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Nybom H, Ruan C, Rumpunen K. The Systematics, Reproductive Biology, Biochemistry, and Breeding of Sea Buckthorn-A Review. Genes (Basel) 2023; 14:2120. [PMID: 38136942 PMCID: PMC10743242 DOI: 10.3390/genes14122120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Revised: 11/11/2023] [Accepted: 11/15/2023] [Indexed: 12/24/2023] Open
Abstract
Both the fruit flesh and seeds of sea buckthorn have multiple uses for medicinal and culinary purposes, including the valuable market for supplementary health foods. Bioactive compounds, such as essential amino acids, vitamins B, C, and E, carotenoids, polyphenols, ursolic acid, unsaturated fatty acids, and other active substances, are now being analyzed in detail for their medicinal properties. Domestication with commercial orchards and processing plants is undertaken in many countries, but there is a large need for improved plant material with high yield, tolerance to environmental stress, diseases, and pests, suitability for efficient harvesting methods, and high contents of compounds that have medicinal and/or culinary values. Applied breeding is based mainly on directed crosses between different subspecies of Hippophae rhamnoides. DNA markers have been applied to analyses of systematics and population genetics as well as for the discrimination of cultivars, but very few DNA markers have as yet been developed for use in selection and breeding. Several key genes in important metabolic pathways have, however, been identified, and four genomes have recently been sequenced.
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Affiliation(s)
- Hilde Nybom
- Department of Plant Breeding–Balsgård, Swedish University of Agricultural Sciences, 29194 Kristianstad, Sweden
| | - Chengjiang Ruan
- Key Laboratory of Biotechnology and Bioresources Utilization, Ministry of Education, Institute of Plant Resources, Dalian Minzu University, Dalian 116600, China;
| | - Kimmo Rumpunen
- Department of Plant Breeding, Swedish University of Agricultural Sciences, 23053 Alnarp, Sweden;
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Newman CS, Andres RJ, Youngblood RC, Campbell JD, Simpson SA, Cannon SB, Scheffler BE, Oakley AT, Hulse-Kemp AM, Dunne JC. Initiation of genomics-assisted breeding in Virginia-type peanuts through the generation of a de novo reference genome and informative markers. Front Plant Sci 2023; 13:1073542. [PMID: 36777543 PMCID: PMC9911918 DOI: 10.3389/fpls.2022.1073542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Virginia-type peanut, Arachis hypogaea subsp. hypogaea, is the second largest market class of peanut cultivated in the United States. It is mainly used for large-seeded, in-shell products. Historically, Virginia-type peanut cultivars were developed through long-term recurrent phenotypic selection and wild species introgression projects. Contemporary genomic technologies represent a unique opportunity to revolutionize the traditional breeding pipeline. While there are genomic tools available for wild and cultivated peanuts, none are tailored specifically to applied Virginia-type cultivar development programs. METHODS AND RESPECTIVE RESULTS Here, the first Virginia-type peanut reference genome, "Bailey II", was assembled. It has improved contiguity and reduced instances of manual curation in chromosome arms. Whole-genome sequencing and marker discovery was conducted on 66 peanut lines which resulted in 1.15 million markers. The high marker resolution achieved allowed 34 unique wild species introgression blocks to be cataloged in the A. hypogaea genome, some of which are known to confer resistance to one or more pathogens. To enable marker-assisted selection of the blocks, 111 PCR Allele Competitive Extension assays were designed. Forty thousand high quality markers were selected from the full set that are suitable for mid-density genotyping for genomic selection. Genomic data from representative advanced Virginia-type peanut lines suggests this is an appropriate base population for genomic selection. DISCUSSION The findings and tools produced in this research will allow for rapid genetic gain in the Virginia-type peanut population. Genomics-assisted breeding will allow swift response to changing biotic and abiotic threats, and ultimately the development of superior cultivars for public use and consumption.
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Affiliation(s)
- Cassondra S. Newman
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Ryan J. Andres
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Ramey C. Youngblood
- Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, Mississippi State, MS, United States
| | - Jacqueline D. Campbell
- United States Department of Agriculture–Agricultural Research Service (USDA–ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
| | - Sheron A. Simpson
- United States Department of Agriculture–Agricultural Research Service Genomics and Bioinformatics Research Unit, Stoneville, MS, United States
| | - Steven B. Cannon
- United States Department of Agriculture–Agricultural Research Service (USDA–ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
| | - Brian E. Scheffler
- United States Department of Agriculture–Agricultural Research Service Genomics and Bioinformatics Research Unit, Stoneville, MS, United States
| | - Andrew T. Oakley
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
| | - Amanda M. Hulse-Kemp
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
- United States Department of Agriculture–Agricultural Research Service Genomics and Bioinformatics Research Unit, Raleigh, NC, United States
| | - Jeffrey C. Dunne
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC, United States
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Backer R, Mandolino G, Wilkins O, ElSohly MA, Smith DL. Editorial: Cannabis Genomics, Breeding and Production. Front Plant Sci 2020; 11:591445. [PMID: 33193546 PMCID: PMC7661384 DOI: 10.3389/fpls.2020.591445] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/22/2020] [Indexed: 05/25/2023]
Affiliation(s)
- Rachel Backer
- Department of Plant Science, McGill University, Montreal, QC, Canada
| | - Giuseppe Mandolino
- Research Center for Industrial Cultures, Council for Agricultural Research and Analysis of Agricultural Economics, Bologna, Italy
| | - Olivia Wilkins
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Mahmoud A. ElSohly
- School of Pharmacy, University of Mississippi, Oxford, MS, United States
| | - Donald L. Smith
- Department of Plant Science, McGill University, Montreal, QC, Canada
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Bishnoi SK, He X, Phuke RM, Kashyap PL, Alakonya A, Chhokar V, Singh RP, Singh PK. Karnal Bunt: A Re-Emerging Old Foe of Wheat. Front Plant Sci 2020; 11:569057. [PMID: 33133115 PMCID: PMC7550625 DOI: 10.3389/fpls.2020.569057] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/09/2020] [Indexed: 05/18/2023]
Abstract
Wheat (Triticum aestivum L.) crop health assumes unprecedented significance in being the second most important staple crop of the world. It is host to an array of fungal pathogens attacking the plant at different developmental stages and accrues various degrees of yield losses owing to these. Tilletia indica that causes Karnal bunt (KB) disease in wheat is one such fungal pathogen of high quarantine importance restricting the free global trade of wheat besides the loss of grain yield as well as quality. With global climate change, the disease appears to be shifting from its traditional areas of occurrence with reports of increased vulnerabilities of new areas across the continents. This KB vulnerability of new geographies is of serious concern because once established, the disease is extremely difficult to eradicate and no known instance of its complete eradication using any management strategy has been reported yet. The host resistance to KB is the most successful as well as preferred strategy for its mitigation and control. However, breeding of KB resistant wheat cultivars has proven to be not so easy, and the low success rate owes to the scarcity of resistance sources, extremely laborious and regulated field screening protocols delaying identification/validation of putative resistance sources, and complex quantitative nature of resistance with multiple genes conferring only partial resistance. Moreover, given a lack of comprehensive understanding of the KB disease epidemiology, host-pathogen interaction, and pathogen evolution. Here, in this review, we attempt to summarize the progress made and efforts underway toward a holistic understanding of the disease itself with a specific focus on the host-pathogen interaction between T. indica and wheat as key elements in the development of resistant germplasm. In this context, we emphasize the tools and techniques being utilized in development of KB resistant germplasm by illuminating upon the genetics concerning the host responses to the KB pathogen including a future course. As such, this article could act as a one stop information primer on this economically important and re-emerging old foe threatening to cause devastating impacts on food security and well-being of communities that rely on wheat.
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Affiliation(s)
| | - Xinyao He
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | | | - Prem Lal Kashyap
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Amos Alakonya
- International Maize and Wheat Improvement Center, Texcoco, Mexico
| | - Vinod Chhokar
- Department of Bio and Nanotechnology, Guru Jambheshwar University of Science and Technology, Hisar, India
| | | | - Pawan Kumar Singh
- International Maize and Wheat Improvement Center, Texcoco, Mexico
- *Correspondence: Pawan Kumar Singh,
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Abstract
Blast, caused by the fungal pathogen Pyricularia grisea, is the most devastating disease of rice worldwide. Knowledge of the pathotype composition of the pathogen in rice fields is essential for rational deployment of resistance genes in rice breeding programs. In this study, we assayed the pathotypes of the pathogen populations using samples recently collected from 13 major rice-growing provinces of central and southern China. In all, 792 single spore isolates were tested for pathogenicity reactions using 13 host differentials consisting of six indica and seven japonica near-isogenic lines (NILs). The compositions of the pathogen populations were complex; 48 pathotypes were identified with the indica NILs, 82 pathotypes were detected with the japonica NILs, and a total of 344 pathotypes were identified with both indica and japonica NILs. There were large differences in distribution of the pathotypes among the different rice-growing areas. Even neighbor provinces seemed to differ sharply in types and frequencies of the most prevalent pathotypes. There was also a large difference in the frequencies of the isolates producing compatible reactions on the NILs, indicating the difference in frequencies of avirulence genes in the pathogen populations. The data provided very useful information for formulating strategies for improving blast resistance in rice breeding programs.
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Affiliation(s)
- H L Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - B T Chen
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - D P Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Y F Xie
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Qifa Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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