scholarly journals Using CRISPR-Cas9 to generate semi-dwarf rice lines in elite landraces

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Xingming Hu ◽  
Yongtao Cui ◽  
Guojun Dong ◽  
Anhui Feng ◽  
Danying Wang ◽  
...  
Keyword(s):  
Gene Editing ◽  
Agronomic Traits ◽  
Genetic Erosion ◽  
Field Trials ◽  
Wild Type ◽  
Biotic And Abiotic Stresses ◽  
Rice Varieties ◽  
Broad Spectrum Resistance ◽  
Mutant Lines ◽  
Better Than

AbstractGenetic erosion refers to the loss of genetic variation in a crop. In China, only a few original landraces of rice (Oryza sativa) were used in breeding and these became the primary genetic background of modern varieties. Expanding the genetic diversity among Chinese rice varieties and cultivating high-yielding and high-quality varieties with resistance to different biotic and abiotic stresses is critical. Here, we used the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein9(Cas9) genome editing system to edit Semi-Dwarf1 (SD1) in the elite landraces Kasalath and TeTePu (TTP), which contain many desired agronomic traits such as tolerance to low phosphorous and broad-spectrum resistance to several diseases and insects. Mutations of SD1 confer shorter plant height for better resistance to lodging. Field trials demonstrated that the yield of the new Kasalath and TTP mutant lines was better than that of the wild type under modern cultivation and that the lines maintained the same desirable agronomic characteristics as their wild-type progenitors. Our results showed that breeding using available landraces in combination with genomic data of different landraces and gene-editing techniques is an effective way to relieve genetic erosion in modern rice varieties.

scholarly journals Improved bacterial leaf blight disease resistance in the major elite Vietnamese rice cultivar TBR225 via editing of the OsSWEET14 promoter

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0255470
Author(s):  
Phuong Nguyen Duy ◽  
Dai Tran Lan ◽  
Hang Pham Thu ◽  
Huong Phung Thi Thu ◽  
Ha Nguyen Thanh ◽  
...  
Keyword(s):  
Agronomic Traits ◽  
Rice Variety ◽  
Rice Cultivar ◽  
Leaf Blight ◽  
Bacterial Leaf Blight ◽  
Transcription Activator ◽  
Rice Varieties ◽  
Sugar Transporters ◽  
Blight Disease ◽  
Mutant Lines

TBR225 is one of the most popular commercial rice varieties in Northern Vietnam. However, this variety is highly susceptible to bacterial leaf blight (BLB), a disease caused by Xanthomonas oryzae pv. oryzae (Xoo) which can lead to important yield losses. OsSWEET14 belongs to the SWEET gene family that encodes sugar transporters. Together with other Clade III members, it behaves as a susceptibility (S) gene whose induction by Asian Xoo Transcription-Activator-Like Effectors (TALEs) is absolutely necessary for disease. In this study, we sought to introduce BLB resistance in the TBR225 elite variety. First, two Vietnamese Xoo strains were shown to up-regulate OsSWEET14 upon TBR225 infection. To investigate if this induction is connected with disease susceptibility, nine TBR225 mutant lines with mutations in the AvrXa7, PthXo3 or TalF TALEs DNA target sequences of the OsSWEET14 promoter were obtained using the CRISPR/Cas9 editing system. Genotyping analysis of T0 and T1 individuals showed that mutations were stably inherited. None of the examined agronomic traits of three transgene-free T2 edited lines were significantly different from those of wild-type TBR225. Importantly, one of these T2 lines, harboring the largest homozygous 6-bp deletion, displayed decreased OsSWEET14 expression as well as a significantly reduced susceptibility to a Vietnamese Xoo strains and complete resistance to another one. Our findings indicate that CRISPR/Cas9 editing conferred an improved BLB resistance to a Vietnamese commercial elite rice variety.

scholarly journals Genetic Variability and Selection Criteria in Rice Mutant Lines as Revealed by Quantitative Traits

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
Yusuff Oladosu ◽  
M. Y. Rafii ◽  
Norhani Abdullah ◽  
Mohammad Abdul Malek ◽  
H. A. Rahim ◽  
...  
Keyword(s):  
Quantitative Traits ◽  
Agronomic Traits ◽  
Field Trials ◽  
Growth And Yield ◽  
Yield Traits ◽  
New Variety ◽  
Rice Mutant ◽  
Group I ◽  
Vegetative Traits ◽  
Mutant Lines

Genetic based knowledge of different vegetative and yield traits play a major role in varietal improvement of rice. Genetic variation gives room for recombinants which are essential for the development of a new variety in any crop. Based on this background, this work was carried out to evaluate genetic diversity of derived mutant lines and establish relationships between their yield and yield components using multivariate analysis. To achieve this objective, two field trials were carried out on 45 mutant rice genotypes to evaluate their growth and yield traits. Data were taken on vegetative traits and yield and its components, while genotypic and phenotypic coefficients, variance components, expected genetic advance, and heritability were calculated. All the genotypes showed variations for vegetative traits and yield and its components. Also, there was positive relationship between the quantitative traits and the final yield with the exception of number of tillers. Finally, the evaluated genotypes were grouped into five major clusters based on the assessed traits with the aid of UPGMA dendrogram. So hybridization of group I with group V or group VI could be used to attain higher heterosis or vigour among the genotypes. Also, this evaluation could be useful in developing reliable selection indices for important agronomic traits in rice.

scholarly journals An Inositol 1,3,4,5,6-Pentakisphosphate 2-Kinase 1 Mutant with a 33-nt Deletion Showed Enhanced Tolerance to Salt and Drought Stress in Rice

Plants ◽  
2020 ◽  
Vol 10 (1) ◽  
pp. 23
Author(s):  
Meng Jiang ◽  
Yanhua Liu ◽  
Ruiqing Li ◽  
Shan Li ◽  
Yuanyuan Tan ◽  
...  
Keyword(s):  
Phytic Acid ◽  
Agronomic Traits ◽  
Inositol Triphosphate ◽  
Rice Grain ◽  
Wild Type ◽  
Low Phytic Acid ◽  
Stress Response Genes ◽  
Potential Applications ◽  
Salt And Drought Stress ◽  
Mutant Lines

OsIPK1 encodes inositol 1,3,4,5,6-pentakisphosphate 2-kinase, which catalyzes the conversion of myo-inositol-1,3,4,5,6-pentakisphosphate to myo-inositol-1,2,3,4,5,6-hexakisphosphate (IP6) in rice. By clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein (Cas9)-mediated mutagenesis in the 3rd exon of the gene, three OsIPK1 mutations, i.e., osipk1_1 (a 33-nt deletion), osipk1_2 (a 1-nt deletion), and osipk1_3 (a 2-nt deletion) were identified in T0 plants of the rice line Xidao #1 (wild type, WT). A transfer DNA free line with the homozygous osipk1_1 mutation was developed; however, no homozygous mutant lines could be developed for the other two mutations. The comparative assay showed that the osipk1_1 mutant line had a significantly lower level of phytic acid (PA, IP6; −19.5%) in rice grain and agronomic traits comparable to the WT. However, the osipk1_1 mutant was more tolerant to salt and drought stresses than the WT, with significantly lower levels of inositol triphosphate (IP3), reactive oxygen species (ROS) and induced IP6, and higher activities of antioxidant enzymes in seedlings subjected to these stresses. Further analyses showed that the transcription of stress response genes was significantly upregulated in the osipk1_1 mutant under stress. Thus, the low phytic acid mutant osipk1_1 should have potential applications in rice breeding and production.

scholarly journals Clarification of the dispensability of PDX1.2 for Arabidopsis viability using CRISPR/Cas9

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Elisa Dell’Aglio ◽  
Ivan Dalvit ◽  
Sylvain Loubéry ◽  
Teresa B. Fitzpatrick
Keyword(s):  
Heat Stress ◽  
Stress Responses ◽  
Gene Editing ◽  
Growth Conditions ◽  
Insertion Mutant ◽  
Wild Type ◽  
Biotic And Abiotic Stress ◽  
Knockout Mutants ◽  
Dna Insertion ◽  
Mutant Lines

Abstract Background PDX1.2 has recently been shown to be a regulator of vitamin B6 biosynthesis in plants and is implicated in biotic and abiotic stress resistance. PDX1.2 expression is strongly and rapidly induced by heat stress. Interestingly, PDX1.2 is restricted to eudicota, wherein it behaves as a non-catalytic pseudoenzyme and is suggested to provide an adaptive advantage to this clade. A first report on an Arabidopsis insertion mutant claims that PDX1.2 is indispensable for viability, being essential for embryogenesis. However, a later study using an independent insertion allele suggests that knockout mutants of pdx1.2 are viable. Therefore, the essentiality of PDX1.2 for Arabidopsis viability is a matter of debate. Given the important implications of PDX1.2 in stress responses, it is imperative to clarify if it is essential for plant viability. Results We have studied the previously reported insertion alleles of PDX1.2, one of which is claimed to be essential for embryogenesis (pdx1.2–1), whereas the other is viable (pdx1.2–2). Our study shows that pdx1.2–1 carries multiple T-DNA insertions, but the T-DNA insertion in PDX1.2 is not responsible for the loss of embryogenesis. By contrast, the pdx1.2–2 allele is an overexpressor of PDX1.2 under standard growth conditions and not a null allele as previously reported. Nonetheless, upregulation of PDX1.2 expression under heat stress is impaired in this mutant line. In wild type Arabidopsis, studies of PDX1.2-YFP fusion proteins show that the protein is enhanced under heat stress conditions. To clarify if PDX1.2 is essential for Arabidopsis viability, we generated several independent mutant lines using the CRISPR-Cas9 gene editing technology. All of these lines are viable and behave similar to wild type under standard growth conditions. Reciprocal crosses of a subset of the CRISPR lines with pdx1.2–1 recovers viability of the latter line and demonstrates that knocking out the functionality of PDX1.2 does not impair embryogenesis. Conclusions Gene editing reveals that PDX1.2 is dispensable for Arabidopsis viability and resolves conflicting reports in the literature on its function.

scholarly journals Fine-tuning Flowering Time via Genome Editing of Upstream Open Reading Frames of Heading Date 2 in Rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Xinxin Liu ◽  
Hualong Liu ◽  
Yuanye Zhang ◽  
Mingliang He ◽  
Rongtian Li ◽  
...  
Keyword(s):  
Genome Editing ◽  
Flowering Time ◽  
Agronomic Traits ◽  
Oryza Sativa L ◽  
Heading Date ◽  
Open Reading Frames ◽  
Fine Tuning ◽  
Wild Type ◽  
Phenotypic Analysis ◽  
Mutant Lines

AbstractFlowering time of rice (Oryza sativa L.) is among the most important agronomic traits for region adaptation and grain yield. In the process of rice breeding, efficient and slightly modulating the flowering time of an elite cultivar would be more popular with breeder. Hence, we are interested in slightly increasing the expression of flowering repressors by CRISPR/Cas9 genome editing system. It was predicated there were three uORFs in 5’ leader sequence of Hd2. In this study, through editing Hd2 uORFs, we got four homozygous mutant lines. Phenotypic analysis showed that the hd2 urf edited lines flowered later by 4.6–11.2 days relative to wild type SJ2. Supporting the later flowering phenotype, the expression of Ehd1, Hd3a, and RFT1 is significantly decreased in hd2 urf than that in wild type. Moreover, we found that the transcription level of Hd2 is not affected, whereas the Hd2 protein level was increased in hd2 urf compared with wild type, which indicated that Hd2 uORFs indeed affect the translation of a downstream Hd2 pORF. In summary, we developed a efficient approach for delaying rice heading date based on editing uORF region of flowering repressor, which is time and labor saving compared to traditional breeding. In future, uORF of other flowering time related genes, including flowering promoter and flowering repressor genes, can also be used as targets to fine-tune the flowering time of varieties.

scholarly journals Genetic mapping and transcriptomic characterization of a new fuzzless-tufted cottonseed mutant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Qian-Hao Zhu ◽  
Warwick Stiller ◽  
Philippe Moncuquet ◽  
Stuart Gordon ◽  
Yuman Yuan ◽  
...  
Keyword(s):  
Molecular Mechanisms ◽  
Agronomic Traits ◽  
Gene Families ◽  
Mutant Phenotype ◽  
Wild Type ◽  
Calcium Dependent ◽  
Dependent Protein ◽  
Flanking Region ◽  
Comparative Transcriptomic Analysis

Abstract Fiber mutants are unique and valuable resources for understanding the genetic and molecular mechanisms controlling initiation and development of cotton fibers that are extremely elongated single epidermal cells protruding from the seed coat of cottonseeds. In this study, we reported a new fuzzless-tufted cotton mutant (Gossypium hirsutum) and showed that fuzzless-tufted near-isogenic lines (NILs) had similar agronomic traits and a higher ginning efficiency compared to their recurrent parents with normal fuzzy seeds. Genetic analysis revealed that the mutant phenotype is determined by a single incomplete dominant locus, designated N5. The mutation was fine mapped to an approximately 250-kb interval containing 33 annotated genes using a combination of bulked segregant sequencing, SNP chip genotyping, and fine mapping. Comparative transcriptomic analysis using 0–6 days post-anthesis (dpa) ovules from NILs segregating for the phenotypes of fuzzless-tufted (mutant) and normal fuzzy cottonseeds (wild-type) uncovered candidate genes responsible for the mutant phenotype. It also revealed that the flanking region of the N5 locus is enriched with differentially expressed genes (DEGs) between the mutant and wild-type. Several of those DEGs are members of the gene families with demonstrated roles in cell initiation and elongation, such as calcium-dependent protein kinase and expansin. The transcriptome landscape of the mutant was significantly reprogrammed in the 6 dpa ovules and, to a less extent, in the 0 dpa ovules, but not in the 2 and 4 dpa ovules. At both 0 and 6 dpa, the reprogrammed mutant transcriptome was mainly associated with cell wall modifications and transmembrane transportation, while transcription factor activity was significantly altered in the 6 dpa mutant ovules. These results imply a similar molecular basis for initiation of lint and fuzz fibers despite certain differences.

scholarly journals Meta-QTL and ortho-MQTL analyses identified genomic regions controlling rice yield, yield-related traits and root architecture under water deficit conditions

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Bahman Khahani ◽  
Elahe Tavakol ◽  
Vahid Shariati ◽  
Laura Rossini
Keyword(s):  
Water Deficit ◽  
Root Architecture ◽  
Agronomic Traits ◽  
Heading Date ◽  
Dry Weight ◽  
Genetic Dissection ◽  
Rice Varieties ◽  
Average Confidence ◽  
Stable Qtls ◽  
Genomic Regions

AbstractMeta-QTL (MQTL) analysis is a robust approach for genetic dissection of complex quantitative traits. Rice varieties adapted to non-flooded cultivation are highly desirable in breeding programs due to the water deficit global problem. In order to identify stable QTLs for major agronomic traits under water deficit conditions, we performed a comprehensive MQTL analysis on 563 QTLs from 67 rice populations published from 2001 to 2019. Yield and yield-related traits including grain weight, heading date, plant height, tiller number as well as root architecture-related traits including root dry weight, root length, root number, root thickness, the ratio of deep rooting and plant water content under water deficit condition were investigated. A total of 61 stable MQTLs over different genetic backgrounds and environments were identified. The average confidence interval of MQTLs was considerably refined compared to the initial QTLs, resulted in the identification of some well-known functionally characterized genes and several putative novel CGs for investigated traits. Ortho-MQTL mining based on genomic collinearity between rice and maize allowed identification of five ortho-MQTLs between these two cereals. The results can help breeders to improve yield under water deficit conditions.

scholarly journals Advances in Cereal Crop Genomics for Resilience under Climate Change

Life ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 502
Author(s):  
Tinashe Zenda ◽  
Songtao Liu ◽  
Anyi Dong ◽  
Huijun Duan
Keyword(s):  
Climate Change ◽  
Genome Sequencing ◽  
Gene Editing ◽  
Agronomic Traits ◽  
Cereal Crops ◽  
Agricultural System ◽  
Plant Genomics ◽  
Crop Species ◽  
Underutilized Species ◽  
Recent Developments

Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.

scholarly journals Directed Evolution of AraC for Improved Compatibility of Arabinose- and Lactose-Inducible Promoters

2007 ◽  
Vol 73 (18) ◽  
pp. 5711-5715 ◽  
Author(s):  
Sung Kuk Lee ◽  
Howard H. Chou ◽  
Brian F. Pfleger ◽  
Jack D. Newman ◽  
Yasuo Yoshikuni ◽  
...  
Keyword(s):  
Directed Evolution ◽  
Cross Talk ◽  
Biological Systems ◽  
Wild Type ◽  
Dimerization Domain ◽  
Expression Levels ◽  
Inducible Promoters ◽  
C Terminus ◽  
Increased Sensitivity ◽  
Better Than

ABSTRACT Synthetic biological systems often require multiple, independently inducible promoters in order to control the expression levels of several genes; however, cross talk between the promoters limits this ability. Here, we demonstrate the directed evolution of AraC to construct an arabinose-inducible (PBAD) system that is more compatible with IPTG (isopropyl-β-d-1-thiogalactopyranoside) induction of a lactose-inducible (Plac) system. The constructed system is 10 times more sensitive to arabinose and tolerates IPTG significantly better than the wild type. Detailed studies indicate that the AraC dimerization domain and C terminus are important for the increased sensitivity of AraC to arabinose.

Efficacy of Clonostachys rosea strain ACM941 and fungicide seed treatments for controlling the root rot complex of field pea

2003 ◽  
Vol 83 (3) ◽  
pp. 519-524 ◽  
Author(s):  
A. G. Xue
Keyword(s):  
Root Rot ◽  
Untreated Control ◽  
Seedling Emergence ◽  
Field Trials ◽  
Field Pea ◽  
Seed Treatments ◽  
Clonostachys Rosea ◽  
Pea Root ◽  
Pea Root Rot ◽  
Better Than

The efficacy of seed treatments with bioagent ACM941 (a strain of Clonostachys rosea), its formulated products GB116 and ACM941-Pro, and common fungicides for the control of pea root rot complex were examined in six field trials in western Canada from 1996 to 2000. The effects on seedling emergence, root rot severity, and yield varied among years. In trials 1 and 2 (1996–1997), none of the treatments significantly reduced root rot severity or increased yield. ACM941 + Thiram 75WP was the most effective treatment, increasing emergence by 17.4% and was significantly better than that of the untreated controls. In trials 3 and 4 (1997–1998), Apron FL alone and ACM941 + Apron FL were significantly better than the untreated control, increasing emergence by 6.2 and 7.7%, and yield by 10.8 and 11.5%, respectively. In trials 5 and 6 (1999–2000), AC M 941 and GB116 were equally the most effective treatments, increasing emergence by 11.5 and 12.2%, and yield by 8.2 and 6.3%, respectively. These effects were significantly greater than that of the untreated control, but not significantly different from those of Apron FL or Vitaflo-280. ACM941-Pro was developed and tested in 2000 only, and it increased emergence by 17.1% and reduced root rot severity by 29.6%. Key words: Bioagent, Clonostachys rosea, field pea, Pisum sativum, pea root rot complex (PRRC), seed treatment, fungicide

Sign in / Sign up

Export Citation Format

Share Document