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Plant genomics

Section edited by David Lightfoot and Keiichi Mochida

This section covers all aspects of the genome structure and function of plants, including crop species.

Page 4 of 30

  1. Content type: Research article

    Temperature stress is a major environmental factor affecting not only plant growth and development, but also fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that pla...

    Authors: Hong Zhu, Yu Zhang, Ruifang Tang, Hongxia Qu, Xuewu Duan and Yueming Jiang

    Citation: BMC Genomics 2019 20:33

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  2. Content type: Research article

    Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants la...

    Authors: Rongzhi Zhang, Shuaifeng Geng, Zhengrui Qin, Zongxiang Tang, Cheng Liu, Dongfeng Liu, Guoqi Song, Yulian Li, Shujuan Zhang, Wei Li, Jie Gao, Xiaodong Han and Genying Li

    Citation: BMC Genomics 2019 20:29

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  3. Content type: Research article

    B-box (BBX) proteins play important roles in plant growth regulation and development including photomorphogenesis, photoperiodic regulation of flowering, and responses to biotic and abiotic stresses.

    Authors: Abdullah Shalmani, Xiu-Qing Jing, Yi Shi, Izhar Muhammad, Meng-Ru Zhou, Xiao-Yong Wei, Qiong-Qiong Chen, Wen-Qiang Li, Wen-Ting Liu and Kun-Ming Chen

    Citation: BMC Genomics 2019 20:27

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  4. Content type: Research article

    Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus an...

    Authors: Chia-Chi Hsu, Pei-Han Lai, Tien-Chih Chen, Wen-Chieh Tsai, Jui-Lin Hsu, Yu-Yun Hsiao, Wen-Luan Wu, Ching-Hsiu Tsai, Wen-Huei Chen and Hong-Hwa Chen

    Citation: BMC Genomics 2019 20:25

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  5. Content type: Research article

    Euscaphis konishii Hayata, a member of the Staphyleaceae Family, is a plant that has been widely used in Traditional Chinese Medicine and it has been the source for several types of flavonoids. To identify candid...

    Authors: Wenxian Liang, Lin Ni, Rebeca Carballar-Lejarazú, Xiaoxing Zou, Weihong Sun, Lingjiao Wu, Xueyuan Yuan, Yanling Mao, Wei Huang and Shuangquan Zou

    Citation: BMC Genomics 2019 20:24

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  6. Content type: Research article

    Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QT...

    Authors: Hongju Jian, Aoxiang Zhang, Jinqi Ma, Tengyue Wang, Bo Yang, Lan Shuan Shuang, Min Liu, Jiana Li, Xinfu Xu, Andrew H. Paterson and Liezhao Liu

    Citation: BMC Genomics 2019 20:21

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  7. Content type: Research article

    Research on the submergence stress of rice has concentrated on the quiescence strategy to survive in long-term flooding conditions based on Submergence-1A (SUB1A). In the case of the ripening period, it is imp...

    Authors: Hyeon Seok Lee, Woon Ha Hwang, Jae Hyeok Jeong, Seung Hyeon Ahn, Jeong Seon Baek, Han Yong Jeong, Hong Kyu Park, Bon Il Ku, Jong Tak Yun, Geon Hwi Lee and Kyung Jin Choi

    Citation: BMC Genomics 2019 20:18

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  8. Content type: Research article

    It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications.

    Authors: Yanling Ma, Miao Liu, Jiri Stiller and Chunji Liu

    Citation: BMC Genomics 2019 20:12

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  9. Content type: Research article

    Canker disease caused by Neoscytalidium dimidiatum is the most serious disease that attacks the pitaya industry. One pathogenic fungus, referred to as ND8, was isolated from the wild-type red-fleshed pitaya (Hylo...

    Authors: Min Xu, Cheng-Li Liu, Juan Luo, Zhao Qi, Zhen Yan, Yu Fu, Shuang-Shuang Wei and Hua Tang

    Citation: BMC Genomics 2019 20:10

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  10. Content type: Research article

    Celastrus angulatus Maxim is a kind of crucial and traditional insecticidal plant widely distributed in the mountains of southwest China. Celangulin V is the efficient insecticidal sesquiterpenoid of C. angulatus

    Authors: Weiguo Li, Ranran Xu, Xiaoguang Yan, Dongmei Liang, Lei Zhang, Xiaoyu Qin, Qinggele Caiyin, Guangrong Zhao, Wenhai Xiao, Zhaonong Hu and Jianjun Qiao

    Citation: BMC Genomics 2019 20:7

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  11. Content type: Research article

    Dendrobium huoshanense C.Z. Tang et S.J. Cheng is a traditional Chinese herbal medicine with high medicinal value in China. Polysaccharides and alkaloids are its main active ingredients. To understand the differe...

    Authors: Yingdan Yuan, Maoyun Yu, Zhaohui Jia, Xue’er Song, Yingquan Liang and Jinchi Zhang

    Citation: BMC Genomics 2018 19:978

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  12. Content type: Methodology article

    Chloroplasts are organelles that conduct photosynthesis in plant and algal cells. The information chloroplast genome contained is widely used in agriculture and studies of evolution and ecology. Correctly asse...

    Authors: Weiwen Wang, Miriam Schalamun, Alejandro Morales-Suarez, David Kainer, Benjamin Schwessinger and Robert Lanfear

    Citation: BMC Genomics 2018 19:977

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  13. Content type: Research article

    Somatic embryogenesis receptor-like kinases (SERKs) are leucine-rich repeat receptor-like kinases associated with various signaling pathways. These kinases have a relationship with stress signals, and they are...

    Authors: Liwei Zheng, Juanjuan Ma, Jiangping Mao, Sheng Fan, Dong Zhang, Caiping Zhao, Na An and Mingyu Han

    Citation: BMC Genomics 2018 19:962

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  14. Content type: Research article

    Flavonoids are important components that confer upon tea plants a unique flavour and health functions. However, the traditional breeding method for selecting a cultivar with a high or unique flavonoid content ...

    Authors: Li-Yi Xu, Li-Yuan Wang, Kang Wei, Li-Qiang Tan, Jing-Jing Su and Hao Cheng

    Citation: BMC Genomics 2018 19:955

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  15. Content type: Research article

    Guar [Cyamopsis tetragonoloba, L. Taub.] is an important industrial crop because of the commercial applications of the galactomannan gum contained in its seeds. Plant breeding programmes based on marker-assisted ...

    Authors: Omika Thakur and Gursharn Singh Randhawa

    Citation: BMC Genomics 2018 19:951

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  16. Content type: Research article

    Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primar...

    Authors: Sui Wang, Chuanping Yang, Xiyang Zhao, Su Chen and Guan-Zheng Qu

    Citation: BMC Genomics 2018 19:950

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  17. Content type: Research article

    Genomic selection (GS) can increase genetic gain by reducing the length of breeding cycle in forest trees. Here we genotyped 1370 control-pollinated progeny trees from 128 full-sib families in Norway spruce (Pice...

    Authors: Zhi-Qiang Chen, John Baison, Jin Pan, Bo Karlsson, Bengt Andersson, Johan Westin, María Rosario García-Gil and Harry X. Wu

    Citation: BMC Genomics 2018 19:946

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  18. Content type: Research article

    Root-knot nematodes (RKN), genus Meloidogyne, are plant parasitic worms that have the ability to transform root vascular cylinder cells into hypertrophied, multinucleate and metabolically over-active feeding cell...

    Authors: Clémence Medina, Martine da Rocha, Marc Magliano, Alizée Raptopoulo, Nathalie Marteu, Kevin Lebrigand, Pierre Abad, Bruno Favery and Stéphanie Jaubert-Possamai

    Citation: BMC Genomics 2018 19:943

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  19. Content type: Research article

    Norway spruce [Picea abies (L.) Karst.] is ecologically and economically one of the most important conifer worldwide. Our main goal was to develop a large catalog of annotated high confidence gene SNPs that shoul...

    Authors: Aïda Azaiez, Nathalie Pavy, Sébastien Gérardi, Jérôme Laroche, Brian Boyle, France Gagnon, Marie-Josée Mottet, Jean Beaulieu and Jean Bousquet

    Citation: BMC Genomics 2018 19:942

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  20. Content type: Software

    Democratising the growing body of whole genome sequencing data available for Triticum aestivum (bread wheat) has been impeded by the lack of a genome reference and the large computational requirements for analysi...

    Authors: Nathan S. Watson-Haigh, Radosław Suchecki, Elena Kalashyan, Melissa Garcia and Ute Baumann

    Citation: BMC Genomics 2018 19:941

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  21. Content type: Research article

    Phosphorus is an important macronutrient that is severely lacking in soils. In plants, specific microRNAs (miRNAs) essential for nutrient management and the regulation of stress responses are responsible for t...

    Authors: Amanda Huen, Julia Bally and Penelope Smith

    Citation: BMC Genomics 2018 19:940

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  22. Content type: Research article

    Nicotiana attenuata is an ecological model plant whose 2.57 Gb genome has recently been sequenced and assembled and for which miRNAs and their genomic locations have been identified. To understand how this plant’...

    Authors: Priyanka Pandey, Ming Wang, Ian T. Baldwin, Shree P. Pandey and Karin Groten

    Citation: BMC Genomics 2018 19:937

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  23. Content type: Research article

    Vaccinium uliginosum (Ericaceae) is an important wild berry having high economic value. The white-fruited V. uliginosum variety found in the wild lacks anthocyanin and bears silvery white fruits. Hence, it is a g...

    Authors: Yang Yang, Baihui Cui, Zhiwen Tan, Bingxue Song, Hounan Cao and Chengwen Zong

    Citation: BMC Genomics 2018 19:930

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  24. Content type: Research article

    Carotenoids are widely distributed in plants and algae, and their biosynthesis has attracted widespread interest. Carotenoid-related research has mostly focused on model species, and there is a lack of data on...

    Authors: Yuan He, Yafeng Ma, Yu Du and Songdong Shen

    Citation: BMC Genomics 2018 19:916

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  25. Content type: Research article

    Quantitative trait loci (QTL) mapping provides a powerful tool to unravel the genetic bases of cotton yield and its components, as well as their heterosis. In the present study, the genetic basis underlying in...

    Authors: Cong Li, Tianlun Zhao, Hurong Yu, Cheng Li, Xiaolei Deng, Yating Dong, Fan Zhang, Yi Zhang, Lei Mei, Jinhong Chen and Shuijin Zhu

    Citation: BMC Genomics 2018 19:910

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  26. Content type: Research article

    Populus nigra is a major tree species of ecological and economic importance for which several initiatives have been set up to create genomic resources. In order to access the large number of Single Nucleotide Pol...

    Authors: Odile Rogier, Aurélien Chateigner, Souhila Amanzougarene, Marie-Claude Lesage-Descauses, Sandrine Balzergue, Véronique Brunaud, José Caius, Ludivine Soubigou-Taconnat, Véronique Jorge and Vincent Segura

    Citation: BMC Genomics 2018 19:909

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  27. Content type: Research article

    Wucai (Brassica campestris L. ssp. chinensis var. rosularis Tsen) is a variant of nonheading Chinese cabbage (Brassica campestris L.), which is one of the major vegetables in China. Cytoplasmic male sterility (CM...

    Authors: Guohu Chen, Xinyu Ye, Shengyun Zhang, Shidong Zhu, Lingyun Yuan, Jinfeng Hou and Chenggang Wang

    Citation: BMC Genomics 2018 19:908

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  28. Content type: Research article

    Members of the Early Salt Induced 3 (Esi3/RCI2/PMP3) gene family in plants have been shown to be induced in response to both biotic and abiotic stresses and to enhance stress tolerance in both transgenic plants a...

    Authors: Sabrina C. Brunetti, Michelle K. M. Arseneault and Patrick J. Gulick

    Citation: BMC Genomics 2018 19:898

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  29. Content type: Research article

    Expression patterns of many laticifer-specific gens are closely correlative with rubber yield of Hevea brasiliensis (para rubber tree). To unveil the mechanisms underlying the rubber yield, transcript levels of n...

    Authors: Chuntai Wu, Li Lan, Yu Li, Zhiyi Nie and Rizhong Zeng

    Citation: BMC Genomics 2018 19:897

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  30. Content type: Research article

    The application of genomic data and bioinformatics for the identification of restricted or illegally-sourced natural products is urgently needed. The taxonomic identity and geographic provenance of raw and pro...

    Authors: Kujin Tang, Jie Ren, Richard Cronn, David L. Erickson, Brook G. Milligan, Meaghan Parker-Forney, John L. Spouge and Fengzhu Sun

    Citation: BMC Genomics 2018 19:896

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  31. Content type: Research article

    The most common infusion in southern Latin-American countries is prepared with dried leaves of Ilex paraguariensis A. St.-Hil., an aboriginal ancestral beverage known for its high polyphenols concentration curren...

    Authors: Jessica V. Fay, Christopher J. Watkins, Ram K. Shrestha, Sergio L. Litwiñiuk, Liliana N. Talavera Stefani, Cristian A. Rojas, Carina F. Argüelles, Julian A. Ferreras, Mario Caccamo and Marcos M. Miretti

    Citation: BMC Genomics 2018 19:891

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  32. Content type: Research article

    Many large-effect quantitative trait loci (QTLs) for yield and disease resistance related traits have been identified in different mapping populations of peanut (Arachis hypogaea L.) under multiple environments. ...

    Authors: Qing Lu, Hao Liu, Yanbin Hong, Haifen Li, Haiyan Liu, Xingyu Li, Shijie Wen, Guiyuan Zhou, Shaoxiong Li, Xiaoping Chen and Xuanqiang Liang

    Citation: BMC Genomics 2018 19:887

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  33. Content type: Research article

    In upland cotton (Gossypium hirsutum L.), genotypes with the same mature fiber length (FL) might possess different genes and exhibit differential expression of genes related to fiber elongation at different fiber...

    Authors: Jianjiang Ma, Yanhui Geng, Wenfeng Pei, Man Wu, Xingli Li, Guoyuan Liu, Dan Li, Qifeng Ma, XinShan Zang, Shuxun Yu, Jinfa Zhang and Jiwen Yu

    Citation: BMC Genomics 2018 19:882

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  34. Content type: Research article

    Upland Cotton (Gossypium hirsutum) is a very important cash crop known for its high quality natural fiber. Recent advances in sequencing technologies provide powerful tools with which to explore the cotton genome...

    Authors: Iftikhar Ali, Zhonghua Teng, Yuting Bai, Qing Yang, Yongshui Hao, Juan Hou, Yongbin Jia, Lixia Tian, Xueying Liu, Zhaoyun Tan, Wenwen Wang, Kiirya Kenneth, Abdalla Yousef Ahmed Sharkh, Dexin Liu, Kai Guo, Jian Zhang…

    Citation: BMC Genomics 2018 19:879

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  35. Content type: Research article

    Taraxacum kok-saghyz R. (Tks) is a promising alternative species to Hevea brasiliensis for production of high quality natural rubber (NR). A comparative transcriptome analysis of plants with differential producti...

    Authors: Francesco Panara, Loredana Lopez, Loretta Daddiego, Elio Fantini, Paolo Facella and Gaetano Perrotta

    Citation: BMC Genomics 2018 19:875

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  36. Content type: Research article

    Silene vulgaris (bladder campion) is a gynodioecious species existing as two genders – male-sterile females and hermaphrodites. Cytoplasmic male sterility (CMS) is generally encoded by mitochondrial genes, which ...

    Authors: Helena Štorchová, James D. Stone, Daniel B. Sloan, Oushadee A. J. Abeyawardana, Karel Müller, Jana Walterová and Marie Pažoutová

    Citation: BMC Genomics 2018 19:874

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  37. Content type: Research article

    Similar to other urban trees, holm oaks (Quercus ilex L.) provide a physiological, ecological and social service in the urban environment, since they remove atmospheric pollution. However, the urban environment h...

    Authors: Lucia Natali, Alberto Vangelisti, Lucia Guidi, Damiano Remorini, Lorenzo Cotrozzi, Giacomo Lorenzini, Cristina Nali, Elisa Pellegrini, Alice Trivellini, Paolo Vernieri, Marco Landi, Andrea Cavallini and Tommaso Giordani

    Citation: BMC Genomics 2018 19:872

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  38. Content type: Research article

    Nicotiana rustica (Aztec tobacco), like common tobacco (Nicotiana tabacum), is an allotetraploid formed through a recent hybridization event; however, it originated from completely different progenitor species. H...

    Authors: N. Sierro, J. N. D. Battey, L. Bovet, V. Liedschulte, S. Ouadi, J. Thomas, H. Broye, H. Laparra, A. Vuarnoz, G. Lang, S. Goepfert, M. C. Peitsch and N. V. Ivanov

    Citation: BMC Genomics 2018 19:855

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  39. Content type: Research article

    Nε-Acetylation of lysine residues, a frequently occurring post-translational modification, plays important functions in regulating physiology and metabolism. However, the information of global overview of protei....

    Authors: Jutang Jiang, Zhongshuai Gai, Yu Wang, Kai Fan, Litao Sun, Hui Wang and Zhaotang Ding

    Citation: BMC Genomics 2018 19:840

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  40. Content type: Research article

    An increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, however, some others reported negative results. Some attributed this divergence to the selective abso...

    Authors: Qi Zhao, Qian Mao, Zheng Zhao, Tongyi Dou, Zhiguo Wang, Xiaoyu Cui, Yuanning Liu and Xiaoya Fan

    Citation: BMC Genomics 2018 19:839

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  41. Content type: Research article

    Chromosomal level reference genomes provide a crucial foundation for genomics research such as genome-wide association studies (GWAS) and whole genome selection. The chromosomal-level sequences of both the Eur...

    Authors: Huabai Xue, Suke Wang, Jia-Long Yao, Cecilia H. Deng, Long Wang, Yanli Su, Huirong Zhang, Huangkai Zhou, Minshan Sun, Xiugen Li and Jian Yang

    Citation: BMC Genomics 2018 19:833

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  42. Content type: Research article

    The marine alga Ulva compressa is the dominant species in coastal areas receiving effluents from copper mines. The alga can accumulate high amounts of copper and possesses a strong antioxidant system. Here, we pe...

    Authors: Felipe E. Rodríguez, Daniel Laporte, Alberto González, Katterinne N. Mendez, Eduardo Castro-Nallar, Claudio Meneses, Juan Pablo Huidobro-Toro and Alejandra Moenne

    Citation: BMC Genomics 2018 19:829

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  43. Content type: Research article

    Despite its relevance, almost no studies account for the genetic control in the early stages of tree development, i.e. from germination on. This study seeks to make a quite complete transcriptome for olive dev...

    Authors: Jaime Jiménez-Ruiz, María de la O Leyva-Pérez, Isabel Vidoy-Mercado, Araceli Barceló and Francisco Luque

    Citation: BMC Genomics 2018 19:824

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  44. Content type: Research article

    The cucumber is one of the most important vegetables worldwide and is used as a research model for study of phloem transport, sex determination and temperature-photoperiod physiology. The shoot apex is the mos...

    Authors: Xiaohui Zhang, Yunsong Lai, Wei Zhang, Jalil Ahmad, Yang Qiu, Xiaoxue Zhang, Mengmeng Duan, Tongjin Liu, Jiangping Song, Haiping Wang and Xixiang Li

    Citation: BMC Genomics 2018 19:819

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  45. Content type: Research article

    The basidiomycete Phanerochaete carnosa is a white-rot species that has been mainly isolated from coniferous softwood. Given the particular recalcitrance of softwoods to bioconversion, we conducted a comparative ...

    Authors: E. Jurak, H. Suzuki, G. van Erven, J. A. Gandier, P. Wong, K. Chan, C. Y. Ho, Y. Gong, E. Tillier, M.-N. Rosso, M. A. Kabel, S. Miyauchi and E. R. Master

    Citation: BMC Genomics 2018 19:815

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  46. Content type: Research article

    Anthocyanins are water-soluble colored flavonoids present in multiple organs of various plant species including flowers, fruits, leaves, stems and roots. DNA-binding R2R3-MYB transcription factors, basic helix–lo...

    Authors: Miyako Kodama, Henrik Brinch-Pedersen, Shrikant Sharma, Inger Bæksted Holme, Bjarne Joernsgaard, Tsaneta Dzhanfezova, Daniel Buchvaldt Amby, Filipe Garrett Vieira, Shanlin Liu and M Thomas P Gilbert

    Citation: BMC Genomics 2018 19:811

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  47. Content type: Research article

    Alfalfa (Medicago sativa) is a widely cultivated, essential commercial forage crop. The protein content in its leaves is the critical factor in determining the quality of alfalfa. Thus far, the understanding of t...

    Authors: Qiming Cheng, Shiqie Bai, Gentu Ge, Ping Li, Liying Liu, Chengdong Zhang and Yushan Jia

    Citation: BMC Genomics 2018 19:807

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  48. Content type: Research article

    Ornamental cabbage (Brassica oleracea var. acephala) is an attractive landscape plant that remains colorful at low temperatures during winter. Its key feature is its inner leaf coloration, which can include red, ...

    Authors: Si-Won Jin, Md Abdur Rahim, Khandker Shazia Afrin, Jong-In Park, Jong-Goo Kang and Ill-Sup Nou

    Citation: BMC Genomics 2018 19:797

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