scholarly journals Applications of the CRISPR/Cas9 System for Rice Grain Quality Improvement: Perspectives and Opportunities

2019 ◽  
Vol 20 (4) ◽  
pp. 888 ◽  
Author(s):  
Sajid Fiaz ◽  
Shakeel Ahmad ◽  
Mehmood Noor ◽  
Xiukang Wang ◽  
Afifa Younas ◽  
...  
Keyword(s):  
Quality Improvement ◽  
Genome Editing ◽  
Reverse Genetics ◽  
Grain Quality ◽  
Rice Genome ◽  
Targeted Mutagenesis ◽  
High Yield ◽  
Genomic Alteration ◽  
Rice Grain ◽  
The Past

Grain quality improvement is a key target for rice breeders, along with yield. It is a multigenic trait that is simultaneously influenced by many factors. Over the past few decades, breeding for semi-dwarf cultivars and hybrids has significantly contributed to the attainment of high yield demands but reduced grain quality, which thus needs the attention of researchers. The availability of rice genome sequences has facilitated gene discovery, targeted mutagenesis, and revealed functional aspects of rice grain quality attributes. Some success has been achieved through the application of molecular markers to understand the genetic mechanisms for better rice grain quality; however, researchers have opted for novel strategies. Genomic alteration employing genome editing technologies (GETs) like clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) for reverse genetics has opened new avenues of research in the life sciences, including for rice grain quality improvement. Currently, CRISPR/Cas9 technology is widely used by researchers for genome editing to achieve the desired biological objectives, because of its simple targeting. Over the past few years many genes that are related to various aspects of rice grain quality have been successfully edited via CRISPR/Cas9 technology. Interestingly, studies on functional genomics at larger scales have become possible because of the availability of GETs. In this review, we discuss the progress made in rice by employing the CRISPR/Cas9 editing system and its eminent applications. We also elaborate possible future avenues of research with this system, and our understanding regarding the biological mechanism of rice grain quality improvement.

scholarly journals Applications and Potential of Genome-Editing Systems in Rice Improvement: Current and Future Perspectives

Agronomy ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1359
Author(s):  
Javaria Tabassum ◽  
Shakeel Ahmad ◽  
Babar Hussain ◽  
Amos Musyoki Mawia ◽  
Aqib Zeb ◽  
...  
Keyword(s):  
Genome Editing ◽  
Crop Production ◽  
Grain Quality ◽  
High Efficiency ◽  
Abiotic Stress Tolerance ◽  
Mutation Breeding ◽  
Rice Grain ◽  
Rice Varieties ◽  
Rice Improvement ◽  
Breeding Techniques

Food crop production and quality are two major attributes that ensure food security. Rice is one of the major sources of food that feeds half of the world’s population. Therefore, to feed about 10 billion people by 2050, there is a need to develop high-yielding grain quality of rice varieties, with greater pace. Although conventional and mutation breeding techniques have played a significant role in the development of desired varieties in the past, due to certain limitations, these techniques cannot fulfill the high demands for food in the present era. However, rice production and grain quality can be improved by employing new breeding techniques, such as genome editing tools (GETs), with high efficiency. These tools, including clustered, regularly interspaced short palindromic repeats (CRISPR) systems, have revolutionized rice breeding. The protocol of CRISPR/Cas9 systems technology, and its variants, are the most reliable and efficient, and have been established in rice crops. New GETs, such as CRISPR/Cas12, and base editors, have also been applied to rice to improve it. Recombinases and prime editing tools have the potential to make edits more precisely and efficiently. Briefly, in this review, we discuss advancements made in CRISPR systems, base and prime editors, and their applications, to improve rice grain yield, abiotic stress tolerance, grain quality, disease and herbicide resistance, in addition to the regulatory aspects and risks associated with genetically modified rice plants. We also focus on the limitations and future prospects of GETs to improve rice grain quality.

scholarly journals Substitution Mapping of Two Closely Linked QTLs Controlling Grain Chalkiness and Grain Shape on Rice Chromosome 8

2021 ◽  
Author(s):  
Weifeng Yang ◽  
Liang Xiong ◽  
Jiayan Liang ◽  
Qingwen Hao ◽  
Xin Luan ◽  
...  
Keyword(s):  
Grain Quality ◽  
Grain Shape ◽  
Rice Chromosome ◽  
Chromosome 8 ◽  
High Yield ◽  
Rice Grain ◽  
Rice Varieties ◽  
Substitution Mapping ◽  
Grain Width ◽  
Grain Chalkiness

Abstract Background: Rice varieties are required to have high yield and good grain quality. Grain chalkiness and grain shape are two important traits of rice grain quality. Low chalkiness slender grains are preferred by most rice consumers. Here, we dissected two closely linked quantitative trait loci (QTLs) controlling grain chalkiness and grain shape on rice chromosome 8 by substitution mapping. Results: Two closely linked QTLs controlling grain chalkiness and grain shape were identified using single-segment substitution lines (SSSLs). The two QTLs were then dissected on rice chromosome 8 by secondary substitution mapping. qPGC8.1 was located in an interval of 1382.6 kb and qPGC8.2 was mapped in a 2057.1 kb region. The maximum distance of the two QTLs was 4.37 Mb and the space distance of two QTL intervals was 0.72 Mb. qPGC8.1 controlled grain chalkiness and grain width. qPGC8.2 was responsible for grain chalkiness and for grain length and grain width. The additive effects of qPGC8.1 and qPGC8.2 on grain chalkiness were not affected by heat stress. Conclusions: Two closely linked QTLs qPGC8.1 and qPGC8.2 were dissected on rice chromosome 8. They controlled the phenotypes of grain chalkiness and grain shape. The two QTLs were insensitive to high temperature.

scholarly journals Targeting Cis-Regulatory Elements for Rice Grain Quality Improvement

2021 ◽  
Vol 12 ◽  
Author(s):  
Yu Ding ◽  
Jiannan Zhu ◽  
Dongsheng Zhao ◽  
Qiaoquan Liu ◽  
Qingqing Yang ◽  
...  
Keyword(s):  
Genome Editing ◽  
Grain Quality ◽  
Target Genes ◽  
Gene Expression Regulation ◽  
Gene Knockout ◽  
Critical Role ◽  
Allelic Diversity ◽  
Complex Trait ◽  
Regulatory Elements ◽  
Rice Grain

Rice is the most important source of food worldwide, providing energy, and nutrition for more than half of the population worldwide. Rice grain quality is a complex trait that is affected by several factors, such as the genotype and environment, and is a major target for rice breeders. Cis-regulatory elements (CREs) are the regions of non-coding DNA, which play a critical role in gene expression regulation. Compared with gene knockout, CRE modifications can fine-tune the expression levels of target genes. Genome editing has provided opportunities to modify the genomes of organisms in a precise and predictable way. Recently, the promoter modifications of coding genes using genome editing technologies in plant improvement have become popular. In this study, we reviewed the results of recent studies on the identification, characterization, and application of CREs involved in rice grain quality. We proposed CREs as preferred potential targets to create allelic diversity and to improve quality traits via genome editing strategies in rice. We also discussed potential challenges and experimental considerations for the improvement in grain quality in crop plants.

scholarly journals Heat-shock inducible CRISPR/Cas9 system generates heritable mutations in rice

2018 ◽  
Author(s):  
Soumen Nandy ◽  
Bhuvan Pathak ◽  
Shan Zhao ◽  
Vibha Srivastava
Keyword(s):  
Heat Shock ◽  
Genome Editing ◽  
Rice Genome ◽  
Gene Promoter ◽  
Targeted Mutagenesis ◽  
High Rate ◽  
Induced Mutations ◽  
Promising Tool ◽  
Before And After ◽  
Transgenic Lines

SummaryTransient expression of CRISPR/Cas9 is an effective approach for limiting its activities and improving its precision in genome editing. Here, we describe the heat-shock inducible CRISPR/Cas9 system for controlled genome editing, and demonstrate its efficiency in the model crop, rice. Using a soybean heat-shock protein gene promoter and the rice U3 promoter to express Cas9 and sgRNA, respectively, we developed the heat-shock (HS) inducible CRISPR/Cas9 system, and tested its efficacy in targeted mutagenesis. Two loci were targeted by transforming rice with HS-CRISPR/Cas9 vectors, and the presence of targeted mutations was determined before and after the HS treatment. We found only a low rate of targeted mutagenesis before HS, but an increased rate of mutagenesis after HS treatment among the transgenic lines. Specifically, only ∼11% of transformants showed characteristic insertions-deletions at the ambient room temperature, but a higher percentage (∼45%) of callus lines developed mutations after a few days of HS treatment. Analysis of regenerated plants harboring HS-CRISPR/Cas9 revealed that targeted mutagenesis was suppressed in the plants but induced by HS, which was detectable by Sanger sequencing after several weeks of HS treatments. Most importantly, the HS-induced mutations were transmitted to the progeny at a high rate, generating monoallelic and biallelic mutant lines that independently segregated from Cas9. Taken together, this work shows that HS-CRISPR/Cas9 is a controlled and reasonably efficient platform for genome editing, and therefore, a promising tool for limiting genome-wide off-target effects and improving the precision of genome editing.Significance StatementA method for the temporal control on gene editing based on the use of heat-shock induced expression of CRISPR/Cas9 is described, which was efficient in producing heritable mutations in the rice genome. We assume this method will be useful for targeting essential genes and improving the precision of CRISPR/Cas9.

scholarly journals The Role of Post Harvest Handling on Rice Quality in Indonesia

2016 ◽  
Vol 30 (1) ◽  
pp. 1 ◽  
Author(s):  
Dewa Ketut Sadra Swastika
Keyword(s):  
Quality Improvement ◽  
Grain Quality ◽  
Rice Grain ◽  
Milled Rice ◽  
Rice Quality ◽  
Post Harvest ◽  
National Welfare ◽  
Rice Milling ◽  
End Use ◽  
Improved Technology

<p><strong>Indonesian</strong><br />Beras berfungsi sebagai makanan pokok dan bahan baku berbagai produk pangan lainnya yang memerlukan kualitas tertentu. Perbaikan kualitas beras tidak memberikan insentif bagi petani dan pedagang di Indonesia, khususnya melalui perontokan, pengeringan, dan penggilingan. Di pihak lain, sebagian besra negara-negara penghasil padi member perhatian lebih pada peningkatan kualitas beras. Kualitas beras meliputi sifat-sifat fisik yang mempengaruhi penampilan maupun sifat-sifat kimia yang menentukan kualitas jika dimasak. Proses produksi, pasca panen, penggilingan dan pemasaran mempengaruhi kualitas beras. Peningkatan kualitas beras akan menguntungkan produsen maupun konsumen beras. Agar pedagang beras bersedia melakukan pasca panen secara baik diperlukan insentif harga yang memadai untuk gabah kering giling dan beras, misalnya harga pembelian oleh pemerintah. Teknologi pasca panen juga harus diperbaiki agar kualitas beras yang dihasilkan menjadi lebih baik.</p><p> </p><p><strong>English</strong><br />Aside from being a staple food, rice also has many uses, especially for food industry. Various rice uses require quality evaluation according to the requirement for a specific end use. Whether rice is acceptable for an intended use is determined by quality testing based on a fixed set of criteria. In Indonesia, the main problem of rice quality improvement is the absence of incentive for farmers and traders to improve rice quality, especially through proper threshing, drying, and milling. On the other hands, most rice producing countries are currently paying more attention to the development of post harvest handling and processing to ensure higher rice grain quality. Rice quality is multidimensional. It includes both physical characteristics that influence appearance, and chemical characteristics that determine cooking quality. Thus, rice grain quality is determined by: production process, post harvest handling, milling and marketing techniques. Among rice post harvest handling, proper threshing, drying, milling, and storage are the key points to produce good quality rice. Rice quality improvement is expected to increase national welfare by raising the value of rice to either consumers or producers. In order to encourage rice businessmen to do the proper post harvest handling, there should be attractive price incentives policy for selling dried paddy (GKG) and milled rice (beras). Price incentive could be in the form of government purchasing price (HPP). In other words, there should be an attractive incentive to do a proper threshing, drying and rice milling by using improved technology in order to produce high quality rice.</p>

scholarly journals Substitution Mapping of Two Closely Linked QTLs on Chromosome 8 Controlling Grain Chalkiness in Rice

Rice ◽  
2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Weifeng Yang ◽  
Liang Xiong ◽  
Jiayan Liang ◽  
Qingwen Hao ◽  
Xin Luan ◽  
...  
Keyword(s):  
Grain Quality ◽  
Grain Shape ◽  
Rice Chromosome ◽  
Chromosome 8 ◽  
High Yield ◽  
Rice Grain ◽  
Rice Varieties ◽  
Substitution Mapping ◽  
Higher Temperature ◽  
Grain Chalkiness

AbstractRice varieties are required to have high yield and good grain quality. Grain chalkiness and grain shape are two important traits of rice grain quality. Low chalkiness slender grains are preferred by most rice consumers. Here, we dissected two closely linked quantitative trait loci (QTLs) controlling grain chalkiness and grain shape on rice chromosome 8 by substitution mapping. Two closely linked QTLs controlling grain chalkiness and grain shape were identified using single-segment substitution lines (SSSLs). The two QTLs were then dissected on rice chromosome 8 by secondary substitution mapping. qPGC8.1 was located in an interval of 1382.6 kb and qPGC8.2 was mapped in a 2057.1 kb region. The maximum distance of the two QTLs was 4.37 Mb and the space distance of two QTL intervals was 0.72 Mb. qPGC8.1 controlled grain chalkiness and grain width. qPGC8.2 was responsible for grain chalkiness, grain length and width. The additive effects of qPGC8.1 and qPGC8.2 on grain chalkiness were not affected by higher temperature. Two closely linked QTLs qPGC8.1 and qPGC8.2 were dissected on rice chromosome 8. They controlled the phenotypes of grain chalkiness and grain shape. The two QTLs were insensitive to higher temperature.

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