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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 5 of 33

  1. The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although a...

    Authors: Maria José Gonzalo, Aurora Díaz, Narinder P. S. Dhillon, Umesh K. Reddy, Belén Picó and Antonio J. Monforte

    Citation: BMC Genomics 2019 20:448

    Content type: Research article

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  2. For spring-type Chinese cabbage production, premature bolting refers to the excessive elongation of dwarf stems before harvesting. Although quantitative trait loci (QTL) mapping for bolting-related traits have...

    Authors: Shuantao Liu, Ronghua Wang, Zhigang Zhang, Qiaoyun Li, Lihua Wang, Yongqiang Wang and Zhizhong Zhao

    Citation: BMC Genomics 2019 20:437

    Content type: Research article

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  3. Cotton is the most essential textile crop worldwide, and phytohormones are critical for cotton fiber development. One example is the role of auxin in fiber initiation, but we know little molecular basis. Micro...

    Authors: Tianlun Zhao, Xiaojian Xu, Min Wang, Cheng Li, Cong Li, Rubing Zhao, Shuijin Zhu, Qiuling He and Jinhong Chen

    Citation: BMC Genomics 2019 20:421

    Content type: Research article

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  4. The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subse...

    Authors: Elizabeth A. Cooper, Zachary W. Brenton, Barry S. Flinn, Jerry Jenkins, Shengqiang Shu, Dave Flowers, Feng Luo, Yunsheng Wang, Penny Xia, Kerrie Barry, Chris Daum, Anna Lipzen, Yuko Yoshinaga, Jeremy Schmutz, Christopher Saski, Wilfred Vermerris…

    Citation: BMC Genomics 2019 20:420

    Content type: Research article

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  5. Cotton (Gossypium spp.) is the most important natural fiber crop worldwide, and cottonseed oil is its most important byproduct. Phospholipid: diacylglycerol acyltransferase (PDAT) is important in TAG biosynthesis...

    Authors: Xinshan Zang, Xiaoli Geng, Lei Ma, Nuohan Wang, Wenfeng Pei, Man Wu, Jinfa Zhang and Jiwen Yu

    Citation: BMC Genomics 2019 20:402

    Content type: Research article

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  6. Peanut embryo development is a complex process involving a series of gene regulatory pathways and is easily affected by various elements in the soil. Calcium deficiency in the soil induces early embryo abortio...

    Authors: Hua Chen, Qiang Yang, Kun Chen, Shanshan Zhao, Chong Zhang, Ronglong Pan, Tiecheng Cai, Ye Deng, Xingjun Wang, Yuting Chen, Wenting Chu, Wenping Xie and Weijian Zhuang

    Citation: BMC Genomics 2019 20:392

    Content type: Research article

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  7. Phytohormones are key regulators of plant growth, development, and signalling networks involved in responses to diverse biotic and abiotic stresses. Transcriptional reference maps of hormone responses have bee...

    Authors: Peng-Fei Qi, Yun-Feng Jiang, Zhen-Ru Guo, Qing Chen, Thérèse Ouellet, Lu-Juan Zong, Zhen-Zhen Wei, Yan Wang, Ya-Zhou Zhang, Bin-Jie Xu, Li Kong, Mei Deng, Ji-Rui Wang, Guo-Yue Chen, Qian-Tao Jiang, Xiu-Jin Lan…

    Citation: BMC Genomics 2019 20:390

    Content type: Research article

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  8. Panax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from ...

    Authors: Le Xue, Zilong He, Xiaochun Bi, Wei Xu, Ting Wei, Shuangxiu Wu and Songnian Hu

    Citation: BMC Genomics 2019 20:383

    Content type: Research article

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  9. Discovering a genome-wide set of avocado (Persea americana Mill.) single nucleotide polymorphisms and characterizing the diversity of germplasm collection is a powerful tool for breeding. However, discovery is a ...

    Authors: Mor Rubinstein, Ravit Eshed, Ada Rozen, Tali Zviran, David N. Kuhn, Vered Irihimovitch, Amir Sherman and Ron Ophir

    Citation: BMC Genomics 2019 20:379

    Content type: Research article

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  10. Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate int...

    Authors: Rocío M. Gamez, Fernando Rodríguez, Newton Medeiros Vidal, Sandra Ramirez, Roberto Vera Alvarez, David Landsman and Leonardo Mariño-Ramírez

    Citation: BMC Genomics 2019 20:378

    Content type: Research article

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  11. Plant non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are abundant in higher plants. They have been reported to play an important role in various plant physiological processes, suc...

    Authors: Guojun Li, Menglu Hou, Yaxue Liu, Yue Pei, Minghui Ye, Yao Zhou, Chenxi Huang, Yaqi Zhao and Haoli Ma

    Citation: BMC Genomics 2019 20:375

    Content type: Research article

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  12. Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering ro...

    Authors: Sovanna Tan, Frédéric Debellé, Pascal Gamas, Florian Frugier and Mathias Brault

    Citation: BMC Genomics 2019 20:373

    Content type: Research article

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  13. Barbarea vulgaris is a wild cruciferous plant and include two distinct types: the G- and P-types named after their glabrous and pubescent leaves, respectively. The types differ significantly in resistance to a ra...

    Authors: Tong-jin Liu, You-jun Zhang, Niels Agerbirk, Hai-ping Wang, Xiao-chun Wei, Jiang-ping Song, Hong-ju He, Xue-zhi Zhao, Xiao-hui Zhang and Xi-xiang Li

    Citation: BMC Genomics 2019 20:371

    Content type: Research article

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  14. Heat shock proteins have important functions in regulating plant growth and response to abiotic stress. HSP70 family genes have been described in several plant species, but a comprehensive analysis of the HSP70 f...

    Authors: Henan Su, Miaomiao Xing, Xing Liu, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yong Wang and Honghao Lv

    Citation: BMC Genomics 2019 20:369

    Content type: Research article

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  15. Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids ...

    Authors: Joanna Majka, Katarzyna Bzdęga, Agnieszka Janiak, Hanna Ćwiek-Kupczyńska, Paweł Krajewski, Tomasz Książczyk and Zbigniew Zwierzykowski

    Citation: BMC Genomics 2019 20:367

    Content type: Research article

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  16. The glyoxalase system usually comprises two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII). This system converts cytotoxic methylglyoxal (MG) into non-toxic D-lactate in the presence of reduced glutath...

    Authors: Tiemei Li, Xin Cheng, Yuting Wang, Xiao Yin, Zhiqian Li, Ruiqi Liu, Guotian Liu, Yuejin Wang and Yan Xu

    Citation: BMC Genomics 2019 20:362

    Content type: Research article

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  17. Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties.

    Authors: Jing Yang, Kai Sun, Dongxiu Li, Lixin Luo, Yongzhu Liu, Ming Huang, Guili Yang, Hong Liu, Hui Wang, Zhiqiang Chen and Tao Guo

    Citation: BMC Genomics 2019 20:355

    Content type: Research article

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  18. Bagging is commonly used to enhance red pigmentation and thereby improve fruit quality of apples (Malus domestica). The green-skinned apple cultivar ‘Granny Smith’ develops red pigmentation after bagging removal,...

    Authors: Changqing Ma, Bowen Liang, Bo Chang, Jiuying Yan, Li Liu, Ying Wang, Yazhou Yang and Zhengyang Zhao

    Citation: BMC Genomics 2019 20:353

    Content type: Research article

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  19. Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridiz...

    Authors: Zengxiang Wu, Kaining Hu, Mengjiao Yan, Liping Song, Jing Wen, Chaozhi Ma, Jinxiong Shen, Tingdong Fu, Bin Yi and Jinxing Tu

    Citation: BMC Genomics 2019 20:348

    Content type: Research article

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  20. Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part ...

    Authors: Gui-Hua Li, Han-Cai Chen, Jia-Li Liu, Wen-Long Luo, Da-Sen Xie, Shao-Bo Luo, Ting-Quan Wu, Waheed Akram and Yu-Juan Zhong

    Citation: BMC Genomics 2019 20:343

    Content type: Research article

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  21. Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behi...

    Authors: Sara Montanari, Luca Bianco, Brian J. Allen, Pedro J. Martínez-García, Nahla V. Bassil, Joseph Postman, Mareike Knäbel, Biff Kitson, Cecilia H. Deng, David Chagné, Marc W. Crepeau, Charles H. Langley, Kate Evans, Amit Dhingra, Michela Troggio and David B. Neale

    Citation: BMC Genomics 2019 20:331

    Content type: Research article

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  22. Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. E3 ligases play a central role in subj...

    Authors: Moon Young Ryu, Seok Keun Cho, Yourae Hong, Jinho Kim, Jong Hum Kim, Gu Min Kim, Yan-Jun Chen, Eva Knoch, Birger Lindberg Møller, Woo Taek Kim, Michael Foged Lyngkjær and Seong Wook Yang

    Citation: BMC Genomics 2019 20:326

    Content type: Research article

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  23. Water deficit and soil salinity substantially influence plant growth and productivity. When occurring individually, plants often exhibit reduced growth resulting in yield losses. The simultaneous occurrence of...

    Authors: Alina Osthoff, Petra Donà dalle Rose, Jutta A. Baldauf, Hans-Peter Piepho and Frank Hochholdinger

    Citation: BMC Genomics 2019 20:325

    Content type: Research article

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  24. Crocins are soluble apocarotenoids that mainly accumulate in the stigma tissue of Crocus sativus and provide the characteristic red color to saffron spice, in addition to being responsible for many of the medicin...

    Authors: Oussama Ahrazem, Javier Argandoña, Alessia Fiore, Andrea Rujas, Ángela Rubio-Moraga, Raquel Castillo and Lourdes Gómez-Gómez

    Citation: BMC Genomics 2019 20:320

    Content type: Research article

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  25. Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage...

    Authors: Tuyen D. Do, Tri D. Vuong, David Dunn, Michael Clubb, Babu Valliyodan, Gunvant Patil, Pengyin Chen, Dong Xu, Henry T. Nguyen and J. Grover Shannon

    Citation: BMC Genomics 2019 20:318

    Content type: Research article

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  26. Climate change models predict more frequent incidents of heat stress worldwide. This trend will contribute to food insecurity, particularly for some of the most vulnerable regions, by limiting the productivity...

    Authors: Ali Soltani, Sarathi M. Weraduwage, Thomas D. Sharkey and David B. Lowry

    Citation: BMC Genomics 2019 20:312

    Content type: Research article

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  27. Integration of T-DNA into plant genomes via Agrobacterium may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in p...

    Authors: Huixin Gang, Guifeng Liu, Manman Zhang, Yuming Zhao, Jing Jiang and Su Chen

    Citation: BMC Genomics 2019 20:311

    Content type: Research article

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  28. Although rapeseed (Brassica napus L.) mutant forming multiple siliques was morphologically described and considered to increase the silique number per plant, an important agronomic trait in this crop, the molecul...

    Authors: Liang Chai, Jinfang Zhang, Kun Lu, Haojie Li, Lintao Wu, Hongshen Wan, Benchuan Zheng, Cheng Cui, Jun Jiang and Liangcai Jiang

    Citation: BMC Genomics 2019 20:304

    Content type: Research article

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  29. Genomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their prompt operational implementation b...

    Authors: Marie Pégard, Odile Rogier, Aurélie Bérard, Patricia Faivre-Rampant, Marie-Christine Le Paslier, Catherine Bastien, Véronique Jorge and Leopoldo Sánchez

    Citation: BMC Genomics 2019 20:302

    Content type: Research article

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  30. Dasypyrum villosum is an important wild species of wheat (Triticum aestivum L.) and harbors many desirable genes that can be used to improve various traits of wheat. Compared with other D. villosum accessions, D....

    Authors: Shijin Li, Jing Wang, Kunyang Wang, Jingnan Chen, Ke Wang, Lipu Du, Zhongfu Ni, Zhishan Lin and Xingguo Ye

    Citation: BMC Genomics 2019 20:289

    Content type: Research article

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  31. The trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization ...

    Authors: Jie Xiao, Rui Hu, Ting Gu, Jiapeng Han, Ding Qiu, Peipei Su, Jialu Feng, Junli Chang, Guangxiao Yang and Guangyuan He

    Citation: BMC Genomics 2019 20:287

    Content type: Research article

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  32. The tetraploid durum wheat (Triticum turgidum L. ssp. durum Desf. Husnot) is an important crop which provides the raw material for pasta production and a valuable source of genetic diversity for breeding hexaploi...

    Authors: Vera Vendramin, Danara Ormanbekova, Simone Scalabrin, Davide Scaglione, Marco Maccaferri, Pierluigi Martelli, Silvio Salvi, Irena Jurman, Rita Casadio, Federica Cattonaro, Roberto Tuberosa, Andrea Massi and Michele Morgante

    Citation: BMC Genomics 2019 20:278

    Content type: Research article

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  33. Chinese kale (Brassica alboglabra) contains high nutritional elements and functional molecules, especially anticarcinogenic and antioxidant glucosinolates (GS), which was highly affected by environment temperatur...

    Authors: Rongfang Guo, Xingru Wang, Xiaoyun Han, Wenjing Li, Tao Liu, Bingxing Chen, Xiaodong Chen and Gefu Wang-Pruski

    Citation: BMC Genomics 2019 20:269

    Content type: Research article

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  34. The two original plants of the oolong tea cultivar (‘Tieguanyin’) are “Wei shuo” ‘Tieguanyin’—TGY (Wei) and “Wang shuo” ‘Tieguanyin’—TGY (Wang). Another cultivar, ‘Benshan’ (BS), is similar to TGY in its aroma...

    Authors: Yuqiong Guo, Chen Zhu, Shanshan Zhao, Shuting Zhang, Wenjian Wang, Haifeng Fu, Xiaozhen Li, Chengzhe Zhou, Lan Chen, Yuling Lin and Zhongxiong Lai

    Citation: BMC Genomics 2019 20:265

    Content type: Research article

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  35. Genic male sterility (GMS) line is an important approach to utilize heterosis in Brassica rapa, one of the most widely cultivated vegetable crops in Northeast Asia. However, the molecular genetic mechanisms of GM...

    Authors: Xiuping Shen, Liai Xu, Yanhong Liu, Heng Dong, Dong Zhou, Yuzhi Zhang, Sue Lin, Jiashu Cao and Li Huang

    Citation: BMC Genomics 2019 20:264

    Content type: Research article

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  36. The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to ident...

    Authors: Liang Wang, Yanbo Cheng, Qibin Ma, Yinghui Mu, Zhifeng Huang, Qiuju Xia, Gengyun Zhang and Hai Nian

    Citation: BMC Genomics 2019 20:260

    Content type: Research article

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  37. Histone methylation mainly occurs on the lysine residues and plays a crucial role during flowering and stress responses of plants, through changing the methylation status or ratio of lysine residues. Histone l...

    Authors: Yexiong Qian, Changle Chen, Lingyu Jiang, Jing Zhang and Qiaoyu Ren

    Citation: BMC Genomics 2019 20:256

    Content type: Research article

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  38. Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, f...

    Authors: Alberto Cenci, Yann Hueber, Yasmin Zorrilla-Fontanesi, Jelle van Wesemael, Ewaut Kissel, Marie Gislard, Julie Sardos, Rony Swennen, Nicolas Roux, Sebastien Christian Carpentier and Mathieu Rouard

    Citation: BMC Genomics 2019 20:244

    Content type: Research article

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  39. Brassica oleracea exhibits extensive phenotypic diversity. As an important trait, petal color varies among different B. oleracea cultivars, enabling the study of the genetic basis of this trait. In a previous stu...

    Authors: Fengqing Han, Huilin Cui, Bin Zhang, Xiaoping Liu, Limei Yang, Mu Zhuang, Honghao Lv, Zhansheng Li, Yong Wang, Zhiyuan Fang, Jianghua Song and Yangyong Zhang

    Citation: BMC Genomics 2019 20:242

    Content type: Research article

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  40. Common cutworm (CCW) is highly responsible for destabilizing soybean productivity. Wild soybean is a resource used by breeders to discover elite defensive genes.

    Authors: Haiping Du, Xiao Li, Lihua Ning, Rui Qin, Qing Du, Qing Wang, Haina Song, Fang Huang, Hui Wang and Deyue Yu

    Citation: BMC Genomics 2019 20:237

    Content type: Research article

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  41. Pigeonpea has considerable extent of insect-aided natural out-crossing that impedes genetic purity of seeds. Pre-anthesis cleistogamy in pigeonpea promotes self-pollination which helps in maintaining genetic p...

    Authors: Pooja Yadav, K. B. Saxena, Anupama Hingane, C. V. Sameer Kumar, V. S. Kandalkar, Rajeev K. Varshney and Rachit K. Saxena

    Citation: BMC Genomics 2019 20:235

    Content type: Research article

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  42. Flowering time and maturity are among the most important adaptive traits in soybean (Glycine max (L.) Merill). Flowering Locus T (FT) family genes function as key flowering integrators, with flowering-promoting m...

    Authors: Bingjun Jiang, Shouwei Zhang, Wenwen Song, Mohammad Abdul Awal Khan, Shi Sun, Chengsheng Zhang, Tingting Wu, Cunxiang Wu and Tianfu Han

    Citation: BMC Genomics 2019 20:230

    Content type: Research article

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  43. Abiotic stresses like drought, heat, cold and salinity cause major productivity loss in the rapeseed-mustard crops (Brassica). Major efforts have been made in the past to identify genes that provide resistance ag...

    Authors: Deepika Verma, Neha Lakhanpal and Kashmir Singh

    Citation: BMC Genomics 2019 20:227

    Content type: Research article

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  44. Aquaporins (AQPs) facilitate transport of water and small solutes across cell membranes and play an important role in different physiological processes in plants. Despite their importance, limited data is avai...

    Authors: S. M. Shivaraj, Rupesh Deshmukh, Humira Sonah and Richard R. Bélanger

    Citation: BMC Genomics 2019 20:222

    Content type: Research article

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  45. Long noncoding RNAs (lncRNAs) have emerged as playing crucial roles in abiotic stress responsive regulation, however, the mechanism of lncRNAs underlying drought-tolerance remains largely unknown in cassava, a...

    Authors: Zehong Ding, Weiwei Tie, Lili Fu, Yan Yan, Guanghua Liu, Wei Yan, Yanan Li, Chunlai Wu, Jiaming Zhang and Wei Hu

    Citation: BMC Genomics 2019 20:214

    Content type: Research article

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  46. The SnRK2s (Plant specific protein kinase) are involved in various biological processes, such as plant defense and environmental challenges. In Arabidopsis, AtSnRK2s regulate the expression of some metal transpor...

    Authors: Ruijiao Wang, Chao Wang, Qin Yao, Xue Xiao, Xing Fan, Lina Sha, Jian Zeng, Houyang Kang, Haiqin Zhang, Yonghong Zhou and Yi Wang

    Citation: BMC Genomics 2019 20:210

    Content type: Research article

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  47. Plants adapted to diverse environments on Earth throughout their evolutionary history, and developed mechanisms to thrive in a variety of terrestrial habitats. When plants are grown in the novel environment of...

    Authors: Mingqi Zhou, Natasha J. Sng, Collin E. LeFrois, Anna-Lisa Paul and Robert J. Ferl

    Citation: BMC Genomics 2019 20:205

    Content type: Research article

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  48. Glyceollins are isoflavonoid-derived pathogen-inducible defense metabolites (phytoalexins) from soybean (Glycine max L. Merr) that have important roles in providing defense against pathogens. They also have impre...

    Authors: Md Asraful Jahan, Brianna Harris, Matthew Lowery, Katie Coburn, Aniello M. Infante, Ryan J. Percifield, Amanda G. Ammer and Nik Kovinich

    Citation: BMC Genomics 2019 20:149

    Content type: Research article

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  49. Trichoderma spp. are effective biocontrol agents for many plant pathogens, thus the mechanism of Trichoderma-induced plant resistance is not fully understood. In this study, a novel Trichoderma strain was identif...

    Authors: Min Yuan, Yuanyuan Huang, Weina Ge, Zhenhua Jia, Shuishan Song, Lan Zhang and Yali Huang

    Citation: BMC Genomics 2019 20:144

    Content type: Research article

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