Pub Date : 2021-11-02DOI: 10.1080/07352689.2022.2031674
Shanshan Jiang, Jin-Long Cui, Xiao-ke Li
Abstract Plant microRNAs (miRNAs), a class of about 21-nucleotide-long small noncoding RNAs (ncRNAs), generally act as key regulators of their target genes by guiding mRNA cleavage or translational repression. Recent researches have reported that miRNAs can interact with pathway-related structural genes, transcription factors (TFs) and noncoding RNAs (ncRNAs) to form regulatory network in secondary metabolite (SM) biosynthetic pathways. The validated interactions can better reflect the real regulatory mechanism of miRNA and convert miRNAs into more efficient tools to control the production of precious SMs. However, there is no systematic review available on this topic especially in plants, particularly model plants and crops. Here, we firstly overviewed the critical secondary metabolic pathways in plants, especially those biosynthetic pathways related structural genes which were well-studied and representative SMs, including phenylpropanoids, terpenoids, alkaloids. Principally, we summarized miRNAs involved in the biosynthesis of SMs, miRNA-target modules and their regulation on the mentioned pathways in the last decade. Significantly, the modules included miRNA-structural gene, miRNA-TF, miRNA-ncRNA interaction pairs carried out by target validation or functional confirmation. This knowledge will promote understanding the sophisticated miRNA-mediated gene regulatory network of SM biosynthesis, and drive the development of synthetic biology.
{"title":"MicroRNA-Mediated Gene Regulation of Secondary Metabolism in Plants","authors":"Shanshan Jiang, Jin-Long Cui, Xiao-ke Li","doi":"10.1080/07352689.2022.2031674","DOIUrl":"https://doi.org/10.1080/07352689.2022.2031674","url":null,"abstract":"Abstract Plant microRNAs (miRNAs), a class of about 21-nucleotide-long small noncoding RNAs (ncRNAs), generally act as key regulators of their target genes by guiding mRNA cleavage or translational repression. Recent researches have reported that miRNAs can interact with pathway-related structural genes, transcription factors (TFs) and noncoding RNAs (ncRNAs) to form regulatory network in secondary metabolite (SM) biosynthetic pathways. The validated interactions can better reflect the real regulatory mechanism of miRNA and convert miRNAs into more efficient tools to control the production of precious SMs. However, there is no systematic review available on this topic especially in plants, particularly model plants and crops. Here, we firstly overviewed the critical secondary metabolic pathways in plants, especially those biosynthetic pathways related structural genes which were well-studied and representative SMs, including phenylpropanoids, terpenoids, alkaloids. Principally, we summarized miRNAs involved in the biosynthesis of SMs, miRNA-target modules and their regulation on the mentioned pathways in the last decade. Significantly, the modules included miRNA-structural gene, miRNA-TF, miRNA-ncRNA interaction pairs carried out by target validation or functional confirmation. This knowledge will promote understanding the sophisticated miRNA-mediated gene regulatory network of SM biosynthesis, and drive the development of synthetic biology.","PeriodicalId":10854,"journal":{"name":"Critical Reviews in Plant Sciences","volume":"40 1","pages":"459 - 478"},"PeriodicalIF":6.9,"publicationDate":"2021-11-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45956028","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-03DOI: 10.1080/07352689.2021.1985819
Fan Li, Chunlian Jin, Liangsheng Zhang, Jihua Wang
Abstract Novelty is the primary requirement and breeding target for plant breeding, which can make a significant contribution to the new cultivar. The key factor for successful breeding is the genetic variation in the progeny, which depends on the degree of genetic material mixing after meiosis. However, meiotic recombination is tightly astricting in plants, resulting in a limited number of crossovers (COs). Recently, several anti-CO factors have been identified that limiting the meiotic recombination in plants, and the knock-out mutants displayed a significant increase in recombination frequency. This provides a universal tool to manipulate the meiotic recombination in plants by applying anti-CO genes, which will facilitate the breeding procedure. Due to the rapid development of genome sequencing and gene editing technologies, the genomes of more and more plants have been sequenced. In the meanwhile, the efficient CRISPR-Cas9 system has also been established in plants. Thus, it’s time to break the shackles of meiotic recombination to create novel cultivars in the biological era of genomics. Here we summarize the functional studies of the main meiotic recombination suppressors in plants, with the discussion of the possibility to apply the anti-CO genes in plant breeding as an emerging tool, especially for ornamental plant breeding.
{"title":"Hyper-Recombinant Plants: An Emerging Field for Plant Breeding","authors":"Fan Li, Chunlian Jin, Liangsheng Zhang, Jihua Wang","doi":"10.1080/07352689.2021.1985819","DOIUrl":"https://doi.org/10.1080/07352689.2021.1985819","url":null,"abstract":"Abstract Novelty is the primary requirement and breeding target for plant breeding, which can make a significant contribution to the new cultivar. The key factor for successful breeding is the genetic variation in the progeny, which depends on the degree of genetic material mixing after meiosis. However, meiotic recombination is tightly astricting in plants, resulting in a limited number of crossovers (COs). Recently, several anti-CO factors have been identified that limiting the meiotic recombination in plants, and the knock-out mutants displayed a significant increase in recombination frequency. This provides a universal tool to manipulate the meiotic recombination in plants by applying anti-CO genes, which will facilitate the breeding procedure. Due to the rapid development of genome sequencing and gene editing technologies, the genomes of more and more plants have been sequenced. In the meanwhile, the efficient CRISPR-Cas9 system has also been established in plants. Thus, it’s time to break the shackles of meiotic recombination to create novel cultivars in the biological era of genomics. Here we summarize the functional studies of the main meiotic recombination suppressors in plants, with the discussion of the possibility to apply the anti-CO genes in plant breeding as an emerging tool, especially for ornamental plant breeding.","PeriodicalId":10854,"journal":{"name":"Critical Reviews in Plant Sciences","volume":"40 1","pages":"446 - 458"},"PeriodicalIF":6.9,"publicationDate":"2021-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44997047","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-09-03DOI: 10.1080/07352689.2021.1969504
Yifan Jiang, Wanbo Zhang, Xinlu Chen, Weijiao Wang, Tobias G. Köllner, Sumei Chen, Fadi Chen, F. Chen
Abstract Chrysanthemum is a significant genus belonging to one of the largest plant families, the Asteraceae. Among the over 40 recognized species, C. morifolium is best-known for its long history of cultivation and countless varieties. Like some other genera of this family, many Chrysanthemum species are producers of high levels of secondary metabolites. This review focuses on the largest class of plant secondary metabolites, namely terpenoids produced by Chrysanthemum species. An extensive literature search revealed a total of 390 terpenoids from these species, which include 183 monoterpenoids and 207 sesquiterpenoids. While some terpenes are produced by almost all of the investigated varieties/species of Chrysanthemum, many terpenoids show specificity to certain varieties or species, indicating species-specific functions. The enzymes and genes participating in the pathways for terpene biosynthesis are also described. In addition to a general overview, in this review we focus on isoprenyl diphosphate synthases and terpene synthases, two enzyme classes pivotal for generating the chemical diversity of terpenes, as established by our analysis of two sequenced genomes of Chrysanthemum. While our knowledge about the biological functions of terpenoids in Chrysanthemum is limited, we discuss their functions in chemical defenses against insects and microbial pathogens. Finally, we present the prospects of understanding the molecular basis of terpene biosynthesis in Chrysanthemum and elucidating its biological significance, as well as the prospects of translational research on terpene-based applications.
{"title":"Diversity and Biosynthesis of Volatile Terpenoid Secondary Metabolites in the Chrysanthemum Genus","authors":"Yifan Jiang, Wanbo Zhang, Xinlu Chen, Weijiao Wang, Tobias G. Köllner, Sumei Chen, Fadi Chen, F. Chen","doi":"10.1080/07352689.2021.1969504","DOIUrl":"https://doi.org/10.1080/07352689.2021.1969504","url":null,"abstract":"Abstract Chrysanthemum is a significant genus belonging to one of the largest plant families, the Asteraceae. Among the over 40 recognized species, C. morifolium is best-known for its long history of cultivation and countless varieties. Like some other genera of this family, many Chrysanthemum species are producers of high levels of secondary metabolites. This review focuses on the largest class of plant secondary metabolites, namely terpenoids produced by Chrysanthemum species. An extensive literature search revealed a total of 390 terpenoids from these species, which include 183 monoterpenoids and 207 sesquiterpenoids. While some terpenes are produced by almost all of the investigated varieties/species of Chrysanthemum, many terpenoids show specificity to certain varieties or species, indicating species-specific functions. The enzymes and genes participating in the pathways for terpene biosynthesis are also described. In addition to a general overview, in this review we focus on isoprenyl diphosphate synthases and terpene synthases, two enzyme classes pivotal for generating the chemical diversity of terpenes, as established by our analysis of two sequenced genomes of Chrysanthemum. While our knowledge about the biological functions of terpenoids in Chrysanthemum is limited, we discuss their functions in chemical defenses against insects and microbial pathogens. Finally, we present the prospects of understanding the molecular basis of terpene biosynthesis in Chrysanthemum and elucidating its biological significance, as well as the prospects of translational research on terpene-based applications.","PeriodicalId":10854,"journal":{"name":"Critical Reviews in Plant Sciences","volume":"40 1","pages":"422 - 445"},"PeriodicalIF":6.9,"publicationDate":"2021-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44792651","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-11DOI: 10.1080/07352689.2021.1959137
S. Dubey, Shilpi Sharma
Abstract In an attempt to attain sustainability in agriculture, microbiome-based approaches have been investigated as “next-generation biologicals”. The top-down strategy of plant-mediated indirect selection of rhizospheric microbiome holds potential in generating a robust and efficient microbiome for enhancement of desired plant phenotype and its overall fitness. It involves multiple rounds of plant growth experiments under selection pressure such that the plant recruits a microbiome optimal for its fitness over the course of selection. In the review, we have critically discussed various aspects related to the approach, viz. methodological details, the current challenges faced by the technique, and the concerns related to the adoption of the plant-mediated indirect selection of microbiome at a larger scale. Besides, based on recent methodological developments and knowledge gained, we have proposed solutions for some of the issues, which will aid in popularizing the strategy.
{"title":"Rhizospheric Engineering by Plant-Mediated Indirect Selection of Microbiome for Agricultural Sustainability","authors":"S. Dubey, Shilpi Sharma","doi":"10.1080/07352689.2021.1959137","DOIUrl":"https://doi.org/10.1080/07352689.2021.1959137","url":null,"abstract":"Abstract In an attempt to attain sustainability in agriculture, microbiome-based approaches have been investigated as “next-generation biologicals”. The top-down strategy of plant-mediated indirect selection of rhizospheric microbiome holds potential in generating a robust and efficient microbiome for enhancement of desired plant phenotype and its overall fitness. It involves multiple rounds of plant growth experiments under selection pressure such that the plant recruits a microbiome optimal for its fitness over the course of selection. In the review, we have critically discussed various aspects related to the approach, viz. methodological details, the current challenges faced by the technique, and the concerns related to the adoption of the plant-mediated indirect selection of microbiome at a larger scale. Besides, based on recent methodological developments and knowledge gained, we have proposed solutions for some of the issues, which will aid in popularizing the strategy.","PeriodicalId":10854,"journal":{"name":"Critical Reviews in Plant Sciences","volume":"40 1","pages":"379 - 397"},"PeriodicalIF":6.9,"publicationDate":"2021-08-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47205947","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-08-10DOI: 10.1080/07352689.2021.1954778
Virender Kumar, Sanskriti Vats, S. Kumawat, Ashita Bisht, Vacha D. Bhatt, S. M. Shivaraj, Gunashri Padalkar, V. Goyal, S. Zargar, S. Gupta, Giriraj Kumawat, S. Chandra, V. Chalam, M. Ratnaparkhe, B. Gill, M. Jean, G. Patil, T. Vuong, I. Rajcan, R. Deshmukh, F. Belzile, T. Sharma, H. Nguyen, H. Sonah
Abstract Genetic improvement of soybean, one of the major crops providing edible oil and protein-rich food, is important to ensure balanced nutrition for the growing world population. To make soybean cultivation more rewarding, an increase in seed oil and protein content is most desirable. Here, a critical review of the efforts employed over a half-century to accomplish the improvement of soybean oil and protein content has been presented. Many studies have used diverse parental lines to map and characterize quantitative trait loci (QTL)/genes regulating these two essential traits. Here, we highlighted such genomic loci that were consistently identified with different mapping approaches, like QTL mapping, genome-wide association studies (GWAS), and meta-QTL analysis. In addition, the information generated through efforts utilizing omics approaches, such as genomics, transcriptomics, and proteomics has also been compiled to anticipate the molecular mechanism. Several innovative approaches like multi-parental mapping, induced mutagenesis, genomic selection, transgenics, and genome-editing have been discussed in terms of effective utilization of technological advances to improve the oil and protein content in soybean. Information provided here will be helpful for better understanding and designing an effective strategy for simultaneous improvement in seed oil and protein content in soybean.
{"title":"Omics advances and integrative approaches for the simultaneous improvement of seed oil and protein content in soybean (Glycine max L.)","authors":"Virender Kumar, Sanskriti Vats, S. Kumawat, Ashita Bisht, Vacha D. Bhatt, S. M. Shivaraj, Gunashri Padalkar, V. Goyal, S. Zargar, S. Gupta, Giriraj Kumawat, S. Chandra, V. Chalam, M. Ratnaparkhe, B. Gill, M. Jean, G. Patil, T. Vuong, I. Rajcan, R. Deshmukh, F. Belzile, T. Sharma, H. Nguyen, H. Sonah","doi":"10.1080/07352689.2021.1954778","DOIUrl":"https://doi.org/10.1080/07352689.2021.1954778","url":null,"abstract":"Abstract Genetic improvement of soybean, one of the major crops providing edible oil and protein-rich food, is important to ensure balanced nutrition for the growing world population. To make soybean cultivation more rewarding, an increase in seed oil and protein content is most desirable. Here, a critical review of the efforts employed over a half-century to accomplish the improvement of soybean oil and protein content has been presented. Many studies have used diverse parental lines to map and characterize quantitative trait loci (QTL)/genes regulating these two essential traits. Here, we highlighted such genomic loci that were consistently identified with different mapping approaches, like QTL mapping, genome-wide association studies (GWAS), and meta-QTL analysis. In addition, the information generated through efforts utilizing omics approaches, such as genomics, transcriptomics, and proteomics has also been compiled to anticipate the molecular mechanism. Several innovative approaches like multi-parental mapping, induced mutagenesis, genomic selection, transgenics, and genome-editing have been discussed in terms of effective utilization of technological advances to improve the oil and protein content in soybean. Information provided here will be helpful for better understanding and designing an effective strategy for simultaneous improvement in seed oil and protein content in soybean.","PeriodicalId":10854,"journal":{"name":"Critical Reviews in Plant Sciences","volume":"40 1","pages":"398 - 421"},"PeriodicalIF":6.9,"publicationDate":"2021-08-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44138749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-04DOI: 10.1080/07352689.2021.1951491
Yuqi He, Kaixuan Zhang, M. Georgiev, Meiliang Zhou
Abstract The ubiquitin proteasome system is a key pathway, regulating targeted proteins degradation. A critical step is regulated by E3 ubiquitin ligases, which facilitates the transfer of ubiquitin moieties to substrate proteins, leading proteins degradation via 26S proteasome. However, the number of known ubiquitin dependent processes is still relatively small. Since some stress-related transcription factors are usually essential under stress conditions, while playing negative roles during normal growth, hence their protein levels need to be precisely regulated. However, the mechanism of ubiquitin pathway, regulating transcription factors stability has not been yet summarized. In this review, we attempted to outline the mechanism of E3 ligases dependent transcription factors degradation and discuss the comprehensive role of E3 ligases in phytohormone signaling.
{"title":"Ubiquitin Proteins and the Orchestration of Transcription Factors Activity","authors":"Yuqi He, Kaixuan Zhang, M. Georgiev, Meiliang Zhou","doi":"10.1080/07352689.2021.1951491","DOIUrl":"https://doi.org/10.1080/07352689.2021.1951491","url":null,"abstract":"Abstract The ubiquitin proteasome system is a key pathway, regulating targeted proteins degradation. A critical step is regulated by E3 ubiquitin ligases, which facilitates the transfer of ubiquitin moieties to substrate proteins, leading proteins degradation via 26S proteasome. However, the number of known ubiquitin dependent processes is still relatively small. Since some stress-related transcription factors are usually essential under stress conditions, while playing negative roles during normal growth, hence their protein levels need to be precisely regulated. However, the mechanism of ubiquitin pathway, regulating transcription factors stability has not been yet summarized. In this review, we attempted to outline the mechanism of E3 ligases dependent transcription factors degradation and discuss the comprehensive role of E3 ligases in phytohormone signaling.","PeriodicalId":10854,"journal":{"name":"Critical Reviews in Plant Sciences","volume":"40 1","pages":"366 - 377"},"PeriodicalIF":6.9,"publicationDate":"2021-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/07352689.2021.1951491","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46850922","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-04DOI: 10.1080/07352689.2021.1938397
S. Nigris, Greta D'Apice, Silvia Moschin, Riccardo Ciarle, B. Baldan
Abstract Fleshy structures associated with the ovule/seed arose independently several times during gymnosperm evolution. Fleshy structures are linked to ovule/seed protection and dispersal, and are present in all the four lineages of extant gymnosperms. The ontogenetic origin of the fleshy structures could be different, and spans from the ovule funiculus in the Taxus baccata aril, the ovule integument in Ginkgo biloba, to modified bracts as in case of Ephedra species. This variability in ontogeny is reflected in the morphology and characteristics that these tissues display among the different species. This review aims to provide a complete overview of these ovule/seed-associated fleshy structures in living gymnosperms, reporting detailed descriptions for every genus. The evolution of these independently evolved structures is still unclear, and different hypotheses have been presented—protection for the seeds, protection to desiccation—each plausible but no one able to account for all their independent origins. Our purpose is to offer an extensive discussion on these fleshy structures, under different points of view (morphology, evolution, gene involvement), to stimulate further studies on their origin and evolution on both ecological and molecular levels.
{"title":"Fleshy Structures Associated with Ovule Protection and Seed Dispersal in Gymnosperms: A Systematic and Evolutionary Overview","authors":"S. Nigris, Greta D'Apice, Silvia Moschin, Riccardo Ciarle, B. Baldan","doi":"10.1080/07352689.2021.1938397","DOIUrl":"https://doi.org/10.1080/07352689.2021.1938397","url":null,"abstract":"Abstract Fleshy structures associated with the ovule/seed arose independently several times during gymnosperm evolution. Fleshy structures are linked to ovule/seed protection and dispersal, and are present in all the four lineages of extant gymnosperms. The ontogenetic origin of the fleshy structures could be different, and spans from the ovule funiculus in the Taxus baccata aril, the ovule integument in Ginkgo biloba, to modified bracts as in case of Ephedra species. This variability in ontogeny is reflected in the morphology and characteristics that these tissues display among the different species. This review aims to provide a complete overview of these ovule/seed-associated fleshy structures in living gymnosperms, reporting detailed descriptions for every genus. The evolution of these independently evolved structures is still unclear, and different hypotheses have been presented—protection for the seeds, protection to desiccation—each plausible but no one able to account for all their independent origins. Our purpose is to offer an extensive discussion on these fleshy structures, under different points of view (morphology, evolution, gene involvement), to stimulate further studies on their origin and evolution on both ecological and molecular levels.","PeriodicalId":10854,"journal":{"name":"Critical Reviews in Plant Sciences","volume":"40 1","pages":"285 - 302"},"PeriodicalIF":6.9,"publicationDate":"2021-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/07352689.2021.1938397","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"44827186","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-07-04DOI: 10.1080/07352689.2021.1941605
Ivan Simko, Mengyuan Jia, J. Venkatesh, B. Kang, Y. Weng, G. Barcaccia, S. Lanteri, G. Bhattarai, M. Foolad
Abstract Vegetables are an integral part of the human diet worldwide. Traditional breeding approaches have been used extensively to develop new cultivars of vegetables with desirable characteristics, including resistance/tolerance to biotic and abiotic stresses, high yield, and an elevated content of compounds beneficial to human health. The technological progress since the early 1980s has revolutionized our ability to study and manipulate genetic variation in crop plants. The development of high-throughput sequencing platforms and accompanying analytical methods have led to sequencing and assembly of a large number of plant genomes, construction of dense and ultra-dense molecular linkage maps, identification of structural variants, and application of molecular markers in breeding programs. Linkage mapping and genome-wide association mapping studies have been used to identify chromosomal locations of genes and QTLs associated with plant phenotypic variations important for crop improvement. This review provides up-to-date information on the status of genomics and marker-assisted improvement of vegetable crops with the focus on tomato, pepper, eggplant, lettuce, spinach, cucumber, and chicory. For each vegetable crop, we present the most recent information on genetic resources, mapping populations, genetic maps, genome sequences, mapped genes and QTLs, the status of marker-assisted selection and genomic selection, and discuss future research prospects and application of novel techniques and approaches.
{"title":"Genomics and Marker-Assisted Improvement of Vegetable Crops","authors":"Ivan Simko, Mengyuan Jia, J. Venkatesh, B. Kang, Y. Weng, G. Barcaccia, S. Lanteri, G. Bhattarai, M. Foolad","doi":"10.1080/07352689.2021.1941605","DOIUrl":"https://doi.org/10.1080/07352689.2021.1941605","url":null,"abstract":"Abstract Vegetables are an integral part of the human diet worldwide. Traditional breeding approaches have been used extensively to develop new cultivars of vegetables with desirable characteristics, including resistance/tolerance to biotic and abiotic stresses, high yield, and an elevated content of compounds beneficial to human health. The technological progress since the early 1980s has revolutionized our ability to study and manipulate genetic variation in crop plants. The development of high-throughput sequencing platforms and accompanying analytical methods have led to sequencing and assembly of a large number of plant genomes, construction of dense and ultra-dense molecular linkage maps, identification of structural variants, and application of molecular markers in breeding programs. Linkage mapping and genome-wide association mapping studies have been used to identify chromosomal locations of genes and QTLs associated with plant phenotypic variations important for crop improvement. This review provides up-to-date information on the status of genomics and marker-assisted improvement of vegetable crops with the focus on tomato, pepper, eggplant, lettuce, spinach, cucumber, and chicory. For each vegetable crop, we present the most recent information on genetic resources, mapping populations, genetic maps, genome sequences, mapped genes and QTLs, the status of marker-assisted selection and genomic selection, and discuss future research prospects and application of novel techniques and approaches.","PeriodicalId":10854,"journal":{"name":"Critical Reviews in Plant Sciences","volume":"40 1","pages":"303 - 365"},"PeriodicalIF":6.9,"publicationDate":"2021-07-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"59480614","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-05-04DOI: 10.1080/07352689.2021.1911034
A. Horn, A. Pascal, Isidora Lončarević, Raíssa Volpatto Marques, Yi Lu, Sissi Miguel, F. Bourgaud, M. Thorsteinsdóttir, N. Cronberg, J. Becker, R. Reski, H. T. Simonsen
Abstract Natural products from plants have served mankind in a wide range of applications, such as medicines, perfumes, or flavoring agents. For this reason, synthesis, regulation and function of plant-derived chemicals, as well as the evolution of metabolic diversity, has attracted researchers all around the world. In particular, vascular plants have been subject to such analyses due to prevalent characteristics such as appearance, fragrance, and ecological settings. In contrast, bryophytes, constituting the second largest group of plants in terms of species number, have been mostly overlooked in this regard, potentially due to their seemingly tiny, simple and obscure nature. However, the identification of highly interesting chemicals from bryophytes with potential for biotechnological exploitation is changing this perception. Bryophytes offer a high degree of biochemical complexity, as a consequence of their ecological and genetic diversification, which enable them to prosper in various, often very harsh habitats. The number of bioactive compounds isolated from bryophytes is growing rapidly. The rapidly increasing wealth of bryophyte genetics opens doors to functional and comparative genomics approaches, including disentangling of the biosynthesis of potentially interesting chemicals, mining for novel gene families and tracing the evolutionary history of metabolic pathways. Throughout the last decades, the moss Physcomitrella (Physcomitrium patens) has moved from being a model plant together with Marchantia polymorpha in fundamental biology into an attractive host for the production of biotechnologically relevant compounds such as biopharmaceuticals. In the future, bryophytes like the moss P. patens might also be attractive candidates for the production of novel bryophyte-derived chemicals of commercial interest. This review provides a comprehensive overview of natural product research in bryophytes from different perspectives together with biotechnological advances throughout the last decade.
{"title":"Natural Products from Bryophytes: From Basic Biology to Biotechnological Applications","authors":"A. Horn, A. Pascal, Isidora Lončarević, Raíssa Volpatto Marques, Yi Lu, Sissi Miguel, F. Bourgaud, M. Thorsteinsdóttir, N. Cronberg, J. Becker, R. Reski, H. T. Simonsen","doi":"10.1080/07352689.2021.1911034","DOIUrl":"https://doi.org/10.1080/07352689.2021.1911034","url":null,"abstract":"Abstract Natural products from plants have served mankind in a wide range of applications, such as medicines, perfumes, or flavoring agents. For this reason, synthesis, regulation and function of plant-derived chemicals, as well as the evolution of metabolic diversity, has attracted researchers all around the world. In particular, vascular plants have been subject to such analyses due to prevalent characteristics such as appearance, fragrance, and ecological settings. In contrast, bryophytes, constituting the second largest group of plants in terms of species number, have been mostly overlooked in this regard, potentially due to their seemingly tiny, simple and obscure nature. However, the identification of highly interesting chemicals from bryophytes with potential for biotechnological exploitation is changing this perception. Bryophytes offer a high degree of biochemical complexity, as a consequence of their ecological and genetic diversification, which enable them to prosper in various, often very harsh habitats. The number of bioactive compounds isolated from bryophytes is growing rapidly. The rapidly increasing wealth of bryophyte genetics opens doors to functional and comparative genomics approaches, including disentangling of the biosynthesis of potentially interesting chemicals, mining for novel gene families and tracing the evolutionary history of metabolic pathways. Throughout the last decades, the moss Physcomitrella (Physcomitrium patens) has moved from being a model plant together with Marchantia polymorpha in fundamental biology into an attractive host for the production of biotechnologically relevant compounds such as biopharmaceuticals. In the future, bryophytes like the moss P. patens might also be attractive candidates for the production of novel bryophyte-derived chemicals of commercial interest. This review provides a comprehensive overview of natural product research in bryophytes from different perspectives together with biotechnological advances throughout the last decade.","PeriodicalId":10854,"journal":{"name":"Critical Reviews in Plant Sciences","volume":"40 1","pages":"191 - 217"},"PeriodicalIF":6.9,"publicationDate":"2021-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/07352689.2021.1911034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41915756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2021-05-04DOI: 10.1080/07352689.2021.1923185
A. Das, M. Choudhary, Pardeep Kumar, Chikkappa Gangadhar Karjagi, Yathish Kr, Ramesh Kumar, Alla Singh, Santosh Kumar, S. Rakshit
Abstract Heterosis has been widely exploited in plants and animals, and also revolutionized agriculture by improving important agronomic traits. However, the molecular mechanism is still remaining elusive. Though different classical models, viz., dominance, overdominance and epistasis still holds true, the recent studies on epigenomics, transcriptomic, proteomic, metabolomics and circadian model have provided new insights. Multigene models have been proposed as the basis of complementation of allelic and gene expression variation, which is a major probable contributor to heterosis. The evolving epigenetic and genomic field put forward the role of interaction of alleles from different parental genomes in reprogramming the genes involved in stress tolerance, fitness and growth of hybrids. In the majority of the studies, transcriptomic, proteomic and metabolomic studies have found many complex regulatory network changes in genetic, epigenetic, regulatory and biochemical levels and only a few patterns could be established. Thus, heterosis is the outcome of the series of interactions in the genomes. Furthermore, epigenetic modifications of the circadian clock genes and their reciprocal regulators were reported to regulate the expression of downstream genes and pathways leading to more product accumulation in hybrids. Moreover, the majority of the epigenetic studies are limited to Arabidopsis thaliana and Zea mays, however, such studies on different crops may further bring more insights on the role of epigenetic mechanisms in determining heterosis. Further, none of the models is capable to explain heterosis alone which reflects the limitations of the individual model. The present review critically assesses different theories from different fields and also unravels the existing rapid methods to exploit them.
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