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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 1 of 34

  1. Among several TF families unique to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important. Chinese jujube (Ziziphus jujuba Mill.) is a popular fruit tree species in Asia, and its fruits ...

    Authors: Yao Zhang, Weilin Gao, Hongtai Li, Yongkang Wang, Dengke Li, Chaoling Xue, Zhiguo Liu, Mengjun Liu and Jin Zhao

    Citation: BMC Genomics 2020 21:483

    Content type: Research article

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  2. The genus Brassica mainly comprises three diploid and three recently derived allotetraploid species, most of which are highly important vegetable, oil or ornamental crops cultivated worldwide. Despite being exten...

    Authors: Jiangwei Qiao, Xiaojun Zhang, Biyun Chen, Fei Huang, Kun Xu, Qian Huang, Yi Huang, Qiong Hu and Xiaoming Wu

    Citation: BMC Genomics 2020 21:480

    Content type: Research article

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  3. Whole-Genome Bisulfite Sequencing (WGBS) is a Next Generation Sequencing (NGS) technique for measuring DNA methylation at base resolution. Continuing drops in sequencing costs are beginning to enable high-thro...

    Authors: Yadollah Shahryary, Rashmi R. Hazarika and Frank Johannes

    Citation: BMC Genomics 2020 21:479

    Content type: Software

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  4. Walnut (Juglans regia) is an important tree cultivated worldwide and is exposed to a series of both abiotic and biotic stress during their life-cycles. The heat stress transcription factors (HSFs) play a crucial ...

    Authors: Xuejiao Liu, Panpan Meng, Guiyan Yang, Mengyan Zhang, Shaobing Peng and Mei Zhi Zhai

    Citation: BMC Genomics 2020 21:474

    Content type: Research article

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  5. VviERF6Ls are an uncharacterized gene clade in Vitis with only distant Arabidopsis orthologs. Preliminary data indicated these transcription factors may play a role in berry development and extreme abiotic stress...

    Authors: Haley S. Toups, Noé Cochetel, Dennis Gray and Grant R. Cramer

    Citation: BMC Genomics 2020 21:472

    Content type: Research article

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  6. Genome sequencing technologies have been improved at an exponential pace but precise chromosome-scale genome assembly still remains a great challenge. The draft genome of cultivated G. arboreum was sequenced and ...

    Authors: Javaria Ashraf, Dongyun Zuo, Hailiang Cheng, Waqas Malik, Qiaolian Wang, Youping Zhang, Muhammad Ali Abid, Qiuhong Yang, Xiaoxu Feng, John Z. Yu and Guoli Song

    Citation: BMC Genomics 2020 21:470

    Content type: Research article

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  7. Genetic improvement of pearl millet is lagging behind most of the major crops. Development of genomic resources is expected to expedite breeding for improved agronomic traits, stress tolerance, yield, and nutr...

    Authors: Ghislain Kanfany, Desalegn D. Serba, Davina Rhodes, Paul St. Amand, Amy Bernardo, Prakash I Gangashetty, Ndjido Ardo Kane and Guihua Bai

    Citation: BMC Genomics 2020 21:469

    Content type: Research article

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  8. In viticulture, rootstock genotype plays a critical role to improve scion physiology, berry quality and to adapt grapevine (Vitis vinifera L.) to different environmental conditions. This study aimed at investigat...

    Authors: A. Zombardo, C. Crosatti, P. Bagnaresi, L. Bassolino, N. Reshef, S. Puccioni, P. Faccioli, A. Tafuri, M. Delledonne, A. Fait, P. Storchi, L. Cattivelli and E. Mica

    Citation: BMC Genomics 2020 21:468

    Content type: Research article

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  9. Soybean (Glycine max) is an important oil provider and ecosystem participant. The protein phosphatase 2C (PP2C) plays important roles in key biological processes. Molecular evolution and functional analysis of th...

    Authors: Kai Fan, Yunrui Chen, Zhijun Mao, Yao Fang, Zhaowei Li, Weiwei Lin, Yongqiang Zhang, Jianping Liu, Jinwen Huang and Wenxiong Lin

    Citation: BMC Genomics 2020 21:465

    Content type: Research article

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  10. Tea plant (Camellia sinensis) is one of the world’s most important beverage crops due to its numerous secondary metabolites conferring tea quality and health effects. However, only a small fraction of tea genes (...

    Authors: Rui Zhang, Yong Ma, Xiaoyi Hu, Ying Chen, Xiaolong He, Ping Wang, Qi Chen, Chi-Tang Ho, Xiaochun Wan, Youhua Zhang and Shihua Zhang

    Citation: BMC Genomics 2020 21:461

    Content type: Database

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  11. Restoration of fertility (Rf) is an important trait for pigeonpea hybrid breeding. Few coarse quantitative trait locus (QTL) studies conducted in the past identified QTLs with large confidence intervals on the ge...

    Authors: Rachit K. Saxena, Johiruddin Molla, Pooja Yadav and Rajeev K. Varshney

    Citation: BMC Genomics 2020 21:460

    Content type: Research article

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  12. In plants, the plasma membrane is enclosed by the cell wall and anchors RLK and RLP proteins, which play a fundamental role in perception of developmental and environmental cues and are crucial in plant develo...

    Authors: Daniel Restrepo-Montoya, Robert Brueggeman, Phillip E. McClean and Juan M. Osorno

    Citation: BMC Genomics 2020 21:459

    Content type: Research article

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  13. Multiple C2 domains and transmembrane region proteins (MCTPs) may act as transport mediators of other regulators. Although increased number of MCTPs in higher plants implies their diverse and specific functions i...

    Authors: Pengbo Hao, Hantao Wang, Liang Ma, Aimin Wu, Pengyun Chen, Shuaishuai Cheng, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2020 21:445

    Content type: Research article

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  14. The class III peroxidases (PODs) are involved in a broad range of physiological activities, such as the formation of lignin, cell wall components, defense against pathogenicity or herbivore, and abiotic stress...

    Authors: Huilin Xiao, Chaoping Wang, Nadeem Khan, Mengxia Chen, Weihong Fu, Le Guan and Xiangpeng Leng

    Citation: BMC Genomics 2020 21:444

    Content type: Research article

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  15. Order Chaetophorales currently includes six families, namely Schizomeridaceae, Aphanochaetaceae, Barrancaceae, Uronemataceae, Fritschiellaceae, and Chaetophoraceae. The phylogenetic relationships of Chaetophor...

    Authors: Benwen Liu, Yuxin Hu, Zhengyu Hu, Guoxiang Liu and Huan Zhu

    Citation: BMC Genomics 2020 21:442

    Content type: Research article

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  16. It was demonstrated in our previous research that trypsin scavenges superoxide anions. In this study, the mechanisms of storage quality improvement by trypsin were evaluated in H. undatus.

    Authors: Xin Li, Xueru Liu, Xinyue Pang, Yong Yin, Huichun Yu, Yunxia Yuan and Bairu Li

    Citation: BMC Genomics 2020 21:437

    Content type: Research article

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  17. Wheat (Triticum aestivium L.) is an important crop globally which has a complex genome. To identify the parents with useful agronomic characteristics that could be used in the various breeding programs, it is ver...

    Authors: Amira M. I. Mourad, Vikas Belamkar and P. Stephen Baenziger

    Citation: BMC Genomics 2020 21:434

    Content type: Research article

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  18. The low genetic diversity of Upland cotton limits the potential for genetic improvement. Making full use of the genetic resources of Sea-island cotton will facilitate genetic improvement of widely cultivated U...

    Authors: De Zhu, Ximei Li, Zhiwei Wang, Chunyuan You, Xinhui Nie, Jie Sun, Xianlong Zhang, Dawei Zhang and Zhongxu Lin

    Citation: BMC Genomics 2020 21:431

    Content type: Research article

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  19. Cellular reprogramming in response to environmental stress involves alteration of gene expression, changes in the protein and metabolite profile for ensuring better stress management in plants. Similar to othe...

    Authors: Pratiti Dasgupta, Abhishek Das, Sambit Datta, Ishani Banerjee, Sucheta Tripathy and Shubho Chaudhuri

    Citation: BMC Genomics 2020 21:425

    Content type: Research article

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  20. Salinity, alkalinity, and drought stress are the main abiotic stress factors affecting plant growth and development. Sophora alopecuroides L., a perennial leguminous herb in the genus Sophora, is a highly salt-to...

    Authors: Fan Yan, Youcheng Zhu, Yanan Zhao, Ying Wang, Jingwen Li, Qingyu Wang and Yajing Liu

    Citation: BMC Genomics 2020 21:423

    Content type: Research article

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  21. Cold hardiness is an important agronomic trait and can significantly affect grape production and quality. Until now, there are no reports focusing on cold hardiness quantitative trait loci (QTL) mapping. In th...

    Authors: Kai Su, Huiyang Xing, Yinshan Guo, Fangyuan Zhao, Zhendong Liu, Kun Li, Yuanyuan Li and Xiuwu Guo

    Citation: BMC Genomics 2020 21:419

    Content type: Research article

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  22. Recent literature on the differential role of genes within networks distinguishes core from peripheral genes. If previous works have shown contrasting features between them, whether such categorization matters...

    Authors: Aurélien Chateigner, Marie-Claude Lesage-Descauses, Odile Rogier, Véronique Jorge, Jean-Charles Leplé, Véronique Brunaud, Christine Paysant-Le Roux, Ludivine Soubigou-Taconnat, Marie-Laure Martin-Magniette, Leopoldo Sanchez and Vincent Segura

    Citation: BMC Genomics 2020 21:416

    Content type: Research article

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  23. Artemisia in East Asia includes a number of economically important taxa that are widely used for food, medicinal, and ornamental purposes. The identification of taxa, however, has been hampered by insufficient di...

    Authors: Goon-Bo Kim, Chae Eun Lim, Jin-Seok Kim, Kyeonghee Kim, Jeong Hoon Lee, Hee-Ju Yu and Jeong-Hwan Mun

    Citation: BMC Genomics 2020 21:415

    Content type: Research article

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  24. Fulvic acid (FA) is a kind of plant growth regulator, which can promote plant growth, play an important role in fighting against drought, improve plant stress resistance, increase production and improve qualit...

    Authors: Jianhao Sun, Chen Qiu, Yiqian Ding, Yu Wang, Litao Sun, Kai Fan, Zhongshuai Gai, Guoqiang Dong, Jiguo Wang, Xinghui Li, Lubin Song and Zhaotang Ding

    Citation: BMC Genomics 2020 21:411

    Content type: Research article

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  25. Jute (Corchorus spp.), belonging to the Malvaceae family, is an important natural fiber crop, second only to cotton, and a multipurpose economic crop. Corchorus capsularis L. is one of the only two commercially c...

    Authors: Zemao Yang, Zhigang Dai, Xiaojun Chen, Dongwei Xie, Qing Tang, Chaohua Cheng, Ying Xu, Canhui Deng, Chan Liu, Jiquan Chen and Jianguang Su

    Citation: BMC Genomics 2020 21:406

    Content type: Research article

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  26. Proline-rich extension-like receptor protein kinases (PERKs) are an important class of receptor kinases located in the plasma membrane, most of which play a vital role in pollen development.

    Authors: Guohu Chen, Jian Wang, Hao Wang, Chenggang Wang, Xiaoyan Tang, Jie Li, Lei Zhang, Jianghua Song, Jinfeng Hou and Lingyun Yuan

    Citation: BMC Genomics 2020 21:401

    Content type: Research article

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  27. Associations of tree roots with diverse symbiotic mycorrhizal fungi have distinct effects on whole plant functioning. An untested explanation might be that such effect variability is associated with distinct i...

    Authors: Marie-Lara Bouffaud, Sylvie Herrmann, Mika T. Tarkka, Markus Bönn, Lasse Feldhahn and François Buscot

    Citation: BMC Genomics 2020 21:399

    Content type: Research article

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  28. The severity and frequency of drought has increased around the globe, creating challenges in ensuring food security for a growing world population. As a consequence, improving water use efficiency by crops has...

    Authors: Caitlin M. A. Simopoulos, Mitchell J. R. MacLeod, Solmaz Irani, Wilson W. L. Sung, Marc J. Champigny, Peter S. Summers, G. Brian Golding and Elizabeth A. Weretilnyk

    Citation: BMC Genomics 2020 21:396

    Content type: Research Article

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  29. Cultivated rice consists of two subspecies, Indica and Japonica, that exhibit well-characterized differences at the morphological and genetic levels. However, the differences between these subspecies at the trans...

    Authors: Malachy T. Campbell, Qian Du, Kan Liu, Sandeep Sharma, Chi Zhang and Harkamal Walia

    Citation: BMC Genomics 2020 21:394

    Content type: Research Article

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  30. SPL (SQUAMOSA-promoter binding protein-like) proteins form a large family of plant-specific transcription factors that play essential roles in various aspects of plant growth and development. They are potentia...

    Authors: Niu Yu, Jin-Chang Yang, Guang-Tian Yin, Rong-Sheng Li and Wen-Tao Zou

    Citation: BMC Genomics 2020 21:368

    Content type: Research article

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  31. Sweetpotato root rot is a devastating disease caused by Fusarium solani that seriously endangers the yield of sweetpotato in China. Although there is currently no effective method to control the disease, breeding...

    Authors: Zhimin Ma, Wenchuan Gao, Lanfu Liu, Minghui Liu, Ning Zhao, Meikun Han, Zhao Wang, Weijing Jiao, Zhiyuan Gao, Yaya Hu and Qingchang Liu

    Citation: BMC Genomics 2020 21:366

    Content type: Research article

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  32. Pumpkins (Cucurbita moschata; Cucurbitaceae) are valued for their fruits and seeds and are rich in nutrients. Carotenoids and sugar contents, as main feature of pumpkin pulp, are used to determine the fruit quali...

    Authors: Hafiz Muhammad Khalid Abbas, He-Xun Huang, An-Jun Wang, Ting-Quan Wu, Shu-Dan Xue, Aqeel Ahmad, Da-Sen Xie, Jun-Xing Li and Yu-Juan Zhong

    Citation: BMC Genomics 2020 21:365

    Content type: Research article

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  33. Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cl...

    Authors: Yabin Wu, Zijian Zhou, Chaopei Dong, Jiafa Chen, Junqiang Ding, Xuecai Zhang, Cong Mu, Yuna Chen, Xiaopeng Li, Huimin Li, Yanan Han, Ruixia Wang, Xiaodong Sun, Jingjing Li, Xiaodong Dai, Weibin Song…

    Citation: BMC Genomics 2020 21:357

    Content type: Research article

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  34. The fluctuation of nitrogen (N) contents profoundly affects the root growth and architecture in maize by altering the expression of thousands of genes. The differentially expressed genes (DEGs) in response to ...

    Authors: Yuancong Wang, Jinyan Xu, Min Ge, Lihua Ning, Mengmei Hu and Han Zhao

    Citation: BMC Genomics 2020 21:353

    Content type: Research article

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  35. The narrow genetic base of elite germplasm compromises long-term genetic gain and increases the vulnerability to biotic and abiotic stresses in unpredictable environmental conditions. Therefore, an efficient s...

    Authors: Antoine Allier, Simon Teyssèdre, Christina Lehermeier, Laurence Moreau and Alain Charcosset

    Citation: BMC Genomics 2020 21:349

    Content type: Research article

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  36. Heavy metal cadmium (Cd) is a common environmental pollutant in soils, which has an negative impacts on crop growth and development. At present, cadmium has become a major soil and water heavy metal pollutant,...

    Authors: Mingyang Jian, Dazhong Zhang, Xiaoying Wang, Shuwei Wei, Yue Zhao, Qin Ding, Yucui Han and Lingjian Ma

    Citation: BMC Genomics 2020 21:343

    Content type: Research article

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  37. Root systems are critical for plant growth and development. The Casparian strip in root systems is involved in stress resistance and maintaining homeostasis. Casparian strip membrane domain proteins (CASPs) ar...

    Authors: Xiaoyang Wang, Yuanming Zhang, Liyuan Wang, Zhaoe Pan, Shoupu He, Qiong Gao, Baojun Chen, Wenfang Gong and Xiongming Du

    Citation: BMC Genomics 2020 21:340

    Content type: Research article

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  38. Schizaphis graminum is one of the most important and devastating cereal aphids worldwide, and its feeding can cause chlorosis and necrosis in wheat. However, little information is available on the wheat defence r...

    Authors: Yong Zhang, Yu Fu, Qian Wang, Xiaobei Liu, Qian Li and Julian Chen

    Citation: BMC Genomics 2020 21:339

    Content type: Research article

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  39. Norway spruce trees in subalpine forests frequently face infections by the needle rust fungus Chrysomyxa rhododendri, which causes significant growth decline and increased mortality of young trees. Yet, it is unk...

    Authors: Carlos Trujillo-Moya, Andrea Ganthaler, Wolfgang Stöggl, Ilse Kranner, Silvio Schüler, Reinhard Ertl, Sarah Schlosser, Jan-Peter George and Stefan Mayr

    Citation: BMC Genomics 2020 21:336

    Content type: Research article

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  40. Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the fr...

    Authors: Enrique J. Schwarzkopf, Juan C. Motamayor and Omar E. Cornejo

    Citation: BMC Genomics 2020 21:332

    Content type: Research article

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  41. Pitayas are currently attracting considerable interest as a tropical fruit with numerous health benefits. However, as a long-day plant, pitaya plants cannot flower in the winter season from November to April i...

    Authors: Rui Xiong, Chengli Liu, Min Xu, Shuang-shuang Wei, Jia-quan Huang and Hua Tang

    Citation: BMC Genomics 2020 21:329

    Content type: Research article

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  42. Physic nut (Jatropha curcas), an inedible oilseed plant, is among the most promising alternative energy sources because of its high oil content, rapid growth and extensive adaptability. Proteins encoded by MADS-b...

    Authors: Yuehui Tang, Jian Wang, Xinxin Bao, Qian Wu, Tongwen Yang, Han Li, Wenxia Wang, Yizhen Zhang, Nannan Bai, Yaxin Guan, Jiaxi Dai, Yanjie Xie, Shen Li, Rui Huo and Wei Cheng

    Citation: BMC Genomics 2020 21:325

    Content type: Research article

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  43. Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for op...

    Authors: Linghua Zhou, Zhiqiang Chen, Lars Olsson, Thomas Grahn, Bo Karlsson, Harry X. Wu, Sven-Olof Lundqvist and María Rosario García-Gil

    Citation: BMC Genomics 2020 21:323

    Content type: Research article

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  44. Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective metho...

    Authors: Min Yao, Mei Guan, Zhenqian Zhang, Qiuping Zhang, Yixin Cui, Hao Chen, Wei Liu, Habib U. Jan, Kai P. Voss-Fels, Christian R. Werner, Xin He, Zhongsong Liu, Chunyun Guan, Rod J. Snowdon, Wei Hua and Lunwen Qian

    Citation: BMC Genomics 2020 21:320

    Content type: Research article

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  45. Climate change, including higher temperatures (HT) has a detrimental impact on wheat productivity and modeling studies predict more frequent heat waves in the future. Wheat growth can be impaired by high dayti...

    Authors: Sumit Pradhan, Md Ali Babar, Guihua Bai, Jahangir Khan, Dipendra Shahi, Muhsin Avci, Jia Guo, Jordan McBreen, Senthold Asseng, Salvador Gezan, Byung-Kee Baik, Ann Blount, Stephen Harrison, Suraj Sapkota, Paul St. Amand and Sanju Kunwar

    Citation: BMC Genomics 2020 21:315

    Content type: Research article

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  46. Puccinellia tenuiflora, a forage grass, is considered a model halophyte given its strong tolerance for multiple stress conditions and its close genetic relationship with cereals. This halophyte has enormous value...

    Authors: Rui Guo, Long Zhao, Kaijian Zhang, Dan Gao and Chunwu Yang

    Citation: BMC Genomics 2020 21:311

    Content type: Database

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  47. In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogene...

    Authors: Zheng Liu, Xiao-Xia Ge, Xiao-Meng Wu, Qiang Xu, Ross G. Atkinson and Wen-Wu Guo

    Citation: BMC Genomics 2020 21:305

    Content type: Research article

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  48. Walnut kernels contain a large amount of unsaturated fatty acids, such as linoleic acid and linolenic acid, which are essential fatty acids for humans and have important effects on growth and health. The main ...

    Authors: Kai Liu, Shugang Zhao, Shuang Wang, Hongxia Wang and Zhihua Zhang

    Citation: BMC Genomics 2020 21:299

    Content type: Research article

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