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Recent Progress in Molecular Investigations of Crop Plants and Crop...
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Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (31 January 2023) | Viewed by 17682

Special Issue Editor

Dr. Fengjie Sun

E-Mail Website
Guest Editor
School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
Interests: plant protection; flower development; molecular systematics and evolution; phylogenetics; plant responses to environmental stress; genetics; genomics; bioinformatics; bioremediation; soil microorganisms
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

With the increasing demand for food and energy supply worldwide, it is becoming extremely important to investigate effective and efficient methodologies for cultivating soil, growing crop plants, and raising livestock with a changing planetary landscape. Agricultural products are also widely applied in various systems for multiple purposes, including developing products important for engineering and medicine. Facilitated by next-generation DNA sequencing technology, our understanding of the interactions between crop plants, the soil, and the soil’s inhabitants has been dramatically improved from a wide range of perspectives. We invite you to contribute to this Special Issue with a genetic, genomic, or biological study of a crop and its environment. We plan to cover a wide range of topics including, but not limited to:

(1) application of genetics, genomics, and other molecular methodologies in crop plants or other model plant systems;

(2) developmental and evolutionary studies of major crops;

(3) crop-supporting microbial structures and bioremediation of the environment;

(4) molecular investigations of applications of agricultural products in various systems, including medicinal plants;

(5) traditional and modern research areas, such as plant physiology, development, ecology, and bioinformatics in a greenhouse or field.

We strongly believe that this Special Issue of Agronomy will greatly enhance our understanding of the applications of advanced techniques and innovative approaches that can help to address food, energy, and related global-change crises worldwide.

Dr. Fengjie Sun
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. Agronomy 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
  • breeding
  • abiotic and biotic stresses
  • domestication
  • fruit
  • genetic diversity
  • molecular mechanisms
  • bioremediation

Published Papers (9 papers)

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Research

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17 pages, 8080 KiB  
Article
Morphological Characterization of Metamorphosis in Stamens of Anemone barbulata Turcz. (Ranunculaceae)
by Hongli Chang, Weihong Ji, Yule Xie, Shujun He, Zhenfeng Xie and Fengjie Sun
Agronomy 2023, 13(2), 554; https://doi.org/10.3390/agronomy13020554 - 15 Feb 2023
Cited by 1 | Viewed by 1567
Abstract
The morphological characteristics of metamorphosis in stamens of Anemone barbulata Turcz. were investigated using morphological and histological analyses. The results showed that stamens were transformed into either white sepaloid organs or more frequently green leaflike structures with successive variations. The extreme metamorphic stamen [...] Read more.
The morphological characteristics of metamorphosis in stamens of Anemone barbulata Turcz. were investigated using morphological and histological analyses. The results showed that stamens were transformed into either white sepaloid organs or more frequently green leaflike structures with successive variations. The extreme metamorphic stamen was represented as a three-lobed leaflike structure with a long stalk, highly consistent with the morphological characters of the normal leaves of the plant. It was hypothesized that the connective and two pollen sacs of the anther were transformed into the three lobes of the metamorphosed stamen, respectively. The depression and circinate stages were identified as the important and necessary processes in the transformation of stamens from axial to foliar organs, suggesting probably the alternative evolutionary process of the formation of anthers derived from foliar organs. The morphological traces of leaf, sepal, and carpel observed in the metamorphosed stamens suggested the homeotic transformations among these organs. The foliar stage in the ancestral stamens of angiosperms was reflected ontogenically in the metamorphosed stamens of A. barbulata. Our findings of a series of metamorphic stamens probably represent the morphological evidence to support the hypothesis that the flowers of angiosperms were derived from metamorphic leaves with the progressive development mode in the evolution of floral organs. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II)
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17 pages, 11152 KiB  
Article
The Complete Chloroplast Genomes of Two Physalis Species, Physalis macrophysa and P. ixocarpa: Comparative Genomics, Evolutionary Dynamics and Phylogenetic Relationships
by Zhenhao Zhang, Yanyun Jin, Yadi Gao, Yong Zhang, Qicai Ying, Chenjia Shen, Jiangjie Lu, Xiaori Zhan, Huizhong Wang and Shangguo Feng
Agronomy 2023, 13(1), 135; https://doi.org/10.3390/agronomy13010135 - 30 Dec 2022
Cited by 4 | Viewed by 1484
Abstract
Physalis macrophysa (PMA) and Physalis ixocarpa (PIX) have significant economic, medicinal, and ornamental value and are often used in the fields of edible fruits, medicinal herbs, and ornamental plants. In the present study, we obtained the complete chloroplast (cp) genome sequences of PMA [...] Read more.
Physalis macrophysa (PMA) and Physalis ixocarpa (PIX) have significant economic, medicinal, and ornamental value and are often used in the fields of edible fruits, medicinal herbs, and ornamental plants. In the present study, we obtained the complete chloroplast (cp) genome sequences of PMA and PIX, compared to the cp genome sequences of 10 Physalis species, and constructed the phylogenetic tree among the tribe Physaleae. The results showed that the cp genomes of PMA and PIX consisted of a large single copy (LSC) region (87,115 bp and 87,103 bp, respectively), a small single copy (SSC) region (18,412 bp and 18,420 bp, respectively), and a pair of same-length inverted-repeat (IRa and IRb) regions (25,604 bp and 25,674 bp, respectively). The two species contained 132 genes, including 87 encoding proteins, eight encoding ribosomal RNAs (rRNAs), and 37 encoding transfer RNAs (tRNAs), which indicated that the two species have strong similarities with respect to genome structure and gene content. PMA and PIX contained repeat sequences (35 and 40, respectively) and simple-sequence repeats (SSRs) (61 and 60, respectively). Nine regions with considerable nucleotide divergence were found, most of which were located in the LSC and SSC regions. The gene selective pressure analysis indicated that eight genes were affected by positive selection, the Ka/Ks values of which were greater than one. Our phylogenetic results indicated that PMA and PIX had the closest genetic relationship and are closely adjacent to Physalis philadelphica (PPH) in the subtribe Physalinae. Our analysis of the cp genomes in both Physalis species will be beneficial for further research into species identification, phylogeny, evolution, and the potential for germplasm resource exploitation in Physalis. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II)
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21 pages, 4858 KiB  
Article
Molecular Mechanisms Regulating the Oil Biosynthesis in Olive (Olea europaea L.) Fruits Revealed by Transcriptomic Analysis
by Jipeng Qu, Zhenyong Chen, Bixia Wang, Shiling Feng, Zhaoguo Tong, Tao Chen, Lijun Zhou, Zhengsong Peng and Chunbang Ding
Agronomy 2022, 12(11), 2718; https://doi.org/10.3390/agronomy12112718 - 2 Nov 2022
Cited by 1 | Viewed by 1443
Abstract
As one of the most important crops for oil, olive (Olea europaea L.) is well-known worldwide for its commercial product “virgin olive oil” containing high-content fatty acids and many secondary metabolites. The molecular mechanisms underlying the enhanced oil content in olive remain [...] Read more.
As one of the most important crops for oil, olive (Olea europaea L.) is well-known worldwide for its commercial product “virgin olive oil” containing high-content fatty acids and many secondary metabolites. The molecular mechanisms underlying the enhanced oil content in olive remain unclear. To further investigate the molecular mechanisms of olive oil biosynthesis, we selected two olive cultivars, i.e., Kalinjot (JZ) and Coratina (KLD), at three maturity stages (MI-1, MI-3, and MI-6) for transcriptomic analysis based on Nanopore sequencing. Significant differences were observed in oil content between JZ and KLD during three maturity stages. Enrichment analysis revealed significant enrichment of differentially expressed genes (DEGs) in metabolic pathways of photosynthesis, amino acid biosynthesis, response to stress, and energy metabolism, in particular, fatty acid metabolism. A total of 170 (31.54% of 539 genes involved in oil synthesis) DEGs were further investigated based on expression analysis to identify their molecular functions in oil biosynthesis in olive. A co-expression network based on 714 transcription factors and their targeted genes in oil biosynthesis was constructed. Our study provided novel experimental evidence to investigate the molecular mechanisms of olive oil biosynthesis and to improve the breeding of olive varieties with enhanced oil contents. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II)
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18 pages, 9635 KiB  
Article
GmDNAJC7 from Soybean Is Involved in Plant Tolerance to Alkaline-Salt, Salt, and Drought Stresses
by Ting Jin, Zhong Shan, Shuang Zhou, Qianqian Yang, Junyi Gai and Yan Li
Agronomy 2022, 12(6), 1419; https://doi.org/10.3390/agronomy12061419 - 13 Jun 2022
Cited by 13 | Viewed by 2302
Abstract
Soybean [Glycine max (L.) Merri.] is an important oilseed and food crop. In recent years, environmental degradation has accelerated soil alkalization, salinization, and water deficit, which have seriously threatened the soybean quality and yield. Chaperone DNAJ proteins play important roles in plant [...] Read more.
Soybean [Glycine max (L.) Merri.] is an important oilseed and food crop. In recent years, environmental degradation has accelerated soil alkalization, salinization, and water deficit, which have seriously threatened the soybean quality and yield. Chaperone DNAJ proteins play important roles in plant response to a number of abiotic and biotic stresses. Here, we investigated the function of a soybean DNAJ gene, GmDNAJC7, in plant tolerance to abiotic stresses. GmDNAJC7 gene expression was induced by alkaline-salt, salt, and drought treatments in soybean roots, suggesting its possible role in soybean response to these stresses. GmDNAJC7 overexpression improved the alkaline-salt tolerance of soybean composite plants, which showed a higher SPAD (Soil and Plant Analysis Development) value for chlorophyll content and leaf relative water content than the control plants after NaHCO3 treatment. Moreover, the GmDNAJC7 overexpressing Arabidopsis had a higher germination rate and average root length than the wild type and dnajc7 mutant, under NaHCO3, NaCl, and mannitol stresses, indicating that the ectopic expression of the GmDNAJC7 gene enhanced the alkaline-salt, salt, and drought tolerance in Arabidopsis. These findings suggest that GmDNAJC7 is involved in the alkaline-salt, salt, and drought tolerance in Arabidopsis and soybean. This study provides new insights into the role of DNAJ proteins in plant tolerance to abiotic stress. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II)
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23 pages, 6802 KiB  
Article
Transcriptomic Characterizations of the Molecular Mechanisms Regulating Lipid Production and Composition in Mortierella alpina in Response to Cold Stress
by Jiali Ren, Haijun Wang, Fengjie Sun, Chunxiao Meng, Xiangyu Zhu, Zuoxi Wei, Zhengquan Gao and Demao Li
Agronomy 2022, 12(3), 599; https://doi.org/10.3390/agronomy12030599 - 28 Feb 2022
Cited by 1 | Viewed by 2223
Abstract
Cold stress causes changes in the lipid composition of Mortierella alpina. In order to investigate the molecular mechanisms of M. alpina in response to cold stress, transcriptome analyses were performed on three groups of M. alpina cultured at (1) 25 °C, (2) [...] Read more.
Cold stress causes changes in the lipid composition of Mortierella alpina. In order to investigate the molecular mechanisms of M. alpina in response to cold stress, transcriptome analyses were performed on three groups of M. alpina cultured at (1) 25 °C, (2) 15 °C, and (3) first at 25 °C for 2 days and then 15 °C for 7 days, respectively. The results of a gas chromatography–mass spectrometry (GC–MS) analysis suggested that, compared with 25 °C conditions, dry weight and lipid production were significantly decreased in M. alpina grown at 15 °C, with a total of 1552 differentially expressed genes (DEGs) identified in response to cold stress. The quantitative real-time PCR (qRT-PCR) analysis was conducted to verify the expression patterns of six DEGs involved in lipid metabolism. Results of the enrichment analyses of the DEGs based on the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) databases showed that fatty acid compositions were regulated by genes involved in the glycolysis pathway, fatty acid synthesis, the pentose phosphate pathway, the glycerolipid pathway, the tricarboxylic acid (TCA) cycle, and the glycerophospholipid pathway. Our study provided solid experimental evidence and novel insights into the metabolic engineering and the molecular mechanisms regulating the response to cold stress in M. alpina. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II)
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12 pages, 2050 KiB  
Article
Identification of Genetic Loci on Chromosome 4B for Improving the Grain Number per Spike in Pre-Breeding Lines of Wheat
by Jinpeng Zhang, Qifu Yao, Ruixin Li, Yuqing Lu, Shenghui Zhou, Haiming Han, Weihua Liu, Xiuquan Li, Xinming Yang and Lihui Li
Agronomy 2022, 12(1), 171; https://doi.org/10.3390/agronomy12010171 - 11 Jan 2022
Cited by 7 | Viewed by 1824
Abstract
The grain number per spike (GNPS) is an important yield component, and much attention is given to the increase in GNPS for current yield improvement of common wheat. Here, a panel of 259 pre-breeding lines and elite commercial varieties were collected for the [...] Read more.
The grain number per spike (GNPS) is an important yield component, and much attention is given to the increase in GNPS for current yield improvement of common wheat. Here, a panel of 259 pre-breeding lines and elite commercial varieties were collected for the investigation of 12 agronomic traits, especially for spike-related traits, with 2-year replicates. The high correlation between GNPS and kernel number per spikelet (KNS) suggested that the high GNPS trait in our pre-breeding lines was mainly controlled by grain set number per spikelet. Genome-wide association studies (GWAS) using the 660K SNP genotyping assay suggested that a major locus on chromosomes 4BS contributed to the high GNPS trait, which contributed to 33% and 48% of the variation in KNS and GNPS, respectively. A good diagnostic KASP marker AX-109286577 flanking the 4BS locus was developed for easy selection of the large spike trait. Taken together, the results suggested that untapped rare allele variation in our pre-breeding lines can be used for improvement of the yield component of set grain number per spike. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II)
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16 pages, 4424 KiB  
Article
Analyses of Chloroplast Genome of Eutrema japonicum Provide New Insights into the Evolution of Eutrema Species
by Mengyao Li, Ran Zhang, Jie Li, Kaimin Zheng, Jiachang Xiao and Yangxia Zheng
Agronomy 2021, 11(12), 2546; https://doi.org/10.3390/agronomy11122546 - 15 Dec 2021
Cited by 7 | Viewed by 2243
Abstract
Wasabi (Eutrema japonicum) is a vegetable of Brassicaceae family, currently cultivated in Southwest Asia. It is rich in nutritional and has a spicy flavour. It is regarded as a rare condiment worldwide. Its genetic profile for yield improvement and the development [...] Read more.
Wasabi (Eutrema japonicum) is a vegetable of Brassicaceae family, currently cultivated in Southwest Asia. It is rich in nutritional and has a spicy flavour. It is regarded as a rare condiment worldwide. Its genetic profile for yield improvement and the development of E. japonicum germplasm resources remains unknown. Cognizant of this, this study sequenced and assembled the chloroplast (cp) genome of E. japonicum to enrich our genomic information of wasabi and further understand genetic relationships within the Eutrema species. The structural characteristics, phylogeny, and evolutionary relationship of cp genomes among other Brassicaceae plants were analyzed and compared to those of Eutrema species. The cp genome of E. japonicum has 153,851 bp with a typical quadripartite structure, including 37 tRNA genes, 8 rRNA genes, and 87 protein-coding genes. It contains 290 simple sequence repeats and prefers to end their codons with an A or T, which is the same as other Brassicaceae species. Moreover, the cp genomes of the Eutrema species had a high degree of collinearity and conservation during the evolution process. Nucleotide diversity analysis revealed that genes in the IR regions had higher Pi values than those in LSC (Large single copy) and SSC (Small single copy) regions, making them potential molecular markers for wasabi diversity studies. The analysis of genetic distance between Eutrema plants and other Brassicacea plants showed that intraspecies variation was found to be low, while large differences were found between genera and species. Phylogenetic analysis based on 29 cp genomes revealed the existence of a close relationship amongst the Eutrema species. Overall, this study provides baseline information for cp genome-based molecular breeding and genetic transformation studies of Eutrema plants. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II)
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17 pages, 6747 KiB  
Article
Characterization of Molecular Properties and Expression of Gene GmPLMT and Its Effects on the Production of Lipid Metabolites in Soybean and Arabidopsis thaliana
by Zhanyu Chen, Yushuang Wang, Yanbo Chen, Xiaoqin Yang, Shuang Wang, Tingting Yu, Ying Zhou and Xiyan Cui
Agronomy 2021, 11(12), 2454; https://doi.org/10.3390/agronomy11122454 - 1 Dec 2021
Cited by 1 | Viewed by 1479
Abstract
Phospholipid N-methyltransferase (PLMT) plays an important role in the synthesis of phosphatidylcholine (PtdCho). The aim of this study was to characterize the molecular properties of GmPLMT and the expression of soybean GmPLMT and its effects on the production of lipid metabolites. Results showed [...] Read more.
Phospholipid N-methyltransferase (PLMT) plays an important role in the synthesis of phosphatidylcholine (PtdCho). The aim of this study was to characterize the molecular properties of GmPLMT and the expression of soybean GmPLMT and its effects on the production of lipid metabolites. Results showed that GmPLMT composed of mainly α-helix was a hydrophobic and transmembrane protein. In soybean leaves, GmPLMT was highly expressed during seedling and flowering stages. In transgenic Arabidopsis thaliana, the highest and lowest expression levels of GmPLMT were detected at flowering and maturity stages, respectively. The total phospholipid contents in soybean grains were decreased from 7.2% (35 days after flowering) to 4.8% (55 days after flowering) and then increased to 7.0% (75 days after flowering). The contents of PtdCho showed a similar pattern to that of total phospholipids. In transgenic A. thaliana seeds, the contents of total phospholipids and PtdCho were significantly increased. Significantly positive correlations were revealed between expression of GmPLMT and contents of both PtdCho and crude fats, and between the contents of PtdCho and both linoleic acid and linolenic acid, suggesting that increased expression of GmPLMT improved the production of lipid metabolites. This study provided solid experimental evidence for further improvement of soybean quality based on GmPLMT in the molecular breeding of soybeans. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II)
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Review

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13 pages, 575 KiB  
Review
Advances in Barley Breeding for Improving Nitrogen Use Efficiency
by Zhiwei Chen, Luli Li, Nigel G. Halford, Hongwei Xu, Linli Huang, Runhong Gao, Ruiju Lu and Chenghong Liu
Agronomy 2022, 12(7), 1682; https://doi.org/10.3390/agronomy12071682 - 15 Jul 2022
Cited by 3 | Viewed by 2118
Abstract
Crop breeding for high nitrogen use efficiency (NUE) or tolerance to low nitrogen fertilization is thought to be an ideal solution to reduce the cost, carbon footprint, and other environmental problems caused by the excess use of nitrogen fertilizers. As a model plant [...] Read more.
Crop breeding for high nitrogen use efficiency (NUE) or tolerance to low nitrogen fertilization is thought to be an ideal solution to reduce the cost, carbon footprint, and other environmental problems caused by the excess use of nitrogen fertilizers. As a model plant for cereal crops, barley has many advantages, including good adaptability, a short growth period, and high natural stress resistance or tolerance. Therefore, research on improving NUE in barley is not only beneficial for nitrogen-efficient barley breeding but will also inform NUE improvement in other cereal crops. In this review, recent progress in understanding barley’s response to nitrogen nutrition, evaluation of NUE or low-nitrogen tolerance, quantitative trait loci (QTL) mapping and gene cloning associated with improving NUE, and breeding of nitrogen-efficient barley is summarized. Furthermore, several biotechnological tools that could be used for revealing the molecular mechanisms of NUE or breeding for improving NUE in barley are introduced, including GWAS, omics, and gene editing. The latest research ideas in unraveling the molecular mechanisms of improving NUE in other crops are also discussed. Thus, this review provides a better understanding of improving the NUE of barley and some directions for future research in this area. Full article
(This article belongs to the Special Issue Recent Progress in Molecular Investigations of Crop Plants and Crop Plant–Environment Interactions from Genetic and Genomic Perspectives: Applications and Challenges—Series II)
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