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Agronomy, Production Systems, Advanced Phenotyping, Breeding, Genetics and Genomics of...
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Agronomy, Production Systems, Advanced Phenotyping, Breeding, Genetics and Genomics of Horticulture Crops

A special issue of Agriculture (ISSN 2077-0472). This special issue belongs to the section "Genotype Evaluation and Breeding".

Deadline for manuscript submissions: closed (15 December 2023) | Viewed by 7128

Special Issue Editors

Dr. Fawad Ali

E-Mail Website
Guest Editor
Centre for Planetary Health and Food Security, Griffith University, Nathan Campus, Brisbane, QLD 4111, Australia
Interests: agronomy and crop production; breeding for food and feed; advanced phenomics tools; genomics for adaptive technology; outcome
Special Issues, Collections and Topics in MDPI journals
Dr. Asjad Ali

E-Mail Website1 Website2
Guest Editor
Department of Agriculture and Fisheries, Mareeba, QLD 4880, Australia
Interests: agronomy; breeding; genetics; plant physiology; plant biotecnology; molecular breeding

Special Issue Information

Dear Colleagues,

Horticulture crop production and fruit quality traits are influenced by genetic and non-genetic factors. It is important to understand the production systems, agronomy, crop physiology, and pre- and post-harvest factors that affect overall production (yields) and fruit quality. There is limited knowledge about the use of advanced phenotyping tools coupled with a genomics-assisted program to measure the gene metrics of key desirable fruit quality traits when key developmental stages of horticulture crops face detrimental effects due to environmental changes. Further, we need to evaluate advanced phenotyping platforms for the measurement of tree agronomic and productivity traits coupled with consumer-driven fruit quality traits, as well as evaluate substantial changes in the environment where the plants are grown. This would help us develop novel pathways to mitigate the effect of the environment and several biotic and abiotic factors that limit yields (production) and fruit quality.

Therefore, it is important to study agronomy, physiology, genetics, and genomics by using advanced phenotyping tools and best management practices at the farm level to improve crop productivity and fruit quality.

This Special Issue deliberates on the approaches to measure the potential effect of environmental and biotic factors coupled with farm-level management practices in elucidating and improving horticulture crop productivity and consumer-driven fruit quality traits.

Dr. Fawad Ali
Dr. Asjad Ali
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

  • agronomy
  • digital agronomy
  • advanced phenotyping
  • image-based phenotyping
  • crop physiology
  • effect of biotic and abiotic factors
  • pre- and post-harvest factors
  • classical breeding
  • molecular breeding
  • quantitative genetics
  • allele mining
  • association mapping of grain quality traits
  • genetic mapping
  • agronomic factors
  • root physiology and genetics
  • carbon partitioning and translocation and their potential impact on crop productivity and fruit quality
  • optimization of the pre- and post-harvest methods to improve crop productivity and fruit quality
  • productivity traits
  • fruit quality traits

Published Papers (5 papers)

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Research

13 pages, 1589 KiB  
Article
In Vitro Regeneration of Chrysanthemum from Ovaries and Ovules Treated with Thermal and Chemical Stimuli: Morphogenic and Cytogenetic Effects
by Natalia Miler, Alicja Tymoszuk, Monika Rewers and Dariusz Kulus
Agriculture 2023, 13(11), 2069; https://doi.org/10.3390/agriculture13112069 - 28 Oct 2023
Viewed by 1176
Abstract
Chrysanthemum (Chrysanthemum × morifolium (Ramat.) Hemsl.) holds a prominent position in the market of ornamental plants. To further advance chrysanthemum breeding efforts, the development of haploids may be useful. Therefore, the effect of various chemical and thermal treatments on regeneration efficiency and [...] Read more.
Chrysanthemum (Chrysanthemum × morifolium (Ramat.) Hemsl.) holds a prominent position in the market of ornamental plants. To further advance chrysanthemum breeding efforts, the development of haploids may be useful. Therefore, the effect of various chemical and thermal treatments on regeneration efficiency and ploidy level in chrysanthemum was studied. Ovaries and ovules of three chrysanthemum cultivars, i.e., ‘Brasil,’ ‘Capitola,’ and ‘Jewel Time Yellow,’ were cultured either on a medium with 1 mg·L−1 2,4-dichlorophenoxyacetic acid (2,4-D) and different concentrations (0.5–1.5 mg·L−1) of thidiazuron (TDZ) or subjected to thermal shock (pretreatment temperature of 4 °C or 32 °C) and cultured on a medium with 1 mg·L−1 2,4-D and 1 mg·L−1 6-benzylaminopurine (BAP). It was found that ovaries had a greater organogenic potential (both in terms of callogenesis and shoot formation) than ovules. Microscopic analyses revealed that shoots mainly developed via indirect somatic embryogenesis from a callus developed from the ovary wall. The highest number of shoots was produced in cooled (at 4 °C) ovaries of chrysanthemum ‘Brasil’ and in ‘Jewel Time Yellow’ ovaries cultured on a medium with 1.0–1.5 mg·L−1 TDZ. The latter cultivar also had the highest potential to produce plants with an altered ploidy level (doubled and halved the number of chromosomes). This study demonstrates that manipulating factors such as temperature and thidiazuron concentration can enhance regeneration efficiency and induce altered ploidy levels in selected cultivars, offering valuable insights for chrysanthemum breeding programs. Full article
(This article belongs to the Special Issue Agronomy, Production Systems, Advanced Phenotyping, Breeding, Genetics and Genomics of Horticulture Crops)
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20 pages, 3343 KiB  
Article
Combined Transcriptomic and Metabolomic Analyses of Defense Mechanisms against Phytoplasma Infection in Camptotheca acuminata Decne
by Kai Qiao, Weiyi Huang, Xuemei Li, Jiahui Liang and Hong Cai
Agriculture 2023, 13(10), 1943; https://doi.org/10.3390/agriculture13101943 - 5 Oct 2023
Viewed by 1108
Abstract
Camptotheca acuminata Witches’-broom disease (CaWB) is the most destructive disease affecting C. acuminata in China. Previous studies on CaWB have failed to clarify the incidence pattern in C. acuminata after infection with phytoplasma. The time interval between phytoplasma infection of C. acuminata and [...] Read more.
Camptotheca acuminata Witches’-broom disease (CaWB) is the most destructive disease affecting C. acuminata in China. Previous studies on CaWB have failed to clarify the incidence pattern in C. acuminata after infection with phytoplasma. The time interval between phytoplasma infection of C. acuminata and the onset of Witches’-broom symptoms in C. acuminata was very long. C. acuminata inoculated with CaWB showed leaf margin scorching symptoms at 4 weeks in inoculated leaves. At 16 weeks after infection (WAI), old leaves were shed, while new leaves showed a mild leaf margin scorch; at 28 WAI, typical symptoms appeared. Transcriptomic and metabolomic analyses of the three sampling periods revealed 194 differentially expressed genes, mainly enriched in MAPK signaling, plant–pathogen interaction, phenylpropanoid biosynthesis, starch and phenylpropanoid biosynthesis, and phenylpropanoid biosynthesis pathways. The expression of calcium-dependent protein kinase (CDPK), β Ketoacyl-CoA Synthase1/10 (KCS1/10), and WRKY22/29 genes in the plant–pathogen interaction pathway significantly increased, indicating that they may be key genes in the CaWB phytoplasma-mediated maintenance of ROS homeostasis. Moreover, isochlorogenic acid B, atractylenolide II, and 3-methoxybenzoic acid were found, which might serve as signaling or functional substances in the defense response. Our results provide novel insights into the pathogenesis of CaWB and the defense response of C. acuminata under the influence of phytoplasma. Additionally, we identified potential candidate genes related to the defense response of C. acuminata, laying the foundation for further research. Full article
(This article belongs to the Special Issue Agronomy, Production Systems, Advanced Phenotyping, Breeding, Genetics and Genomics of Horticulture Crops)
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12 pages, 2021 KiB  
Article
Flowering Phenology of Olive Cultivars in Two Climate Zones with Contrasting Temperatures (Subtropical and Mediterranean)
by María G. Medina-Alonso, Jose M. Cabezas, Domingo Ríos-Mesa, Ignacio J. Lorite, Lorenzo León and Raúl de la Rosa
Agriculture 2023, 13(7), 1312; https://doi.org/10.3390/agriculture13071312 - 27 Jun 2023
Viewed by 933
Abstract
The large amount of olive cultivars conserved in germplasm banks can be used to overcome some of the challenges faced by the olive growing industry, including climate warming. One effect of climate warming in olive is the difficulty to fulfill the chilling requirements [...] Read more.
The large amount of olive cultivars conserved in germplasm banks can be used to overcome some of the challenges faced by the olive growing industry, including climate warming. One effect of climate warming in olive is the difficulty to fulfill the chilling requirements for flowering due to mild winter temperatures. In the present work, we evaluate seven olive cultivars for their adaptation to high winter temperatures by comparing their flowering phenology in the standard Mediterranean climate of Cordoba, Southern Iberian Peninsula, with the subtropical climate of Tenerife, Canary Islands. Flowering phenology in Tenerife was significantly earlier and longer than in Cordoba. However, genotype seems to have little influence on the effects of the lack of winter chilling temperatures, as in Tenerife. This was found even though the cultivars studied had a high genetic distance between them. In fact, all the cultivars tested in Tenerife flowered during the three-year study but showed asynchronous flowering bud burst. ‘Arbequina’ showed an earlier day of full flowering compared with the rest of the cultivars. The results observed here could be of interest to refine the phenological simulation models, including the length of the flowering period. More genetic variability should be evaluated in warm winter conditions to look for adaptation to climate warming. Full article
(This article belongs to the Special Issue Agronomy, Production Systems, Advanced Phenotyping, Breeding, Genetics and Genomics of Horticulture Crops)
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21 pages, 9875 KiB  
Article
Genome Identification and Characterization of WRKY Transcription Factor Gene Family in Mandarin (Citrus reticulata)
by Nimra Maheen, Muhammad Shafiq, Saleha Sadiq, Muhammad Farooq, Qurban Ali, Umer Habib, Muhammad Adnan Shahid, Asjad Ali and Fawad Ali
Agriculture 2023, 13(6), 1182; https://doi.org/10.3390/agriculture13061182 - 1 Jun 2023
Viewed by 1801
Abstract
WRKY proteins are an important group of transcription factors (TFs) gene family and were identified primarily in plants. WRKY TFs play vital roles in modulating gene expression when plants face detrimental effects due to the environment. In the current study, we focused on [...] Read more.
WRKY proteins are an important group of transcription factors (TFs) gene family and were identified primarily in plants. WRKY TFs play vital roles in modulating gene expression when plants face detrimental effects due to the environment. In the current study, we focused on using the mandarin citrus (Citrus reticulata) genome to understand the impact of the WRKY gene family on the extraction of alleles mining in mandarins. The mining of the C. reticulata genome identified 46 CrWRKY genes that were classified into three main groups (G1, G2, and G3) further with five subclasses (IIa, IIb, IIc, Iid, and IIe) in the G2 group, and all were presented on 29 scaffolds representing numerous segmental duplications of 100% events established. Multiple sequence analysis predicted the presence of the “WRKYGQK” domain and metal-chelating zinc-finger motif C2H2 in 45 genes, while the “WRKYGQK” domain was replaced with “WRKYGKK” only in CrWRKY20. The comparative relationship of CrWRKY with other plant species using dual synteny analysis revealed that the divergence between C. reticulata and C. grandis occurred after the evolutionary divergence of C. clementine, C. sinensis, C. medica, and C. ichangensis. The possible functions of the CrWRKY genes in mitigating environmental effects were predicted using cis-regulatory elements analysis and in silico RNAseq analysis, for the development of plants. These results provide a robust platform and absence of knowledge for the functional identification from key genes of CrWRKY genes in the mandarin for the possible use to improve key desirable agronomic and consumer-driven fruit quality traits in mandarins and related species. Full article
(This article belongs to the Special Issue Agronomy, Production Systems, Advanced Phenotyping, Breeding, Genetics and Genomics of Horticulture Crops)
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19 pages, 4826 KiB  
Article
Estimating Freezing Injury on Olive Trees: A Comparative Study of Computing Models Based on Electrolyte Leakage and Tetrazolium Tests
by Mehdi Rezaei and Abbas Rohani
Agriculture 2023, 13(6), 1137; https://doi.org/10.3390/agriculture13061137 - 29 May 2023
Cited by 1 | Viewed by 1460
Abstract
Winter frost injury is a major limiting factor for olive cultivation in temperate regions. The response of olive shoots to freezing stress can be used for selecting genotypes resistant to freezing. The electrolyte leakage (EL) and tetrazolium tests (TZ) are commonly used to [...] Read more.
Winter frost injury is a major limiting factor for olive cultivation in temperate regions. The response of olive shoots to freezing stress can be used for selecting genotypes resistant to freezing. The electrolyte leakage (EL) and tetrazolium tests (TZ) are commonly used to evaluate dead tissues in cold stress studies. The temperature–response curve of dead tissues to lethal temperature (LT) is measured with models to calculate LT50 and LT90. In this study, we evaluated the accuracy and efficiency of eighteen nonlinear regression models (NLRs) in calculating LT50 and LT90 of freezing stress in different olive cultivars at various stages of dormancy. After evaluating the prediction performance of NLR models, it was found that only eight models were suitable for the purpose of this research out of the eighteen models examined. The 2p-logistic and Gompertz models were selected for modeling EL and TZ, respectively. Our research findings indicate that the Roughani, Kawi, and Zard varieties of olive trees exhibit the best performance under artificial temperature-controlled conditions. Our findings provide valuable insights into selecting frost-resistant cultivars and designing effective strategies for cold acclimation in olive cultivation. Full article
(This article belongs to the Special Issue Agronomy, Production Systems, Advanced Phenotyping, Breeding, Genetics and Genomics of Horticulture Crops)
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