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Agronomy
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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 Volume II

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

Deadline for manuscript submissions: 30 September 2024 | Viewed by 5451

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

Published Papers (6 papers)

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Research

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 (registering DOI) - 26 Apr 2024
Viewed by 195
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 Volume II)
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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
Viewed by 525
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 Volume II)
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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 749
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 Volume II)
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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 - 05 Oct 2023
Viewed by 784
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 Volume II)
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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 3 | Viewed by 1539
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 Volume II)
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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 985
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 Volume II)
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