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Agriculture
Special Issues
Genetic Diversity Assessment and Phenotypic Characterization of Crops
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Genetic Diversity Assessment and Phenotypic Characterization of Crops

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

Deadline for manuscript submissions: 31 March 2025 | Viewed by 2581

Special Issue Editors

Prof. Dr. Andrijana Rebekić

E-Mail Website
Guest Editor
Faculty of Agrobiotechincal Sciences Osijek, Josip Juraj Strossmayer University of Osijek, Vladimira Preloga 1, 31000 Osijek, Croatia
Interests: nutritional quality; wheatgrass; in vitro digestion; phenotypic diversity; genetic diversity
Dr. Ankica Kondić-Špika

E-Mail Website
Guest Editor
Institute of Field and Vegetable Crops, 21000 Novi Sad, Serbia
Interests: genetics; plant breeding; molecular biology; biotechnology; plant phenotyping; cereal and oil crops
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Genetic diversity assessment involves studying the genetic variations present within a crop species, which can help to understand their potential for adaptation and resilience and identify unique traits that may be beneficial for breeding purposes. Phenotypic characterization, on the other hand, focuses on observing and measuring the physical traits of crops such as yield, disease resistance, nutritional content, etc., providing valuable information on their performance in different environments. By combining genetic diversity assessment with phenotypic characterization, researchers can better understand the relationship between genotypes and phenotypes, leading to the development of improved crop varieties. This integrated approach allows for the selection of crops with desirable traits, such as high yield, disease resistance, and nutritional quality, contributing to sustainable agriculture and food security. Both genetic diversity assessment and phenotypic characterization are crucial areas of research in crop improvement efforts, and ongoing studies in these fields aim to address the challenges of sustainable agriculture, food security, and climate change.

Topics of interest for this Special Issue include, but are not limited to, the following:

  • Investigating the role of genetic diversity in crop adaptation to changing environments;
  • Utilizing advanced technologies such as genomics and bioinformatics for more accurate and efficient assessment;
  • Evaluating the performance of crops under different environmental conditions;
  • Assessing the nutritional quality and health benefits of crop varieties;
  • Studying the interactions between genotypes and phenotypes;
  • Exploring the potential of precision agriculture techniques for phenotypic data collection;
  • Integrating phenotypic data with genomic information for a more comprehensive understanding of crop traits.

Prof. Dr. Andrijana Rebekić
Dr. Ankica Kondić-Špika
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 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

  • genetic diversity
  • genomic analysis
  • phenotypic diversity
  • high-throughput phenotyping
  • crop improvement
  • crop adaptation
  • crop resilience
  • nutritional quality
  • big data analysis
  • bioinformatics

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

Published Papers (4 papers)

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Research

21 pages, 10488 KiB  
Article
Genome-Wide Identification and Exogenous Hormone and Stress Response Expression Analysis of the GARP Gene Family in Soybean (Glycine max)
by Lijun Cai, Zhenhua Guo, Junjie Ding, Zhijia Gai, Jingqi Liu, Qingying Meng, Xu Yang, Na Zhang and Qingsheng Wang
Agriculture 2024, 14(12), 2109; https://doi.org/10.3390/agriculture14122109 - 22 Nov 2024
Viewed by 81
Abstract
The GARP transcription factor family is integral to the regulation of plant growth, development, hormone signaling pathways, circadian rhythms, and responses to both biotic and abiotic stressors. Despite its recognized importance, a comprehensive characterization of the GARP gene family in Glycine max remains [...] Read more.
The GARP transcription factor family is integral to the regulation of plant growth, development, hormone signaling pathways, circadian rhythms, and responses to both biotic and abiotic stressors. Despite its recognized importance, a comprehensive characterization of the GARP gene family in Glycine max remains unexplored. In this study, we identified 126 GmGARP genes across the 16 chromosomes of G. max and elucidated their diverse physicochemical properties. Phylogenetic classification grouped the GmGARP genes into eight distinct subfamilies, based on conserved motifs and gene structures, suggesting functional and evolutionary conservation within these clusters. The discovery of 56 segmentally duplicated gene pairs highlights gene duplication as a key driver of family expansion. Promoter analysis revealed various cis-regulatory elements, while expression profiling demonstrated that GmGARP genes possess significant tissue specificity. Furthermore, qRT-PCR analysis indicated that GmGARP genes are highly responsive to exogenous hormones, such as ABA, MeJA, and GA, as well as to abiotic stresses, including cold, salt, and drought conditions. Notably, GmGARP120 and GmGARP98 contain specific cis-elements linked to hormone responses, with their interaction verified through yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays. Additionally, 11,195 potential target genes were predicted, underscoring the regulatory potential of the GmGARP transcription factors. These findings provide significant insights into the GmGARP gene family, laying a strong foundation for future studies on its role in G. max development and adaptive responses to environmental stressors. Full article
(This article belongs to the Special Issue Genetic Diversity Assessment and Phenotypic Characterization of Crops)
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15 pages, 7381 KiB  
Article
Genome-Wide Association Studies for Wheat Height Under Different Nitrogen Conditions
by Tingzhi Yang, Wenjiao Zhang, Yutao Cui, Yalin Wang, Huimin Qin, Xinru Lv, Xiaohan Xie, Fulin Yang, Kangzhen Ren, Jinlan Ni, Xuehuan Dai, Jianbin Zeng, Wenxing Liu, Wujun Ma, Hongsheng Zhang and Dengan Xu
Agriculture 2024, 14(11), 1998; https://doi.org/10.3390/agriculture14111998 - 7 Nov 2024
Viewed by 483
Abstract
Lodging causes a reduction in wheat (Triticum aestivum L.) yield and quality. A shorter plant height (PH) can reduce the incidence of lodging. The overuse of nitrogen promotes excessive vegetative growth, leads to taller plants, and increases lodging risk. Here, we utilized [...] Read more.
Lodging causes a reduction in wheat (Triticum aestivum L.) yield and quality. A shorter plant height (PH) can reduce the incidence of lodging. The overuse of nitrogen promotes excessive vegetative growth, leads to taller plants, and increases lodging risk. Here, we utilized genome-wide association studies (GWASs) to explore the genetic basis of PH and the nitrogen effect index (NEI), a parameter to estimate the responses of PH under varying nitrogen conditions, using 21,201 SNP markers from the Illumina Wheat 90K SNP array. A total of 191 wheat varieties from Yellow and Huai Valley regions of China, as well as other global regions, were analyzed across two growing seasons under four nitrogen treatments, namely N0 (0 kg/ha), N150 (150 kg/ha), N210 (210 kg/ha), and N270 (270 kg/ha). GWAS results showed that 30 genetic markers were associated with PH, explaining phenotypic variance from 5.92% to 13.69%. Additionally, nine significant loci were associated with the NEI. Notably, markers on chromosomes 1A and 6B were linked to both PH and the NEI, which were insensitive to low- and high-nitrogen fertilizers. In addition, the PH of the three cultivars (Zhoumai16, Zhoumai13, and Bima1) showed little variation in four nitrogen fertilizer levels. This study identified key genetic markers associated with wheat PH and the NEI, providing insights for optimizing nitrogen use in wheat breeding. Full article
(This article belongs to the Special Issue Genetic Diversity Assessment and Phenotypic Characterization of Crops)
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11 pages, 1966 KiB  
Communication
Genome-Wide Association Study Reveals Loci and New Candidate Gene Controlling Seed Germination in Rice
by Shaona Chen, Guanlong Chen, Zepeng Peng, Jiping Liu, Yixiong Zheng and Bin Yang
Agriculture 2024, 14(9), 1613; https://doi.org/10.3390/agriculture14091613 - 14 Sep 2024
Viewed by 668
Abstract
Improving seed germination and seedling development can potentially increase crop yield and improve quality in direct-seeded rice. This study aimed to detect loci or genes associated with rice seed germination. We reported the phenotypic analysis of seed germination in 103 rice accessions across [...] Read more.
Improving seed germination and seedling development can potentially increase crop yield and improve quality in direct-seeded rice. This study aimed to detect loci or genes associated with rice seed germination. We reported the phenotypic analysis of seed germination in 103 rice accessions across two years, and a genome-wide association study (GWAS) was conducted to identify loci underlying the genetic regulation of seed germination. A total of seven genetic loci were found to be associated with seed germination, including five loci that overlapped with the previously reported loci/genes, and two novel loci. Of these, two loci (qGP2 and qGP4.1) were stable across different environments. GP4 (Germination percentage 4), encoding a 9-cis-epoxycarotenoid dioxygenase, was identified as the candidate gene of the major locus qGP4.1. A sequence analysis of GP4 revealed that four functional polymorphic sites in the coding region were significantly associated with germination percentage. The disruption of GP4 by gene editing resulted in faster seed germination and seedling establishment. Taken together, we have identified GP4 as a novel gene involved in rice seed germination, and we provide a potential target gene for improving rice seed vigor via gene editing or molecular breeding. Full article
(This article belongs to the Special Issue Genetic Diversity Assessment and Phenotypic Characterization of Crops)
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14 pages, 2840 KiB  
Article
Comprehensive Genome-Wide Identification and Characterization of the AP2 Subfamily in Beta vulgaris L. in Response to Exogenous Abscisic Acid
by Yan Zhai, Yuanrong Ni, Hao Wang, Yuanhang Zhou and Wang Xing
Agriculture 2024, 14(8), 1273; https://doi.org/10.3390/agriculture14081273 - 2 Aug 2024
Viewed by 726
Abstract
APETALA2 (AP2) belongs to transcription factor (TF) families, with crucial roles in regulating plant growth, development, and stress responses. In order to explore the characteristics of sugar beet (Beta vulgaris L.) AP2s (BvAP2s) in response to drought stress hormone abscisic [...] Read more.
APETALA2 (AP2) belongs to transcription factor (TF) families, with crucial roles in regulating plant growth, development, and stress responses. In order to explore the characteristics of sugar beet (Beta vulgaris L.) AP2s (BvAP2s) in response to drought stress hormone abscisic acid (ABA), genome-wide identification, and the phylogeny, gene structure and promoter precursor analysis of the BvAP2s were employed to predict their potential functions. It is shown that there are a total of 13 BvAP2 genes in the Beta vulgaris. Based on the primary amino acid sequence, the BvAP2s can be further subdivided into euAP2, euANT and basalANT. In addition, cis-acting element analysis showed that BvAP2s contained several abiotic stress-related elements, including those associated with ABA and drought stress. Roots are the first to perceive stress signals, and ABA-treated beetroot transcriptome and downstream gene prediction of BvAP2s revealed that BVRB_4g074790, BVRB_6g128480 and BVRB_7g179610 may play an important role involved in ABA signaling pathways during the stress response by regulating downstream GRAM genes, LEAs and U-boxes. Additionally, quantitative real-time polymerase chain reaction (qRT-PCR) further confirmed the downregulation of these three BvAP2s in response to ABA induction in sugar beet roots. These findings provide a basis for future utilization of BvAP2s in developing drought-tolerant Beta vulgaris varieties. Full article
(This article belongs to the Special Issue Genetic Diversity Assessment and Phenotypic Characterization of Crops)
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