽  
A. Ghesquière
Keyword(s):  
Genetic Basis ◽  
Virus Isolate ◽  
Mottle Virus ◽  
F1 Hybrids ◽  
Enzyme Linked Immunosorbent Assay ◽  
Rice Yellow Mottle Virus ◽  
Recessive Resistance ◽  
Cultivated Rice ◽  
Recessive Resistance Gene ◽  
Yellow Mottle

Three cultivars of Oryza sativa (IR64, Azucena, and Gigante) and four cultivars of O. glaberrima (Tog5681, Tog5673, CG14, and SG329) were evaluated for their resistance to two isolates of rice yellow mottle virus (RYMV) by enzyme-linked immunosorbent assay (ELISA) and symptomatology. Cultivars Tog5681 and Gigante were highly resistant, and no symptoms were observed when either virus isolate was inoculated at 10 or 20 days postgermination and assayed by ELISA at 7, 14, 22, 35, 50, or 64 days postinoculation. Azucena showed a partial resistance, whereas the other cultivars were susceptible. Symptom appearance was associated with increase in ELISA absorbance in the systemically infected leaves. The best discrimination among the cultivars occurred when the plants were inoculated at 10 days postgermination. Crosses were made between the highly resistant (Gigante and Tog5681) and the susceptible (IR64) cultivars to determine the genetic basis of resistance to RYMV. Evaluation of F1 hybrids and interspecific progenies, as well as the segregation of resistance in F2 and F3 lines of the IR64 × Gigante cross, provided results consistent with the presence of a single recessive resistance gene common to Tog5681 and Gigante.

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