scholarly journals Improving the Rice Photosynthetic Efficiency and Yield by Editing OsHXK1 via CRISPR/Cas9 System

2021 ◽  
Vol 22 (17) ◽  
pp. 9554
Author(s):  
Shaoyan Zheng ◽  
Chanjuan Ye ◽  
Jingqin Lu ◽  
Jiamin Liufu ◽  
Lin Lin ◽  
...  
Keyword(s):  
Photosynthetic Efficiency ◽  
Gene Editing ◽  
Molecular Breeding ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Rice Breeding ◽  
Phenotypic Analysis ◽  
Rice Varieties ◽  
Crop Species ◽  
Rice Yields

Rice (Oryza sativa L.) is an important food crop species in China. Cultivating high-yielding rice varieties that have a high photosynthetic efficiency is an important goal of rice breeding in China. In recent years, due to the continual innovation of molecular breeding methods, many excellent genes have been applied in rice breeding, which is highly important for increasing rice yields. In this paper, the hexokinase gene OsHXK1 was knocked out via the CRISPR/Cas9 gene-editing method in the indica rice varieties Huanghuazhan, Meixiangzhan, and Wushansimiao, and OsHXK1-CRISPR/Cas9 lines were obtained. According to the results of a phenotypic analysis and agronomic trait statistics, the OsHXK1-CRISPR/Cas9 plants presented increased light saturation points, stomatal conductance, light tolerance, photosynthetic products, and rice yields. Moreover, transcriptome analysis showed that the expression of photosynthesis-related genes significantly increased. Taken together, our results revealed that knocking out OsHXK1 via the CRISPR/Cas9 gene-editing method could effectively lead to the cultivation of high-photosynthetic efficiency and high-yielding rice varieties. They also revealed the important roles of OsHXK1 in the regulation of rice yield and photosynthesis.

scholarly journals OsmiR396/Growth Regulating Factor modulate rice grain size through direct regulation of embryo-specific miR408

2021 ◽  
Author(s):  
Xiaofang Yang ◽  
Xiaoling Zhao ◽  
Zhengyan Dai ◽  
Feilong Ma ◽  
Xuexia Miao ◽  
...  
Keyword(s):  
Grain Size ◽  
Regulatory Networks ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Expression Patterns ◽  
Crop Improvement ◽  
Genetic Regulatory Networks ◽  
Rice Grain ◽  
Rice Varieties ◽  
Size Regulation

Abstract microRNAs (miRNAs) are promising targets for crop improvement of complex agricultural traits. Coordinated activity between/among different miRNAs may fine-tune specific developmental processes in diverse organisms. Grain size is a main factor determining rice (Oryza sativa L.) crop yield, but the network of miRNAs influencing this trait remains uncharacterized. Here we show that sequestering OsmiR396 through target mimicry (MIM396) can substantially increase grain size in several japonica and indica rice subspecies and in plants with excessive tillers and a high panicle density. Thus, OsmiR396 has a major role related to the regulation of rice grain size. The grain shape of Growth Regulating Factor8 (OsGRF8)-overexpressing transgenic plants was most similar to that of MIM396 plants, suggesting OsGRF8 is a major mediator of OsmiR396 in grain size regulation. A miRNA microarray analysis revealed changes to the expression of many miRNAs, including OsmiR408, in the MIM396 plants. Analyses of gene expression patterns and functions indicated OsmiR408 is an embryo-specific miRNA that positively regulates grain size. Silencing OsmiR408 expression (miR408KO) using CRISPR technology resulted in small grains. Moreover, we revealed the direct regulatory effects of OsGRF8 on OsMIR408 expression. A genetic analysis further showed that the large-grain phenotype of MIM396 plants could be complemented by miR408KO. Also, several hormone signaling pathways might be involved in the OsmiR396/GRF-meditated grain size regulation. Our findings suggest that genetic regulatory networks comprising various miRNAs, such as OsmiR396 and OsmiR408, may be crucial for controlling rice grain size. Furthermore, the OsmiR396/GRF module may be important for breeding new high-yielding rice varieties.

scholarly journals Variability in Nutraceutical Lipid Content of Selected Rice (Oryza sativa L. spp. indica) Germplasms

Agronomy ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 823 ◽  
Author(s):  
Bhornchai Harakotr ◽  
Kasidid Prompoh ◽  
Supakorn Boonyuen ◽  
Bhalang Suriharn ◽  
Kamol Lertrat
Keyword(s):  
Oryza Sativa ◽  
Lipid Content ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
Block Design ◽  
Added Value ◽  
Rice Varieties ◽  
Breeding Programs ◽  
Lipid Contents ◽  
Lipid Compounds

Rice (Oryza sativa L.) contains many high-value nutritional compounds, including nutraceutical lipid compounds that offer health benefits. An understanding of the genetic variability in the lipid contents of different rice germplasms is necessary to support breeding programs. The goals of this study were: i) to investigate varietal differences in levels of the nutraceutical lipid α-tocopherol, γ-oryzanol, campesterol, β-sitosterol, octacosanol, and squalene and ii) to identify clusters of rice germplasms based on their lipid contents. Eighty-three indica rice subspecies were evaluated using a randomized complete block design with three replications. Research was conducted in Thailand during the 2016 rice-growing season. Significant differences were found among genotypes across all traits. The largest variation was found for β-sitosterol, followed by campesterol, octacosanol, and α-tocopherol. Variation in squalene content was small. Four principal components were found that accounted for 93.47% of overall variability. β-sitosterol, campesterol, and squalene were the principal discriminatory constituents. No significant correlation was found between color parameters and levels of these compounds, suggesting that former are of little use as an indirect marker for selection of fat-soluble nutraceuticals. Cluster analysis sorted the germplasm into nine clusters, based on their nutraceutical lipid content. TU-010, TU-027, TU-093, and TU-244 genotypes had the highest levels, making them a potentially useful genetic resource in breeding programs for nutraceutically-improved rice. The findings of this study can support the introduction of novel rice varieties with high added-value bioactive properties.

scholarly journals Identification and Validation a Major QTL from “Sea Rice 86” Seedlings Conferred Salt Tolerance

Agronomy ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 410 ◽  
Author(s):  
Fengling Wu ◽  
Jun Yang ◽  
Diqiu Yu ◽  
Peng Xu
Keyword(s):  
Salt Tolerance ◽  
Oryza Sativa L ◽  
Bulked Segregant Analysis ◽  
Indica Rice ◽  
Chromosome 1 ◽  
Saline Stress ◽  
Salt Tolerant ◽  
Rice Varieties ◽  
Target Region ◽  
High Salt Tolerance

Saline stress severely affects rice (Oryza sativa L.) growth and development and reduces crop yield. Therefore, developing salt-tolerant and high-yielding rice using quantitative trait loci (QTLs) and linkage markers is a priority for molecular breeding. Here, the indica rice Sea Rice 86 (SR86) seedlings showed higher tolerance than ordinary rice varieties in saline soil, and a dominant effect on salinity sensitivity was demonstrated by genetic analysis. We constructed bulked segregant analysis pools using F2 populations from parents Dianjingyou 1 as the recipient and SR86 as the donor. We identified a 2.78 Mb region on chromosome 1 as the candidate region. Using simple sequence repeat markers and substitution analysis, we mapped the target region within 5.49 cM in the vicinity of markers RM8904–RM493. We speculated that this QTL, named qST1.1, might contribute significantly to the salt tolerance of SR86. The high salt tolerance of introgression lines obtained by marker assistant selection (MAS) confirmed that the qST1.1 region was associated with salinity tolerance. This newly-discovered QTL will be helpful for the analysis of the salt-tolerant mechanism of rice and breeding high-quality rice varieties using MAS.

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

Genome ◽  
1988 ◽  
Vol 30 (5) ◽  
pp. 782-792 ◽  
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.

scholarly journals Differential Expression Proteins Contribute to Race-Specific Resistant Ability in Rice (Oryza sativa L.)

Plants ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 29 ◽  
Author(s):  
Shiwei Ma ◽  
Shoukai Lin ◽  
Menglin Wang ◽  
Yang Zou ◽  
Huan Tao ◽  
...  
Keyword(s):  
Magnaporthe Grisea ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Differentially Expressed Proteins ◽  
Near Isogenic Lines ◽  
Rice Varieties ◽  
Global Food Security ◽  
Rice Yields ◽  
And Function ◽  
Global Food

Rice blast, caused by the fungus, Magnaporthe grisea (M. grisea), lead to the decrease of rice yields widely and destructively, threatening global food security. Although many resistant genes had been isolated and identified in various rice varieties, it is still not enough to clearly understand the mechanism of race-specific resistant ability in rice, especially on the protein level. In this research, proteomic methods were employed to analyze the differentially expressed proteins (DEPs) in susceptible rice variety CO39 and its two near isogenic lines (NILs), CN-4a and CN-4b, in response to the infection of two isolates with different pathogenicity, GUY11 and 81278ZB15. A total of 50 DEPs with more than 1.5-fold reproducible change were identified. At 24 and 48 hpi of GUY11, 32 and 16 proteins in CN-4b were up-regulated, among which 16 and five were paralleled with the expression of their corresponding RNAs. Moreover, 13 of 50 DEPs were reported to be induced by M. grisea in previous publications. Considering the phenotypes of the three tested rice varieties, we found that 21 and 23 up-regulated proteins were responsible for the rice resistant ability to the two different blast isolates, 81278ZB15 and GUY11, respectively. Two distinct branches corresponding to GUY11 and 81278ZB15 were observed in the expression and function of the module cluster of DEPs, illuminating that the DEPs could be responsible for race-specific resistant ability in rice. In other words, DEPs in rice are involved in different patterns and functional modules’ response to different pathogenic race infection, inducing race-specific resistant ability in rice.

scholarly journals Optimization of in vitro regeneration protocol for a popular Indica rice (Oryza sativa L. cv Swarna)

2016 ◽  
Vol 5 (08) ◽  
pp. 1395 ◽  
Author(s):  
Vijaya Naresh Juturu ◽  
Gopala Krishna Mekala ◽  
Mallikarjuna Garladinne ◽  
Puli Chandra Obul Reddy ◽  
Akila Chandra Sekhar*
Keyword(s):  
Callus Induction ◽  
Oryza Sativa L ◽  
Indica Rice ◽  
In Vitro Regeneration ◽  
Regeneration System ◽  
Embryogenic Calli ◽  
Rice Varieties ◽  
Regenerated Plants ◽  
Rooting Medium

Though regeneration system in rice has been very well established compare to other crop plants, the fact remains that, most of the indica rice varieties are still recalcitrant for regeneration and genetic transformation. Therefore, refinement of tissue culture protocol for generation of embryogenic calli and regeneration of the fertile plants from a single cell should be a pre requisite event for development of transgenic plants. Here, in this study we reported high frequency robust regeneration protocols for a popular Indica cultivar Swarna.Mature seeds were used as initial material as explants. Highest callus induction % was observed in MSCIMP medium containing 2.0 mg-1 2,4, D + 0.5 mg-1 Kn as phytohormonal combinations. In addition, maximum regeneration was observed in 2.0 mg-l KN + 0.5 mg-l NAA. Regenerated plants were shifted to rooting medium followed by polyhouse for hardening. The callus induction and regeneration reported in this study were well suited for transformation agronomical important genes or functional genomics studies.

scholarly journals Optimizing Agrobacterium-Mediated Transformation and CRISPR-Cas9 Gene Editing in the tropical japonica Rice Variety Presidio

2021 ◽  
Vol 22 (20) ◽  
pp. 10909
Author(s):  
Marco Molina-Risco ◽  
Oneida Ibarra ◽  
Mayra Faion-Molina ◽  
Backki Kim ◽  
Endang M. Septiningsih ◽  
...  
Keyword(s):  
Gene Editing ◽  
Oryza Sativa L ◽  
Rice Variety ◽  
Crop Improvement ◽  
Japonica Rice ◽  
Rice Varieties ◽  
Tropical Japonica ◽  
Regenerated Plants ◽  
Efficient Gene ◽  
Japonica Rice Variety

Bottlenecks in plant transformation and regeneration have slowed progress in applying CRISPR/Cas-based genome editing for crop improvement. Rice (Oryza sativa L.) has highly efficient temperate japonica transformation protocols, along with reasonably efficient indica protocols using immature embryos. However, rapid and efficient protocols are not available for transformation and regeneration in tropical japonica varieties, even though they represent the majority of rice production in the U.S. and South America. The current study has optimized a protocol using callus induction from mature seeds with both Agrobacterium-mediated and biolistic transformation of the high-yielding U.S. tropical japonica cultivar Presidio. Gene editing efficiency was tested by evaluating knockout mutations in the phytoene desaturase (PDS) and young seedling albino (YSA) genes, which provide a visible phenotype at the seedling stage for successful knockouts. Using the optimized protocol, transformation of 648 explants with particle bombardment and 532 explants with Agrobacterium led to a 33% regeneration efficiency. The YSA targets had ambiguous phenotypes, but 60% of regenerated plants for PDS showed an albino phenotype. Sanger sequencing of edited progeny showed a number of insertions, deletions, and substitutions at the gRNA target sites. These results pave the way for more efficient gene editing of tropical japonica rice varieties.

Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing

Genome ◽  
2016 ◽  
Vol 59 (3) ◽  
pp. 197-207 ◽  
Author(s):  
Chong-Yun Fu ◽  
Wu-Ge Liu ◽  
Di-Lin Liu ◽  
Ji-Hua Li ◽  
Man-Shan Zhu ◽  
...  
Keyword(s):  
Oryza Sativa L ◽  
Indica Rice ◽  
Copy Number Variations ◽  
Hybrid Vigor ◽  
Dna Polymorphisms ◽  
Whole Genome ◽  
Rice Varieties ◽  
Sequencing Technologies ◽  
Hybrid Weakness ◽  
Sound Foundation

Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica ‘Nipponbare’) reference genome. A total of 2 758 740 polymorphic sites including 2 408 845 SNPs and 349 895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961 791 SNPs and 46 640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.

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