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Research Advances in Rice Breeding and Genetics
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Research Advances in Rice Breeding and Genetics

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: closed (15 March 2023) | Viewed by 5418

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,

The contribution of rice (Oryza sativa L.) to global food security is of paramount importance due to its role in the sustenance of 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 major impact in alleviating hunger around the world. Although classical plant breeding and genetic approaches have been instrumental in ushering in the first green revolution, the further increase in the productivity of major food crops including rice has been challenging. Spectacular advances have been made in many related fields such as genomics, genetic engineering, high-throughput phenotyping, next-generation sequencing, and marker-aided selection, which can strengthen rice breeding and genetics research. It is imperative to devise innovative approaches to exploit world germplasms, understand the molecular and physiological basis of yield and yield component traits and tolerance to various biotic and abiotic stresses, and develop novel molecular tools for selection. The purpose of this Special Issue is to report the recent advances in rice breeding and genetics, which can be helpful for rice researchers to design novel high-yielding rice varieties with superior grain quality and tolerance to climate change-induced biotic and abiotic stresses.

Contributions of both original research articles and reviews are welcome for this Special Issue on the following topics: novel breeding approaches, germplasm utilization, application of next-generation sequencing for rice improvement, mapping and cloning of genes and QTLs, development of tools for marker-assisted selection, genomic 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

  • advanced breeding methods
  • biotic and abiotic stress tolerance
  • gene editing
  • genomic selection
  • germplasm characterization
  • high-throughput phenotyping
  • hybrid rice
  • marker-assisted selection
  • next-generation sequencing
  • physiological mechanisms
  • yield and grain quality traits

Published Papers (3 papers)

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Research

13 pages, 1636 KiB  
Article
Fine Mapping and Cloning of a qRA2 Affect the Ratooning Ability in Rice (Oryza sativa L.)
by Niqing He, Fenghuang Huang and Dewei Yang
Int. J. Mol. Sci. 2023, 24(2), 967; https://doi.org/10.3390/ijms24020967 - 04 Jan 2023
Cited by 2 | Viewed by 1261
Abstract
Ratooning ability is a key factor that influences the ratoon rice yield in areas where light and temperature are not sufficient for second-season rice. Near-isogenic lines (NILs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). [...] Read more.
Ratooning ability is a key factor that influences the ratoon rice yield in areas where light and temperature are not sufficient for second-season rice. Near-isogenic lines (NILs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs). In this study, using 176 NILs, we identified a novel QTL for ratooning ability in NIL128. First, we mapped the QTL between the markers Indel12-29 and Indel12-31, which encompass a region of 233 kb. The rice genome annotation indicated the existence of three candidate genes in this region that may be related to ratooning ability. Through gene prediction and cDNA sequencing, we speculated that the target gene of ratooning ability is LOC_Os02g51930 which encodes cytokinin glucosyl transferases (CGTs), hereafter named qRA2. Further analysis showed that qra2 was a 1-bp substitution in the first exon in NIL128, which resulted in the premature termination of qRA2. The results of the knockdown experiment showed that the Jiafuzhan knockdown mutants exhibited the ratooning ability phenotype of NIL128. Interestingly, the qRA2 gene was found to improve ratooning ability without affecting major agronomic traits. These results will help us better understand the genetic basis of rice ratooning ability and provide a valuable gene resource for breeding strong ratoon rice varieties. Full article
(This article belongs to the Special Issue Research Advances in Rice Breeding and Genetics)
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23 pages, 2517 KiB  
Article
Integration of QTL Mapping and Whole Genome Sequencing Identifies Candidate Genes for Alkalinity Tolerance in Rice (Oryza sativa)
by Lovepreet Singh, Sapphire Coronejo, Rajat Pruthi, Sandeep Chapagain and Prasanta K. Subudhi
Int. J. Mol. Sci. 2022, 23(19), 11791; https://doi.org/10.3390/ijms231911791 - 04 Oct 2022
Cited by 7 | Viewed by 1851
Abstract
Soil alkalinity is an important stressor that impairs crop growth and development, resulting in reduced crop productivity. Unlike salinity stress, research efforts to understand the mechanism of plant adaptation to alkaline stress is limited in rice, a major staple food for the world [...] Read more.
Soil alkalinity is an important stressor that impairs crop growth and development, resulting in reduced crop productivity. Unlike salinity stress, research efforts to understand the mechanism of plant adaptation to alkaline stress is limited in rice, a major staple food for the world population. We evaluated a population of 193 recombinant inbred lines (RIL) developed from a cross between Cocodrie and N22 under alkaline stress at the seedling stage. Using a linkage map consisting of 4849 SNP markers, 42 additive QTLs were identified. There were seven genomic regions where two or more QTLs for multiple traits colocalized. Three important QTL clusters were targeted, and several candidate genes were identified based on high impact variants using whole genome sequences (WGS) of both parents and differential expression in response to alkalinity stress. These genes included two expressed protein genes, the glucan endo-1,3-beta-glucosidase precursor, F-box domain-containing proteins, double-stranded RNA-binding motif-containing protein, aquaporin protein, receptor kinase-like protein, semialdehyde hydrogenase, and NAD-binding domain-containing protein genes. Tolerance to alkaline stress in Cocodrie was most likely due to the low Na+/K+ ratio resulting from reduced accumulation of Na+ ions and higher accumulation of K+ in roots and shoots. Our study demonstrated the utility of integrating QTL mapping with WGS to identify the candidate genes in the QTL regions. The QTLs and candidate genes originating from the tolerant parent Cocodrie should be targeted for introgression to improve alkalinity tolerance in rice and to elucidate the molecular basis of alkali tolerance. Full article
(This article belongs to the Special Issue Research Advances in Rice Breeding and Genetics)
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20 pages, 7402 KiB  
Article
Transcriptome Analysis of the Responses of Rice Leaves to Chilling and Subsequent Recovery
by Zhong Li, Muhammad Umar Khan, Puleng Letuma, Yuebin Xie, Wenshan Zhan, Wei Wang, Yuhang Jiang, Wenxiong Lin and Zhixing Zhang
Int. J. Mol. Sci. 2022, 23(18), 10739; https://doi.org/10.3390/ijms231810739 - 15 Sep 2022
Cited by 3 | Viewed by 1744
Abstract
Improving chilling tolerance at the seedling stage in rice is essential for agricultural research. We combined a physiological analysis with transcriptomics in a variety Dular subjected to chilling followed by recovery at normal temperature to better understand the chilling tolerance mechanisms of rice. [...] Read more.
Improving chilling tolerance at the seedling stage in rice is essential for agricultural research. We combined a physiological analysis with transcriptomics in a variety Dular subjected to chilling followed by recovery at normal temperature to better understand the chilling tolerance mechanisms of rice. Chilling inhibited the synthesis of chlorophyll and non-structural carbohydrate (NSC) and disrupted the ion balance of the plant, resulting in the impaired function of rice leaves. The recovery treatment can effectively reverse the chilling-related injury. Transcriptome results displayed that 21,970 genes were identified at three different temperatures, and 11,732 genes were differentially expressed. According to KEGG analysis, functional categories for differentially expressed genes (DEGs) mainly included ribosome (8.72%), photosynthesis–antenna proteins (7.38%), phenylpropanoid biosynthesis (11.41%), and linoleic acid metabolism (10.07%). The subcellular localization demonstrated that most proteins were located in the chloroplasts (29.30%), cytosol (10.19%), and nucleus (10.19%). We proposed that some genes involved in photosynthesis, ribosome, phenylpropanoid biosynthesis, and linoleic acid metabolism may play key roles in enhancing rice adaptation to chilling stress and their recovery capacity. These findings provide a foundation for future research into rice chilling tolerance mechanisms. Full article
(This article belongs to the Special Issue Research Advances in Rice Breeding and Genetics)
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