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Deng Y, He Z, Li Y, Ye M, Xiang L. Six Express Sequence Tag-Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species. Curr Issues Mol Biol 2023; 45:7183-7196. [PMID: 37754238 PMCID: PMC10529843 DOI: 10.3390/cimb45090454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
Zanthoxylum (Sichuan pepper), with its rich cultivars, has long been widely cultivated in China for its unique seasoning and medicinal uses, but most of its cultivars have similar morphological characteristics. Therefore, we hypothesized that the genetic diversity of Zanthoxylum cultivars is low because of their apomixis and long cultivation history. In this study, we aimed to investigate the genetic diversity of three Zanthoxylum species on the cultivar level based on express sequence tag-simple sequence repeat (EST-SSR) primers. In total, 121 samples of three Zanthoxylum species (Z. bungeanum, Z. armatum and Z. piperitum) were collected from different areas in China for genetic diversity analysis. A total of six specificity and polymorphism EST-SSR primers, which we selected from among 120 primers based on two transcriptomes (Z. bungeanum, Z. armatum) in our earlier study, were used to evaluate genetic diversity based on capillary electrophoresis technology. The results of our analysis using the unweighted pair group method with arithmetic mean (UPGMA) indicated that most of the samples are clustered in one clade in the UPGMA dendrogram, and the average genetic distance was 0.6409. Principal component analysis (PCA) showed that Z. piperitum may have a closer genetic relationship with Z. bungeanum than with Z. armatum. An analysis of molecular variation (AMOVA) showed that the genetic variation mainly stemmed from individuals within populations; the genetic differentiation coefficient (PhiPT) was 0.429, the gene flow (Nm) between populations was 0.333, and the differences among populations were not significant (p > 0.001). For the intraspecific populations of ZB, the percentage of genetic variation was 53% among populations and 47% within populations, with non-significant differences between populations (p > 0.001). The genetic differentiation coefficient (PhiT) was 0.529, and the gene flow (Nm) was 0.223. For the intraspecific populations of ZA, the results indicated that the percentage of genetic variation was 29% among populations and 71% within populations, with non-significant differences between populations (p > 0.001); the genetic differentiation coefficient (PhiPT) was 0.293, and the gene flow (Nm) was 0.223. Through genetic structure analysis (GSA), we predicted that these 121 samples belonged to two optimal subgroups, which means that all the samples probably originated from two gene pools. Above all, this indicated that the genetic diversity of the 121 Zanthoxylum samples was relatively low at both the species and cultivar levels, a finding which was consistent with our initial assumptions. This study provides a reference, with molecular-level data, for the further identification of Zanthoxylum species.
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Affiliation(s)
- Yangchuan Deng
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Zhoujian He
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Yanlin Li
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Meng Ye
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave., Beijing 100700, China
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Li JW, Li H, Liu ZW, Wang YX, Chen Y, Yang N, Hu ZH, Li T, Zhuang J. Molecular markers in tea plant (Camellia sinensis): Applications to evolution, genetic identification, and molecular breeding. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107704. [PMID: 37086694 DOI: 10.1016/j.plaphy.2023.107704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 04/03/2023] [Accepted: 04/13/2023] [Indexed: 05/03/2023]
Abstract
Tea plants have a long cultivation history in the world, and the beverage (tea) made from its leaves is well known in the world. Due to the characteristics of self-incompatibility, long-term natural and artificial hybridization, tea plants have a very complex genetic background, which make the classification of tea plants unclear. Molecular marker, one type of genetic markers, has the advantages of stable inheritance, large amount of information, and high reliability. The development of molecular marker has facilitated the understanding of complex tea germplasm resources. So far, molecular markers had played important roles in the study of the origin and evolution, the preservation and identification of tea germplasms, and the excellent cultivars breeding of tea plants. However, the information is scattered, making it difficult to understand the advance of molecular markers in tea plants. In this paper, we summarized the development process and types of molecular markers in tea plants. In addition, the application advance of these molecular markers in tea plants was reviewed. Perspectives of molecular markers in tea plants were also systematically provided and discussed. The elaboration of molecular markers in this paper should help us to renew understanding of its application in tea plants.
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Affiliation(s)
- Jing-Wen Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Hui Li
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Wei Liu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yong-Xin Wang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yi Chen
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ni Yang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Zhi-Hang Hu
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Tong Li
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhuang
- Tea Science Research Institute, College of Horticulture, Nanjing Agricultural University, Nanjing, China.
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Agafonov AV, Shabanova Kobozeva EV, Asbaganov SV, Mglinets AV, Bogdanova VS. Identification of genome compositions in allopolyploid species of the genus Elymus (Poaceae: Triticeae) in the Asian part of Russia by CAPS analysis. Vavilovskii Zhurnal Genet Selektsii 2020; 24:115-122. [PMID: 33659790 PMCID: PMC7716549 DOI: 10.18699/vj20.606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
The genus Elymus L., together with wheat, rye, and barley, belongs to the tribe Triticeae. Apart from its economic value, this tribe is characterized by abundance of polyploid taxa formed in the course of remote hybridization. Single-copy nuclear genes are convenient markers for identification of source genomes incorporated into polyploids. In the present work, a CAPS-marker is developed to distinguish basic St, H, and Y genomes comprising polyploid genomes of Asiatic species of the genus Elymus. The test is based on electrophoretic analysis of restriction patterns of a PCR-amplified fragment of the gene coding for beta-amylase. There are about 50 Elymus species in Russia, and most of them are supposed to possess one of three haplome combinations, StH, StY and StHY. Boreal StH-genomic species endemic for Russia are the least studied. On the basis of nucleotide sequences from public databases, TaqI restrictase was selected, as it produced patterns of restriction fragments specific for St, H, and Y haplomes easily recognizable in agarose gel. A sample of 68 accessions belonging to 32 species was analyzed. In 15 species, the earlier known genomic constitutions were confirmed, but in E. kamoji this assay failed to reveal the presence of H genome. This unusual H genome was suggested to originate from a different Hordeum species. In 16 species, genomic constitutions were identified for the first time. Fifteen accessions from Asian Russia possessed the genomic constitution StStHH, and E. amurensis, phylogenetically close to the StY-genomic species E. ciliaris, had the genomic constitution StStYY. It is inferred that the center of species diversity of the StH-genomic group is shifted to the north as compared to the center of origin of StY-genomic species, confined to China. Key words: Elymus; taxonomy; allopolyploids; genome constitution; CAPS markers.
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Affiliation(s)
- A V Agafonov
- Central Siberian Botanical Garden of Siberian Branch of the Russian Academy of Sciences, Russia, Novosibirsk, Russia
| | - E V Shabanova Kobozeva
- Central Siberian Botanical Garden of Siberian Branch of the Russian Academy of Sciences, Russia, Novosibirsk, Russia
| | - S V Asbaganov
- Central Siberian Botanical Garden of Siberian Branch of the Russian Academy of Sciences, Russia, Novosibirsk, Russia
| | - A V Mglinets
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - V S Bogdanova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Dubey H, Rawal HC, Rohilla M, Lama U, Kumar PM, Bandyopadhyay T, Gogoi M, Singh NK, Mondal TK. TeaMiD: a comprehensive database of simple sequence repeat markers of tea. Database (Oxford) 2020; 2020:baaa013. [PMID: 32159215 PMCID: PMC7065459 DOI: 10.1093/database/baaa013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 01/05/2020] [Accepted: 01/25/2020] [Indexed: 12/05/2022]
Abstract
Tea is a highly cross-pollinated, woody, perennial tree. High heterozygosity combined with a long gestational period makes conventional breeding a cumbersome process. Therefore, marker-assisted breeding is a better alternative approach when compared with conventional breeding. Considering the large genome size of tea (~3 Gb), information about simple sequence repeat (SSR) is scanty. Thus, we have taken advantage of the recently published tea genomes to identify large numbers of SSR markers in the tea. Besides the genomic sequences, we identified SSRs from the other publicly available sequences such as RNA-seq, GSS, ESTs and organelle genomes (chloroplasts and mitochondrial) and also searched published literature to catalog validated set of tea SSR markers. The complete exercise yielded a total of 935 547 SSRs. Out of the total, 82 SSRs were selected for validation among a diverse set of tea genotypes. Six primers (each with four to six alleles, an average of five alleles per locus) out of the total 27 polymorphic primers were used for a diversity analysis in 36 tea genotypes with mean polymorphic information content of 0.61-0.76. Finally, using all the information generated in this study, we have developed a user-friendly database (TeaMiD; http://indianteagenome.in:8080/teamid/) that hosts SSR from all the six resources including three nuclear genomes of tea and transcriptome sequences of 17 Camellia wild species. Database URL: http://indianteagenome.in:8080/teamid/.
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Affiliation(s)
- Himanshu Dubey
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Hukam C Rawal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Megha Rohilla
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Urvashi Lama
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - P Mohan Kumar
- Darjeeling Tea Research and Development Centre, Tea Board, Ministry of Commerce, B.T.M. Sarani (Brabourne Road), Kolkata, West Bengal 700001, India
| | - Tanoy Bandyopadhyay
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Madhurjya Gogoi
- Department of Biotechnology, Tocklai Experimental Station, Tea Research Association, Jorhat, Assam, India
| | - Nagendra Kumar Singh
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
| | - Tapan Kumar Mondal
- Indian Council Agricultural Research-National Institute for Plant Biotechnology, Lal Bahadur Sashtri Centre, Indian Agricultural Research Institute, Pusa, New Delhi 110012, India
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Shiferaw E, Porceddu E, Pé E, Ponnaiah M. Application of CAPS markers for diversity assessment in grass pea ( Lathyrus sativus L.). BIODIVERSITY: RESEARCH AND CONSERVATION 2019. [DOI: 10.1515/biorc-2017-0012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Genetic diversity among 20 Lathyrus sativus L. accessions from Ethiopia was investigated by using Cleaved Amplified Polymorphic Sequence (CAPS) markers. Genetic diversity statistics showed presence of a moderate level of genetic variation in the analysed accessions (P = 69.77%, Hs = 0.278). Analysis of genetic differentiation showed existence of a low level of differentiation between accessions, which accounted for only 7% of the total variation and most of the variation was due to differences among individuals within accessions (93%). Both cluster and principal coordinate analyses revealed minimal grouping of accessions based on geographical origin implying that local varieties of grass pea with different genetic backgrounds were distributed among various administrative regions in Ethiopia. The CAPS markers employed in our study demonstrated the utility of such markers for genetic diversity assessment in grass pea.
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Affiliation(s)
- Eleni Shiferaw
- Ethiopian Biodiversity Institute , P.O. Box 30726, Addis Ababa , Ethiopia
- Scuola Superiore Sant’Anna, Piazza Martiri della Liberta 33, 56127 Pisa , Italy
| | - Enrico Porceddu
- Scuola Superiore Sant’Anna, Piazza Martiri della Liberta 33, 56127 Pisa , Italy
- University of Tuscia , Via S. C. De Lellis 01100 , Viterbo , Italy
| | - Enrico Pé
- Scuola Superiore Sant’Anna, Piazza Martiri della Liberta 33, 56127 Pisa , Italy
| | - Maharajah Ponnaiah
- Scuola Superiore Sant’Anna, Piazza Martiri della Liberta 33, 56127 Pisa , Italy
- Pierre and Marie Curie University , UPMC-Paris 6, Developmental Biology Laboratory , UMR 7622, Paris , France
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Li YC, Wu CJ, Lin YC, Wu RH, Chen WY, Kuo PC, Tzen JTC. Identification of two teaghrelins in Shy-jih-chuen oolong tea. J Food Biochem 2019; 43:e12810. [PMID: 31353599 DOI: 10.1111/jfbc.12810] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/24/2019] [Accepted: 02/02/2019] [Indexed: 12/25/2022]
Abstract
Teaghrelins are unique acylated flavonoid tetraglycosides originally identified in Chin-shin oolong tea, and proposed to be potential oral analogs of ghrelin. Two acylated flavonoid tetraglycosides were isolated from Shy-jih-chuen oolong tea, and their chemical structures were determined to be quercetin and kaempferol 3-O-[α-L-arabinopyranosyl(1 → 3)][2"-O-(E)-p-coumaroyl] [β-D-glucopyranosyl(1 → 3)-α-L-rhamnopyranosyl(1 → 6)]-β-D-glucoside. These two compounds were extremely similar to the two teaghrelins (teaghrelin-1 and teaghrelin-2) in Chin-shin oolong tea by simply replacing a glucopyranosyl group with an arabinopyranosyl group. Molecular modeling showed that the two putative teaghrelins identified in Shy-jih-chuen docked to and interacted with the ghrelin receptor as well as teaghrelin-1 and teaghrelin-2. Mixture of these two putative teaghrelins was shown to enhance the release of growth hormone from primary anterior pituitary cells of rats. The results suggest that two teaghrelins, named teaghrelin-3 and teaghrelin-4, are present in Shy-jih-chuen oolong tea and possess biological activities analogous to teaghrelins in Chin-shin oolong tea. PRACTICAL APPLICATIONS: According to this study, teaghrelin-3 and teaghrelin-4 may be regarded as active ingredients for the quality control of Shy-jih-chuen oolong tea. The content of teaghrelins may serve as a key factor for the farmers to select new tea plants in their next propagation of Shy-jih-chuen cultivar. Crude water extract of Shy-jih-chuen oolong tea containing teaghrelins is considered to be an adequate food supplement or additive in functional food products.
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Affiliation(s)
- Yue-Chiun Li
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Chieh-Ju Wu
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Yi-Chiao Lin
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Ruo-Hsuan Wu
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Wen-Ying Chen
- Department of Veterinary Medicine, National Chung-Hsing University, Taichung, Taiwan
| | - Ping-Chung Kuo
- School of Pharmacy, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jason T C Tzen
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
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Next generation crop improvement program: Progress and prospect in tea ( Camellia sinensis (L.) O. Kuntze). ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.aasci.2018.02.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Adhikari S, Saha S, Biswas A, Rana TS, Bandyopadhyay TK, Ghosh P. Application of molecular markers in plant genome analysis: a review. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0214-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Fang W, Meinhardt LW, Tan H, Zhou L, Mischke S, Wang X, Zhang D. Identification of the varietal origin of processed loose-leaf tea based on analysis of a single leaf by SNP nanofluidic array. ACTA ACUST UNITED AC 2016. [DOI: 10.1016/j.cj.2016.02.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Fang WP, Meinhardt LW, Tan HW, Zhou L, Mischke S, Zhang D. Varietal identification of tea (Camellia sinensis) using nanofluidic array of single nucleotide polymorphism (SNP) markers. HORTICULTURE RESEARCH 2014; 1:14035. [PMID: 26504544 PMCID: PMC4596320 DOI: 10.1038/hortres.2014.35] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2014] [Revised: 05/20/2014] [Accepted: 05/30/2014] [Indexed: 05/04/2023]
Abstract
Apart from water, tea is the world's most widely consumed beverage. Tea is produced in more than 50 countries with an annual production of approximately 4.7 million tons. The market segment for specialty tea has been expanding rapidly owing to increased demand, resulting in higher revenues and profits for tea growers and the industry. Accurate varietal identification is critically important to ensure traceability and authentication of premium tea products, which in turn contribute to on-farm conservation of tea genetic diversity. Using a set of single nucleotide polymorphism (SNP) markers developed from the expressed sequence tag (EST) database of Camilla senensis, we genotyped deoxyribonucleic acid (DNA) samples extracted from a diverse group of tea varieties, including both fresh and processed commercial loose-leaf teas. The validation led to the designation of 60 SNPs that unambiguously identified all 40 tested tea varieties with high statistical rigor (p<0.0001). Varietal authenticity and genetic relationships among the analyzed cultivars were further characterized by ordination and Bayesian clustering analysis. These SNP markers, in combination with a high-throughput genotyping protocol, effectively established and verified specific DNA fingerprints for all tested tea varieties. This method provides a powerful tool for variety authentication and quality control for the tea industry. It is also highly useful for the management of tea genetic resources and breeding, where accurate and efficient genotype identification is essential.
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Affiliation(s)
- Wan-Ping Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Lyndel W Meinhardt
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Hua-Wei Tan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Lin Zhou
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Sue Mischke
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
| | - Dapeng Zhang
- Sustainable Perennial Crops Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD 20705, USA
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