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 CRISPR/Cas mediated genome-editing for rice improvement

2021 ◽  
Vol 58 (Special) ◽  
pp. 89-102
Author(s):  
BN Devanna ◽  
Kutubuddin A Molla ◽  
C Parameswaran ◽  
Jawahar Lal Katara ◽  
A Kumar ◽  
...  
Keyword(s):  
Genome Editing ◽  
Nutritional Value ◽  
Abiotic Stress Tolerance ◽  
Rice Production ◽  
Biotic And Abiotic Stress ◽  
Important Food ◽  
Biotic And Abiotic Stresses ◽  
Rice Varieties ◽  
Rice Improvement ◽  
Global Population

Rice is one of the important food crops, feeding more than 50% of the global population. The climate change is adversely affecting the rice production across the rice growing regions. The major challenges posing threat to the world rice production are various biotic and abiotic stresses. Rice is grown and consumed largely by the developing countries, and most part of the population in these regions are undernourished with unbalanced and comparatively low nutritional food. Therefore, it is of utmost importance to develop rice varieties for higher nutritional value with attributes for better adaptability to various stresses. In the present review, we have discussed about the different CRISPR/Cas genome editing tools, and their applications for biotic and abiotic stress tolerance, yield and also for grain and nutritional quality improvement in rice.

scholarly journals Efficacy of Irrigation Interval after Anthesis on Grain Quality, Alkali Digestion, and Gel Consistency of Rice

Agriculture ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 325
Author(s):  
Ramin Rayee ◽  
Tran Dang Xuan ◽  
Tran Dang Khanh ◽  
Hoang-Dung Tran ◽  
Kifayatullah Kakar
Keyword(s):  
Protein Content ◽  
Grain Quality ◽  
Cooking Quality ◽  
Amylose Content ◽  
Rice Grain ◽  
Gelatinization Temperature ◽  
Rice Varieties ◽  
Irrigation Interval ◽  
Gel Consistency ◽  
Alkali Digestion

The management of amylose and protein contents and cooking quality are the main challenges in rice macronutrients and quality improvement. This experiment was conducted to examine the rice grain quality, alkali digestion, and gel consistency responses to irrigation interval after anthesis. Three rice varieties (K1, K3, and K4) were subjected to different irrigation intervals (1, 2, and 3 d) after anthesis. The findings of this study showed that the protein content was markedly increased from 6.53–6.63% to 9.93–10.16%, whilst the amylose content was decreased significantly from 22.00–22.43% to 16.33–17.56% under stressed treatments at irrigation intervals, whilst the quantity of fatty acids was not affected. The 3-d irrigation interval recorded the highest protein content but the lowest amylose value. In addition, this treatment shows lower gelatinization temperature, but it is negatively associated with hard gel consistency under irrigation interval. This study highlights that the water management following a 3-d irrigation interval from anthesis is a useful and simple treatment to improve rice nutrients and grain cooking 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.

Mutation breeding in rice for sustainable crop production and food security in India.

2021 ◽  
pp. 83-99
Author(s):  
Vikash Kumar ◽  
Anjali Chauhan ◽  
Avinash Kumar Shinde ◽  
Ramesh L. Kunkerkar ◽  
Deepak Sharma ◽  
...  
Keyword(s):  
Climate Change ◽  
Mutation Breeding ◽  
Crop Diversity ◽  
World Population ◽  
Rice Varieties ◽  
Pests And Diseases ◽  
Crop Varieties ◽  
The World ◽  
Traditional Landraces ◽  
Rice Improvement

Abstract With the inevitable risk posed by global climate change affecting crop yield and the ever-increasing demands of agricultural produce, crop improvement techniques need to be more precise in developing smart crop varieties. The rice crop, a staple food for the majority of the world population, has a significant role to play in alleviating the global hunger problem. With the world population burgeoning at an unprecedented rate, limited fertile land resources, climate change, emerging new races of pests and diseases and consumer preferences for quality attributes, it is imperative to increase crop diversity, and this requires better selection efficiency addressing the challenges of future rice production. Mutation breeding is a fundamental and very successful tool helping to increase crop diversity and allowing plant breeders to exercise their skill in developing desirable crop varieties. The induction of mutations has been used to enhance yield, improve nutritional quality and widen the adaptability of the world's most important crops such as wheat, rice, pulses, millets and oilseeds. India is considered to be one of the primary centres of origin of crop species with the concomitant very high genetic diversity in traditional landraces for different agronomic traits of economic importance. Plant architecture, such as plant height, branching habit (tiller number), leaf shape and patterns, floral and grain traits and quality traits such as aroma, amylose content and cooking quality are of tremendous importance for rice improvement programmes. Traditional landraces of rice have premium grain quality, fetching a premium price, but their cultivation is being marginalized due to their tall stature, proneness to lodging, late maturity and poor yield. Mutation breeding technology has been successfully implemented in rice improvement programmes, which have resulted in the improvement of aromatic rice varieties, such as 'Pusa Basmati 1', 'Dubraj and Jawaphool'. Two high-yielding mutant rice varieties, TCDM-1 ('Trombay Chhattisgarh Dubraj Mutant-1') and TKR Kolam ('Trombay Karjat Rice Kolam'), have been released for cultivation in Chhattisgarh and the Konkan region of Maharashtra. Both these varieties possess dwarf plant stature (110 cm), medium maturity (130 days), premium grain quality and resistance to major pests and diseases. Improvement of other traditional rice varieties is underway which will bring these varieties back into cultivation and help in improving the tribal and marginal farmers' economy.

scholarly journals Morphological Observation and Correlation of Growth and Yield Characteristics with Grain Quality and Antioxidant Activities in Exotic Rice Varieties of Afghanistan

Agriculture ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 167 ◽  
Author(s):  
Kifayatullah Kakar ◽  
Tran Dang Xuan ◽  
Saidajan Abdiani ◽  
Imran Khan Wafa ◽  
Zubair Noori ◽  
...  
Keyword(s):  
Physicochemical Properties ◽  
Grain Yield ◽  
Grain Quality ◽  
Antioxidant Activities ◽  
Growth And Yield ◽  
Yield Potential ◽  
Morphological Observation ◽  
Rice Grain ◽  
Rice Varieties ◽  
Panicle Number

Rice is an important staple food for Afghans. Its production has been increased, and attention is needed to improve grain quality. Experiments were conducted to evaluate the growth, yield, physicochemical properties, antioxidant activity, and morphological structures of four exotic rice varieties widely grown in Afghanistan (Attai-1, Jalalabad-14, Shishambagh-14, and Zodrass). Antioxidant activities, including 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzthiazoline-6-sulphonic acid) (ABTS), of rice grain were determined. A scanning electron microscopic observation was conducted on the cross-cut section of dehulled rice grains. The results showed a wide variation among four rice varieties for growth, grain yield, physicochemical properties, antioxidant activities, and morphology. Tiller and panicle number per hill, 1000-grain weight, grain yield, and antioxidant activities were found to be highest in Jalalabad-14. Attai-1 showed lower amylose, protein, and lipid contents with a high number of perfect grains, consequently enhanced taste point (score of quality). Grain yield, protein, and amylose contents showed a negative correlation with antioxidant activities. Accumulated structures in Attai-1, Shishambagh-14, and Zodrass were normal; however, Jalalabad-14 increased protein bodies and its traces in the amyloplasts. Information on yield potential, grain quality, and nutritional value of these exotic rice varieties may useful for sustainable food provision and nutritional improvement of rice in Afghanistan.

scholarly journals Advanced Breeding Strategies and Future Perspectives of Salinity Tolerance in Rice

Agronomy ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1631
Author(s):  
Md Azadul Haque ◽  
Mohd Y. Rafii ◽  
Martini Mohammad Yusoff ◽  
Nusaibah Syd Ali ◽  
Oladosu Yusuff ◽  
...  
Keyword(s):  
Genome Editing ◽  
Salinity Stress ◽  
Salinity Tolerance ◽  
High Salinity ◽  
Abiotic Factors ◽  
Rice Production ◽  
Salt Tolerant ◽  
Rice Varieties ◽  
Rice Plants ◽  
Breeding Techniques

Rice, generally classified as a typical glycophyte, often faces abiotic stresses such as excessive drought, high salinity, prolonged submergence, cold, and temperature, which significantly affects growth, development, and ultimately, grain yield. Among these negative impacts of abiotic factors in rice production, salinity stress is a major constraint, followed by drought. There is considerable research on the use of marker-assisted selection (MAS), genome editing techniques, and transgenic studies that have profoundly improved the present-day rice breeders’ toolboxes for developing salt-tolerant varieties. Salinity stresses significantly affect rice plants during seedling and reproductive stages. Hence, greater understanding and manipulation of genetic architecture in developing salt-tolerant rice varieties will significantly impact sustainable rice production. Rice plants’ susceptibility or tolerance to high salinity has been reported to be the result of coordinated actions of multiple stress-responsive quantitative trait loci (QTLs)/genes. This paper reviews recent literature, updating the effects of salinity stress on rice plants and germplasm collections and screening for salinity tolerance by different breeding techniques. Mapping and identification of QTLs salt tolerance genes are illuminated. The present review updates recent breeding for improvement in rice tolerance to salinity stress and how state-of-the-art tools such as MAS or genetic engineering and genome editing techniques, including mutagenesis and conventional breeding techniques, can assist in transferring salt-tolerant QTLs genes into elite rice genotypes, accelerating breeding of salt-resistant rice cultivars.

Identifying the Grain Chalkiness Gene Using Molecular Marker Techniques in Rice (Oryza sativa L.)

2017 ◽  
Vol 63 ◽  
pp. 18-26
Author(s):  
Nguyen Thi Lang ◽  
Phan Ho Truc Giang ◽  
Pham Thi Thu Ha ◽  
Tran Bao Toan ◽  
Truong Anh Phuong ◽  
...  
Keyword(s):  
Ssr Marker ◽  
High Efficiency ◽  
Rice Grain ◽  
Key Factors ◽  
Amplification Product ◽  
Rice Varieties ◽  
Indel Markers ◽  
Marker Combination ◽  
Grain Chalkiness

Chalkiness is a major constraint on rice production because it is one of the key factors determining grain quality (appearance, processing, milling, storing, eating, and cooking quality) and price. In this study, we conducted grain chalkiness gene identification using co-dominant insertion/deletion (INDEL) markers and SSR marker combination on 50 different varieties. The application results in 7 InDel markers and SSR marker on chromosome 7 were recorded. Three primers, InDel 5, InDel 14 and RM21938, associated with grain chalkiness. For the InDel 5 primer, the amplification product was 100%. Use of primer InDel 5 in detection and evaluation of genotype to the chalkiness trait of rice grain on 50 rice varieties indicated the suitability level with phenotypic evaluation was 86% and the unsuitability level was 14%. For the InDel 14 primer, the amplification products were 100%. The suitability with phenotypic assessment was 84% and the unsuitability was 16%. For the RM21938 primer, the amplification product was 94%. The suitability with phenotypic assessment was 76% and the unsuitability was 24%. Thirteen of the selected varieties had grain chalkiness gene both InDel 5, InDel 14 and RM21938. Total 13 varieties were detected from InDel 5, InDel 14 and RM12938 primer combinations also showed high efficiency of the InDel technique in identifying chalkiness gene in rice grain. A cluster analysis was performed and a dendrogram was constructed which evinced the nature of phylogenetic classification among the genotypes of the varieties. These markers could be used for developing quality of rice in breeding program.

scholarly journals Rice grain quality and starch digestibility- desired traits for evaluating rice varieties

2021 ◽  
Vol 58 (Special) ◽  
pp. 208-220
Author(s):  
Torit Baran Bagchi ◽  
Sarangadhar Nayak ◽  
Monalisha Biswal ◽  
Soumya Kumar Sahoo ◽  
Awadhesh Kumar
Keyword(s):  
Grain Quality ◽  
Amylose Content ◽  
Energy Requirement ◽  
The Body ◽  
Starch Digestibility ◽  
Rice Grain ◽  
Asian Countries ◽  
Rice Varieties ◽  
Physico Chemical ◽  
Sensory Qualities

Rice grain quality is the most important factor for evaluation of a variety as well as millers, consumers and farmer's point of view. It includes physico-chemical, nutritional and sensory qualities. The consumers of India and other south east Asian countries prefer medium to high amylose content (AC) rice due to their non-stickiness properties of boiled rice but in many Asian countries, waxy rice (having low AC) mainly preferred. The colour of rice grain may be white, purple, red and black; which are mainly associated with pericarp or bran layers of the whole grain. The bran contains most of the phytochemicals like oils, antioxidants, minerals, proteins, vitamins and crude fibers in higher concentration than white endosperm. Pigmented rice is generally rich in nutritional compounds as compared to white one but those are unpopular among the farmers because of many undesirable physiological and agronomic characteristics. Sensory qualities like colour, texture, pasting properties, aroma are essential for consumers as per their preference and acceptance. As rice grain is mainly composed by starch, hydrolyzed by digestive enzymes and converted into glucose which is the major energy source for various metabolic functions. After fulfilling the body energy requirement, extra calories from starch are stored as fats or glycogen for later use. Therefore, overeating food containing rice with sedentary lifestyle potentially leads to some health issues, such as type-II diabetes, obesity and colon diseases in long term particularly in Asian countries. Various biochemical factors affect the starch digestibility and Glycemic index (GI) of a food or its products. These factors are resistant starch, AC and phytic acid which lowers the starch digestibility by various ways and have been negatively correlated with GI value. Now-a-days quality assessment of rice grain in terms of its nutritional as well as physico-chemical parameters is gaining prime importance gradually.

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.

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