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Agriculture
Special Issues
Gene Editing and Molecular Markers for Crops Genetics and Breeding
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Gene Editing and Molecular Markers for Crops Genetics and Breeding

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Crop Genetics, Genomics and Breeding".

Deadline for manuscript submissions: 10 February 2025 | Viewed by 3285

Special Issue Editors

Prof. Dr. Lin Zhang

E-Mail Website
Guest Editor
Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
Interests: rice; quantitative trait loci (QTL); gene cloning; molecular breeding; gene editing
Dr. Guobin Zhang

E-Mail Website
Guest Editor
College of Agriculture, Shandong Agricultural University, Taian 271018, China
Interests: plant genomics; plant molecular genetics; comparative genomics; pangenomics; plant nutrition; nitrogen nutrition
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Improving crop production is facing great challenges due to global population explosion and climate change, and the yield of major crops including rice, wheat, maize and soybean will need to double to satisfy the diet demands by 2050. The advent of new breeding techniques provides an opportunity to develop crops with higher production. Molecular markers are well-known tools for breeding selection, and developing advanced markers is important for both foreground and background selection, such as functional markers directly recognizing the causative sequence variations and non-labor intensive markers with higher genotyping efficiency. Gene editing is becoming the most popular technique to create mutants for both genetic study and crop breeding, and trait improvement of a specific variety can be achieved quickly in a short time period. Therefore, combinational use of marker selection and gene editing will be the best way to break through the ceiling of crop production.

This Special Issue focuses on various dimensions about efficient use of molecular markers or gene editing for crop genetics and breeding research. Submissions of molecular marker research could cover the development of functional markers targeting important genes and middle- or high-throughput marker packages suitable for population discrimination, gene mapping and breeding selection. Gene editing research could include the creation of beneficial alleles of known genes or function validation of unknown genes and clarifying the phenotypic effect of different mutations. We also welcome case studies of efficient crop breeding using either of the techniques described above. We accept both research and review papers matching with the topic.

Prof. Dr. Lin Zhang
Dr. Guobin Zhang
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. Agriculture 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 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

  • crops
  • molecular makers
  • gene editing
  • functional markers
  • association mapping
  • QTL analysis
  • marker-assisted selection (MAS) breeding
  • CRISPR/Cas9
  • base editing

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Published Papers (2 papers)

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Research

17 pages, 1726 KiB  
Article
Genome-Wide Association Analysis for Submergence Tolerance at the Early Vegetative and Germination Stages in Wild Soybean (Glycine soja)
by Hai Anh Tran, Hyun Jo, Thi Cuc Nguyen, Jeong-Dong Lee, Hak Soo Seo and Jong Tae Song
Agriculture 2024, 14(9), 1627; https://doi.org/10.3390/agriculture14091627 - 17 Sep 2024
Viewed by 1099
Abstract
Cultivated soybean is an important legume crop that is generally sensitive to flooding stress, including submergence and waterlogging treatments. Wild soybeans, the ancestor of cultivated soybeans, have been potential genetic resources for resistance to abiotic or biotic stresses. The present study aimed to [...] Read more.
Cultivated soybean is an important legume crop that is generally sensitive to flooding stress, including submergence and waterlogging treatments. Wild soybeans, the ancestor of cultivated soybeans, have been potential genetic resources for resistance to abiotic or biotic stresses. The present study aimed to evaluate 163 wild soybean accessions for foliar damages at the early vegetative stage and 105 accessions for germination rates, normal seedling rates, and electrical conductivity at the germination stage under submergence stress. In addition, a genome-wide association study (GWAS) was conducted to identify genomic regions associated with phenotypic measurements at these two growth stages by using MLM and FarmCPU models with publicly available genotypic data. The phenotypic evaluation revealed six and three accessions were tolerant to submergence at the early vegetative and germination stages, respectively. Notably, only one wild soybean accession showed a tolerance reaction to submergence at two stages. Through GWAS analysis, 16 and 20 SNPs across different chromosomes were determined for the submergence-related traits at the early vegetative and germination stages, respectively. Based on the linkage disequilibrium block on the detected genomic regions, ten and four putative genes were identified at the early vegetative and germination stages, respectively. Of these genes, certain genes may be related to submergence stress in wild soybeans. Further studies should be performed to validate the function of these putative genes in the responses of wild soybeans to submergence stress. Full article
(This article belongs to the Special Issue Gene Editing and Molecular Markers for Crops Genetics and Breeding)
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14 pages, 2297 KiB  
Article
Fine-Tuning Quantitative Trait Loci Identified in Immortalized F2 Population Are Essential for Genomic Prediction of Hybrid Performance in Maize
by Pingxi Wang, Xingye Ma, Xining Jin, Xiangyuan Wu, Xiaoxiang Zhang, Huaisheng Zhang, Hui Wang, Hongwei Zhang, Junjie Fu, Yuxin Xie and Shilin Chen
Agriculture 2024, 14(3), 340; https://doi.org/10.3390/agriculture14030340 - 21 Feb 2024
Viewed by 1547
Abstract
Maize breeding is greatly affected by hybrid vigor, a phenomenon that hybrids exhibit superior performance than parental lines. The immortalized F2 population (IMF2) is ideal for the genetic dissection and prediction of hybrid performance. Here, in this study, we conducted [...] Read more.
Maize breeding is greatly affected by hybrid vigor, a phenomenon that hybrids exhibit superior performance than parental lines. The immortalized F2 population (IMF2) is ideal for the genetic dissection and prediction of hybrid performance. Here, in this study, we conducted the QTL mapping and genomic prediction of six traits related to plant architecture using an IMF2 population. Broad-sense heritability of these traits ranged from 0.85 to 0.94. Analysis of genetic effects showed that additive variance was the main contributor to phenotypic variations. The mapping of quantitative trait loci (QTLs) revealed 10 to 16 QTLs (including pleiotropic loci and epistatic QTLs) for the six traits. Additionally, we identified 15 fine-tuning QTLs for plant height (PH). For genomic prediction (GP), the model of additive and dominance (AD) exhibited higher prediction accuracy than those fitting general combining ability (GCA) and its combination with special combining ability (SCA) effects for all tested traits. And adding the epistasis (E) effect into the AD model did not significantly increase its prediction accuracy. Moreover, the identified 15 fine-tuning QTLs of PH, which exerted large genomic prediction effects, were verified by the marker effect of GP. Our results not only provide an approach for the fine-mapping of fine-tuning QTLs but also serve as references for GP breeding in crops. Full article
(This article belongs to the Special Issue Gene Editing and Molecular Markers for Crops Genetics and Breeding)
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