Agronomy

Editorial

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4 pages, 216 KiB

Open AccessEditorial

Rice Genetics: Trends and Challenges for the Future Crops Production

by Kwon-Kyoo Kang and Yong-Gu Cho

Agronomy 2022, 12(7), 1555; https://doi.org/10.3390/agronomy12071555 - 28 Jun 2022

Viewed by 1152

Abstract

Twenty-first-century agriculture faces serious challenges in every country on the planet due to global population growth, declining genetic resources, climate change, farmland loss due to urbanization, and stagnant crop yields [...] Full article

(This article belongs to the Special Issue Rice Genetics: Trends and Challenges for the Future Crops Production)

Research

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20 pages, 1120 KiB

Open AccessEditor’s ChoiceArticle

Breeding for Low Temperature Germinability in Temperate Japonica Rice Varieties: Analysis of Candidate Genes in Associated QTLs

by Ester Sales, Eva Miedes and Luis Marqués

Agronomy 2021, 11(11), 2125; https://doi.org/10.3390/agronomy11112125 - 23 Oct 2021

Cited by 1 | Viewed by 1710

Abstract

In temperate areas, rice deals with low temperatures that can affect plant growth and crop yield. Rapid germination is required for adequate plant establishment in the field, therefore obtaining cultivars that maintain this phenotype under suboptimal temperature conditions is a challenge for rice [...] Read more.

In temperate areas, rice deals with low temperatures that can affect plant growth and crop yield. Rapid germination is required for adequate plant establishment in the field, therefore obtaining cultivars that maintain this phenotype under suboptimal temperature conditions is a challenge for rice breeders. Our study aimed to investigate temperature-induced expression changes in genes underlying quantitative trait loci (QTLs) associated to this trait (low temperature germinability, LTG) that were detected in a previous genome wide association study (GWAS). In the context of a breeding program for japonica rice cultivars adapted to cultivation in Spain, we obtained two biparental families of lines derived from hybridization with two cold tolerant Italian cultivars, and we have studied the effect on the LTG phenotype of introgressing these QTLs. A wide region in chromosome 3 was related to significant increases in seedling growth rate at 15 °C, although the extent of the effect depended on the analyzed family. In parallel, we studied the pattern of expression during germination at different temperatures of 10 genes located in the LTG-associated QTLs, in five japonica rice cultivars and in a biparental family of recombinant inbred lines (RILs). Cold induced changes in the expression of the 10 analyzed genes, with significant differences among genotypes. Variation in LTG phenotype was consistently associated with changes in the pattern of expression of five genes from the tagged regions in rice chromosome 3, which encoded for enzymes implicated in phytohormone metabolism (OsFBK12, Os3Bglu6), oxidative stress (SPL35, OsSRO1c) and Mn homeostasis maintenance (OsMTP8.1). Differential expression induced by cold in two regulatory genes (Os02g0824000 and Os06g06400) also contributed to explain low temperature tolerance during rice germination. In conclusion, introgression in defective cultivars of favorable alleles for these genes would contribute to the genetic improvement of LTG in japonica rice varieties. Full article

(This article belongs to the Special Issue Rice Genetics: Trends and Challenges for the Future Crops Production)

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15 pages, 2647 KiB

Open AccessArticle

Quantitative Trait Locus Analysis of Microscopic Phenotypic Characteristic Data Obtained Using Optical Coherence Tomography Imaging of Rice Bacterial Leaf Blight Infection in the Field

by Xiao-Xuan Du, Jae-Ryoung Park, Hyeree Kim, Sm Abu Saleah, Byoung-Ju Yun, Mansik Jeon and Kyung-Min Kim

Agronomy 2021, 11(8), 1630; https://doi.org/10.3390/agronomy11081630 - 16 Aug 2021

Cited by 2 | Viewed by 2182

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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17 pages, 4732 KiB

Open AccessArticle

The Role of OsWRKY Genes in Rice When Faced with Single and Multiple Abiotic Stresses

by Rajendran Jeyasri, Pandiyan Muthuramalingam, Lakkakula Satish, Sivakumar Adarshan, Muthukannan Aishwarya Lakshmi, Shunmugiah Karutha Pandian, Jen-Tsung Chen, Sunny Ahmar, Xiukang Wang, Freddy Mora-Poblete and Manikandan Ramesh

Agronomy 2021, 11(7), 1301; https://doi.org/10.3390/agronomy11071301 - 26 Jun 2021

Cited by 13 | Viewed by 3489

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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23 pages, 3621 KiB

Open AccessArticle

Introgression of qDTY1.1 Governing Reproductive Stage Drought Tolerance into an Elite Basmati Rice Variety “Pusa Basmati 1” through Marker Assisted Backcross Breeding

by Gaurav Dhawan, Aruna Kumar, Priyanka Dwivedi, Subbaiyan Gopala Krishnan, Madan Pal, Kunnummal Kurungara Vinod, Mariappan Nagarajan, Prolay Kumar Bhowmick, Haritha Bollinedi, Ranjith Kumar Ellur, Kuram Tirumala Ravikiran, Pankaj Kumar and Ashok Kumar Singh

Agronomy 2021, 11(2), 202; https://doi.org/10.3390/agronomy11020202 - 21 Jan 2021

Cited by 19 | Viewed by 4123

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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22 pages, 4911 KiB

Open AccessArticle

Combined Linkage Mapping and Genome-Wide Association Study Identified QTLs Associated with Grain Shape and Weight in Rice (Oryza sativa L.)

by Ju-Won Kang, Nkulu Rolly Kabange, Zarchi Phyo, So-Yeon Park, So-Myeong Lee, Ji-Yun Lee, Dongjin Shin, Jun Hyeon Cho, Dong-Soo Park, Jong-Min Ko and Jong-Hee Lee

Agronomy 2020, 10(10), 1532; https://doi.org/10.3390/agronomy10101532 - 09 Oct 2020

Cited by 11 | Viewed by 3534

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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22 pages, 2630 KiB

Open AccessReview

Research Trends and Challenges of Using CRISPR/Cas9 for Improving Rice Productivity

by Van Trang Le, Me-Sun Kim, Yu-Jin Jung, Kwon-Kyoo Kang and Yong-Gu Cho

Agronomy 2022, 12(1), 164; https://doi.org/10.3390/agronomy12010164 - 10 Jan 2022

Cited by 6 | Viewed by 4443

Abstract

Nowadays, rice production faces significant challenges due to population pressure, global climate change, and outbreak of various pests and diseases. Breeding techniques used to improve rice traits include mutant breeding, cross breeding, heterogeneity, transformation, molecular markers, genome-wide association study (GWAS), and so on. [...] Read more.

Nowadays, rice production faces significant challenges due to population pressure, global climate change, and outbreak of various pests and diseases. Breeding techniques used to improve rice traits include mutant breeding, cross breeding, heterogeneity, transformation, molecular markers, genome-wide association study (GWAS), and so on. Since the recently developed CRISPR/Cas9 technology can directly target a specific part of a desired gene to induce mutation, it can be used as a powerful means to expand genetic diversity of crops and develop new varieties. So far, CRISPR/Cas9 technology has been used for improving rice characteristics such as high yield, good quality, abundant nutrition, pest and disease resistance, herbicide resistance, and biotic and abiotic stress resistance. This review highlights the mechanisms and optimization of the CRISPR system and its application to rice crop, including resistance to biotic and abiotic stresses, and improved rice quality and yield. Full article

(This article belongs to the Special Issue Rice Genetics: Trends and Challenges for the Future Crops Production)

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17 pages, 706 KiB

Open AccessEditor’s ChoiceReview

Recent Advances on Nitrogen Use Efficiency in Rice

by Sichul Lee

Agronomy 2021, 11(4), 753; https://doi.org/10.3390/agronomy11040753 - 13 Apr 2021

Cited by 32 | Viewed by 6150

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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12 pages, 939 KiB

Open AccessReview

Brassinosteroid Signaling Pathways Interplaying with Diverse Signaling Cues for Crop Enhancement

by Hyeona Hwang, Hojin Ryu and Hyunwoo Cho

Agronomy 2021, 11(3), 556; https://doi.org/10.3390/agronomy11030556 - 15 Mar 2021

Cited by 10 | Viewed by 3061

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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