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Genetic Diversity in Rice Cultivars
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Genetic Diversity in Rice Cultivars

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: closed (28 May 2021) | Viewed by 16912

Special Issue Editor

Prof. Dr. Michael Schläppi

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Guest Editor
Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA

Special Issue Information

Dear Colleagues,

Rice (Oryza sativa) is a model organism for plant biology, and one of the most widely consumed staple foods worldwide, being the most important cereal grain used for human nutrition. Domesticated in Asia, rice is a monocot usually grown as an annual crop plant. As it is a worldwide-spread crop, many varieties (also known as cultivars) exist, each one with its own genotypic and phenotypic characteristics, which makes their exploitation interesting for different causes.

This Special Issue is focused on the genetics and genomics underlying the similarities and distinctions between the different rice cultivars that can be found all across the world, to better understand the changes in the genome that lead to the appearance of the characteristics that make some varieties more suitable than others for their cultivation in different environmental conditions (both biotic- and abiotic-driven) or for different purposes (regarding their phenotypic characteristics).

For this, we welcome submissions of reviews, original research articles, and short communications that focus on genetic and genomic studies of different cultivars from the worldwide rice collection.

Prof. Michael Schläppi
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 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

  • Oryza sativa
  • rice
  • genetic diversity
  • cultivar

Published Papers (5 papers)

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Research

Jump to: Review

20 pages, 2341 KiB  
Article
Low Temperature Antioxidant Activity QTL Associate with Genomic Regions Involved in Physiological Cold Stress Tolerance Responses in Rice (Oryza sativa L.)
by Huy Phan and Michael Schläppi
Genes 2021, 12(11), 1700; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12111700 - 26 Oct 2021
Cited by 6 | Viewed by 2355
Abstract
Boosting cold stress tolerance in crop plants can minimize stress-mediated yield losses. Asian rice (Oryza sativa L.), one of the most consumed cereal crops, originated from subtropical regions and is generally sensitive to low temperature environments. Within the two subspecies of rice, [...] Read more.
Boosting cold stress tolerance in crop plants can minimize stress-mediated yield losses. Asian rice (Oryza sativa L.), one of the most consumed cereal crops, originated from subtropical regions and is generally sensitive to low temperature environments. Within the two subspecies of rice, JAPONICA, and INDICA, the cold tolerance potential of its accessions is highly variable and depends on their genetic background. Yet, cold stress tolerance response mechanisms are complex and not well understood. This study utilized 370 accessions from the Rice Diversity Panel 1 (RDP1) to investigate and correlate four cold stress tolerance response phenotypes: membrane damage, seedling survivability, and catalase and anthocyanin antioxidative activity. Most JAPONICA accessions, and admixed accessions within JAPONICA, had lower membrane damage, higher antioxidative activity, and overall, higher seedling survivability compared to INDICA accessions. Genome-wide association study (GWAS) mapping was done using the four traits to find novel quantitative trait loci (QTL), and to validate and fine-map previously identified QTL. A total of 20 QTL associated to two or more traits were uncovered by our study. Gene Ontology (GO) term enrichment analyses satisfying four layers of filtering retrieved three potential pathways: signal transduction, maintenance of plasma membrane and cell wall integrity, and nucleic acids metabolism as general mechanisms of cold stress tolerance responses involving antioxidant activity. Full article
(This article belongs to the Special Issue Genetic Diversity in Rice Cultivars)
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20 pages, 2153 KiB  
Article
Novel QTL Associated with Shoot Branching Identified in Doubled Haploid Rice (Oryza sativa L.) under Low Nitrogen Cultivation
by Young-Ho Kwon, Nkulu-Rolly Kabange, Ji-Yun Lee, So-Myeong Lee, Jin-Kyung Cha, Dong-Jin Shin, Jun-Hyeon Cho, Ju-Won Kang, Jong-Min Ko and Jong-Hee Lee
Genes 2021, 12(5), 745; https://0-doi-org.brum.beds.ac.uk/10.3390/genes12050745 - 14 May 2021
Cited by 7 | Viewed by 2581
Abstract
Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing [...] Read more.
Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential. In the present study, we evaluated the growth and development, and yield components of a doubled haploid population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica), grown under normal nitrogen and low nitrogen cultivation open field conditions. The results of the phenotypic evaluation indicated that parental lines 93-11 (P1, a high tillering indica cultivar) and Milyang352 (P2, a low tillering japonica cultivar) showed distinctive phenotypic responses, also reflected in their derived population. In addition, the linkage mapping and quantitative trait locus (QTL) analysis detected three QTLs associated with tiller number on chromosome 2 (qTNN2-1, 130 cM, logarithm of the odds (LOD) 4.14, PVE 14.5%; and qTNL2-1, 134 cM, LOD: 6.05, PVE: 20.5%) and chromosome 4 (qTN4-1, 134 cM, LOD 3.92, PVE 14.5%), with qTNL2-1 having the highest phenotypic variation explained, and the only QTL associated with tiller number under low nitrogen cultivation conditions, using Kompetitive Allele-Specific PCR (KASP) and Fluidigm markers. The additive effect (1.81) of qTNL2-1 indicates that the allele from 93-11 (P1) contributed to the observed phenotypic variation for tiller number under low nitrogen cultivation. The breakthrough is that the majority of the candidate genes harbored by the QTLs qTNL2-1 and qTNN4-1 (here associated with the control of shoot branching under low and normal nitrogen cultivation, respectively), were also proposed to be involved in plant stress signaling or response mechanisms, with regard to their annotations and previous reports. Therefore, put together, these results would suggest that a possible crosstalk exists between the control of plant growth and development and the stress response in rice. Full article
(This article belongs to the Special Issue Genetic Diversity in Rice Cultivars)
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33 pages, 2952 KiB  
Article
Diverse Roles of MAX1 Homologues in Rice
by Marek Marzec, Apriadi Situmorang, Philip B. Brewer and Agnieszka Brąszewska
Genes 2020, 11(11), 1348; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11111348 - 13 Nov 2020
Cited by 13 | Viewed by 3975
Abstract
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce [...] Read more.
Cytochrome P450 enzymes encoded by MORE AXILLARY GROWTH1 (MAX1)-like genes produce most of the structural diversity of strigolactones during the final steps of strigolactone biosynthesis. The diverse copies of MAX1 in Oryza sativa provide a resource to investigate why plants produce such a wide range of strigolactones. Here we performed in silico analyses of transcription factors and microRNAs that may regulate each rice MAX1, and compared the results with available data about MAX1 expression profiles and genes co-expressed with MAX1 genes. Data suggest that distinct mechanisms regulate the expression of each MAX1. Moreover, there may be novel functions for MAX1 homologues, such as the regulation of flower development or responses to heavy metals. In addition, individual MAX1s could be involved in specific functions, such as the regulation of seed development or wax synthesis in rice. Our analysis reveals potential new avenues of strigolactone research that may otherwise not be obvious. Full article
(This article belongs to the Special Issue Genetic Diversity in Rice Cultivars)
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14 pages, 1474 KiB  
Article
Genetic Diversity of Hydro Priming Effects on Rice Seed Emergence and Subsequent Growth under Different Moisture Conditions
by Yoshihiro Nakao, Chiharu Sone and Jun-Ichi Sakagami
Genes 2020, 11(9), 994; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11090994 - 25 Aug 2020
Cited by 8 | Viewed by 2908
Abstract
Seed priming refers to seed enhancement methods that stimulate seed metabolism. This study evaluated the genetic diversity of hydro priming efficacy in 27 different genotypes of rice under dry to wet soil moisture conditions. The genotypes included 21 genotypes of Oryza sativa, [...] Read more.
Seed priming refers to seed enhancement methods that stimulate seed metabolism. This study evaluated the genetic diversity of hydro priming efficacy in 27 different genotypes of rice under dry to wet soil moisture conditions. The genotypes included 21 genotypes of Oryza sativa, five genotypes of Oryza glaberrima, and one genotype of NERICA (New Rice for Africa). The treated rice seeds were sown in plastic boxes under four soil moisture conditions (5%, 10%, 15%, and 20% (w/w)). The genotypes were categorized into six groups based on growth parameters using hierarchical cluster analysis. Furthermore, emergence properties were investigated by using principal component analysis based on the mean emergence time of control and primed seeds. Seed priming enhanced growth performance under the moderate dry conditions of 10% and 15% soil moisture. Meanwhile, priming efficacy was low in water stress conditions of 5% and 20% soil moisture. There were wide-ranging genotypic differences of priming efficacy under 20% soil moisture condition. Our findings indicate that the anaerobic-tolerant genotypes tend to exhibit priming efficacy under high soil moisture conditions. Furthermore, one group included all upland genotypes of Oryza sativa. This group originally adapted to 10% and 15% of dry conditions, and seed priming improved their features greatly. Full article
(This article belongs to the Special Issue Genetic Diversity in Rice Cultivars)
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Review

Jump to: Research

13 pages, 1025 KiB  
Review
Snorkeling Strategy: Tolerance to Flooding in Rice and Potential Application for Weed Management
by Tiago Edu Kaspary, Nilda Roma-Burgos and Aldo Merotto, Jr.
Genes 2020, 11(9), 975; https://0-doi-org.brum.beds.ac.uk/10.3390/genes11090975 - 22 Aug 2020
Cited by 9 | Viewed by 4310
Abstract
Flooding is an important strategy for weed control in paddy rice fields. However, terrestrial weeds had evolved mechanisms of tolerance to flooding, resulting in new ‘snorkeling’ ecotypes. The aim of this review is to discuss the mechanisms of flooding tolerance in cultivated and [...] Read more.
Flooding is an important strategy for weed control in paddy rice fields. However, terrestrial weeds had evolved mechanisms of tolerance to flooding, resulting in new ‘snorkeling’ ecotypes. The aim of this review is to discuss the mechanisms of flooding tolerance in cultivated and weedy rice at different plant stages and the putative utility of this trait for weed management. Knowledge about flooding tolerance is derived primarily from crop models, mainly rice. The rice model informs us about the possible flooding tolerance mechanisms in weedy rice, Echinochloa species, and other weeds. During germination, the gene related to carbohydrate mobilization and energy intake (RAmy3D), and genes involved in metabolism maintenance under anoxia (ADH, PDC, and OsB12D1) are the most important for flooding tolerance. Flooding tolerance during emergence involved responses promoted by ethylene and induction of RAmy3D, ADH, PDC, and OsB12D1. Plant species tolerant to complete submersion also employ escape strategies or the ability to become quiescent during the submergence period. In weedy rice, the expression of PDC1, SUS3, and SUB1 genes is not directly related to flooding tolerance, contrary to what was learned in cultivated rice. Mitigation of flooding tolerance in weeds could be achieved with biotechnological approaches and genetic manipulation of flood tolerance genes through RNAi and transposons, providing a potential new tool for weed management. Full article
(This article belongs to the Special Issue Genetic Diversity in Rice Cultivars)
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