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Horticulturae
Special Issues
Analysis, Identification and Utilization of Genetic Resources Related to Peanut
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Analysis, Identification and Utilization of Genetic Resources Related to Peanut

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Genetics, Genomics, Breeding, and Biotechnology (G2B2)".

Deadline for manuscript submissions: 25 December 2024 | Viewed by 6311

Special Issue Editors

Dr. Hui Zhang

E-Mail Website
Guest Editor
College of Agriculture, South China Agriculture University, Guangzhou, China
Interests: peanut quality; genes; breeding
Dr. Xinlei Yang

E-Mail Website
Guest Editor
Department of Agronomy, Agricultural University of Hebei, Baoding, China
Interests: sequencing; agriculture; DNA sequencing; DNA; gene expression; PCR; genomics; cloning; molecular cenetics; RNA; genomics and molecular breeding of peanut
Prof. Dr. Charles Y. Chen

E-Mail Website
Guest Editor
Crop Soil and Environmental Science, Auburn University, Auburn, AL 36830, USA
Interests: peanut; plant breeding; genetics; genomics; GWAS; QTL studies; RNAseq studies
Special Issues, Collections and Topics in MDPI journals
Dr. Ming Li Wang

E-Mail Website
Guest Editor
USDA Agricultural Research Service, Washington, DC, USA
Interests: molecular genetics; biology; biochemistry; genomics; phenomics; plant germplasm

Special Issue Information

Dear Colleagues,

Peanut is an important oil crop belonging to Leguminosae. In this Special Issue, we intend to publish original research reports and reviews concerning the genomics and genetics of peanut. Topics might include, but are not limited to, the effects of genotype/environment/G by E on important peanut traits, using genome-wide association studies, genomic selection, or breeding lines to identify the QTLs/genes that can be potentially used in breeding through marker-assisted selection. In addition, this Special Issue also includes the detection of genes using bioinformatic analysis or omics tools. We will particularly consider manuscripts with a clear genetic component and significant impact on peanut breeding.

Dr. Hui Zhang
Dr. Xinlei Yang
Prof. Dr. Charles Y. Chen
Dr. Ming Li Wang
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. Horticulturae 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 2200 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

  • genetic resources
  • genomic selection
  • GWAS
  • bioinformatics
  • genes
  • omics
  • marker-assisted selection
  • G by E
  • evolution

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Published Papers (4 papers)

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Research

14 pages, 1677 KiB  
Article
Characterization and Phylogenetic Analyses of the Complete Chloroplast Genome Sequence in Arachis Species
by Xiaona Yu, Tianzhu Liang, Yi Guo, Yan Liang, Xiaoxia Zou, Tong Si, Yu Ni and Xiaojun Zhang
Horticulturae 2024, 10(5), 464; https://doi.org/10.3390/horticulturae10050464 - 1 May 2024
Viewed by 1692
Abstract
Peanut is an important oilseed and a widely cultivated crop worldwide. Knowledge of the phylogenetic relationships and information on the chloroplast genomes of wild and cultivated peanuts is crucial for the evolution of peanuts. In this study, we sequenced and assembled 14 complete [...] Read more.
Peanut is an important oilseed and a widely cultivated crop worldwide. Knowledge of the phylogenetic relationships and information on the chloroplast genomes of wild and cultivated peanuts is crucial for the evolution of peanuts. In this study, we sequenced and assembled 14 complete chloroplast genomes of Arachis. The total lengths varied from 156,287 bp to 156, 402 bp, and the average guanine–cytosine content was 36.4% in 14 Arachis species. A total of 85 simple sequence repeats (SSRs) loci were detected, including 3 dinucleotide and 82 polynucleotide SSRs. Based on 110 complete chloroplast genomes of Arachis, a phylogenetic tree was constructed, which was divided into two groups (I and II). A total of 79 different genes were identified, of which six double-copy genes (ndhB, rpl2, rpl23, rps7, ycf1, and ycf2) and one triple-copy gene (rps12) are present in all 14 Arachis species, implying that these genes may be critical for photosynthesis. The dN/dS ratios for four genes (rps18, accD, clpP, ycf1) were larger than 1, indicating that these genes are subject to positive selection. These results not only provided rich genetic resources for molecular breeding but also candidate genes for further functional gene research. Full article
(This article belongs to the Special Issue Analysis, Identification and Utilization of Genetic Resources Related to Peanut)
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16 pages, 10307 KiB  
Article
Genome-Wide Identification, Characterization and Expression Profile of F-Box Protein Family Genes Shed Light on Lateral Branch Development in Cultivated Peanut (Arachis hypogaea L.)
by Chuheng Li, Liguo Guo, Weiqian Wang, Penghui Miao, Guojun Mu, Charles Y. Chen, Chengsheng Meng and Xinlei Yang
Horticulturae 2024, 10(3), 255; https://doi.org/10.3390/horticulturae10030255 - 7 Mar 2024
Viewed by 1270
Abstract
F-box proteins are a large gene family in plants, and play crucial roles in plant growth, development, and stress response. To date, a comprehensive investigation of F-box family genes in peanuts, and their expression pattern in lateral branch development has not been performed. [...] Read more.
F-box proteins are a large gene family in plants, and play crucial roles in plant growth, development, and stress response. To date, a comprehensive investigation of F-box family genes in peanuts, and their expression pattern in lateral branch development has not been performed. In this study, a total of 95 F-box protein family members on 18 chromosomes, named AhFBX1-AhFBX95, were identified in cultivated peanut (Arachis hypogaea L.), which were classified into four groups (Group I–IV). The gene structures and protein motifs of these peanut FBX genes were highly conserved among most FBXs. We found that significant segmental duplication events occurred between wild diploid species and the allotetraploid of peanut FBXs, and observed that AhFBXs underwent strong purifying selection throughout evolution. Cis-acting elements related to development, hormones, and stresses were identified in the promoters of AhFBX genes. In silico analysis of AhFBX genes revealed expression patterns across 22 different tissues. A total of 32 genes were predominantly expressed in leaves, pistils, and the aerial gynophore tip. Additionally, 37 genes displayed tissue-specific expression specifically at the apex of both vegetative and reproductive shoots. During our analysis of transcriptome data for lateral branch development in spreading and erect varieties, namely M130 and JH5, we identified nine deferentially expressed genes (DEGs). Quantitative real-time PCR (qRT-PCR) results further confirmed the expression patterns of these DEGs. These DEGs exhibited significant differences in their expression levels at different stages between M130 and JH5, suggesting their potential involvement in the regulation of lateral branch development. This systematic research offers valuable insights into the functional dissection of AhFBX genes in regulating plant growth habit in peanut. Full article
(This article belongs to the Special Issue Analysis, Identification and Utilization of Genetic Resources Related to Peanut)
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18 pages, 4079 KiB  
Article
Characterization and Comprehensive Evaluation of Phenotypic and Yield Traits in Salt-Stress-Tolerant Peanut Germplasm for Conservation and Breeding
by Nan Zhang, He Zhang, Jingyao Ren, Baiyi Bai, Pei Guo, Zhenghao Lv, Shuli Kang, Xinhua Zhao, Haiqiu Yu and Tianhong Zhao
Horticulturae 2024, 10(2), 147; https://doi.org/10.3390/horticulturae10020147 - 4 Feb 2024
Cited by 3 | Viewed by 1401
Abstract
Salt stress is a limiting factor affecting the growth, development, and yield of peanuts. Breeding improvement is a possible solution to overcome salt stress. The salt tolerance of 57 peanut cultivars in Northeast China was identified using indoor simulation at the germination stage, [...] Read more.
Salt stress is a limiting factor affecting the growth, development, and yield of peanuts. Breeding improvement is a possible solution to overcome salt stress. The salt tolerance of 57 peanut cultivars in Northeast China was identified using indoor simulation at the germination stage, the seedling stage, and field natural identification. At the germination stage, 75 mM NaCl was the most suitable screening concentration, and the seed vitality index of 57 cultivars was analyzed using the membership function and cluster analysis. Among these cultivars, 11 were identified as salt-tolerant and 19 were salt-sensitive during germination. In the seedling stage, six salt tolerance coefficients (STCs) showed significant correlation. A gray relational analysis was used in combination with evaluation grading, resulting in the identification of 14 salt-tolerant cultivars and 12 salt-sensitive cultivars. In the field screening, a comprehensive analysis was conducted using a principal component analysis of nine indices, including agronomic characteristics, yield characteristics, and SPAD. This analysis led to the determination of three comprehensive indices. The weighted membership function was used for comprehensive evaluation. Finally, three salt-tolerant cultivars and four salt-sensitive cultivars suitable for planting in Northeast China were screened out to provide an excellent germplasm for researching the salt-tolerant mechanism of peanuts. Full article
(This article belongs to the Special Issue Analysis, Identification and Utilization of Genetic Resources Related to Peanut)
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14 pages, 3585 KiB  
Article
Development and Evaluation of a New Spectral Index to Detect Peanut Southern Blight Disease Using Canopy Hyperspectral Reflectance
by Tiantian Wen, Juan Liu, Yuanyuan Fu, Jibo Yue, Yuheng Li and Wei Guo
Horticulturae 2024, 10(2), 128; https://doi.org/10.3390/horticulturae10020128 - 30 Jan 2024
Cited by 1 | Viewed by 1278
Abstract
Peanut southern blight is a soil-borne fungal disease caused by Agroathelia rolfsii (syn. Sclerotium rolfsii) Sacc, which seriously affects peanut yield. The disease mainly affects the stem, pod, and root of the plant, and it is difficult to detect the disease [...] Read more.
Peanut southern blight is a soil-borne fungal disease caused by Agroathelia rolfsii (syn. Sclerotium rolfsii) Sacc, which seriously affects peanut yield. The disease mainly affects the stem, pod, and root of the plant, and it is difficult to detect the disease by visual interpretation. Detecting peanut southern blight using existing technology is an urgent problem that needs to be solved. To address this issue, field experiments were conducted in September 2022 to determine whether hyperspectral techniques could be used to assess the severity of peanut southern blight. In this study, we obtained 610 canopy-scale spectral data through field experiments. Firstly, 18 traditional spectral features were calculated. Then, wavelengths of 544 nm, 678 nm, and 769 nm were selected as sensitive by the Relief-F algorithm, and the NDSISB and NSISB were constructed using normalization and ratio calculation methods. Finally, Support Vector Machine (SVM), Light Gradient Boosting Machine (LightGBM), Categorical Boosting (CatBoost), and ANN were used to evaluate the diagnostic ability of all spectral features to assess disease severity levels. The results showed that the NSISB had the highest association with peanut southern blight (R2 = 0.817), exceeding the other spectral features. Compared to the other three models, CatBoost demonstrated superior accuracy, with an overall accuracy (OA) and Kappa coefficient of 84.18% and 78.31%, respectively. The findings of this study can serve as a reference for estimating the severity levels of peanut southern blight using ground-based hyperspectral data. Full article
(This article belongs to the Special Issue Analysis, Identification and Utilization of Genetic Resources Related to Peanut)
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