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Molecular Research in Rice, 2nd Edition
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Molecular Research in Rice, 2nd Edition

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 30 July 2024 | Viewed by 4231

Special Issue Editor

Prof. Dr. Prasanta K. Subudhi

E-Mail Website
Guest Editor
School of Plant, Environmental, and Soil Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
Interests: abiotic stress; rice; maize
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue follows the publication of the first edition on “Molecular Research in Rice”.

Rice (Oryza sativa L.) is a crop of global importance because it provides sustenance to more than half of the world population. Since the global population is expected to reach 9 billion by 2050, increased rice production will have a significant positive impact on global food security. However, rice farming in many parts of the world is threatened by a number of biotic and abiotic stresses due to climate change. To design novel rice genotypes, it is imperative to devise novel approaches to exploit world germplasm, understand the molecular basis of yield and yield component traits, tolerance to various biotic and abiotic stresses, and development of molecular tools to transfer desirable traits/genes. Due to spectacular advances in molecular biology, genetic engineering, and various omics fields, new molecular tools and technologies have been developed to realize these goals. As a model cereal crop due to its small genome size and genetic closeness to major cereal crops, advances in molecular research in rice will not only accelerate development of high yielding and stress tolerant rice varieties but also will help improve other cereal crops.

Contributions of both original research articles and reviews are welcome for this Special Issue on the following topics: novel approaches of germplasm utilization, application of next generation sequencing for rice improvement, mapping and cloning of genes and QTLs, development of tools for marker-assisted selection, molecular basis of biotic and abiotic stress tolerance, nutrient use efficiency, grain quality, and yield enhancing traits.

Prof. Dr. Prasanta K. Subudhi
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • molecular breeding and marker-assisted selection
  • QTL/Gene cloning
  • next generation sequencing
  • genetic engineering
  • candidate genes
  • germplasm enhancement
  • biotic and abiotic stresses
  • yield and quality traits

Published Papers (5 papers)

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Research

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15 pages, 10295 KiB  
Article
Genome-Wide Association Analysis of Effective Tillers in Rice under Different Nitrogen Gradients
by Yuzhuo Liu, Wei Xin, Liqiang Chen, Yuqi Liu, Xue Wang, Cheng Ma, Laiyuan Zhai, Yingying Feng, Jiping Gao and Wenzhong Zhang
Int. J. Mol. Sci. 2024, 25(5), 2969; https://doi.org/10.3390/ijms25052969 - 04 Mar 2024
Viewed by 530
Abstract
Nitrogen is a crucial element that impacts rice yields, and effective tillering is a significant agronomic characteristic that can influence rice yields. The way that reduced nitrogen affects effective tillering is a complex quantitative trait that is controlled by multiple genes, and its [...] Read more.
Nitrogen is a crucial element that impacts rice yields, and effective tillering is a significant agronomic characteristic that can influence rice yields. The way that reduced nitrogen affects effective tillering is a complex quantitative trait that is controlled by multiple genes, and its genetic basis requires further exploration. In this study, 469 germplasm varieties were used for a genome-wide association analysis aiming to detect quantitative trait loci (QTL) associated with effective tillering at low (60 kg/hm2) and high (180 kg/hm2) nitrogen levels. QTLs detected over multiple years or under different treatments were scrutinized in this study, and candidate genes were identified through haplotype analysis and spatio-temporal expression patterns. A total of seven genes (NAL1, OsCKX9, Os01g0690800, Os02g0550300, Os02g0550700, Os04g0615700, and Os04g06163000) were pinpointed in these QTL regions, and were considered the most likely candidate genes. These results provide favorable information for the use of auxiliary marker selection in controlling effective tillering in rice for improved yields. Full article
(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)
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12 pages, 1454 KiB  
Article
The QTL and Candidate Genes Regulating the Early Tillering Vigor Traits of Late-Season Rice in Double-Cropping Systems
by Wei Wu, Tian-Tian Zhang, Li-Li You, Zi-Yi Wang, Si-Qi Du, Hai-Yan Song, Zao-Hai Wang, Ying-Jin Huang and Jiang-Lin Liao
Int. J. Mol. Sci. 2024, 25(3), 1497; https://doi.org/10.3390/ijms25031497 - 25 Jan 2024
Viewed by 618
Abstract
Rice effective panicle is a major trait for grain yield and is affected by both the genetic tiller numbers and the early tillering vigor (ETV) traits to survive environmental adversities. The mechanism behind tiller bud formation has been well described, while the genes [...] Read more.
Rice effective panicle is a major trait for grain yield and is affected by both the genetic tiller numbers and the early tillering vigor (ETV) traits to survive environmental adversities. The mechanism behind tiller bud formation has been well described, while the genes and the molecular mechanism underlying rice-regulating ETV traits are unclear. In this study, the candidate genes in regulating ETV traits have been sought by quantitative trait locus (QTL) mapping and bulk-segregation analysis by resequencing method (BSA-seq) conjoint analysis using rice backcross inbred line (BIL) populations, which were cultivated as late-season rice of double-cropping rice systems. By QTL mapping, seven QTLs were detected on chromosomes 1, 3, 4, and 9, with the logarithm of the odds (LOD) values ranging from 3.52 to 7.57 and explained 3.23% to 12.98% of the observed phenotypic variance. By BSA-seq analysis, seven QTLs on chromosomes 1, 2, 4, 5, 7, and 9 were identified using single-nucleotide polymorphism (SNP) and insertions/deletions (InDel) index algorithm and Euclidean distance (ED) algorithm. The overlapping QTL resulting from QTL mapping and BSA-seq analysis was shown in a 1.39 Mb interval on chromosome 4. In the overlap interval, six genes, including the functional unknown genes Os04g0455650, Os04g0470901, Os04g0500600, and ethylene-insensitive 3 (Os04g0456900), sialyltransferase family domain containing protein (Os04g0506800), and ATOZI1 (Os04g0497300), showed the differential expression between ETV rice lines and late tillering vigor (LTV) rice lines and have a missense base mutation in the genomic DNA sequences of the parents. We speculate that the six genes are the candidate genes regulating the ETV trait in rice, which provides a research basis for revealing the molecular mechanism behind the ETV traits in rice. Full article
(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)
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18 pages, 2673 KiB  
Article
Genetic Enhancement for Biotic Stress Resistance in Basmati Rice through Marker-Assisted Backcross Breeding
by Gagandeep Singh, Niraj Singh, Ranjith Kumar Ellur, Alexander Balamurugan, G. Prakash, Rajeev Rathour, Kalyan Kumar Mondal, Prolay Kumar Bhowmick, S. Gopala Krishnan, Mariappan Nagarajan, Rakesh Seth, K. K. Vinod, Varsha Singh, Haritha Bollinedi and Ashok Kumar Singh
Int. J. Mol. Sci. 2023, 24(22), 16081; https://doi.org/10.3390/ijms242216081 - 08 Nov 2023
Cited by 1 | Viewed by 988
Abstract
Pusa Basmati 1509 (PB1509) is one of the major foreign-exchange-earning varieties of Basmati rice; it is semi-dwarf and early maturing with exceptional cooking quality and strong aroma. However, it is highly susceptible to various biotic stresses including bacterial blight and blast. Therefore, bacterial [...] Read more.
Pusa Basmati 1509 (PB1509) is one of the major foreign-exchange-earning varieties of Basmati rice; it is semi-dwarf and early maturing with exceptional cooking quality and strong aroma. However, it is highly susceptible to various biotic stresses including bacterial blight and blast. Therefore, bacterial blight resistance genes, namely, xa13 + Xa21 and Xa38, and fungal blast resistance genes Pi9 + Pib and Pita were incorporated into the genetic background of recurrent parent (RP) PB1509 using donor parents, namely, Pusa Basmati 1718 (PB1718), Pusa 1927 (P1927), Pusa 1929 (P1929) and Tetep, respectively. Foreground selection was carried out with respective gene-linked markers, stringent phenotypic selection for recurrent parent phenotype, early generation background selection with Simple sequence repeat (SSR) markers, and background analysis at advanced generations with Rice Pan Genome Array comprising 80K SNPs. This has led to the development of Near isogenic lines (NILs), namely, Pusa 3037, Pusa 3054, Pusa 3060 and Pusa 3066 carrying genes xa13 + Xa21, Xa38, Pi9 + Pib and Pita with genomic similarity of 98.25%, 98.92%, 97.38% and 97.69%, respectively, as compared to the RP. Based on GGE-biplot analysis, Pusa 3037-1-44-3-164-20-249-2 carrying xa13 + Xa21, Pusa 3054-2-47-7-166-24-261-3 carrying Xa38, Pusa 3060-3-55-17-157-4-124-1 carrying Pi9 + Pib, and Pusa 3066-4-56-20-159-8-174-1 carrying Pita were identified to be relatively stable and better-performing individuals in the tested environments. Intercrossing between the best BC3F1s has led to the generation of Pusa 3122 (xa13 + Xa21 + Xa38), Pusa 3124 (Xa38 + Pi9 + Pib) and Pusa 3123 (Pi9 + Pib + Pita) with agronomy, grain and cooking quality parameters at par with PB1509. Cultivation of such improved varieties will help farmers reduce the cost of cultivation with decreased pesticide use and improve productivity with ensured safety to consumers. Full article
(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)
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13 pages, 8510 KiB  
Article
Regulation of Grain Chalkiness and Starch Metabolism by FLO2 Interaction Factor 3, a bHLH Transcription Factor in Oryza sativa
by Xianyu Tang, Weiping Zhong, Kunmei Wang, Xin Gong, Yunong Xia, Jieying Nong, Langtao Xiao and Shitou Xia
Int. J. Mol. Sci. 2023, 24(16), 12778; https://doi.org/10.3390/ijms241612778 - 14 Aug 2023
Viewed by 970
Abstract
Chalkiness is a key determinant that directly affects the appearance and cooking quality of rice grains. Previously, Floury endosperm 2 (FLO2) was reported to be involved in the formation of rice chalkiness; however, its regulation mechanism is still unclear. Here, FLO2 [...] Read more.
Chalkiness is a key determinant that directly affects the appearance and cooking quality of rice grains. Previously, Floury endosperm 2 (FLO2) was reported to be involved in the formation of rice chalkiness; however, its regulation mechanism is still unclear. Here, FLO2 interaction factor 3 (OsFIF3), a bHLH transcription factor, was identified and analyzed in Oryza sativa. A significant increase in chalkiness was observed in OsFIF3-overexpressed grains, coupled with a round, hollow filling of starch granules and reduced grain weight. OsFIF3 is evolutionarily conserved in monocotyledons, but variable in dicotyledons. Subcellular localization revealed the predominant localization of OsFIF3 in the nucleus. The DAP-seq (DNA affinity purification sequencing) results showed that OsFIF3 could affect the transcriptional accumulation of β-amylase 1, α-amylase isozyme 2A-like, pectinesterase 11, β-glucosidase 28 like, pectinesterase, sucrose transport protein 1 (SUT1), and FLO2 through the binding of the CACGTG motif on their promoters. Moreover, FLO2 and SUT1 with abundant OsFIF3 binding signals showed significant expression reduction in OsFIF3 overexpression lines, further confirming OsFIF3’s role in starch metabolism regulation and energy material allocation. Taken together, these findings show that the overexpression of OsFIF3 inhibits the expression of FLO2 and SUT1, thereby increasing grain chalkiness and affecting grain weight. Full article
(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)
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Review

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14 pages, 2819 KiB  
Review
Glutaredoxin in Rice Growth, Development, and Stress Resistance: Mechanisms and Research Advances
by Rongrong Zhai, Shenghai Ye, Jing Ye, Mingming Wu, Guofu Zhu, Faming Yu, Xingyu Wang, Yue Feng and Xiaoming Zhang
Int. J. Mol. Sci. 2023, 24(23), 16968; https://doi.org/10.3390/ijms242316968 - 30 Nov 2023
Viewed by 777
Abstract
Rice (Oryza sativa L.) is a staple food for more than half of the global population. Various abiotic and biotic stresses lead to accumulation of reactive oxygen species in rice, which damage macromolecules and signaling pathways. Rice has evolved a variety of [...] Read more.
Rice (Oryza sativa L.) is a staple food for more than half of the global population. Various abiotic and biotic stresses lead to accumulation of reactive oxygen species in rice, which damage macromolecules and signaling pathways. Rice has evolved a variety of antioxidant systems, including glutaredoxin (GRX), that protect against various stressors. A total of 48 GRX gene loci have been identified on 11 of the 12 chromosomes of the rice genome; none were found on chromosome 9. GRX proteins were classified into four categories according to their active sites: CPYC, CGFS, CC, and GRL. In this paper, we summarized the recent research advances regarding the roles of GRX in rice development regulation and response to stresses, and discussed future research perspectives related to rice production. This review could provide information for rice researchers on the current status of the GRX and serve as guidance for breeding superior varieties. Full article
(This article belongs to the Special Issue Molecular Research in Rice, 2nd Edition)
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