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Recognition and Utilization of Natural Genetic Resources for Advances in...
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Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition

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

Deadline for manuscript submissions: closed (30 September 2024) | Viewed by 17025

Special Issue Editors

Prof. Dr. Jian Zhang

E-Mail Website1 Website2
Guest Editor
1. Department of Biology, University of British Columbia, Okanagan, Kelowna, BC V1V 1V7, Canada
2. Faculty of Agronomy, Jilin Agricultural University, Changchun 131018, China
Interests: digital agriculture; bioinformatics; genomics; plant phenomics; indoor breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Guofei Tan

E-Mail Website
Guest Editor
Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, China
Interests: biotechnology; genomics; vegetable biology; germplasm; secondary metabolism; breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Feng Que

E-Mail Website
Guest Editor
Bamboo Research Institute, Nanjing Forestry University, Nanjing 210037, China
Interests: growth and development of bamboo plants; hormones in bamboo plants; cell wall development
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Following the success of the first Special Issue on “Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology” (https://www.mdpi.com/journal/agronomy/special_issues/genetic_resources_biotechnology) in Agronomy, the Editorial Office is pleased to launch a second series of the Special Issue.

Biological diversity is the most important of nature’s gifts, and many elite or superior gene alleles that confer favorable traits remain to be discovered and utilized. With the advancement of “omics” disciplines, plant genetic resources and biodiversity have become more critical for future agricultural and horticultural development. The data mining of these genetic resources to advance domestication has great potential in enhancing crop vegetable yields and quality through molecular breeding and genetic engineering. A better knowledge of accumulated genomic plant resources for seeds, tubers, bamboo, etc., would help provide a fundamental understanding of the underlying genetics, physiology, biochemistry and metabolism, with the aim of developing improved breeding regimes for future agriculture and horticulture.

The introduction of newly identified germplasms for major crops improves their important traits, such as oil, fiber and bioproduct production, and increases the understanding of the genetic background, genome information, proteome and metabolome of plants.

Second and third generation sequencing, GWAS, transcriptomics, proteomics, metabolomics, and genetic basis of quality and production.

What kind of papers we are soliciting: crop genomics; genetic improvement; molecular markers; genetic engineering/transformation; organ formation and development and their genetic basis; digital agriculture.

Prof. Dr. Jian Zhang
Dr. Guofei Tan
Dr. Feng Que
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. 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

  • genetic resources
  • genomics biotechnology
  • genetic transformation
  • tissue culture

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Published Papers (12 papers)

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Research

13 pages, 2462 KiB  
Article
Medium-Term Monitoring of Greenhouse Gases above Rice-Wheat Rotation System Based on Mid-Infrared Laser Heterodyne Radiometer
by Zhengyue Xue, Jun Li, Fengjiao Shen, Sheng Zhang, Xueyou Hu and Tu Tan
Agronomy 2024, 14(9), 2162; https://doi.org/10.3390/agronomy14092162 - 22 Sep 2024
Viewed by 3293
Abstract
The rice-wheat rotation system is a major agricultural practice in China as well as an important source of greenhouse gas (GHG) emissions. In this study, the developed mid-infrared laser heterodyne radiometer (MIR-LHR) was used for the remote sensing of atmospheric CH4 and [...] Read more.
The rice-wheat rotation system is a major agricultural practice in China as well as an important source of greenhouse gas (GHG) emissions. In this study, the developed mid-infrared laser heterodyne radiometer (MIR-LHR) was used for the remote sensing of atmospheric CH4 and N2O concentrations above the rice-wheat rotation system. From April 2019 to May 2022, the atmospheric column concentrations of CH4 and N2O above the rice-wheat rotation system were continuously observed in Hefei, China. The peak values of the N2O column concentration appeared 7~10 days after wheat seasonal fertilization, with additional peaks during the drainage period of rice cultivation. During the three-year rice-wheat crop rotation cycle, a consistent trend was observed in the CH4 column concentrations, which increased during the rice-growing season and subsequently decreased during the wheat-growing season. The data reveal different seasonal patterns and the impact of agricultural activities on their emissions. During the observation period, the fluctuations in the CH4 and N2O column concentrations associated with the rice-wheat rotation system were about 40 ppbv and 6 ppbv, respectively. The MIR-LHR developed for this study shows great potential for analyzing fluctuations in atmospheric column concentrations caused by GHG emissions in the rice-wheat rotation system. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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14 pages, 2417 KiB  
Article
Multi-Year Insights into Industrial Hemp Growth in a Mediterranean Climate
by Eleni Tsaliki, Theodoros Moysiadis, Apostolos Kalivas, Ioannis Panoras and Ioannis Grigoriadis
Agronomy 2024, 14(9), 1946; https://doi.org/10.3390/agronomy14091946 - 28 Aug 2024
Viewed by 617
Abstract
Hemp (Cannabis sativa L.) is a rapidly growing plant with multipurpose uses, and the optimal combination of yield and quality of hemp products (fibers, inflorescences, or seeds) may provide economic opportunities to uncover the full spectrum of its capabilities. The presented experimentation [...] Read more.
Hemp (Cannabis sativa L.) is a rapidly growing plant with multipurpose uses, and the optimal combination of yield and quality of hemp products (fibers, inflorescences, or seeds) may provide economic opportunities to uncover the full spectrum of its capabilities. The presented experimentation took place over seven years (2017–2023) in Greek climatic conditions for fourteen (14) registered monoecious and dioecious varieties. It can be concluded that the production of biomass, fiber, and seed weight were different not only between varieties but also from year to year. Despite significant variation between harvest years in biomass yield, the extracted fiber was relatively constant. Moreover, not only the dioecious varieties but also the monecious varieties could be effectively grown for biomass production in Greece. Regarding fiber production, monoecious varieties had the highest yields, apart from the dioecious Kompolti variety, which was the most fiber-productive. Under the experimentation conditions, early flowering varieties were most suited for seed production, and the KC Dora variety produced the heavier seeds. Generally, the Futura 75 variety was one of the most productive varieties for biomass and seed weight, while the Bialobrzeskie variety produced the greatest amounts of fiber. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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15 pages, 5989 KiB  
Article
Instance Segmentation of Lentinus edodes Images Based on YOLOv5seg-BotNet
by Xingmei Xu, Xiangyu Su, Lei Zhou, Helong Yu and Jian Zhang
Agronomy 2024, 14(8), 1808; https://doi.org/10.3390/agronomy14081808 - 16 Aug 2024
Viewed by 739
Abstract
The shape and quantity of Lentinus edodes (commonly known as shiitake) fruiting bodies significantly affect their quality and yield. Accurate and rapid segmentation of these fruiting bodies is crucial for quality grading and yield prediction. This study proposed the YOLOv5seg-BotNet, a model for [...] Read more.
The shape and quantity of Lentinus edodes (commonly known as shiitake) fruiting bodies significantly affect their quality and yield. Accurate and rapid segmentation of these fruiting bodies is crucial for quality grading and yield prediction. This study proposed the YOLOv5seg-BotNet, a model for the instance segmentation of Lentinus edodes, to research its application for the mushroom industry. First, the backbone network was replaced with the BoTNet, and the spatial convolutions in the local backbone network were replaced with global self-attention modules to enhance the feature extraction ability. Subsequently, the PANet was adopted to effectively manage and integrate Lentinus edodes images in complex backgrounds at various scales. Finally, the Varifocal Loss function was employed to adjust the weights of different samples, addressing the issues of missed segmentation and mis-segmentation. The enhanced model demonstrated improvements in the precision, recall, Mask_AP, F1-Score, and FPS, achieving 97.58%, 95.74%, 95.90%, 96.65%, and 32.86 frames per second, respectively. These values represented the increases of 2.37%, 4.55%, 4.56%, 3.50%, and 2.61% compared to the original model. The model achieved dual improvements in segmentation accuracy and speed, exhibiting excellent detection and segmentation performance on Lentinus edodes fruiting bodies. This study provided technical fundamentals for future application of image detection and decision-making processes to evaluate mushroom production, including quality grading and intelligent harvesting. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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15 pages, 4479 KiB  
Article
Metabolic Profiling and Transcriptome Analysis Provide Insights into the Anthocyanin Types and Biosynthesis in Zingiber striolatum Diels Flower Buds in Three Planting Modes
by Dan Zhou, Tianhong Wang, Qian Zhao and Guofei Tan
Agronomy 2024, 14(7), 1414; https://doi.org/10.3390/agronomy14071414 - 28 Jun 2024
Viewed by 869
Abstract
The flower buds of Zingiber striolatum Diels are considered a special vegetable in China, and they are rich in anthocyanins. However, the detailed composition types and the molecular mechanism of anthocyanin biosynthesis in Z. striolatum flower buds are still unclear. In this study, [...] Read more.
The flower buds of Zingiber striolatum Diels are considered a special vegetable in China, and they are rich in anthocyanins. However, the detailed composition types and the molecular mechanism of anthocyanin biosynthesis in Z. striolatum flower buds are still unclear. In this study, targeted metabolites were used to analyze and identify the anthocyanin types of Z. striolatum in three planting modes: monoculture (CK), intercropping with maize (ZP), and intercropping with soybean (SP). A total of 48 anthocyanins were identified with significant differential accumulation in Z. striolatum flower buds. Among them, cyanidin-3-O-glucoside was the main composition type of anthocyanins. Furthermore, the composition types of blue anthocyanin were identified in flower buds. A total of 15 structure genes were obtained from the transcriptome database of Z. striolatum flower buds. The qRT-PCR results revealed that the expression levels of ZsC4H-1, ZsC4H-2, ZsCHS-2, ZsCHI, ZsF3H, ZsF3′H, ZsDFR, ZsF3′5′H-3, and ZsANS genes were the highest in the ZP model. This study showed that the ZP model contributes to anthocyanin synthesis and accumulation of Z. striolatum flower buds among the three planting modes of Z. striolatum. These findings provide valuable information for research on the planting model and anthocyanin biosynthesis in Z. striolatum flower buds. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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20 pages, 6356 KiB  
Article
The Effects of Exogenous Iron on the Photosynthetic Performance and Transcriptome of Rice under Salt–Alkali Stress
by Dapeng Gao, Shuting Zhao, Rang Huang, Yanqiu Geng and Liying Guo
Agronomy 2024, 14(6), 1253; https://doi.org/10.3390/agronomy14061253 - 10 Jun 2024
Viewed by 911
Abstract
Saline-sodic stress induces iron deficiency in rice, reduces leaf photosynthetic performance, and inhibits yield enhancement. In this study, we investigated the effects of exogenous Fe on the photosynthetic performance and transcriptomics of two different tolerant rice cultivars CB9 (Changbai9: saline tolerant cultivar) and [...] Read more.
Saline-sodic stress induces iron deficiency in rice, reduces leaf photosynthetic performance, and inhibits yield enhancement. In this study, we investigated the effects of exogenous Fe on the photosynthetic performance and transcriptomics of two different tolerant rice cultivars CB9 (Changbai9: saline tolerant cultivar) and TH899 (Tonghe899: saline sensitive cultivar) with 4-week-old Fe-deficient rice seedlings under saline stress, Fe deficiency stress, and both co-stresses. The results showed that under saline and alkaline stress, spraying exogenous iron favored the growth of the two cultivars of rice, with a 32.68% and 39.82 increase in fresh weight, a 2.20-fold and 2.16-fold increase in pigment, respectively, and an 80.28% and 100.00% increase in net photosynthetic rate, respectively, as compared with the iron-deficiency treatment. Transcriptome analysis showed that we found a higher number of differentially expressed genes (7785 differentially expressed genes) in response to exogenous Fe spraying in the soda-salt sensitive variety TH899. The differentially expressed genes that are common to the two cultivars are primarily enriched in metabolic pathways, including plant hormone signal transduction (map04075) and phenylpropanoid biosynthesis (map00940). Specifically, among these genes, 14 are differentially expressed in the carotenoid biosynthetic metabolic pathway. The differentially expressed genes specific to the salinity-tolerant variety CB9 were mainly enriched in the metabolic pathways of glyoxylate and dicarboxylic acid methyl metabolism (map00630), and carbon fixation in photosynthetic organisms (map00710), among which 20 genes were significantly expressed in the pathway for carbon fixation in photosynthetic organisms (map00710). The research results offer specific theoretical support for enhancing the salt tolerance of rice. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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14 pages, 2853 KiB  
Article
Whole-Genome Evolutionary Analyses of Non-Endosymbiotic Organelle-Targeting Nuclear Genes Reveal Their Genetic Evolution in 12 Representative Poaceae Species
by Yanan Yu, Yue Yu, Yuefan Dong, Guo Li, Ning Li, Bao Liu, Tianya Wang, Lei Gong and Zhibin Zhang
Agronomy 2024, 14(6), 1177; https://doi.org/10.3390/agronomy14061177 - 30 May 2024
Viewed by 777
Abstract
Chloroplasts and mitochondria, descendants of ancient prokaryotes via endosymbiosis, occupy a pivotal position in plant growth and development due to their intricate connections with the nuclear genome. Genes encoded by the nuclear genome but relocated to or being functional within these organelles are [...] Read more.
Chloroplasts and mitochondria, descendants of ancient prokaryotes via endosymbiosis, occupy a pivotal position in plant growth and development due to their intricate connections with the nuclear genome. Genes encoded by the nuclear genome but relocated to or being functional within these organelles are commonly referred as organelle-targeting nuclear genes (ONGs). These genes are essential for maintaining cytonuclear coordination, thereby determining the stability of the life cycle. While molecular function and cytonuclear coordination of some endosymbiosis-derived ONGs (E-ONGs) have been extensively studied, the evolutionary history and characteristics from a more widespread range of non-endosymbiosis-derived ONGs (NE-ONGs) remain largely enigmatic. In this study, we focused on 12 representative species within the Poaceae family to systematically identify NE-ONGs and investigated their evolutionary history and functional significance on a phylogenetic timescale. Upon aligning these 12 species’ evolutionary histories, we observed the following phenomena: (i) an exploration of NE-ONGs between the BOP and PACMAD clades unveiled dynamic compositions, potentially influencing their photosynthetic divergence; (ii) the majority of the abundant species-specific NE-ONGs exist in a single-copy status, and functional enrichment analysis further underscored their specialized roles, which could be crucial for species adaptation; and (iii) comparative analyses between plasmid- and mitochondria-related NE-ONGs (pNE-ONGs and mNE-ONGs) revealed a prevalence of pNE-ONGs, indicating tighter control for chloroplast function in Poaceae. In summary, this study offers novel insights into the cytonuclear co-evolutionary dynamics in Poaceae speciation and draws attention to crop improvement by using NE-ONGs. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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16 pages, 7031 KiB  
Article
Complete Plastomes of Ten Rorippa Species (Brassicaceae): Comparative Analysis and Phylogenetic Relationships
by Ting Ren, Lulu Xun, Yun Jia and Bin Li
Agronomy 2024, 14(5), 913; https://doi.org/10.3390/agronomy14050913 - 26 Apr 2024
Cited by 1 | Viewed by 1092
Abstract
The genus Rorippa belongs to the family Brassicaceae, and its members usually have high medicinal value. The genus consists of approximately 75 species and mainly grows in the Northern Hemisphere, occurring in every continent except Antarctica. The taxonomy and phylogenetic relationships of Rorippa [...] Read more.
The genus Rorippa belongs to the family Brassicaceae, and its members usually have high medicinal value. The genus consists of approximately 75 species and mainly grows in the Northern Hemisphere, occurring in every continent except Antarctica. The taxonomy and phylogenetic relationships of Rorippa are still unsettled, largely due to complex morphological variations in Rorippa, which were caused by frequent hybridization events. Here, we sequenced four complete plastid genomes of Rorippa species by Illumina paired-end sequencing. The four new plastid genomes of Rorippa ranged in total size from 154,671 bp for R. palustris to 154,894 bp for R. sylvestris. There are 130 genes in the four plastomes, embodying 8 rRNA, 37 tRNA, and 85 protein-coding genes. Combining with six published plastid genomes, we carried on comparative and phylogenetic analyses. We found that the ten Rorippa plastid genomes were conservative in gene number and order, total size, genomic structure, codon usage, long repeat sequence, and SSR. Fourteen mutational hotspot regions could be selected as candidate DNA barcoding to distinguish Rorippa plants. The phylogenetic trees clearly identified that ten Rorippa species displayed monophyletic relationships within the tribe Cardamineae based on plastomes and nrDNA ITS sequences. However, there are significant cytonuclear discordances in the interspecific relationships within Rorippa, as well as the intergeneric relationships between Rorippa and its related genera. We inferred that the cytonuclear discordance is most likely a result of interspecific hybridization within Rorippa, as well as intergeneric hybridization with its related genera. These plastid genomes can offer precious information for studies of species authentication, evolutionary history, and the phylogeny of Rorippa. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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13 pages, 4455 KiB  
Article
Effect of Ecological Factors on Nutritional Quality of Foxtail Millet (Setaria italica L.)
by Ke Ma, Xiatong Zhao, Boyu Lu, Yiru Wang, Zhongxiao Yue, Liguang Zhang, Xianmin Diao and Xiangyang Yuan
Agronomy 2024, 14(2), 387; https://doi.org/10.3390/agronomy14020387 - 17 Feb 2024
Cited by 1 | Viewed by 1200
Abstract
Foxtail millet (Setaria italica [L.] P. Beauv.) is a climate-change-ready crop, and it is crucial for predicting the impact of ecological factors on grain quality. In this study, multivariate statistical analysis was used to explore the relationship between ecological factors and the [...] Read more.
Foxtail millet (Setaria italica [L.] P. Beauv.) is a climate-change-ready crop, and it is crucial for predicting the impact of ecological factors on grain quality. In this study, multivariate statistical analysis was used to explore the relationship between ecological factors and the key nutritional quality of Jingu 21 from twelve production areas. The results showed that the crude fat and amylopectin content of foxtail millets showed a downward trend from south to north. The nutritional quality was significantly affected by geographical, climatic, and soil factors, and the foxtail millet produced in geographically close areas was extremely similar in nutritional quality. Most nutritional quality indicators of Jingu 21 had a strong correlation with the latitude and climatic factors such as average temperature, diurnal temperature range, and average precipitation, while the content of mineral elements was greatly affected by soil factors. Moreover, higher average precipitation in the jointing, booting–heading, and heading stages, a higher average temperature, and a lower diurnal temperature range in the heading and grain-filling stages are conducive to the establishment of nutritional quality. The findings could facilitate the rational distribution of high-quality foxtail millets under global climate change. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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17 pages, 2239 KiB  
Article
A Comparison of the Physiological Traits and Gene Expression of Brassinosteroids Signaling under Drought Conditions in Two Chickpea Cultivars
by Khatereh Felagari, Bahman Bahramnejad, Adel Siosemardeh, Khaled Mirzaei, Xiujuan Lei and Jian Zhang
Agronomy 2023, 13(12), 2963; https://doi.org/10.3390/agronomy13122963 - 30 Nov 2023
Cited by 2 | Viewed by 1204
Abstract
This study aimed to investigate the effects of drought stress at the flowering stage on the physiological and molecular responses of the genes involved in the brassinosteroid pathway of two chickpea cultivars (ILC1799: drought tolerant, and ILC3279: drought sensitive). The drought resulted in [...] Read more.
This study aimed to investigate the effects of drought stress at the flowering stage on the physiological and molecular responses of the genes involved in the brassinosteroid pathway of two chickpea cultivars (ILC1799: drought tolerant, and ILC3279: drought sensitive). The drought resulted in significant reductions in chlorophyll a, chlorophyll b, total chlorophyll and carotenoid content in both cultivars, and had significantly lesser effects on the tolerant cultivar, Samin, compared to that of ILC3279. However, the relative water content, the osmotic potential and the cell membrane stability were less affected by drought in both cultivars. The proline content and peroxidase activity increased significantly under drought stress in both cultivars, with a higher amount in Samin (ILC1799). Members of the BES1 family positively mediate brassinosteroid signaling and play an important role in regulating plant stress responses. The expression of these genes was analyzed in chickpea cultivars under drought. Further, a genome-wide analysis of BES1 genes in the chickpea genome was conducted. Six CaBES1 genes were identified in total, and their phylogenetic tree, gene structures, and conserved motifs were determined. CaBES1 gene expression patterns were analyzed using a transcription database and quantitative real-time PCR analysis. The results revealed that the expression of CaBES1 genes are different in response to various plant stresses. The expression levels of CaBES1.1, CaBES1.2, CaNAC72 and CaRD26 genes were measured by using qRT-PCR. The relative expression of CaBES1.2 in the drought conditions was significantly downregulated. In contrast to CaBES1.1 and CaBES1.2, the expression of CaRD26 and CaNAC72 showed a significant increase under drought stress. The expression of CaRD26 and CaNAC72 genes was significantly higher in the Samin cultivar compared to that of ILC3279 cultivars. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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21 pages, 13159 KiB  
Article
Studying the Effect of Dense Planting on the Mechanism of Flower Abscission in Soybean through Combined Transcriptome-Metabolome Analysis
by Nan Wang, Dexin He, Hexiang Sun, Xingdong Yao and Futi Xie
Agronomy 2023, 13(10), 2561; https://doi.org/10.3390/agronomy13102561 - 5 Oct 2023
Viewed by 1205
Abstract
A high pod abscission rate in soybean plants results in a significant decrease in the yield per plant. Under dense planting conditions, dense tolerant soybean cultivars had a relatively low rate of pod abscission, thereby facilitating higher yield. In this experiment, two planting [...] Read more.
A high pod abscission rate in soybean plants results in a significant decrease in the yield per plant. Under dense planting conditions, dense tolerant soybean cultivars had a relatively low rate of pod abscission, thereby facilitating higher yield. In this experiment, two planting densities were used to analyze the differentially expressed genes and metabolites between the abscised and non-abscised flowers of two soybean cultivars on the basis of transcriptomic and metabolomic techniques. The flower abscission rate of LD32 was significantly lower than that of SND28. Both cultivars were enriched in the photosynthesis, sugar, and starch metabolism; MAPK signaling; and phenylalanine metabolism pathways at different planting densities. However, under dense planting, the trend of differential gene changes in the density-tolerant CV LD32 was opposite to that of the conventional CV SND28. The results of the joint analysis indicated that the co-regulation of cytokinin dehydrogenase 6 (CKX6) and cis-zeatin riboside monophosphate (CZRM) in the zeatin biosynthesis pathway of LD32 under dense planting conditions was the main factor for the relatively low rate of pod abscission under dense planting conditions. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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14 pages, 2198 KiB  
Article
Optimization of Protoplast Preparation System from Leaves and Establishment of a Transient Transformation System in Apium graveolens
by Jiageng Du, Huitao Zhang, Weilong Li, Xiaoyan Li, Zhuo Wang, Ying Zhang, Aisheng Xiong and Mengyao Li
Agronomy 2023, 13(8), 2154; https://doi.org/10.3390/agronomy13082154 - 17 Aug 2023
Cited by 5 | Viewed by 2408
Abstract
Protoplast culture and transformation technology offer a novel method for developing new plant varieties. Nonetheless, the effective preparation of protoplasts and transformation technology specific to celery has yet to be achieved. This study utilized celery seedling leaves as the primary materials to examine [...] Read more.
Protoplast culture and transformation technology offer a novel method for developing new plant varieties. Nonetheless, the effective preparation of protoplasts and transformation technology specific to celery has yet to be achieved. This study utilized celery seedling leaves as the primary materials to examine the key factors influencing protoplast isolation. The aim was to prepare leaf protoplasts with a high yield and of high quality and subsequently conduct transient gene transformation and expression. The findings indicated that the most effective procedure for isolating and purifying protoplasts was enzymatic digestion using an enzyme solution consisting of 2.0% cellulase, 0.1% pectolase, and 0.6 M mannitol for a duration of 8 h. Subsequently, the protoplasts were filtered through a 400-mesh sieve and purified through centrifugation at 200× g. Within this system, the overall protoplast yield was exceptionally high, reaching a viability rate of up to 95%. The transient transformation system yielded a maximum transformation efficiency of approximately 53%, as evaluated using the green fluorescent protein (GFP) as a reporter gene. The parameters of the transient transformation system were as follows: a protoplast concentration of 5 × 105 cells·mL−1, exogenous DNA concentration of 500 μg·mL−1, final concentration of PEG4000 at 40%, and transformation duration of 15 min. The transient transformation system was also utilized to further analyze the protein localization characteristics of the celery transcription factor AgMYB80. The findings indicated that AgMYB80 predominantly localizes in the nucleus, thereby confirming the reliability and effectiveness of the transient transformation system. This study successfully established an efficient system for isolating, purifying, and transforming celery protoplasts, and will serve as a basis for future studies on molecular biology and gene function. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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15 pages, 3758 KiB  
Article
Comparative Transcriptomics Reveal the Mechanisms Underlying the Glucosinolate Metabolic Response in Leaf Brassica juncea L. under Cold Stress
by Bing Tang, Bao-Hui Zhang, Chuan-Yuan Mo, Wen-Yuan Fu, Wei Yang, Qing-Qing Wang, Ning Ao, Fei Qu, Guo-Fei Tan, Lian Tao and Ying Deng
Agronomy 2023, 13(7), 1922; https://doi.org/10.3390/agronomy13071922 - 20 Jul 2023
Cited by 1 | Viewed by 1494
Abstract
Glucosinolates (GSLs) are not only a unique flavor substance from leaf B. juncea but also a major secondary metabolite produced in response to abiotic stresses. Cold stress is one of the most common abiotic stresses in leaf B. juncea; however, the metabolic [...] Read more.
Glucosinolates (GSLs) are not only a unique flavor substance from leaf B. juncea but also a major secondary metabolite produced in response to abiotic stresses. Cold stress is one of the most common abiotic stresses in leaf B. juncea; however, the metabolic response pattern of GSLs in leaf B. juncea under cold stress has not yet been reported. In the present study, we analyzed the GSLs content of leaf B. juncea under cold stress and found that it increased and subsequently decreased. According to RNA-seq data, genes related to the synthesis of aliphatic GSLs were significantly upregulated following 24 h of cold stress; genes related to the synthesis of indole GSLs were significantly upregulated following 48 h of cold stress; and BjBGLU25 and BjBGLU27 were significantly upregulated. Further analysis of the correlation between transcription factors and GSLs content revealed that MYB, ERF, IQD, and bHLH may be involved in regulating the GSLs response pattern in leaf B. juncea under cold stress. In particular, an unreported transcription factor, BjMYBS3 (BjuVA05G33250), was found to play a possible role in the synthesis of aliphatic GSLs. And the external application of GSLs increased the ability of leaf B. juncea to cope with cold stress. Full article
(This article belongs to the Special Issue Recognition and Utilization of Natural Genetic Resources for Advances in Plant Biology through Genomics and Biotechnology—2nd Edition)
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