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Recent Advances in Plant Genetics and Genomics
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Recent Advances in Plant Genetics and Genomics

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 31 July 2025 | Viewed by 793

Special Issue Editors

Prof. Dr. Longbiao Guo

E-Mail Website
Guest Editor
State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 311401, China
Interests: rice; molecular biology; gene mapping; functional genome
Dr. Qian-Hao Zhu

E-Mail Website
Guest Editor
CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
Interests: cotton biology; genomics; molecular breeding; plant noncoding RNAs; biostress tolerance
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The publication of the genomic sequence of A. thaliana in 2000 and of a O. sativa in 2002 marked the beginning of an exciting era in which advances in technology and methodology uncovered the genetic blueprints of hundreds of plant species. This, in turn, promotes functional genome development; for example, in rice, over 4100 functionally characterized rice genes and more than 6000 gene family members have been confirmed. In recent years, a rice pangenome and genome navigation system—RiceNavi—has been developed for QTN polymerization and breeding route optimization. The Oryza super pangenome, which has the largest population size of plants and fully annotated genomes, has also been constructed. Several nitrogen-efficient genes have been identified and their molecular mechanism of nitrogen efficiency has been dissected. The expression of some genes can significantly increase rice yield under experimental conditions. Significant progress has also been made in research relating to the mechanism of rice broad-spectrum disease resistance, temperature response, and salt–alkali resistance. In gene editing, a new polynucleotide-targeted deletion system—AFIDs (APOBEC-Cas9 fusion induced deletion systems)—has been established, successfully achieving accurate and predictable polynucleotide deletion in rice and wheat genomes. Using CRISPR/Cas9 technology, gene editing has produced many practical new materials including the rice apomixis material. This Special Issue of Plants will highlight the allelic gene identification, function, evolution, and diversity of rice germplasm resources in genomic and RNA-seq levels, as well as their breeding applications.

Prof. Dr. Longbiao Guo
Dr. Qian-Hao Zhu
Guest Editors

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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • rice
  • genomic selection
  • multi-omics
  • genetic analysis
  • gene editing
  • molecular design breeding

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Published Papers (2 papers)

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15 pages, 4324 KiB  
Article
QTL-Seq and Fine-Mapping Analyses Identify QTL and Candidate Genes Controlling Snake-like Pod Surface Trait in Vegetable Cowpea Yardlong Bean
by Khwanruedee Thepphomwong, Makawan Srichan, Artitaya Deeroum, Kularb Laosatit and Prakit Somta
Plants 2025, 14(10), 1447; https://doi.org/10.3390/plants14101447 - 12 May 2025
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Abstract
Yardlong bean is a vegetable type of cowpea grown for fresh and immature pods. “Thua Ngu” is a specialty yardlong bean cultivar with its unique snake-like pod surface and highly crispy pods that may be useful for the breeding of a new cultivar(s). [...] Read more.
Yardlong bean is a vegetable type of cowpea grown for fresh and immature pods. “Thua Ngu” is a specialty yardlong bean cultivar with its unique snake-like pod surface and highly crispy pods that may be useful for the breeding of a new cultivar(s). The objectives of this study were to determine the mode of inheritance of the snake-like pod trait and locate the genome region controlling this trait in Thua Ngu. Microscopic observation revealed that the shape, size, and organization of cells of immature and mature pods of Thua Ngu were clearly different from those of “Raya” (normal yardlong bean). Fiber analysis showed that lignin content in immature and mature pods of Thua Ngu was 2.05- and 3.45-fold higher than that in Raya. Segregation analysis using F2 and F2:3 populations of the cross Thua Ngu × Raya demonstrated that a single gene controls the snake-like pod trait. QTL-seq analysis using the F2 population revealed a major locus, qSlp4.1, for the snake-like pod trait. Fine-mapping using F2 and F2:3 populations delimited qSlp4.1 to a 152.88 Kbp region containing nine genes. Genes with functions involved in cell morphology and/or lignin formation, including Vigun04g163400, Vigun04g163600, and Vigun04g163700, were identified as candidate genes for the snake-like pod trait. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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12 pages, 2521 KiB  
Brief Report
Expression of the Nicotiana benthamiana Retrozyme 1 (NbRZ1) Genomic Locus
by Alexander A. Lezzhov, Anastasia K. Atabekova, Denis A. Chergintsev, Andrey G. Solovyev and Sergey Y. Morozov
Plants 2025, 14(8), 1205; https://doi.org/10.3390/plants14081205 - 14 Apr 2025
Viewed by 303
Abstract
Retrozymes are a class of non-autonomous plant retrotransposons that have long terminal repeats (LTRs) containing hammerhead ribozymes (HHRs) that facilitate the circularization of the retrozyme RNA. The LTR of Nicotiana benthamiana retrozyme 1 (NbRZ1) has been shown to contain a promoter that directs [...] Read more.
Retrozymes are a class of non-autonomous plant retrotransposons that have long terminal repeats (LTRs) containing hammerhead ribozymes (HHRs) that facilitate the circularization of the retrozyme RNA. The LTR of Nicotiana benthamiana retrozyme 1 (NbRZ1) has been shown to contain a promoter that directs transcription of this retroelement. In this study, we identified the transcription start site of the promoter contained in the LTR of NbRZ1 and mapped the promoter region essential for its transcriptional activity. Using transgenic Arabidopsis thaliana plants carrying the GUS gene under the control of the NbRZ1 LTR, the NbRZ1 transcript was demonstrated to potentially encode a protein targeted for proteasomal degradation in the plant cell. Overexpression of this protein in plants using a viral expression vector was found to cause severe necrosis. The data presented suggest a tight regulation of the expression of the NbRZ1-encoded polypeptide in plants and its potential functional importance, although further research is needed to determine whether circular and/or linear retrozyme RNA forms can be translated in plants. Full article
(This article belongs to the Special Issue Recent Advances in Plant Genetics and Genomics)
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