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Advances in Plant Genetics and Breeding Improvement
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Advances in Plant Genetics and Breeding Improvement

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

Deadline for manuscript submissions: 30 June 2025 | Viewed by 1893

Special Issue Editor

Prof. Dr. Jiaquan Huang

E-Mail Website
Guest Editor
School of Tropical Agriculture and Forestry, Hainan University, Haikou 570228, China
Interests: plant genetics; plant breeding; crop nutrients

Special Issue Information

Dear Colleagues,

In recent years, significant progress has been made in the field of plant genetics and breeding, which has greatly promoted agricultural production and crop improvement. These advances provide strong support for meeting the world's growing food demand and promoting sustainable agricultural development, showing broad prospects in the field of plant genetics and breeding improvement.

The present Topic aims to create a representative and updated collection of research articles and reviews regarding plant genetics and breeding improvement. Submissions may encompass a spectrum of topics, including but not limited to genomic technology, marker-assisted selection, genetic engineering and plant breeding.

Prof. Dr. Jiaquan Huang
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. 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

  • plant genetics
  • plant breeding
  • genomic technology
  • marker-assisted selection
  • genetic engineering

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (3 papers)

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Research

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13 pages, 2384 KiB  
Article
Unravelling the Chloroplast Genome of the Kazakh Apricot (Prunus armeniaca L.) Through MinION Long-Read Sequencing
by Imanbayeva Akzhunis, Zharassova Dinara, Duisenova Nurzhaugan, Orazov Aidyn, Tolep Nazerke and Tlepiyeva Gulmira
Plants 2025, 14(5), 638; https://doi.org/10.3390/plants14050638 - 20 Feb 2025
Cited by 1 | Viewed by 506
Abstract
The study of the genetic diversity and adaptation mechanisms of the Kazakh apricot (Prunus armeniaca L.) is essential for breeding programs and the conservation of plant genetic resources in arid environments. Despite this species’ ecological and agricultural significance, its chloroplast genome remains [...] Read more.
The study of the genetic diversity and adaptation mechanisms of the Kazakh apricot (Prunus armeniaca L.) is essential for breeding programs and the conservation of plant genetic resources in arid environments. Despite this species’ ecological and agricultural significance, its chloroplast genome remains poorly studied due to its complex repetitive structure and secondary metabolites that hinder high-molecular-weight DNA (HMW-DNA) extraction and long-read sequencing. To address this gap, our study aims to develop and optimise sequencing protocols for P. armeniaca under arid conditions using Oxford Nanopore’s MinION technology. We successfully extracted HMW-DNA with 50–100 ng/μL concentrations and purity (A260/A280) between 1.8 and 2.0, ensuring high sequencing quality. A total of 10 GB of sequencing data was generated, comprising 155,046 reads, of which 74,733 (48.2%) had a Q-score ≥ 8. The average read length was 1679 bp, with a maximum of 31,144 bp. Chloroplast genome assembly resulted in 33,000 contigs with a total length of 1.1 Gb and a BUSCO completeness score of 97.3%. Functional annotation revealed key genes (nalC, AcrE, and mecC-type BlaZ) associated with stress tolerance and a substantial proportion (≈40%) of hypothetical proteins requiring further investigation. GC content analysis (40.25%) and GC skew data suggest the presence of specific regulatory elements linked to environmental adaptation. This study demonstrates the feasibility of using third-generation sequencing technologies to analyse complex plant genomes and highlights the genetic resilience of P. armeniaca to extreme conditions. The findings provide a foundation for breeding programs to improve drought tolerance and conservation strategies to protect Kazakhstan’s unique arid ecosystems. Full article
(This article belongs to the Special Issue Advances in Plant Genetics and Breeding Improvement)
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Review

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16 pages, 760 KiB  
Review
Application and Progress of Genomics in Deciphering the Genetic Regulation Mechanisms of Plant Secondary Metabolites
by Chong Liu, Hang Xu, Zheng Li, Yukun Wang, Siwei Qiao and Hao Zhang
Plants 2025, 14(9), 1316; https://doi.org/10.3390/plants14091316 - 26 Apr 2025
Viewed by 442
Abstract
This review aims to systematically dissect the genetic regulatory mechanisms of plant secondary metabolites in the era of genomics, while comprehensively summarizing the progress and potential impact of genomics in plant secondary metabolism research. By integrating methodologies such as high-throughput sequencing, structural genomics, [...] Read more.
This review aims to systematically dissect the genetic regulatory mechanisms of plant secondary metabolites in the era of genomics, while comprehensively summarizing the progress and potential impact of genomics in plant secondary metabolism research. By integrating methodologies such as high-throughput sequencing, structural genomics, comparative genomics, and functional genomics, we elucidate the principles underlying plant secondary metabolism and identify functional genes. The application of these technologies has deepened our understanding of secondary metabolic pathways and driven advancements in plant molecular genetics and genomics. The development of genomics has enabled scientists to gain profound insights into the biosynthetic pathways of secondary metabolites in plants such as ginseng (Panax ginseng) and grapevine (Vitis vinifera), while offering novel possibilities for precise regulation of these pathways. Despite remarkable progress in studying the genetic regulation of plant secondary metabolites, significant challenges persist. Future research must focus on integrating multi-omics data, developing advanced bioinformatics tools, and exploring effective genetic improvement strategies to fully harness the medicinal potential of plants and enhance their capacity to synthesize secondary metabolites. Full article
(This article belongs to the Special Issue Advances in Plant Genetics and Breeding Improvement)
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13 pages, 1177 KiB  
Review
Advances and Future Prospects of Pigment Deposition in Pigmented Rice
by Hong Lang, Xingtian Jia, Bing He and Xiaoming Yu
Plants 2025, 14(6), 963; https://doi.org/10.3390/plants14060963 - 19 Mar 2025
Viewed by 500
Abstract
Pigmented rice, particularly the black and red varieties, is popular due to its better nutritional value. Anthocyanins and proanthocyanidins are two major flavonoid subcategories with broad physiological functions and therapeutic significance. However, pigment deposition is a complex process, and the molecular mechanism involved [...] Read more.
Pigmented rice, particularly the black and red varieties, is popular due to its better nutritional value. Anthocyanins and proanthocyanidins are two major flavonoid subcategories with broad physiological functions and therapeutic significance. However, pigment deposition is a complex process, and the molecular mechanism involved remains unknown. This review explores the metabolites responsible for the pigmentation in various rice tissues. Moreover, the current challenges, feasible strategies, and potential future directions in pigmented rice research are reported. Full article
(This article belongs to the Special Issue Advances in Plant Genetics and Breeding Improvement)
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