Special Issue "Rice Genetics: Trends and Challenges for the Future Crops Production"

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: 15 December 2021.

Special Issue Editors

Prof. Dr. Kwon-Kyoo Kang
E-Mail Website
Guest Editor
Division of Horticultural Biotechnology, Hankyung National University, Anseong 17579, Korea
Interests: functional analysis of genes by CRISPR/Cas9; functional genomics; MABc (marker-assisted backcross); transcriptomics; plant biotechnology; molecular breeding in plants
Special Issues and Collections in MDPI journals
Prof. Dr. Yong-Gu Cho
E-Mail Website
Guest Editor
Department of Crop Science, College of Agriculture, Life and Environment Sciences, Chungbuk National University, 1 Chungdae-ro, Seowon-gu, Chongju 28644, Korea
Interests: marker-assisted breeding (MAS); plant breeding by CRISPR/Cas9; functional genomics; GWAS; biotic and abiotic tolerance; transcriptomics; functional analysis of genes; plant biotechnology; molecular breeding in rice
Special Issues and Collections in MDPI journals

Special Issue Information

Dear Colleagues, 

Future food security will require reducing crop losses due to environmental factors, including climate change, as well as transformative advances that provide major gains in yields. More recent genomic technologies have expedited breeding and trait development for increased environmental resilience and productivity. Complementary to breeding approaches, advances in the spatial and temporal regulation of engineered genes and pathways are increasingly accelerated by the targeted editing of genomes using CRISPR?Cas technology. A greater understanding of plant mechanisms that increase yields in variable environments is essential to drive the necessary gains in crop improvement, which can be fuelled by genetic diversity and implemented by genome-scale breeding, finely-tuned gene engineering and more precise agronomic management practices. This Special Issue will provide a platform to present and discuss related topics of research progress and trends in the genetics, genomics, and breeding of rice.

Prof. Dr. Kwon-Kyoo Kang
Prof. Dr. Yong-Gu Cho
Guest Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Functional genomics
  • Nutrient acquisition and use efficiency
  • Genome editing
  • Metabolic regulation
  • Biotic and abiotic resistance
  • Grain quality
  • Molecular breeding
  • Transcription factors

Published Papers (6 papers)

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Research

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Article
Quantitative Trait Locus Analysis of Microscopic Phenotypic Characteristic Data Obtained Using Optical Coherence Tomography Imaging of Rice Bacterial Leaf Blight Infection in the Field
Agronomy 2021, 11(8), 1630; https://doi.org/10.3390/agronomy11081630 - 16 Aug 2021
Viewed by 407
Abstract
Rapid climate change has increased the incidence of various pests and diseases, and these threaten global food security. In particular, BLB (bacterial leaf blight) is caused by Xoo (Xanthomonas oryzae pv. oryzae) and its main characteristic is that the rice suddenly [...] Read more.
Rapid climate change has increased the incidence of various pests and diseases, and these threaten global food security. In particular, BLB (bacterial leaf blight) is caused by Xoo (Xanthomonas oryzae pv. oryzae) and its main characteristic is that the rice suddenly dries and withers. Recently, omics have been effectively used in agriculture. In particular, it is a key technology that can accurately diagnose diseases in the field. Until now, QTL (quantitative trait loci) mapping has been analyzed using only subjective phenotypic data by experts. However, in this study, diseases were accurately diagnosed using OCT (optical coherence tomography), and QTL mapping was performed using leaf thickness and leaf angles after Xoo inoculation. After Xoo inoculation of a 120 Cheongcheong/Nagdong double haploid (CNDH) population, QTL mapping was performed using the changing leaf angle, and OsWRKY34q1 was detected in RM811-RM14323 of chromosome 1. OsWRKY34q1 always had a higher expression level in the BLB-resistant population than in the susceptible population after Xoo inoculation. OsWRKY34q1 belongs to the WRKY family of genes. OsWRKY34q1 could be effectively used to develop BLB-resistant rice varieties in response to the current era of unpredictable climate change. Full article
(This article belongs to the Special Issue Rice Genetics: Trends and Challenges for the Future Crops Production)
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Article
The Role of OsWRKY Genes in Rice When Faced with Single and Multiple Abiotic Stresses
Agronomy 2021, 11(7), 1301; https://doi.org/10.3390/agronomy11071301 - 26 Jun 2021
Cited by 1 | Viewed by 435
Abstract
The WRKY genes are one of the largest families of transcription factors (TFs) and play a crucial role in certain processes in plants including stress signaling, regulation of transcriptional reprogramming associated with stress responses, and other regulatory networks. This study aims to investigate [...] Read more.
The WRKY genes are one of the largest families of transcription factors (TFs) and play a crucial role in certain processes in plants including stress signaling, regulation of transcriptional reprogramming associated with stress responses, and other regulatory networks. This study aims to investigate the WRKY gene family in the C3 model plant, Oryza sativa L., using a genome-wide in silico expression analysis. Firstly, 104 WRKY TF family members were identified, and then their molecular properties and expression signatures were analyzed systematically. In silico spatio-temporal and hormonal expression profiling revealed the roles of OsWRKY genes and their dynamism in diverse developmental tissues and hormones, respectively. Comparative mapping between OsWRKY genes and their synteny with C4 panicoid genomes showed the evolutionary insights of the WRKY TF family. Interactions of OsWRKY coding gene sequences represented the complexity of abiotic stress (AbS) and their molecular cross-talks. The expression signature of 26 novel candidate genes in response to stresses exhibited the putative involvement of individual and combined AbS (CAbS) responses. These novel findings unravel the in-depth insights into OsWRKY TF genes and delineate the plant developmental metabolisms and their functional regulations in individual and CAbS conditions. Full article
(This article belongs to the Special Issue Rice Genetics: Trends and Challenges for the Future Crops Production)
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Article
Introgression of qDTY1.1 Governing Reproductive Stage Drought Tolerance into an Elite Basmati Rice Variety “Pusa Basmati 1” through Marker Assisted Backcross Breeding
Agronomy 2021, 11(2), 202; https://doi.org/10.3390/agronomy11020202 - 21 Jan 2021
Cited by 4 | Viewed by 918
Abstract
Drought stress at the reproductive stage in rice is one of the most important cause for yield reduction, affecting both productivity and quality. All Basmati rice varieties, including the popular cultivar “Pusa Basmati 1 (PB1)” is highly sensitive to reproductive stage drought stress [...] Read more.
Drought stress at the reproductive stage in rice is one of the most important cause for yield reduction, affecting both productivity and quality. All Basmati rice varieties, including the popular cultivar “Pusa Basmati 1 (PB1)” is highly sensitive to reproductive stage drought stress (RSDS). We report for the first time, improvement of a Basmati cultivar for RSDS tolerance, with the introgression of a major quantitative trait locus (QTL), “qDTY1.1” into PB1. The QTL was sourced from an aus variety, Nagina 22 (N22). A microsatellite (simple sequence repeat (SSR)) marker “RM 431” located at telomeric end (38.89 mb) of chromosome 1, and located within a 1.04 mb QTL region was employed for foreground selection for qDTY1.1 in the marker assisted backcross breeding process. A set of 113 SSR markers polymorphic between N22 and PB1 were utilized for background selection to ensure higher recurrent parent genome recovery. After three backcrosses followed by five generations of selfing, eighteen near isogenic lines (NILs) were developed, through combinatory selection for agro-morphological, grain and cooking quality traits. The NILs were evaluated for three consecutive Kharif seasons, 2017, 2018 and 2019 under well-watered and drought stress conditions. RSDS tolerance and yield stability indicated that P1882-12-111-3, P1882-12-111-5, P1882-12-111-6, P1882-12-111-7, P1882-12-111-12, P1882-12-111-15 and P1882-12-111-17 were best in terms of overall agronomic and grain quality under RSDS. Additionally, NILs exhibited high yield potential under normal condition as well. The RSDS tolerant Basmati NILs with high resilience to water stress, is a valuable resource for sustaining Basmati rice production under water limiting production environments. Full article
(This article belongs to the Special Issue Rice Genetics: Trends and Challenges for the Future Crops Production)
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Article
Combined Linkage Mapping and Genome-Wide Association Study Identified QTLs Associated with Grain Shape and Weight in Rice (Oryza sativa L.)
Agronomy 2020, 10(10), 1532; https://doi.org/10.3390/agronomy10101532 - 09 Oct 2020
Cited by 3 | Viewed by 1185
Abstract
In the current study, we used a linkage mapping–Genome-Wide Association Study (GWAS) joint strategy to investigate quantitative trait loci (QTLs) governing rice grain shape and weight in a doubled haploid (DH) population, using Kompetitive Allele-Specific PCR (KASP) markers. Results revealed the co-detection of [...] Read more.
In the current study, we used a linkage mapping–Genome-Wide Association Study (GWAS) joint strategy to investigate quantitative trait loci (QTLs) governing rice grain shape and weight in a doubled haploid (DH) population, using Kompetitive Allele-Specific PCR (KASP) markers. Results revealed the co-detection of the QTLs, qGLE-12-1 and qGLE-12-2 (Chromosome 12), qGTE-3-1 (Chromosome 3), and qGWL-5-1 and qLWRL-5-1 (Chromosome 5), associated with grain length, width, and length–width ratio, by both linkage mapping and GWAS. In addition, qGLL-7-1 (logarithm of the odds (LOD): 18.0, late-transplanted rice) and qGLE-3-1 (LOD: 8.1, early-transplanted rice), and qLWRL-7-1 (LOD: 34.5), detected only by linkage mapping, recorded a high phenotypic variation explained (PVE) of 32.5%, 19.3%, and 37.7% for grain length, and grain length–width ratio, respectively, contributed by the allele from 93-11. Meanwhile, qGWL-5-1 (LOD: 17.2) recorded a high PVE (31.7%) for grain width, and the allele from Milyang352 contributed to the observed phenotypic variation. Furthermore, qGTL-5-1 (LOD: 21.9) had a high PVE (23.3%) for grain thickness. Similarly, qTGWE-5-1 (LOD: 8.6) showed a high contribution to the PVE for grain weight (23.4%). Moreover, QTLs, qGW-5-1, qGT-5-1, qLWR-5-1, and qTGW-5-1 coincided on chromosome 5, flanked with KJ05_17 and KJ05_13 markers. Therefore, these QTLs are suggested to govern rice grain shape and weight. Additionally, the identified candidate genes could play active roles in the regulation of rice grain shape and weight, regarding their predicted functions, and similarity with previously reported genes. Downstream breeding and functional studies are required to elucidate the roles of these candidate genes in the regulation of grain shape and weight in rice. Full article
(This article belongs to the Special Issue Rice Genetics: Trends and Challenges for the Future Crops Production)
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Review

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Review
Recent Advances on Nitrogen Use Efficiency in Rice
Agronomy 2021, 11(4), 753; https://doi.org/10.3390/agronomy11040753 - 13 Apr 2021
Viewed by 685
Abstract
Rice (Oryza sativa L.) is a daily staple food crop for more than half of the global population and improving productivity is an important task to meet future demands of the expanding world population. The application of nitrogen (N) fertilization improved rice [...] Read more.
Rice (Oryza sativa L.) is a daily staple food crop for more than half of the global population and improving productivity is an important task to meet future demands of the expanding world population. The application of nitrogen (N) fertilization improved rice growth and productivity in the world, but excess use causes environmental and economic issues. One of the main goals of rice breeding is reducing N fertilization while maintaining productivity. Therefore, enhancing rice nitrogen use efficiency (NUE) is essential for the development of sustainable agriculture and has become urgently needed. Many studies have been conducted on the main steps in the use of N including uptake and transport, reduction and assimilation, and translocation and remobilization, and on transcription factors regulating N metabolism. Understanding of these complex processes provides a base for the development of novel strategies to improve NUE for rice productivity under varying N conditions. Full article
(This article belongs to the Special Issue Rice Genetics: Trends and Challenges for the Future Crops Production)
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Review
Brassinosteroid Signaling Pathways Interplaying with Diverse Signaling Cues for Crop Enhancement
Agronomy 2021, 11(3), 556; https://doi.org/10.3390/agronomy11030556 - 15 Mar 2021
Cited by 1 | Viewed by 607
Abstract
The signaling pathways of brassinosteroids (BRs), a unique plant steroid hormone, are critically involved in a diverse range of plant growth and developmental processes as well as many important agronomic traits. Recent advances in the understanding of BR biosynthetic and signaling pathways in [...] Read more.
The signaling pathways of brassinosteroids (BRs), a unique plant steroid hormone, are critically involved in a diverse range of plant growth and developmental processes as well as many important agronomic traits. Recent advances in the understanding of BR biosynthetic and signaling pathways in model organisms and crops have increased the feasibility of modulating BR responses in crop plants to enhance adaptation to various vulnerable environmental changes. In particular, the identification and functional analysis of BR signaling components in rice (Oryza sativa) present the possibility of their utilization to improve many agricultural traits involved in crop yields. In this review, we summarize recent advances and progress in the understanding of the BR signaling pathway and its interactions with diverse internal and external signaling cues. We also discuss how these physiological modulations of BR and the abundant signaling crosstalk can be applied to enhance rice productivity through the manipulation of plant architecture and fine-tuning of stress responses. Finally, we discuss how the complex regulation of BR signaling pathways could favor application in the molecular design of plant growth and development, precise breeding strategies, and cultivation methods for rice crop improvement. Full article
(This article belongs to the Special Issue Rice Genetics: Trends and Challenges for the Future Crops Production)
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