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Molecular Genetics and Plant Breeding 3.0

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2023) | Viewed by 17487

Special Issue Editor

Special Issue Information

Dear Colleagues,

Plant breeding is a historical academic discipline which laid the foundations of modern agriculture. The principles of classical breeding are still the nucleus of modern breeding science and industry. On the other hand, recent methodological advancements in genomics, biotechnology, molecular biology, and bioinformatics have revolutionized the area of plant breeding and its linkages with related disciplines. These developments have opened new interdisciplinary areas of plant breeding with quantitative genetics, genomics, agro-biotechnology, and bioinformatics.

In this second compilation of the special issue on Molecular Genetics and Plant Breeding 3.0 will focus on innovative research on the exploration and utilization of crop biodiversity for improving essential breeding traits using molecular techniques and to replenish the genetic potential of the cultivated gene pool for yield and sustainability.

Prof. Dr. Hai Du
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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • Crop biodiversity
  • Wild accessions
  • Molecular breeding
  • QTL and gene mapping 
  • Comparative genomics
  • Drought stress adaptation
  • Disease resistance
  • Yield and sustainability
  • GWAS mapping
  • Predictive breeding
  • Genomic prediction

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Published Papers (12 papers)

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Research

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17 pages, 5478 KiB  
Article
Joint-GWAS, Linkage Mapping, and Transcriptome Analysis to Reveal the Genetic Basis of Plant Architecture-Related Traits in Maize
by Xuefeng Lu, Pengfei Liu, Liang Tu, Xiangyang Guo, Angui Wang, Yunfang Zhu, Yulin Jiang, Chunlan Zhang, Yan Xu, Zehui Chen and Xun Wu
Int. J. Mol. Sci. 2024, 25(5), 2694; https://doi.org/10.3390/ijms25052694 - 26 Feb 2024
Viewed by 710
Abstract
Plant architecture is one of the key factors affecting maize yield formation and can be divided into secondary traits, such as plant height (PH), ear height (EH), and leaf number (LN). It is a viable approach for exploiting genetic resources to improve plant [...] Read more.
Plant architecture is one of the key factors affecting maize yield formation and can be divided into secondary traits, such as plant height (PH), ear height (EH), and leaf number (LN). It is a viable approach for exploiting genetic resources to improve plant density. In this study, one natural panel of 226 inbred lines and 150 family lines derived from the offspring of T32 crossed with Qi319 were genotyped by using the MaizeSNP50 chip and the genotyping by sequence (GBS) method and phenotyped under three different environments. Based on the results, a genome-wide association study (GWAS) and linkage mapping were analyzed by using the MLM and ICIM models, respectively. The results showed that 120 QTNs (quantitative trait nucleotides) and 32 QTL (quantitative trait loci) related to plant architecture were identified, including four QTL and 40 QTNs of PH, eight QTL and 41 QTNs of EH, and 20 QTL and 39 QTNs of LN. One dominant QTL, qLN7-2, was identified in the Zhangye environment. Six QTNs were commonly identified to be related to PH, EH, and LN in different environments. The candidate gene analysis revealed that Zm00001d021574 was involved in regulating plant architecture traits through the autophagy pathway, and Zm00001d044730 was predicted to interact with the male sterility-related gene ms26. These results provide abundant genetic resources for improving maize plant architecture traits by using approaches to biological breeding. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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21 pages, 8317 KiB  
Article
Genome-Wide Identification and Expression Analysis of Chitinase Genes in Watermelon under Abiotic Stimuli and Fusarium oxysporum Infection
by Changqing Xuan, Mengjiao Feng, Xin Li, Yinjie Hou, Chunhua Wei and Xian Zhang
Int. J. Mol. Sci. 2024, 25(1), 638; https://doi.org/10.3390/ijms25010638 - 04 Jan 2024
Cited by 1 | Viewed by 937
Abstract
Chitinases, which catalyze the hydrolysis of chitin, the primary components of fungal cell walls, play key roles in defense responses, symbiotic associations, plant growth, and stress tolerance. In this study, 23 chitinase genes were identified in watermelon (Citrullus lanatus [Thunb.]) and classified [...] Read more.
Chitinases, which catalyze the hydrolysis of chitin, the primary components of fungal cell walls, play key roles in defense responses, symbiotic associations, plant growth, and stress tolerance. In this study, 23 chitinase genes were identified in watermelon (Citrullus lanatus [Thunb.]) and classified into five classes through homology search and phylogenetic analysis. The genes with similar exon-intron structures and conserved domains were clustered into the same class. The putative cis-elements involved in the responses to phytohormone, stress, and plant development were identified in their promoter regions. A tissue-specific expression analysis showed that the ClChi genes were primarily expressed in the roots (52.17%), leaves (26.09%), and flowers (34.78%). Moreover, qRT-PCR results indicate that ClChis play multifaceted roles in the interaction between plant/environment. More ClChi members were induced by Race 2 of Fusarium oxysporum f. sp. niveum, and eight genes were expressed at higher levels on the seventh day after inoculation with Races 1 and 2, suggesting that these genes play a key role in the resistance of watermelon to Fusarium wilt. Collectively, these results improve knowledge of the chitinase gene family in watermelon species and help to elucidate the roles played by chitinases in the responses of watermelon to various stresses. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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15 pages, 2887 KiB  
Article
Identification and Analysis of Candidate Genes Associated with Maize Fusarium Cob Resistance Using Next-Generation Sequencing Technology
by Aleksandra Sobiech, Agnieszka Tomkowiak, Jan Bocianowski, Grażyna Szymańska, Bartosz Nowak and Maciej Lenort
Int. J. Mol. Sci. 2023, 24(23), 16712; https://doi.org/10.3390/ijms242316712 - 24 Nov 2023
Cited by 2 | Viewed by 841
Abstract
The pressure to reduce mineral fertilization and the amount of pesticides used has become a factor limiting production growth, as has the elimination of many crop protection chemicals from the market. A key condition for this to be an effective form of protection [...] Read more.
The pressure to reduce mineral fertilization and the amount of pesticides used has become a factor limiting production growth, as has the elimination of many crop protection chemicals from the market. A key condition for this to be an effective form of protection is the use of varieties with higher levels of resistance. The most effective and fastest way to assist in the selection and control of pathogens is the conducting of genome-wide association studies. These are useful tools for identifying candidate genes, especially when combined with QTL mapping to map and validate loci for quantitative traits. The aim of this study was to identify new markers coupled to genes that determine maize plant resistance to fusarium head blight through the use of next-generation sequencing, association and physical mapping, and to optimize diagnostic procedures to identify selected molecular markers coupled to plant resistance to this fungal disease. As a result of field experiments and molecular analyses, molecular markers coupled to potential genes for resistance to maize ear fusariosis were selected. The newly selected markers were tested against reference genotypes. As a result of the analyses, it was found that two markers (11801 and 20607) out of the ten that were tested differentiated between susceptible and resistant genotypes. Marker number 11801 proved to be the most effective, with a specious product of 237 bp appearing for genotypes 1, 3, 5, 9 and 10. These genotypes were characterized by a field resistance of 4–6 on the 9° scale (1 being susceptible, 9 being resistant) and for all genotypes except 16 and 20, which were characterized by a field resistance of 9. In the next step, this marker will be tested on a wider population of extreme genotypes in order to use it for the preliminary selection of fusarium-resistant genotypes, and the phosphoenolpyruvate carboxylase kinase 1 gene coupled to it will be subjected to expression analysis. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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20 pages, 3769 KiB  
Article
Genomic Regions Associated with Resistance to Three Rusts in CIMMYT Wheat Line “Mokue#1”
by Naeela Qureshi, Ravi Prakash Singh, Blanca Minerva Gonzalez, Hedilberto Velazquez-Miranda and Sridhar Bhavani
Int. J. Mol. Sci. 2023, 24(15), 12160; https://doi.org/10.3390/ijms241512160 - 29 Jul 2023
Cited by 1 | Viewed by 992
Abstract
Understanding the genetic basis of rust resistance in elite CIMMYT wheat germplasm enhances breeding and deployment of durable resistance globally. “Mokue#1”, released in 2023 in Pakistan as TARNAB Gandum-1, has exhibited high levels of resistance to stripe rust, leaf rust, and stem rust [...] Read more.
Understanding the genetic basis of rust resistance in elite CIMMYT wheat germplasm enhances breeding and deployment of durable resistance globally. “Mokue#1”, released in 2023 in Pakistan as TARNAB Gandum-1, has exhibited high levels of resistance to stripe rust, leaf rust, and stem rust pathotypes present at multiple environments in Mexico and Kenya at different times. To determine the genetic basis of resistance, a F5 recombinant inbred line (RIL) mapping population consisting of 261 lines was developed and phenotyped for multiple years at field sites in Mexico and Kenya under the conditions of artificially created rust epidemics. DArTSeq genotyping was performed, and a linkage map was constructed using 7892 informative polymorphic markers. Composite interval mapping identified three significant and consistent loci contributed by Mokue: QLrYr.cim-1BL and QLrYr.cim-2AS on chromosome 1BL and 2AS, respectively associated with stripe rust and leaf rust resistance, and QLrSr.cim-2DS on chromosome 2DS for leaf rust and stem rust resistance. The QTL on 1BL was confirmed to be the Lr46/Yr29 locus, whereas the QTL on 2AS represented the Yr17/Lr37 region on the 2NS/2AS translocation. The QTL on 2DS was a unique locus conferring leaf rust resistance in Mexico and stem rust resistance in Kenya. In addition to these pleiotropic loci, four minor QTLs were also identified on chromosomes 2DL and 6BS associated with stripe rust, and 3AL and 6AS for stem rust, respectively, using the Kenya disease severity data. Significant decreases in disease severities were also demonstrated due to additive effects of QTLs when present in combinations. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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17 pages, 7058 KiB  
Article
Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella
by Yue Qin, Han Zhao, Hongwei Han, Gaopu Zhu, Zhaoshan Wang and Fangdong Li
Int. J. Mol. Sci. 2023, 24(14), 11735; https://doi.org/10.3390/ijms241411735 - 21 Jul 2023
Cited by 1 | Viewed by 1138
Abstract
Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research into molecular breeding and genetic evolution has been severely restricted due [...] Read more.
Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research into molecular breeding and genetic evolution has been severely restricted due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231 Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32,088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibits many presence/absence variants. Moreover, a large inversion at the 7588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protection, developing, and utilizing P. tenella germplasm resources. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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14 pages, 17704 KiB  
Article
Anatomy and Comparative Transcriptome Reveal the Mechanism of Male Sterility in Salvia miltiorrhiza
by Jinqiu Liao, Zhizhou Zhang, Yukun Shang, Yuanyuan Jiang, Zixuan Su, Xuexue Deng, Xiang Pu, Ruiwu Yang and Li Zhang
Int. J. Mol. Sci. 2023, 24(12), 10259; https://doi.org/10.3390/ijms241210259 - 17 Jun 2023
Cited by 1 | Viewed by 1135
Abstract
Salvia miltiorrhiza Bunge is an important traditional herb. Salvia miltiorrhiza is distributed in the Sichuan province of China (here called SC). Under natural conditions, it does not bear seeds and its sterility mechanism is still unclear. Through artificial cross, there was defective pistil [...] Read more.
Salvia miltiorrhiza Bunge is an important traditional herb. Salvia miltiorrhiza is distributed in the Sichuan province of China (here called SC). Under natural conditions, it does not bear seeds and its sterility mechanism is still unclear. Through artificial cross, there was defective pistil and partial pollen abortion in these plants. Electron microscopy results showed that the defective pollen wall was caused by delayed degradation of the tapetum. Due to the lack of starch and organelle, the abortive pollen grains showed shrinkage. RNA-seq was performed to explore the molecular mechanisms of pollen abortion. KEGG enrichment analysis suggested that the pathways of phytohormone, starch, lipid, pectin, and phenylpropanoid affected the fertility of S. miltiorrhiza. Moreover, some differentially expressed genes involved in starch synthesis and plant hormone signaling were identified. These results contribute to the molecular mechanism of pollen sterility and provide a more theoretical foundation for molecular-assisted breeding. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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18 pages, 4178 KiB  
Article
Abundance of Transgene Transcript Variants Associated with Somatically Active Transgenic Helitrons from Multiple T-DNA Integration Sites in Maize
by Chuxi Li, Chunsheng Cong, Fangyuan Liu, Qian Yu, Yuan Zhan, Li Zhu and Yubin Li
Int. J. Mol. Sci. 2023, 24(7), 6574; https://doi.org/10.3390/ijms24076574 - 31 Mar 2023
Cited by 1 | Viewed by 1263
Abstract
Helitrons, a novel type of mysterious DNA transposons discovered computationally prior to bench work confirmation, are components ubiquitous in most sequenced genomes of various eukaryotes, including plants, animals, and fungi. There is a paucity of empirical evidence to elucidate the mechanism of [...] Read more.
Helitrons, a novel type of mysterious DNA transposons discovered computationally prior to bench work confirmation, are components ubiquitous in most sequenced genomes of various eukaryotes, including plants, animals, and fungi. There is a paucity of empirical evidence to elucidate the mechanism of Helitrons transposition in plants. Here, by constructing several artificial defective Helitron (dHel) reporter systems, we aim to identify the autonomous Helitrons (aHel) in maize genetically and to demonstrate the transposition and repair mechanisms of Helitrons upon the dHel-GFP excision in maize. When crossing with various inbred lines, several transgenic lines produced progeny of segregated, purple-blotched kernels, resulting from a leaky expression of the C1 gene driven by the dHel-interrupted promoter. Transcription analysis indicated that the insertion of different dHels into the C1 promoter or exon would lead to multiple distinct mRNA transcripts corresponding to transgenes in the host genome. Simple excision products and circular intermediates of dHel-GFP transposition have been detected from the leaf tissue of the seedlings in F1 hybrids of transgenic lines with corresponding c1 tester, although they failed to be detected in all primary transgenic lines. These results revealed the transposition and repair mechanism of Helitrons in maize. It is strongly suggested that this reporter system can detect the genetic activity of autonomic Helitron at the molecular level. Sequence features of dHel itself, together with the flanking regions, impact the excision activity of dHel and the regulation of the dHel on the transcription level of the host gene. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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17 pages, 4140 KiB  
Article
Genome-Scale Analysis of the Grapevine KCS Genes Reveals Its Potential Role in Male Sterility
by Huan Zheng, Yueting Liang, Ben Hong, Yingyi Xu, Mengfan Ren, Yixu Wang, Liyuan Huang, Lina Yang and Jianmin Tao
Int. J. Mol. Sci. 2023, 24(7), 6510; https://doi.org/10.3390/ijms24076510 - 30 Mar 2023
Cited by 2 | Viewed by 1282
Abstract
Very long-chain fatty acid (VLCFA) synthesis in plants, is primarily rate-limited by the enzyme 3-ketoacyl CoA synthase (KCS), which also controls the rate and carbon chain length of VLCFA synthesis. Disruption of VLCFA during pollen development, may affect the pollen wall formation and [...] Read more.
Very long-chain fatty acid (VLCFA) synthesis in plants, is primarily rate-limited by the enzyme 3-ketoacyl CoA synthase (KCS), which also controls the rate and carbon chain length of VLCFA synthesis. Disruption of VLCFA during pollen development, may affect the pollen wall formation and ultimately lead to male sterility. Our study identified 24 grapevine KCS (VvKCS) genes and provided new names based on their relative chromosome distribution. Based on sequence alignment and phylogenetic investigation, these genes were grouped into seven subgroups, members of the same subgroup having similar motif structures. Synteny analysis of VvKCS genes, showed that the segmental duplication events played an important role in expanding this gene family. Expression profiles obtained from the transcriptome data showed different expression patterns of VvKCS genes in different tissues. Comparison of transcriptome and RT-qPCR data of the male sterile grape ‘Y−14’ and its fertile parent ‘Shine Muscat’, revealed that 10 VvKCS genes were significantly differentially expressed at the meiosis stage, which is a critical period of pollen wall formation. Further, joint analysis by weighted gene co-expression network analysis (WGCNA) and Kyoto Encyclopedia of Genes and Genomes (KEGG), revealed that five of these VvKCS (VvKCS6/15/19/20/24) genes were involved in the fatty acid elongation pathway, which may ultimately affect the structural integrity of the pollen wall in ‘Y−14’. This systematic analysis provided a foundation for further functional characterization of VvKCS genes, with the aim of grapevine precision breeding improvement. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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16 pages, 3683 KiB  
Article
The Effects of Epicuticular Wax on Anthracnose Resistance of Sorghum bicolor
by Wangdan Xiong, Longxin Liao, Yu Ni, Hanchi Gao, Jianfeng Yang and Yanjun Guo
Int. J. Mol. Sci. 2023, 24(4), 3070; https://doi.org/10.3390/ijms24043070 - 04 Feb 2023
Cited by 3 | Viewed by 1694
Abstract
Cuticular waxes are mixtures of hydrophobic compounds covering land plant surfaces and play key roles in plant resistance to abiotic and biotic stresses. However, it is still not clear whether the epicuticular wax could protect the plants from infection by anthracnose, one of [...] Read more.
Cuticular waxes are mixtures of hydrophobic compounds covering land plant surfaces and play key roles in plant resistance to abiotic and biotic stresses. However, it is still not clear whether the epicuticular wax could protect the plants from infection by anthracnose, one of the most important plant diseases worldwide, which seriously infects sorghum and causes great yield loss. In this study, Sorghum bicolor L., an important C4 crop with high wax coverage, was selected to analyze the relationship between epicuticular wax (EW) and anthracnose resistance. In vitro analysis indicated that the sorghum leaf wax significantly inhibited the anthracnose mycelium growth of anthracnose on potato dextrose agar (PDA) medium, with the plaque diameter smaller than that grown on medium without wax. Then, the EWs were removed from the intact leaf with gum acacia, followed by the inoculation of Colletotrichum sublineola. The results indicated that the disease lesion was remarkably aggravated on leaves without EW, which showed decreased net photosynthetic rate and increased intercellular CO2 concentrations and malonaldehyde content three days after inoculation. Transcriptome analysis further indicated that 1546 and 2843 differentially expressed genes (DEGs) were regulated by C. sublineola infection in plants with and without EW, respectively. Among the DEG encoded proteins and enriched pathways regulated by anthracnose infection, the cascade of the mitogen-activated protein kinases (MAPK) signaling pathway, ABC transporters, sulfur metabolism, benzoxazinoid biosynthesis, and photosynthesis were mainly regulated in plants without EW. Overall, the EW increases plant resistance to C. sublineola by affecting physiological and transcriptome responses through sorghum epicuticular wax, improving our understanding of its roles in defending plants from fungi and ultimately benefiting sorghum resistance breeding. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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15 pages, 3305 KiB  
Article
Genome-Wide Characterization of Trehalose-6-Phosphate Synthase Gene Family of Brassica napus and Potential Links with Agronomic Traits
by Ming Hu, Meili Xie, Xiaobo Cui, Junyan Huang, Xiaohui Cheng, Lijiang Liu, Shengyi Liu and Chaobo Tong
Int. J. Mol. Sci. 2022, 23(24), 15714; https://doi.org/10.3390/ijms232415714 - 11 Dec 2022
Cited by 2 | Viewed by 1360
Abstract
Trehalose and trehalose-6 phosphate played important roles in floral organ development, embryonic development, cell morphogenesis, and signal transduction under abiotic stress. However, little is known about the trehalose-6-phosphate synthase (TPS) gene family in Brassica napus. In this study, in total, [...] Read more.
Trehalose and trehalose-6 phosphate played important roles in floral organ development, embryonic development, cell morphogenesis, and signal transduction under abiotic stress. However, little is known about the trehalose-6-phosphate synthase (TPS) gene family in Brassica napus. In this study, in total, 26 TPS genes in B. napus (BnTPS genes) were identified and classified into two groups. In each group, the BnTPS genes showed relatively conserved gene structures. The protein–protein interaction (PPI) network and enrichment analysis indicated that BnTPS genes were involved in the glycolysis/gluconeogenesis, fructose and mannose metabolism, galactose metabolism, pentose phosphate pathway, carbohydrate transmembrane transport, trehalose–phosphatase activity, etc. The expression of BnTPS genes varied greatly across different tissues, while most of the BnTPS genes showed a considerable improvement in expression under different abiotic stresses, indicating that BnTPS genes were significantly responsive to the abiotic treatments. In addition, the association mapping analysis revealed that eight BnTPS genes were potential regulators of particular agronomic traits. Among them, the gene BnTPS23 was significantly associated with the primary flowering time (PFT), full flowering time (FFT1), and final flowering time (FFT2), suggesting that BnTPS genes may play an important role in regulating key agronomic traits in B. napus. In summary, our research provides a better understanding of BnTPS genes, facilitates the breeding of superior B. napus varieties, and paves the way for future functional studies. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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Review

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15 pages, 2604 KiB  
Review
Biogenesis, Mode of Action and the Interactions of Plant Non-Coding RNAs
by Xin Zhang, Mingjun Du, Zhengfu Yang, Zhengjia Wang and Kean-Jin Lim
Int. J. Mol. Sci. 2023, 24(13), 10664; https://doi.org/10.3390/ijms241310664 - 26 Jun 2023
Viewed by 1154
Abstract
The central dogma of genetics, which outlines the flow of genetic information from DNA to RNA to protein, has long been the guiding principle in molecular biology. In fact, more than three-quarters of the RNAs produced by transcription of the plant genome are [...] Read more.
The central dogma of genetics, which outlines the flow of genetic information from DNA to RNA to protein, has long been the guiding principle in molecular biology. In fact, more than three-quarters of the RNAs produced by transcription of the plant genome are not translated into proteins, and these RNAs directly serve as non-coding RNAs in the regulation of plant life activities at the molecular level. The breakthroughs in high-throughput transcriptome sequencing technology and the establishment and improvement of non-coding RNA experiments have now led to the discovery and confirmation of the biogenesis, mechanisms, and synergistic effects of non-coding RNAs. These non-coding RNAs are now predicted to play important roles in the regulation of gene expression and responses to stress and evolution. In this review, we focus on the synthesis, and mechanisms of non-coding RNAs, and we discuss their impact on gene regulation in plants. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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23 pages, 2390 KiB  
Review
Functional Endophytes Regulating Plant Secondary Metabolism: Current Status, Prospects and Applications
by Zhaogao Li, Keyi Xiong, Weie Wen, Lin Li and Delin Xu
Int. J. Mol. Sci. 2023, 24(2), 1153; https://doi.org/10.3390/ijms24021153 - 06 Jan 2023
Cited by 18 | Viewed by 3597
Abstract
Endophytes, which are widely found in host plants and have no harmful effects, are a vital biological resource. Plant endophytes promote plant growth and enhance plants’ resistance to diseases, pests, and environmental stresses. In addition, they enhance the synthesis of important secondary metabolites [...] Read more.
Endophytes, which are widely found in host plants and have no harmful effects, are a vital biological resource. Plant endophytes promote plant growth and enhance plants’ resistance to diseases, pests, and environmental stresses. In addition, they enhance the synthesis of important secondary metabolites in plants and improve the potential applicability of plants in agriculture, medicine, food, and horticulture. In this review, we summarize the recent progress in understanding the interaction between endophytes and plants and summarize the construction of synthetic microbial communities (SynComs) and metaomics analysis of the interaction between endophytes and plants. The application and development prospects of endophytes in agriculture, medicine, and other industries are also discussed to provide a reference for further study of the interaction between endophytes and plants and further development and utilization of endophytes. Full article
(This article belongs to the Special Issue Molecular Genetics and Plant Breeding 3.0)
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