1
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Das P, Chandra T, Negi A, Jaiswal S, Iquebal MA, Rai A, Kumar D. A comprehensive review on genomic resources in medicinally and industrially important major spices for future breeding programs: Status, utility and challenges. Curr Res Food Sci 2023; 7:100579. [PMID: 37701635 PMCID: PMC10494321 DOI: 10.1016/j.crfs.2023.100579] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 08/21/2023] [Accepted: 08/26/2023] [Indexed: 09/14/2023] Open
Abstract
In the global market, spices possess a high-value but low-volume commodities of commerce. The food industry depends largely on spices for taste, flavor, and therapeutic properties in replacement of cheap synthetic ones. The estimated growth rate for spices demand in the world is ∼3.19%. Since spices grow in limited geographical regions, India is one of the leading producer of spices, contributing 25-30 percent of total world trade. Hitherto, there has been no comprehensive review of the genomic resources of industrially important major medicinal spices to overcome major impediments in varietal improvement and management. This review focuses on currently available genomic resources of 24 commercially significant spices, namely, Ajwain, Allspice, Asafoetida, Black pepper, Cardamom large, Cardamom small, Celery, Chillies, Cinnamon, Clove, Coriander, Cumin, Curry leaf, Dill seed, Fennel, Fenugreek, Garlic, Ginger, Mint, Nutmeg, Saffron, Tamarind, Turmeric and Vanilla. The advent of low-cost sequencing machines has contributed immensely to the voluminous data generation of these spices, cracking the complex genomic architecture, marker discovery, and understanding comparative and functional genomics. This review of spice genomics resources concludes the perspective and way forward to provide footprints by uncovering genome assemblies, sequencing and re-sequencing projects, transcriptome-based studies, non-coding RNA-mediated regulation, organelles-based resources, developed molecular markers, web resources, databases and AI-directed resources in candidate spices for enhanced breeding potential in them. Further, their integration with molecular breeding could be of immense use in formulating a strategy to protect and expand the production of the spices due to increased global demand.
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Affiliation(s)
- Parinita Das
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Tilak Chandra
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ankita Negi
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sarika Jaiswal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Anil Rai
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Division of Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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2
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Kour D, Khan SS, Kaur T, Kour H, Singh G, Yadav A, Yadav AN. Drought adaptive microbes as bioinoculants for the horticultural crops. Heliyon 2022; 8:e09493. [PMID: 35647359 PMCID: PMC9130543 DOI: 10.1016/j.heliyon.2022.e09493] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/24/2022] [Accepted: 05/14/2022] [Indexed: 12/20/2022] Open
Abstract
Drought stress is among the most destructive stresses for agricultural productivity. It interferes with normal metabolic activities of the plants resulting, a negative impact on physiology and morphology of the plants. The management of drought stress requires various adaptive and alleviation strategies in which stress adaptive microbiomes are exquisite bioresources for plant growth and alleviation of drought stress. Diverse drought adaptive microbes belonging to genera Achromobacter, Arthrobacter, Aspergillus, Bacillus, Pseudomonas, Penicillium and Streptomyces have been reported worldwide. These bioresources exhibit a wide range of mechanisms such as helping plant in nutrient acquisition, producing growth regulators, lowering the levels of stress ethylene, increasing the concentration of osmolytes, and preventing oxidative damage under water deficit environmental conditions. Horticulture is one of the potential agricultural sectors to speed up the economy, poverty and generation of employment for livelihood. The applications of drought adaptive plant growth promoting (PGP) microbes as biofertilizers and biopesticides for horticulture is a potential strategy to improve the productivity and protection of horticultural crops from abiotic and biotic stresses for agricultural sustainability.
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Affiliation(s)
- Divjot Kour
- Department of Microbiology, Akal College of Basic Sciences, Eternal University, Baru Sahib, Sirmour 173101, India
| | - Sofia Shareif Khan
- Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir, 182320, India
| | - Tanvir Kaur
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour 173101, India
| | - Harpreet Kour
- Department of Botany, University of Jammu, Jammu and Kashmir, 180006, India
| | - Gagandeep Singh
- Department of Animal Husbandary, National Dairy Research Institute, Karnal, 132001, India
| | - Ashok Yadav
- Department of Botany, Institute of Science, Banaras Hindu University, Varanasi, Uttar Pradesh, India
| | - Ajar Nath Yadav
- Department of Biotechnology, Dr. Khem Singh Gill Akal College of Agriculture, Eternal University, Baru Sahib, Sirmour 173101, India
- Corresponding author.
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3
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Wang XJ, Luo Q, Li T, Meng PH, Pu YT, Liu JX, Zhang J, Liu H, Tan GF, Xiong AS. Origin, evolution, breeding, and omics of Apiaceae: a family of vegetables and medicinal plants. HORTICULTURE RESEARCH 2022; 9:uhac076. [PMID: 38239769 PMCID: PMC10795576 DOI: 10.1093/hr/uhac076] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/17/2022] [Indexed: 01/22/2024]
Abstract
Many of the world's most important vegetables and medicinal crops, including carrot, celery, coriander, fennel, and cumin, belong to the Apiaceae family. In this review, we summarize the complex origins of Apiaceae and the current state of research on the family, including traditional and molecular breeding practices, bioactive compounds, medicinal applications, nanotechnology, and omics research. Numerous molecular markers, regulatory factors, and functional genes have been discovered, studied, and applied to improve vegetable and medicinal crops in Apiaceae. In addition, current trends in Apiaceae application and research are also briefly described, including mining new functional genes and metabolites using omics research, identifying new genetic variants associated with important agronomic traits by population genetics analysis and GWAS, applying genetic transformation, the CRISPR-Cas9 gene editing system, and nanotechnology. This review provides a reference for basic and applied research on Apiaceae vegetable and medicinal plants.
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Affiliation(s)
- Xiao-Jing Wang
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guizhou 550025, China
| | - Qing Luo
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guizhou 550006, China
| | - Tong Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ping-Hong Meng
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guizhou 550006, China
| | - Yu-Ting Pu
- Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), Guizhou University, Guizhou 550025, China
| | - Jie-Xia Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jian Zhang
- College of Agronomy, Jilin Agricultural University, Changchun 210095, China
| | - Hui Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Guo-Fei Tan
- Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guizhou 550006, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Ministry of Agriculture and Rural Affairs Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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4
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Yu T, Gao J, Liao PC, Li JQ, Ma WB. Insights Into Comparative Analyses and Phylogenomic Implications of Acer (Sapindaceae) Inferred From Complete Chloroplast Genomes. Front Genet 2022; 12:791628. [PMID: 35047013 PMCID: PMC8762318 DOI: 10.3389/fgene.2021.791628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/02/2021] [Indexed: 01/04/2023] Open
Abstract
Acer L. (Sapindaceae) is one of the most diverse and widespread plant genera in the Northern Hemisphere. It comprises 124-156 recognized species, with approximately half being native to Asia. Owing to its numerous morphological features and hybridization, this genus is taxonomically and phylogenetically ranked as one of the most challenging plant taxa. Here, we report the complete chloroplast genome sequences of five Acer species and compare them with those of 43 published Acer species. The chloroplast genomes were 149,103-158,458 bp in length. We conducted a sliding window analysis to find three relatively highly variable regions (psbN-rps14, rpl32-trnL, and ycf1) with a high potential for developing practical genetic markers. A total of 76-103 SSR loci were identified in 48 Acer species. The positive selection analysis of Acer species chloroplast genes showed that two genes (psaI and psbK) were positively selected, implying that light level is a selection pressure for Acer species. Using Bayes empirical Bayes methods, we also identified that 20 cp gene sites have undergone positive selection, which might result from adaptation to specific ecological niches. In phylogenetic analysis, we have reconfirmed that Acer pictum subsp. mono and A. truncatum as sister species. Our results strongly support the sister relationships between sections Platanoidea and Macrantha and between sections Trifoliata and Pentaphylla. Moreover, series Glabra and Arguta are proposed to promote to the section level. The chloroplast genomic resources provided in this study assist taxonomic and phylogenomic resolution within Acer and the Sapindaceae family.
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Affiliation(s)
- Tao Yu
- CECEP Eco-Product Development Research Center, Beijing, China.,Forestry College, Beijing Forestry University, Beijing, China
| | - Jian Gao
- Faculty of Resources and Environment, Baotou Teachers' College, Inner Mongolia University of Science and Technology, Baotou, China
| | - Pei-Chun Liao
- Department of Life Science, National Taiwan Normal University, Taipei, Taiwan
| | - Jun-Qing Li
- Forestry College, Beijing Forestry University, Beijing, China
| | - Wen-Bao Ma
- Key Laboratory of National Forestry and Grassland Administration on Sichuan Forest Ecology and Resources and Environment, Sichuan Academy of Forestry, Chengdu, China
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5
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Jamal A, Wen J, Ma ZY, Ahmed I, Abdullah, Chen LQ, Nie ZL, Liu XQ. Comparative Chloroplast Genome Analyses of the Winter-Blooming Eastern Asian Endemic Genus Chimonanthus (Calycanthaceae) With Implications For Its Phylogeny and Diversification. Front Genet 2021; 12:709996. [PMID: 34917123 PMCID: PMC8670589 DOI: 10.3389/fgene.2021.709996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 10/18/2021] [Indexed: 11/13/2022] Open
Abstract
Chimonanthus of Calycanthaceae is a small endemic genus in China, with unusual winter-blooming sweet flowers widely cultivated for ornamentals and medicinal uses. The evolution of Chimonanthus plastomes and its phylogenetic relationships remain unresolved due to limited availability of genetic resources. Here, we report fully assembled and annotated chloroplast genomes of five Chimonanthus species. The chloroplast genomes of the genus (size range 153,010 – 153,299 bp) reveal high similarities in gene content, gene order, GC content, codon usage, amino acid frequency, simple sequence repeats, oligonucleotide repeats, synonymous and non-synonymous substitutions, and transition and transversion substitutions. Signatures of positive selection are detected in atpF and rpoB genes in C. campanulatus. The correlations among substitutions, InDels, and oligonucleotide repeats reveal weak to strong correlations in distantly related species at the intergeneric levels, and very weak to weak correlations among closely related Chimonanthus species. Chloroplast genomes are used to reconstruct a well-resolved phylogenetic tree, which supports the monophyly of Chimonanthus. Within Chimonanthus, C. praecox and C. campanulatus form one clade, while C. grammatus, C. salicifolius, C. zhejiangensis, and C. nitens constitute another clade. Chimonanthus nitens appears paraphyletic and is closely related to C. salicifolius and C. zhejiangensis, suggesting the need to reevaluate the species delimitation of C. nitens. Chimonanthus and Calycanthus diverged in mid-Oligocene; the radiation of extant Chimonanthus species was dated to the mid-Miocene, while C. grammatus diverged from other Chimonanthus species in the late Miocene. C. salicifolius, C. nitens(a), and C. zhejiangensis are inferred to have diverged in the Pleistocene of the Quaternary period, suggesting recent speciation of a relict lineage in the subtropical forest regions in eastern China. This study provides important insights into the chloroplast genome features and evolutionary history of Chimonanthus and family Calycanthaceae.
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Affiliation(s)
- Abbas Jamal
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
| | - Jun Wen
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Zhi-Yao Ma
- Department of Botany, National Museum of Natural History, MRC166, Smithsonian Institution, Washington, DC, United States
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Abdullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Long-Qing Chen
- Southwest Engineering Technology and Research Center of Landscape Architecture, State Forestry Administration, Southwest Forestry University, Kunming, China
| | - Ze-Long Nie
- Key Laboratory of Plant Resources Conservation and Utilization, College of Biology and Environmental Sciences, Jishou University, Jishou, China
| | - Xiu-Qun Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan, China
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6
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Devanna BN, Mandlik R, Raturi G, Sudhakaran SS, Sharma Y, Sharma S, Rana N, Bansal R, Barvkar V, Tripathi DK, Shivaraj SM, Deshmukh R. Versatile role of silicon in cereals: Health benefits, uptake mechanism, and evolution. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 165:173-186. [PMID: 34044226 DOI: 10.1016/j.plaphy.2021.03.060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2020] [Accepted: 03/30/2021] [Indexed: 06/12/2023]
Abstract
Silicon (Si) is an omnipresent and second most abundant element in the soil lithosphere after oxygen. Silicon being a beneficial element imparts several benefits to the plants and animals. In many plant species, including the cereals the uptake of Si from the soil even exceeds the uptake of essential nutrients. Cereals are the monocots which are known to accumulate a high amount of Si, and reaping maximum benefits associated with it. Cereals contribute a high amount of Si to the human diet compared to other food crops. In the present review, we have summarized distribution of the dietary Si in cereals and its role in the animal and human health. The Si derived benefits in cereals, specifically with respect to biotic and abiotic stress tolerance has been described. We have also discussed the molecular mechanism involved in the Si uptake in cereals, evolution of the Si transport mechanism and genetic variation in the Si concentration among different cultivars of the same species. Various genetic mutants deficient in the Si uptake have been developed and many QTLs governing the Si accumulation have been identified in cereals. The existing knowledge about the Si biology and available resources needs to be explored to understand and improve the Si accumulation in crop plants to achieve sustainability in agriculture.
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Affiliation(s)
- B N Devanna
- ICAR-National Rice Research Institute, Cuttack, Odisha, India
| | - Rushil Mandlik
- National Agri-Food Biotechnology Institute (NABI) Mohali, Punjab, India; Department of Biotechnology Panjab University, Chandigarh, India
| | - Gaurav Raturi
- National Agri-Food Biotechnology Institute (NABI) Mohali, Punjab, India; Department of Biotechnology Panjab University, Chandigarh, India
| | - Sreeja S Sudhakaran
- National Agri-Food Biotechnology Institute (NABI) Mohali, Punjab, India; Department of Biotechnology Panjab University, Chandigarh, India
| | - Yogesh Sharma
- National Agri-Food Biotechnology Institute (NABI) Mohali, Punjab, India
| | - Shivani Sharma
- National Agri-Food Biotechnology Institute (NABI) Mohali, Punjab, India
| | - Nitika Rana
- National Agri-Food Biotechnology Institute (NABI) Mohali, Punjab, India; Department of Biotechnology Panjab University, Chandigarh, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI) Mohali, Punjab, India; Department of Biotechnology Panjab University, Chandigarh, India
| | - Vitthal Barvkar
- Department of Botany, Savitribai Phule Pune University, Pune, India
| | - Durgesh K Tripathi
- Amity Institute of Organic Agriculture, Amity University Uttar Pradesh, AUUP Campus Sector-125, Noida, India
| | - S M Shivaraj
- National Agri-Food Biotechnology Institute (NABI) Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI) Mohali, Punjab, India.
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7
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Kushanov FN, Turaev OS, Ernazarova DK, Gapparov BM, Oripova BB, Kudratova MK, Rafieva FU, Khalikov KK, Erjigitov DS, Khidirov MT, Kholova MD, Khusenov NN, Amanboyeva RS, Saha S, Yu JZ, Abdurakhmonov IY. Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2021; 12:779386. [PMID: 34975965 PMCID: PMC8716771 DOI: 10.3389/fpls.2021.779386] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023]
Abstract
Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.
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Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
- *Correspondence: Fakhriddin N. Kushanov, ;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Kuvandik K. Khalikov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Doston Sh. Erjigitov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Naim N. Khusenov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Sukumar Saha
- Crop Science Research Laboratory, USDA-ARS, Washington, DC, United States
| | - John Z. Yu
- Southern Plains Agricultural Research Center, USDA-ARS, Washington, DC, United States
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
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8
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Aremu AO, Fawole OA, Makunga NP, Masondo NA, Moyo M, Buthelezi NMD, Amoo SO, Spíchal L, Doležal K. Applications of Cytokinins in Horticultural Fruit Crops: Trends and Future Prospects. Biomolecules 2020; 10:biom10091222. [PMID: 32842660 PMCID: PMC7563339 DOI: 10.3390/biom10091222] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 08/15/2020] [Accepted: 08/17/2020] [Indexed: 12/15/2022] Open
Abstract
Cytokinins (CKs) are a chemically diverse class of plant growth regulators, exhibiting wide-ranging actions on plant growth and development, hence their exploitation in agriculture for crop improvement and management. Their coordinated regulatory effects and cross-talk interactions with other phytohormones and signaling networks are highly sophisticated, eliciting and controlling varied biological processes at the cellular to organismal levels. In this review, we briefly introduce the mode of action and general molecular biological effects of naturally occurring CKs before highlighting the great variability in the response of fruit crops to CK-based innovations. We present a comprehensive compilation of research linked to the application of CKs in non-model crop species in different phases of fruit production and management. By doing so, it is clear that the effects of CKs on fruit set, development, maturation, and ripening are not necessarily generic, even for cultivars within the same species, illustrating the magnitude of yet unknown intricate biochemical and genetic mechanisms regulating these processes in different fruit crops. Current approaches using genomic-to-metabolomic analysis are providing new insights into the in planta mechanisms of CKs, pinpointing the underlying CK-derived actions that may serve as potential targets for improving crop-specific traits and the development of new solutions for the preharvest and postharvest management of fruit crops. Where information is available, CK molecular biology is discussed in the context of its present and future implications in the applications of CKs to fruits of horticultural significance.
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Affiliation(s)
- Adeyemi O. Aremu
- Indigenous Knowledge Systems Centre, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2745, South Africa;
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2745, South Africa
- Correspondence: (A.O.A.); (O.A.F.); (N.P.M.); Tel.: +27-18-389-2573 (A.O.A.); +27-11-559-7237 (O.A.F.); +27-21-808-3061 (N.P.M.)
| | - Olaniyi A. Fawole
- Postharvest Research Laboratory, Department of Botany and Plant Biotechnology, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa;
- Correspondence: (A.O.A.); (O.A.F.); (N.P.M.); Tel.: +27-18-389-2573 (A.O.A.); +27-11-559-7237 (O.A.F.); +27-21-808-3061 (N.P.M.)
| | - Nokwanda P. Makunga
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
- Correspondence: (A.O.A.); (O.A.F.); (N.P.M.); Tel.: +27-18-389-2573 (A.O.A.); +27-11-559-7237 (O.A.F.); +27-21-808-3061 (N.P.M.)
| | - Nqobile A. Masondo
- Department of Botany and Zoology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa;
| | - Mack Moyo
- Department of Horticulture, Faculty of Applied Sciences, Durban University of Technology, P.O. Box 1334, Durban 4000, South Africa;
| | - Nana M. D. Buthelezi
- Postharvest Research Laboratory, Department of Botany and Plant Biotechnology, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa;
| | - Stephen O. Amoo
- Indigenous Knowledge Systems Centre, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho 2745, South Africa;
- Postharvest Research Laboratory, Department of Botany and Plant Biotechnology, Faculty of Science, University of Johannesburg, Auckland Park Kingsway Campus, P.O. Box 524, Auckland Park 2006, South Africa;
- Agricultural Research Council, Roodeplaat Vegetable and Ornamental Plants, Private Bag X293, Pretoria 0001, South Africa
| | - Lukáš Spíchal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (L.S.); (K.D.)
| | - Karel Doležal
- Department of Chemical Biology and Genetics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Šlechtitelů 27, CZ-783 71 Olomouc, Czech Republic; (L.S.); (K.D.)
- Laboratory of Growth Regulators, Faculty of Science, Palacký University & Institute of Experimental Botany AS CR, Šlechtitelů 11, CZ-783 71 Olomouc, Czech Republic
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9
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Comparative Plastome Analyses and Phylogenetic Applications of the Acer Section Platanoidea. FORESTS 2020. [DOI: 10.3390/f11040462] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Acer L. (Sapindaceae) is one of the most diverse and widespread genera in the Northern Hemisphere. Section Platanoidea harbours high genetic and morphological diversity and shows the phylogenetic conflict between A. catalpifolium and A. amplum. Chloroplast (cp) genome sequencing is efficient for the enhancement of the understanding of phylogenetic relationships and taxonomic revision. Here, we report complete cp genomes of five species of Acer sect. Platanoidea. The length of Acer sect. Platanoidea cp genomes ranged from 156,262 bp to 157,349 bp and detected the structural variation in the inverted repeats (IRs) boundaries. By conducting a sliding window analysis, we found that five relatively high variable regions (trnH-psbA, psbN-trnD, psaA-ycf3, petA-psbJ and ndhA intron) had a high potential for developing effective genetic markers. Moreover, with an addition of eight plastomes collected from GenBank, we displayed a robust phylogenetic tree of the Acer sect. Platanoidea, with high resolutions for nearly all identified nodes, suggests a promising opportunity to resolve infrasectional relationships of the most species-rich section Platanoidea of Acer.
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Rana N, Rahim MS, Kaur G, Bansal R, Kumawat S, Roy J, Deshmukh R, Sonah H, Sharma TR. Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.). Crit Rev Food Sci Nutr 2019; 60:3304-3320. [DOI: 10.1080/10408398.2019.1685454] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Nitika Rana
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | | | - Gazaldeep Kaur
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Ruchi Bansal
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Surbhi Kumawat
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Joy Roy
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Rupesh Deshmukh
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Humira Sonah
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
| | - Tilak Raj Sharma
- National Agri-Food Biotechnology Institute (NABI), Mohali, Punjab, India
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Wei X, Jin X, Ndayambaza B, Min X, Zhang Z, Wang Y, Liu W. Transcriptome-Wide Characterization and Functional Identification of the Aquaporin Gene Family During Drought Stress in Common Vetch. DNA Cell Biol 2019; 38:374-384. [PMID: 30807211 DOI: 10.1089/dna.2018.4562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Aquaporins (AQPs) are transmembrane channels that are essential for the movement of water and other small molecules between biofilms in various physiological processes in plants. In this study, based on transcriptome-wide data, we identified and described a total of 21 AQP genes in common vetch (Vicia sativa subsp. sativa), which is an economically important pasture legume worldwide. Based on phylogenetic analyses, the VsAQPs were sorted into four subfamilies, including four plasma membrane intrinsic proteins (PIPs), six tonoplast intrinsic proteins (TIPs), seven NOD26-like intrinsic proteins, and four small basic intrinsic proteins. Furthermore, chemical and physical properties of these VsAQPs, including the isoelectric point and theoretical molecular weight, were analyzed. Analyses of the AQP signature sequences and key residues indicated the substrate specificity of each VsAQP. A set of VsAQPs was selected for gene expression analysis in a number of tissues and after drought stress treatments using real-time quantitative reverse transcription/polymerase chain reaction assays. Most of the PIPs and TIPs were proposed to have critical roles in regulating the flow of water during drought stress. Heterologous expression experiments in yeast indicated that VsPIP1;2 and VsPIP2;2 are key candidate genes for improving drought stress tolerance. The results reported in this study could be a crucial resource for further practical analyses and for genetic improvement of drought stress tolerance in common vetch.
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Affiliation(s)
- Xingyi Wei
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Xiaoyu Jin
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Boniface Ndayambaza
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Xueyang Min
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Zhengshe Zhang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Yanrong Wang
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
| | - Wenxian Liu
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, P.R. China
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Abu Zaitoun SY, Jamous RM, Shtaya MJ, Mallah OB, Eid IS, Ali-Shtayeh MS. Characterizing Palestinian snake melon (Cucumis melo var. flexuosus) germplasm diversity and structure using SNP and DArTseq markers. BMC PLANT BIOLOGY 2018; 18:246. [PMID: 30340523 PMCID: PMC6194588 DOI: 10.1186/s12870-018-1475-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2018] [Accepted: 10/08/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Crop landraces embody a source of beneficial genes potentially providing endurance to environmental stress and other agronomic qualities including yield. Our study included 88 snake melon accessions (Cucumis melo var. flexuosus) collected from 9 districts in the Palestinian West-Bank. These accessions represent four landraces of Palestinian snake melon: Green, and White Baladi, and Green, and White Sahouri. RESULTS This is the first report on successful application of genotyping by sequencing in snake melon. Nine thousand seven hundred fifty single-nucleotide polymorphism (SNP) and 7400 DArTseq genetic markers were employed to evaluate genetic biodiversity and population structure of Palestinian snake melon germplasm collection. Clustering based on neighbor-joining-analysis, principle coordinate and Bayesian model implemented in Structure showed that patterns of genetic diversity of snake melon landraces depends on their geographical source and unraveled the presence of two major local landraces (Sahouri, and Baladi) with accessions from each group clustering together. A significant correlation was observed between both types of markers in Mantel correlation test. A significant association between genetic and geographic matrices (P < 0.0001) was also detected. AMOVA indicated that majority of variation (90%) was due to the difference within accessions. CONCLUSION The Palestinian landraces seem to have unique genes that may allow the enhancement of the global snake melon gene pool and developments of the plant production worldwide. Our subsequent objective is to detect genotypes with promising qualities and to conduct association mapping studies concentrating on Fusarium-wilt resistance, yield, and environmental stresses.
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Affiliation(s)
| | - Rana M. Jamous
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
| | - Munqez J. Shtaya
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
- Department of Plant Production and Protection, Faculty of Agriculture, An-Najah University, Tulkarm, Palestine
| | - Omar B. Mallah
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
| | - Imad S. Eid
- Biodiversity and Environmental Research Center, BERC, Til, Nablus, Palestine
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Galla SJ, Buckley TR, Elshire R, Hale ML, Knapp M, McCallum J, Moraga R, Santure AW, Wilcox P, Steeves TE. Building strong relationships between conservation genetics and primary industry leads to mutually beneficial genomic advances. Mol Ecol 2016; 25:5267-5281. [PMID: 27641156 DOI: 10.1111/mec.13837] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 08/23/2016] [Accepted: 08/24/2016] [Indexed: 02/06/2023]
Abstract
Several reviews in the past decade have heralded the benefits of embracing high-throughput sequencing technologies to inform conservation policy and the management of threatened species, but few have offered practical advice on how to expedite the transition from conservation genetics to conservation genomics. Here, we argue that an effective and efficient way to navigate this transition is to capitalize on emerging synergies between conservation genetics and primary industry (e.g., agriculture, fisheries, forestry and horticulture). Here, we demonstrate how building strong relationships between conservation geneticists and primary industry scientists is leading to mutually-beneficial outcomes for both disciplines. Based on our collective experience as collaborative New Zealand-based scientists, we also provide insight for forging these cross-sector relationships.
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Affiliation(s)
- Stephanie J Galla
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand.
| | - Thomas R Buckley
- Landcare Research, Private Bag 92170, Auckland Mail Centre, Auckland, 1142, New Zealand.,School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Rob Elshire
- The Elshire Group, Ltd., 52 Victoria Avenue, Palmerston North, 4410, New Zealand
| | - Marie L Hale
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
| | - Michael Knapp
- Department of Anatomy, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand
| | - John McCallum
- Breeding and Genomics, New Zealand Institute for Plant and Food Research, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Roger Moraga
- AgResearch, Ruakura Research Centre, Bisley Road, Private Bag 3115, Hamilton, 3240, New Zealand
| | - Anna W Santure
- School of Biological Sciences, University of Auckland, Auckland, 1010, New Zealand
| | - Phillip Wilcox
- Department of Mathematics and Statistics, University of Otago, P.O. Box 56, 710 Cumberland Street, Dunedin, 9054, New Zealand
| | - Tammy E Steeves
- School of Biological Sciences, University of Canterbury, Private Bag 4800, Christchurch, 8140, New Zealand
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Ong Q, Nguyen P, Thao NP, Le L. Bioinformatics Approach in Plant Genomic Research. Curr Genomics 2016; 17:368-78. [PMID: 27499685 PMCID: PMC4955030 DOI: 10.2174/1389202917666160331202956] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Revised: 09/11/2015] [Accepted: 09/18/2015] [Indexed: 11/22/2022] Open
Abstract
The advance in genomics technology leads to the dramatic change in plant biology research. Plant biologists now easily access to enormous genomic data to deeply study plant high-density genetic variation at molecular level. Therefore, fully understanding and well manipulating bioinformatics tools to manage and analyze these data are essential in current plant genome research. Many plant genome databases have been established and continued expanding recently. Meanwhile, analytical methods based on bioinformatics are also well developed in many aspects of plant genomic research including comparative genomic analysis, phylogenomics and evolutionary analysis, and genome-wide association study. However, constantly upgrading in computational infrastructures, such as high capacity data storage and high performing analysis software, is the real challenge for plant genome research. This review paper focuses on challenges and opportunities which knowledge and skills in bioinformatics can bring to plant scientists in present plant genomics era as well as future aspects in critical need for effective tools to facilitate the translation of knowledge from new sequencing data to enhancement of plant productivity.
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Affiliation(s)
- Quang Ong
- Plant Abiotic Stress Research Group, Ton Duc Thang University, Ho Chi Minh City, Vietnam
- Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam
| | - Phuc Nguyen
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Nguyen Phuong Thao
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
| | - Ly Le
- School of Biotechnology, International University, Vietnam National University, Ho Chi Minh City, Vietnam
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15
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Darvishzadeh R. Population structure, linkage disequilibrium and association mapping for morphological traits in sunflower ( Helianthus annuusL.). BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2015.1136568] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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16
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Affiliation(s)
- Rupesh Deshmukh
- Département de phytologie Université Laval Quebec QCG1V 0A6 Canada
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17
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He J, Zhao X, Laroche A, Lu ZX, Liu H, Li Z. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. FRONTIERS IN PLANT SCIENCE 2014; 5:484. [PMID: 25324846 DOI: 10.3389/fpls.2014.00484/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/02/2014] [Indexed: 05/23/2023]
Abstract
Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.
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Affiliation(s)
- Jiangfeng He
- Inner Mongolia Academy of Agriculture and Husbandry Science Hohhot, China ; Lethbridge Research Centre, Agriculture and Agri-Food Canada Lethbridge, AB, Canada
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agriculture and Husbandry Science Hohhot, China
| | - André Laroche
- Lethbridge Research Centre, Agriculture and Agri-Food Canada Lethbridge, AB, Canada
| | - Zhen-Xiang Lu
- Lethbridge Research Centre, Agriculture and Agri-Food Canada Lethbridge, AB, Canada
| | - HongKui Liu
- Inner Mongolia Academy of Agriculture and Husbandry Science Hohhot, China
| | - Ziqin Li
- Inner Mongolia Academy of Agriculture and Husbandry Science Hohhot, China
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18
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Deshmukh R, Sonah H, Patil G, Chen W, Prince S, Mutava R, Vuong T, Valliyodan B, Nguyen HT. Integrating omic approaches for abiotic stress tolerance in soybean. FRONTIERS IN PLANT SCIENCE 2014; 5:244. [PMID: 24917870 PMCID: PMC4042060 DOI: 10.3389/fpls.2014.00244] [Citation(s) in RCA: 110] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 05/13/2014] [Indexed: 05/18/2023]
Abstract
Soybean production is greatly influenced by abiotic stresses imposed by environmental factors such as drought, water submergence, salt, and heavy metals. A thorough understanding of plant response to abiotic stress at the molecular level is a prerequisite for its effective management. The molecular mechanism of stress tolerance is complex and requires information at the omic level to understand it effectively. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. The emerging field of ionomics is also being employed for investigating abiotic stress tolerance in soybean. Omic approaches generate a huge amount of data, and adequate advancements in computational tools have been achieved for effective analysis. However, the integration of omic-scale information to address complex genetics and physiological questions is still a challenge. In this review, we have described advances in omic tools in the view of conventional and modern approaches being used to dissect abiotic stress tolerance in soybean. Emphasis was given to approaches such as quantitative trait loci (QTL) mapping, genome-wide association studies (GWAS), and genomic selection (GS). Comparative genomics and candidate gene approaches are also discussed considering identification of potential genomic loci, genes, and biochemical pathways involved in stress tolerance mechanism in soybean. This review also provides a comprehensive catalog of available online omic resources for soybean and its effective utilization. We have also addressed the significance of phenomics in the integrated approaches and recognized high-throughput multi-dimensional phenotyping as a major limiting factor for the improvement of abiotic stress tolerance in soybean.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Henry T. Nguyen
- National Center for Soybean Biotechnology and Division of Plant Sciences, University of MissouriColumbia, MO, USA
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19
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Abstract
The availability of many genomic resources such as genome sequences, functional genomics resources including microarrays and RNA-seq, sufficient numbers of molecular markers, express sequence tags (ESTs) and high-density genetic maps is causing a rapid acceleration of genetics and genomic research of many fruit plants. This is leading to an increase in our knowledge of the genes that are linked to many horticultural and agronomically important traits. Recently, some progress has also been made on the identification and functional analysis of miRNAs in some fruit plants. This is one of the most active research fields in plant sciences. The last decade has witnessed development of genomic resources in many fruit plants such as apple, banana, citrus, grapes, papaya, pears, strawberry etc.; however, many of them are still not being exploited. Furthermore, owing to lack of resources, infrastructure and research facilities in many lesser-developed countries, development of genomic resources in many underutilized or less-studied fruit crops, which grow in these countries, is limited. Thus, research emphasis should be given to those fruit crops for which genomic resources are relatively scarce. The development of genomic databases of these less-studied fruit crops will enable biotechnologists to identify target genes that underlie key horticultural and agronomical traits. This review presents an overview of the current status of the development of genomic resources in fruit plants with the main emphasis being on genome sequencing, EST resources, functional genomics resources including microarray and RNA-seq, identification of quantitative trait loci and construction of genetic maps as well as efforts made on the identification and functional analysis of miRNAs in fruit plants.
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Affiliation(s)
- Manoj K Rai
- a Department of Botany , Biotechnology Centre, Jai Narain Vyas University , Jodhpur , Rajasthan , India
| | - N S Shekhawat
- a Department of Botany , Biotechnology Centre, Jai Narain Vyas University , Jodhpur , Rajasthan , India
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20
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He J, Zhao X, Laroche A, Lu ZX, Liu H, Li Z. Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. FRONTIERS IN PLANT SCIENCE 2014; 5:484. [PMID: 25324846 PMCID: PMC4179701 DOI: 10.3389/fpls.2014.00484] [Citation(s) in RCA: 264] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 09/02/2014] [Indexed: 05/05/2023]
Abstract
Marker-assisted selection (MAS) refers to the use of molecular markers to assist phenotypic selections in crop improvement. Several types of molecular markers, such as single nucleotide polymorphism (SNP), have been identified and effectively used in plant breeding. The application of next-generation sequencing (NGS) technologies has led to remarkable advances in whole genome sequencing, which provides ultra-throughput sequences to revolutionize plant genotyping and breeding. To further broaden NGS usages to large crop genomes such as maize and wheat, genotyping-by-sequencing (GBS) has been developed and applied in sequencing multiplexed samples that combine molecular marker discovery and genotyping. GBS is a novel application of NGS protocols for discovering and genotyping SNPs in crop genomes and populations. The GBS approach includes the digestion of genomic DNA with restriction enzymes followed by the ligation of barcode adapter, PCR amplification and sequencing of the amplified DNA pool on a single lane of flow cells. Bioinformatic pipelines are needed to analyze and interpret GBS datasets. As an ultimate MAS tool and a cost-effective technique, GBS has been successfully used in implementing genome-wide association study (GWAS), genomic diversity study, genetic linkage analysis, molecular marker discovery and genomic selection under a large scale of plant breeding programs.
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Affiliation(s)
- Jiangfeng He
- Inner Mongolia Academy of Agriculture and Husbandry ScienceHohhot, China
- Lethbridge Research Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agriculture and Husbandry ScienceHohhot, China
| | - André Laroche
- Lethbridge Research Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - Zhen-Xiang Lu
- Lethbridge Research Centre, Agriculture and Agri-Food CanadaLethbridge, AB, Canada
| | - HongKui Liu
- Inner Mongolia Academy of Agriculture and Husbandry ScienceHohhot, China
- *Correspondence: Hongkui Liu and Ziqin Li, Inner Mongolia Academy of Agriculture and Husbandry Science, Zhaojun Road 22, Hohhot, Inner Mongolia 010031, China e-mail: ;
| | - Ziqin Li
- Inner Mongolia Academy of Agriculture and Husbandry ScienceHohhot, China
- *Correspondence: Hongkui Liu and Ziqin Li, Inner Mongolia Academy of Agriculture and Husbandry Science, Zhaojun Road 22, Hohhot, Inner Mongolia 010031, China e-mail: ;
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Gapper NE, Giovannoni JJ, Watkins CB. Understanding development and ripening of fruit crops in an 'omics' era. HORTICULTURE RESEARCH 2014; 1:14034. [PMID: 26504543 PMCID: PMC4596339 DOI: 10.1038/hortres.2014.34] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 05/21/2014] [Accepted: 05/28/2014] [Indexed: 05/17/2023]
Abstract
Next generation sequencing has revolutionized plant biology. Not only has our understanding of plant metabolism advanced using model systems and modern chromatography, but application of 'omics'-based technology has been widely extended to non-model systems as costs have plummeted and efficiency increased. As a result, important fundamental questions relating to important horticultural crops are being answered, and novel approaches with application to industry are in progress. Here we review recent research advances on development and ripening of fruit crops, how next generation sequencing approaches are driving this advance and the emerging future landscape.
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Affiliation(s)
- Nigel E Gapper
- Department of Horticulture, Cornell University, Ithaca, NY 14853, USA
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
- mailto:
| | - James J Giovannoni
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
- Plant, Soil, and Nutrition Laboratory, US Department of Agriculture/Agriculture Research Service, Ithaca, NY 14853, USA
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22
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Deshmukh RK, Vivancos J, Guérin V, Sonah H, Labbé C, Belzile F, Bélanger RR. Identification and functional characterization of silicon transporters in soybean using comparative genomics of major intrinsic proteins in Arabidopsis and rice. PLANT MOLECULAR BIOLOGY 2013; 83:303-15. [PMID: 23771580 DOI: 10.1007/s11103-013-0087-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Accepted: 06/03/2013] [Indexed: 05/18/2023]
Abstract
Silicon (Si) confers several benefits to many plant species when absorbed as silicic acid through nodulin 26-like intrinsic proteins (NIPs). The NIPs belong to major intrinsic protein (MIP) family, members of which form channels with high selectivity to control transport of water and different solutes. Here, comparative genomic analysis of the MIPs was performed to investigate the presence of Si transporter MIPs in soybean. Thorough analysis of phylogeny, gene organization, transcriptome profiling and protein modeling was performed to characterize MIPs in rice, Arabidopsis and soybean. Based on several attributes, two putative Si transporter genes, GmNIP2-1 and GmNIP2-2, were identified, characterized and cloned from soybean. Expression of both genes was detected in shoot and root tissues, and decreased as Si increased. The protein encoded by GmNIP2-2 showed functionality for Si transport when expressed in Xenopus oocytes, thus confirming the genetic capability of soybean to absorb the element. Comparative analysis of MIPs in plants provides opportunities to decipher gene evolution, functionality and selectivity of nutrient uptake mechanisms. Exploitation of this strategy has helped to uncover unique features of MIPs in soybean. The identification and functional characterization of Si transporters can be exploited to optimize the benefits that plants can derive from Si absorption.
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Affiliation(s)
- Rupesh K Deshmukh
- Département de Phytologie, Faculté des Sciences de l'Agriculture et de l'Alimentation, Centre de Recherche en Horticulture, Université Laval, Quebec, Canada
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Agrawal GK, Sarkar A, Righetti PG, Pedreschi R, Carpentier S, Wang T, Barkla BJ, Kohli A, Ndimba BK, Bykova NV, Rampitsch C, Zolla L, Rafudeen MS, Cramer R, Bindschedler LV, Tsakirpaloglou N, Ndimba RJ, Farrant JM, Renaut J, Job D, Kikuchi S, Rakwal R. A decade of plant proteomics and mass spectrometry: translation of technical advancements to food security and safety issues. MASS SPECTROMETRY REVIEWS 2013; 32:335-65. [PMID: 23315723 DOI: 10.1002/mas.21365] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 09/10/2012] [Accepted: 09/10/2012] [Indexed: 05/21/2023]
Abstract
Tremendous progress in plant proteomics driven by mass spectrometry (MS) techniques has been made since 2000 when few proteomics reports were published and plant proteomics was in its infancy. These achievements include the refinement of existing techniques and the search for new techniques to address food security, safety, and health issues. It is projected that in 2050, the world's population will reach 9-12 billion people demanding a food production increase of 34-70% (FAO, 2009) from today's food production. Provision of food in a sustainable and environmentally committed manner for such a demand without threatening natural resources, requires that agricultural production increases significantly and that postharvest handling and food manufacturing systems become more efficient requiring lower energy expenditure, a decrease in postharvest losses, less waste generation and food with longer shelf life. There is also a need to look for alternative protein sources to animal based (i.e., plant based) to be able to fulfill the increase in protein demands by 2050. Thus, plant biology has a critical role to play as a science capable of addressing such challenges. In this review, we discuss proteomics especially MS, as a platform, being utilized in plant biology research for the past 10 years having the potential to expedite the process of understanding plant biology for human benefits. The increasing application of proteomics technologies in food security, analysis, and safety is emphasized in this review. But, we are aware that no unique approach/technology is capable to address the global food issues. Proteomics-generated information/resources must be integrated and correlated with other omics-based approaches, information, and conventional programs to ensure sufficient food and resources for human development now and in the future.
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Affiliation(s)
- Ganesh Kumar Agrawal
- Research Laboratory for Biotechnology and Biochemistry, PO Box 13265, Kathmandu, Nepal.
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Mittler R, Shulaev V. Functional genomics, challenges and perspectives for the future. PHYSIOLOGIA PLANTARUM 2013; 148:317-321. [PMID: 23582101 DOI: 10.1111/ppl.12060] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Accepted: 04/07/2013] [Indexed: 06/02/2023]
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Pedreschi R, Lurie S, Hertog M, Nicolaï B, Mes J, Woltering E. Post-harvest proteomics and food security. Proteomics 2013; 13:1772-83. [PMID: 23483703 DOI: 10.1002/pmic.201200387] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Revised: 10/27/2012] [Accepted: 11/11/2012] [Indexed: 12/12/2022]
Abstract
To guarantee sufficient food supply for a growing world population, efforts towards improving crop yield and plant resistance should be complemented with efforts to reduce post-harvest losses. Post-harvest losses are substantial and occur at different stages of the food chain in developed and developing countries. In recent years, a substantially increasing interest can be seen in the application of proteomics to understand post-harvest events. In the near future post-harvest proteomics will be poised to move from fundamental research to aiding the reduction of food losses. Proteomics research can help in reducing food losses through (i) identification and validation of gene products associated to specific quality traits supporting marker-assisted crop improvement programmes, (ii) delivering markers of initial quality that allow optimisation of distribution conditions and prediction of remaining shelf-life for decision support systems and (iii) delivering early detection tools of physiological or pathogen-related post-harvest problems. In this manuscript, recent proteomics studies on post-harvest and stress physiology are reviewed and discussed. Perspectives on future directions of post-harvest proteomics studies aiming to reduce food losses are presented.
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Affiliation(s)
- Romina Pedreschi
- Food & Biobased Research Centre, Wageningen University, Wageningen, The Netherlands.
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26
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Sonah H, Bastien M, Iquira E, Tardivel A, Légaré G, Boyle B, Normandeau É, Laroche J, Larose S, Jean M, Belzile F. An improved genotyping by sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping. PLoS One 2013; 8:e54603. [PMID: 23372741 PMCID: PMC3553054 DOI: 10.1371/journal.pone.0054603] [Citation(s) in RCA: 339] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2012] [Accepted: 12/14/2012] [Indexed: 11/24/2022] Open
Abstract
Highly parallel SNP genotyping platforms have been developed for some important crop species, but these platforms typically carry a high cost per sample for first-time or small-scale users. In contrast, recently developed genotyping by sequencing (GBS) approaches offer a highly cost effective alternative for simultaneous SNP discovery and genotyping. In the present investigation, we have explored the use of GBS in soybean. In addition to developing a novel analysis pipeline to call SNPs and indels from the resulting sequence reads, we have devised a modified library preparation protocol to alter the degree of complexity reduction. We used a set of eight diverse soybean genotypes to conduct a pilot scale test of the protocol and pipeline. Using ApeKI for GBS library preparation and sequencing on an Illumina GAIIx machine, we obtained 5.5 M reads and these were processed using our pipeline. A total of 10,120 high quality SNPs were obtained and the distribution of these SNPs mirrored closely the distribution of gene-rich regions in the soybean genome. A total of 39.5% of the SNPs were present in genic regions and 52.5% of these were located in the coding sequence. Validation of over 400 genotypes at a set of randomly selected SNPs using Sanger sequencing showed a 98% success rate. We then explored the use of selective primers to achieve a greater complexity reduction during GBS library preparation. The number of SNP calls could be increased by almost 40% and their depth of coverage was more than doubled, thus opening the door to an increase in the throughput and a significant decrease in the per sample cost. The approach to obtain high quality SNPs developed here will be helpful for marker assisted genomics as well as assessment of available genetic resources for effective utilisation in a wide number of species.
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Affiliation(s)
- Humira Sonah
- Département de Phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Maxime Bastien
- Département de Phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Elmer Iquira
- Département de Phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Aurélie Tardivel
- Département de Phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Gaétan Légaré
- Plateforme d’analyses génomiques and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Brian Boyle
- Plateforme d’analyses génomiques and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Éric Normandeau
- Département de Biologie, and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Jérôme Laroche
- Plate-forme de bio-informatique and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Stéphane Larose
- Plate-forme de bio-informatique and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - Martine Jean
- Département de Phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
| | - François Belzile
- Département de Phytologie and Institut de biologie intégrative et des systèmes, Université Laval, Quebec City, Quebec, Canada
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Ren M, Venglat P, Qiu S, Feng L, Cao Y, Wang E, Xiang D, Wang J, Alexander D, Chalivendra S, Logan D, Mattoo A, Selvaraj G, Datla R. Target of rapamycin signaling regulates metabolism, growth, and life span in Arabidopsis. THE PLANT CELL 2012; 24:4850-74. [PMID: 23275579 PMCID: PMC3556962 DOI: 10.1105/tpc.112.107144] [Citation(s) in RCA: 183] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Target of Rapamycin (TOR) is a major nutrition and energy sensor that regulates growth and life span in yeast and animals. In plants, growth and life span are intertwined not only with nutrient acquisition from the soil and nutrition generation via photosynthesis but also with their unique modes of development and differentiation. How TOR functions in these processes has not yet been determined. To gain further insights, rapamycin-sensitive transgenic Arabidopsis thaliana lines (BP12) expressing yeast FK506 Binding Protein12 were developed. Inhibition of TOR in BP12 plants by rapamycin resulted in slower overall root, leaf, and shoot growth and development leading to poor nutrient uptake and light energy utilization. Experimental limitation of nutrient availability and light energy supply in wild-type Arabidopsis produced phenotypes observed with TOR knockdown plants, indicating a link between TOR signaling and nutrition/light energy status. Genetic and physiological studies together with RNA sequencing and metabolite analysis of TOR-suppressed lines revealed that TOR regulates development and life span in Arabidopsis by restructuring cell growth, carbon and nitrogen metabolism, gene expression, and rRNA and protein synthesis. Gain- and loss-of-function Ribosomal Protein S6 (RPS6) mutants additionally show that TOR function involves RPS6-mediated nutrition and light-dependent growth and life span in Arabidopsis.
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Affiliation(s)
- Maozhi Ren
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Prakash Venglat
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Shuqing Qiu
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Li Feng
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Yongguo Cao
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Edwin Wang
- Computational Chemistry and Bioinformatics Group, Biotechnology Research Institute, National Research Council of Canada, Montreal, Quebec H4P 2R2, Canada
| | - Daoquan Xiang
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Jinghe Wang
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | | | | | - David Logan
- Université d’Angers, Institut de Recherche en Horticulture et Semences, SFR 4207 QUASAV, LUNAM Université, Angers cedex 1, France
| | - Autar Mattoo
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture–Agricultural Research Service, Beltsville Agricultural Research Center, Beltsville, Maryland 20705-2350
| | - Gopalan Selvaraj
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
| | - Raju Datla
- Plant Biotechnology Institute, National Research Council of Canada, Saskatoon, Saskatchewan S7N 0W9, Canada
- Address correspondence to
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28
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Sun YD, Liang Y, Wu JM, Li YZ, Cui X, Qin L. Dynamic QTL analysis for fruit lycopene content and total soluble solid content in a Solanum lycopersicum x S. pimpinellifolium cross. GENETICS AND MOLECULAR RESEARCH 2012; 11:3696-710. [PMID: 22930431 DOI: 10.4238/2012.august.17.8] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Fruit lycopene content and total soluble solid content are important factors determining fruit quality of tomatoes; however, the dynamic quantitative trait loci (QTL) controlling lycopene and soluble solid content have not been well studied. We mapped the chromosomal regions controlling these traits in different periods in F(2:3) families derived from a cross between the domestic and wild tomato species Solanum lycopersicum and S. pimpinellifolium. Fifteen QTLs for lycopene and soluble solid content and other related traits analyzed at three different fruit ripening stages were detected with a composite interval mapping method. These QTLs explained 7-33% of the individual phenotypic variation. QTLs detected in the color-changing period were different from those detected in the other two periods. On chromosome 1, the soluble solid content QTL was located in the same region during the color-changing and full-ripe periods. On chromosome 4, the same QTL for lycopene content was found during the color-changing and full-ripe periods. The QTL for lycopene content on chromosome 4 co-located with the QTL for soluble solid content during the full-ripe period. Co-location of lycopene content QTL and soluble solid content QTLs may be due to pleiotropic effects of a single gene or a cluster of genes via physiological relationships among traits. On chromosome 9, the same two QTLs for lycopene content at two different fruit ripening periods may reflect genes controlling lycopene content that are always expressed in tomato fruit development.
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Affiliation(s)
- Y D Sun
- Key Laboratory of Horticulture Plant Germplasm and Genetic Improvement, Ministry of Agriculture, College of Horticulture, Northwest A & F University, Yangling, Shaanxi, China
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Gupta SK, Rai AK, Kanwar SS, Sharma TR. Comparative analysis of zinc finger proteins involved in plant disease resistance. PLoS One 2012; 7:e42578. [PMID: 22916136 PMCID: PMC3419713 DOI: 10.1371/journal.pone.0042578] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 07/10/2012] [Indexed: 11/19/2022] Open
Abstract
A meta-analysis was performed to understand the role of zinc finger domains in proteins of resistance (R) genes cloned from different crops. We analyzed protein sequences of seventy R genes of various crops in which twenty six proteins were found to have zinc finger domains along with nucleotide binding sites - leucine rice repeats (NBS-LRR) domains. We identified thirty four zinc finger domains in the R proteins of nine crops and were grouped into 19 types of zinc fingers. The size of individual zinc finger domain within the R genes varied from 11 to 84 amino acids, whereas the size of proteins containing these domains varied from 263 to 1305 amino acids. The biophysical analysis revealed that molecular weight of Pi54 zinc finger was lowest whereas the highest one was found in rice Pib zinc finger named as Transposes Transcription Factor (TTF). The instability (R(2) =0.95) and the aliphatic (R(2) =0.94) indices profile of zinc finger domains follows the polynomial distribution pattern. The pairwise identity analysis showed that the Lin11, Isl-1 & Mec-3 (LIM) zinc finger domain of rice blast resistance protein pi21 have 12.3% similarity with the nuclear transcription factor, X-box binding-like 1 (NFX) type zinc finger domain of Pi54 protein. For the first time, we reported that Pi54 (Pi-k(h)-Tetep), a rice blast resistance (R) protein have a small zinc finger domain of NFX type located on the C-terminal in between NBS and LRR domains of the R-protein. Compositional analysis depicted by the helical wheel diagram revealed the presence of a hydrophobic region within this domain which might help in exposing the LRR region for a possible R-Avr interaction. This domain is unique among all other cloned plant disease resistance genes and might play an important role in broad-spectrum nature of rice blast resistance gene Pi54.
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Affiliation(s)
- Santosh Kumar Gupta
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
- Department of Biotechnology, Himachal Pradesh University, Summer-Hill, Shimla, India
| | - Amit Kumar Rai
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
- Department of Biotechnology, Himachal Pradesh University, Summer-Hill, Shimla, India
| | - Shamsher Singh Kanwar
- Department of Biotechnology, Himachal Pradesh University, Summer-Hill, Shimla, India
| | - Tilak R. Sharma
- National Research Centre on Plant Biotechnology, Indian Agricultural Research Institute, New Delhi, India
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Korir NK, Han J, Shangguan L, Wang C, Kayesh E, Zhang Y, Fang J. Plant variety and cultivar identification: advances and prospects. Crit Rev Biotechnol 2012; 33:111-25. [PMID: 22698516 DOI: 10.3109/07388551.2012.675314] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Plant variety and cultivar identification is one of the most important aspects in agricultural systems. The large number of varieties or landraces among crop plants has made it difficult to identify and characterize varieties solely on the basis of morphological characters because they are non stable and originate due to environmental and climatic conditions, and therefore phenotypic plasticity is an outcome of adaptation. To mitigate this, scientists have developed and employed molecular markers, statistical tests and software to identify and characterize the required plant cultivars or varieties for cultivation, breeding programs as well as for cultivar-right-protection. The establishment of genome and transcriptome sequencing projects for many crops has led to generation of a huge wealth of sequence information that could find much use in identification of plants and their varieties. We review the current status of plant variety and cultivar identification, where an attempt has been made to describe the different strategies available for plant identification. We have found that despite the availability of methods and suitable markers for a wide range of crops, there is dearth of simple ways of making both morphological descriptors and molecular markers easy, referable and practical to use although there are ongoing attempts at making this possible. Certain limitations present a number of challenges for the development and utilization of modern scientific methods in variety or cultivar identification in many important crops.
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Affiliation(s)
- Nicholas Kibet Korir
- College of Horticulture, Nanjing Agricultural University, Weigang, Nanjing, China
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31
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Barabaschi D, Guerra D, Lacrima K, Laino P, Michelotti V, Urso S, Valè G, Cattivelli L. Emerging knowledge from genome sequencing of crop species. Mol Biotechnol 2012; 50:250-66. [PMID: 21822975 DOI: 10.1007/s12033-011-9443-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Extensive insights into the genome composition, organization, and evolution have been gained from the plant genome sequencing and annotation ongoing projects. The analysis of crop genomes provided surprising evidences with important implications in plant origin and evolution: genome duplication, ancestral re-arrangements and unexpected polyploidization events opened new doors to address fundamental questions related to species proliferation, adaptation, and functional modulations. Detailed paleogenomic analysis led to many speculation on how chromosomes have been shaped over time in terms of gene content and order. The completion of the genome sequences of several major crops, prompted to a detailed identification and annotation of transposable elements: new hypothesis related to their composition, chromosomal distribution, insertion models, amplification rate, and evolution patterns are coming up. Availability of full genome sequence of several crop species as well as from many accessions within species is providing new keys for biodiversity exploitation and interpretation. Re-sequencing is enabling high-throughput genotyping to identify a wealth of SNP and afterward to produce haplotype maps necessary to accurately associate molecular variation to phenotype. Conservation genomics is emerging as a powerful tool to explain adaptation, genetic drift, natural selection, hybridization and to estimate genetic variation, fitness and population's viability.
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Affiliation(s)
- Delfina Barabaschi
- CRA, Viticolture Research Centre, Via Casoni 13/A, 31058 Susegana, TV, Italy
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32
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Translational plant proteomics: a perspective. J Proteomics 2012; 75:4588-601. [PMID: 22516432 DOI: 10.1016/j.jprot.2012.03.055] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2011] [Revised: 02/25/2012] [Accepted: 03/25/2012] [Indexed: 11/21/2022]
Abstract
Translational proteomics is an emerging sub-discipline of the proteomics field in the biological sciences. Translational plant proteomics aims to integrate knowledge from basic sciences to translate it into field applications to solve issues related but not limited to the recreational and economic values of plants, food security and safety, and energy sustainability. In this review, we highlight the substantial progress reached in plant proteomics during the past decade which has paved the way for translational plant proteomics. Increasing proteomics knowledge in plants is not limited to model and non-model plants, proteogenomics, crop improvement, and food analysis, safety, and nutrition but to many more potential applications. Given the wealth of information generated and to some extent applied, there is the need for more efficient and broader channels to freely disseminate the information to the scientific community. This article is part of a Special Issue entitled: Translational Proteomics.
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Scharf KD, Berberich T, Ebersberger I, Nover L. The plant heat stress transcription factor (Hsf) family: structure, function and evolution. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2011; 1819:104-19. [PMID: 22033015 DOI: 10.1016/j.bbagrm.2011.10.002] [Citation(s) in RCA: 539] [Impact Index Per Article: 41.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2011] [Revised: 10/06/2011] [Accepted: 10/07/2011] [Indexed: 12/13/2022]
Abstract
Ten years after the first overview of a complete plant Hsf family was presented for Arabidopsis thaliana by Nover et al. [1], we compiled data for 252 Hsfs from nine plant species (five eudicots and four monocots) with complete or almost complete genome sequences. The new data set provides interesting insights into phylogenetic relationships within the Hsf family in plants and allows the refinement of their classification into distinct groups. Numerous publications over the last decade document the diversification and functional interaction of Hsfs as well as their integration into the complex stress signaling and response networks of plants. This article is part of a Special Issue entitled: Plant gene regulation in response to abiotic stress.
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Affiliation(s)
- Klaus-Dieter Scharf
- Molecular Cellbiology of Plants, Goethe University Frankfurt, Max-von-Laue-Str. 9, D-60438 Frankfurt/M., Germany.
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Genome-wide distribution and organization of microsatellites in plants: an insight into marker development in Brachypodium. PLoS One 2011; 6:e21298. [PMID: 21713003 PMCID: PMC3119692 DOI: 10.1371/journal.pone.0021298] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/25/2011] [Indexed: 11/29/2022] Open
Abstract
Plant genomes are complex and contain large amounts of repetitive DNA including microsatellites that are distributed across entire genomes. Whole genome sequences of several monocot and dicot plants that are available in the public domain provide an opportunity to study the origin, distribution and evolution of microsatellites, and also facilitate the development of new molecular markers. In the present investigation, a genome-wide analysis of microsatellite distribution in monocots (Brachypodium, sorghum and rice) and dicots (Arabidopsis, Medicago and Populus) was performed. A total of 797,863 simple sequence repeats (SSRs) were identified in the whole genome sequences of six plant species. Characterization of these SSRs revealed that mono-nucleotide repeats were the most abundant repeats, and that the frequency of repeats decreased with increase in motif length both in monocots and dicots. However, the frequency of SSRs was higher in dicots than in monocots both for nuclear and chloroplast genomes. Interestingly, GC-rich repeats were the dominant repeats only in monocots, with the majority of them being present in the coding region. These coding GC-rich repeats were found to be involved in different biological processes, predominantly binding activities. In addition, a set of 22,879 SSR markers that were validated by e-PCR were developed and mapped on different chromosomes in Brachypodium for the first time, with a frequency of 101 SSR markers per Mb. Experimental validation of 55 markers showed successful amplification of 80% SSR markers in 16 Brachypodium accessions. An online database ‘BraMi’ (Brachypodium microsatellite markers) of these genome-wide SSR markers was developed and made available in the public domain. The observed differential patterns of SSR marker distribution would be useful for studying microsatellite evolution in a monocot–dicot system. SSR markers developed in this study would be helpful for genomic studies in Brachypodium and related grass species, especially for the map based cloning of the candidate gene(s).
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