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Genetic and Genomic Studies of Crop Breeding
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Genetic and Genomic Studies of Crop Breeding

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

Deadline for manuscript submissions: 25 March 2025 | Viewed by 1694

Special Issue Editor

Prof. Dr. Depeng Wang

E-Mail Website
Guest Editor
College of Life Science, Linyi University, Linyi, China
Interests: plant sciences; crop genetic improvement; crop yield potential; climate change and crop production; crop physiology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Food security is confronted by great threats from crop yield stagnation, growing demand for high-quality crops, and global climate change in the form of frequent extreme weather events, increasing occurrence of various pests and diseases, and shortage of water and other resources. The benefits of genetic studies of crop breeding globally are thought to be imperative for realizing high-yielding crop production. Breeding practices for modern crops are critical in facing these challenges, and a deep understanding of these practices is crucial to uncovering how to identify genetic improvements for productive crops. This Special Issue explores the basic mechanism of the breeding of high-yield and high-quality crops. It is expected that the development and integration of new technology into established breeding schemes will contribute significantly to crop genetic improvements, for instance, with the breeding of varieties with better quality and improved disease resistance, improving yield potential, and enhancing resistance or tolerance to biotic stress such as drought and heat. This Special Issue will prioritize articles that are of direct relevance to plant breeders, in the form of original research, technology reports, opinion articles, perspectives, reviews, and mini reviews. Studies on cereals, beans, potatoes, fiber, oilseeds, sugar, seasoning, medicinal, green manure, and aromatic crops are also welcome.

Prof. Dr. Depeng Wang
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

  • agronomy
  • plant protection
  • biological sciences
  • plant breeding
  • genetics
  • genomics
  • molecular biology
  • biotechnology
  • plant pathology
  • plant biochemistry

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Published Papers (3 papers)

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Research

20 pages, 4551 KiB  
Article
Genome-Wide Identification and Comprehensive Analysis of the PPO Gene Family in Glycine max and Glycine soja
by Ziye Song, Bo Wang, Jia Liu, Nianxi Liu, Zhigang Yi, Zhi Li, Zhimin Dong, Chunbao Zhang, Yingshan Dong and Yuqiu Li
Genes 2025, 16(1), 17; https://doi.org/10.3390/genes16010017 (registering DOI) - 26 Dec 2024
Abstract
Background: Polyphenol oxidases (PPOs) form a multigene family that is widely distributed in plants, animals, and insects. To date, PPOs have been identified in plants such as Populus L. and Solanum tuberosum L., but studies on PPOs in soybean [...] Read more.
Background: Polyphenol oxidases (PPOs) form a multigene family that is widely distributed in plants, animals, and insects. To date, PPOs have been identified in plants such as Populus L. and Solanum tuberosum L., but studies on PPOs in soybean (Glycine max (L.) Merr.) and wild soybean (Glycine soja Sieb. and Zucc.) remain limited. Methods: To clarify the nature, structure, evolution, expression pattern, and interaction network of PPOs in these plants, we performed bioinformatics analysis and evaluated the expression patterns of PPOs in soybean and wild soybean throughout the growth period and under salt stress. Results: We identified 17 and 15 genes belonging to the PPO family. These genes were distributed across chromosomes 7 and 6 and could be divided into three groups. Most of these genes only contained one coding sequence (CDS), and their gene structure, conserved motifs, and 3D structures were very similar. Although there were a few intraspecies gene duplications, 75 gene replication pairs between soybean and wild soybean were detected. A Ka/Ks analysis showed that the PPOs in these plants were mainly subjected to purity selection. Moreover, the expression of the PPO genes varied greatly during different stages of the growth period and under salt stress, showing high temporal and spatial specificity. The protein interaction networks of these genes appeared to be quite distinct. Through the interaction analysis of the candidate gene GmPPO2 selected under salt stress, Glyma.07G059000, Glyma.10G279000, and Glyma.03G167900 were identified as the candidate genes regulating salt stress tolerance in soybean. Conclusions: These findings provide a foundation for further research on the evolution of soybean and wild soybean, as well as the functions of the PPO gene family. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Crop Breeding)
25 pages, 5418 KiB  
Article
Transcriptomic Characterization of Genes Harboring Markers Linked to Maize Yield
by Agnieszka Tomkowiak, Tomasz Jamruszka, Jan Bocianowski, Aleksandra Sobiech, Karolina Jarzyniak, Maciej Lenort, Sylwia Mikołajczyk and Monika Żurek
Genes 2024, 15(12), 1558; https://doi.org/10.3390/genes15121558 - 29 Nov 2024
Viewed by 461
Abstract
Background: It is currently believed that breeding priorities, including maize breeding, should focus on introducing varieties with greater utility value, specifically higher yields, into production. Global modern maize breeding relies on various molecular genetics techniques. Using the above mentioned technologies, we can identify [...] Read more.
Background: It is currently believed that breeding priorities, including maize breeding, should focus on introducing varieties with greater utility value, specifically higher yields, into production. Global modern maize breeding relies on various molecular genetics techniques. Using the above mentioned technologies, we can identify regions of the genome that are associated with various phenotypic traits, including yield, which is of fundamental importance for understanding and manipulating these regions. Objectives: The aim of the study was to analyze the expression of candidate genes associated with maize yield. To better understand the function of the analyzed genes in increasing maize yield, their expression in different organs and tissues was also assessed using publicly available transcriptome data. Methods: RT-qPCR analyses were performed using iTaq Universal SYBR Green Supermix (Bio-Rad, Hercules, CA, USA) and CFX96 Touch Real-Time PCR Detection System (Bio-Rad, Hercules, CA, USA). Each of the performed RT-qPCR experiments consisted of three biological replicates and three technical replicates, the results of which were averaged. Results: The research results allowed us to select three out of six candidate genes (cinnamoyl-CoA reductase 1—CCR1, aspartate aminotransferase—AAT and sucrose transporter 1—SUT1), which can significantly affect grain yield in maize. Not only our studies but also literature reports clearly indicate the participation of CCR1, AAT and SUT1 in the formation of yield. Identified molecular markers located within these genes can be used in breeding programs to select high yielding maize genotypes. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Crop Breeding)
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10 pages, 1200 KiB  
Article
Simple Sequence Repeat Marker-Based Genetic Diversity and Chemical Composition Analysis of Ancient Camellia sinensis in Jiulong County, Sichuan Province, China
by Haitao Huang, Shuwen He, Xuxia Zheng, Daliang Shi, Peixian Bai, Yun Zhao, Jizhong Yu and Xiaojun Niu
Genes 2024, 15(10), 1317; https://doi.org/10.3390/genes15101317 - 14 Oct 2024
Viewed by 824
Abstract
Background/Objectives: The ancient tea plant germplasm resources are rich in genetic diversity and provide an important basis for the genetic diversity in tea germplasm resources. To explore the genetic diversity of ancient tea plant germplasm resources in Jiulong County, Sichuan Province. Methods: 59 [...] Read more.
Background/Objectives: The ancient tea plant germplasm resources are rich in genetic diversity and provide an important basis for the genetic diversity in tea germplasm resources. To explore the genetic diversity of ancient tea plant germplasm resources in Jiulong County, Sichuan Province. Methods: 59 ancient tea tree germplasm resources were analyzed using simple sequence repeat (SSR) molecular markers and chemical composition analysis. Results: The results showed that a total of 83 alleles were amplified by 23 pairs of SSR primers, with an average observed allele number (Na) of 3.6 and an effective allele number (Ne) of 2.335. The average Shannon information index (I) and the polymorphic information content (PIC) of the primers were 0.896 and 0.446, respectively. The results of the UPGMA cluster analysis showed that 59 ancient tea tree samples could be classified into five different subgroups. Based on the results of chemical composition analysis, two specific tea germplasm resources with high amino acid content, 10 excellent germplasm resources with tea polyphenol content over 20% and some other tea germplasm resources were identified. Conclusions: This study reveals that Jiulong’s ancient tea tree germplasm exhibits significant genetic diversity and includes valuable tea tree planting resources. These findings provide a foundational framework for the conservation, detailed exploration and sustainable utilization of these resources. Full article
(This article belongs to the Special Issue Genetic and Genomic Studies of Crop Breeding)
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