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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 25

  1. Content type: Research article

    The leaves of tea plants (Camellia sinensis) are used to produce tea, which is one of the most popular beverages consumed worldwide. The nutritional value and health benefits of tea are mainly related to three ab...

    Authors: Yuling Tai, Chun Liu, Shuwei Yu, Hua Yang, Jiameng Sun, Chunxiao Guo, Bei Huang, Zhaoye Liu, Yi Yuan, Enhua Xia, Chaoling Wei and Xiaochun Wan

    Citation: BMC Genomics 2018 19:616

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  2. Content type: Research article

    Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to L...

    Authors: Shanshan Dong, Chaoxian Zhao, Fei Chen, Yanhui Liu, Shouzhou Zhang, Hong Wu, Liangsheng Zhang and Yang Liu

    Citation: BMC Genomics 2018 19:614

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  3. Content type: Research article

    Peach (Prunus persica) is an important fruit crop that generally softens rapidly after harvest resulting in a short shelf-life. By contrast, stony hard (SH) peach fruit does not soften and hardly produces ethylen...

    Authors: Shaolei Guo, Shahid Iqbal, Ruijuan Ma, Juan Song, Mingliang Yu and Zhihong Gao

    Citation: BMC Genomics 2018 19:612

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  4. Content type: Research article

    Plant lipoxygenase (LOX) genes are members of the non-haeme iron-containing dioxygenase family that catalyze the oxidation of polyunsaturated fatty acids into functionally diverse oxylipins. The LOX family gen...

    Authors: Muhammad Shaban, Muhammad Mahmood Ahmed, Heng Sun, Abid Ullah and Longfu Zhu

    Citation: BMC Genomics 2018 19:599

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  5. Content type: Research article

    Since 2007, bacterial canker caused by Pseudomonas syringae pv. actinidiae (Psa) has become a pandemic disease leading to important economic losses in every country where kiwifruit is widely cultivated. Options f...

    Authors: Vania Michelotti, Antonella Lamontanara, Giampaolo Buriani, Luigi Orrù, Antonio Cellini, Irene Donati, Joel L. Vanneste, Luigi Cattivelli, Gianni Tacconi and Francesco Spinelli

    Citation: BMC Genomics 2018 19:585

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  6. Content type: Research article

    Synthetic hexaploid wheat (SHW) is a reconstitution of hexaploid wheat from its progenitors (Triticum turgidum ssp. durum L.; AABB x Aegilops tauschii Coss.; DD) and has novel sources of genetic diversity for bro...

    Authors: Madhav Bhatta, Alexey Morgounov, Vikas Belamkar, Jesse Poland and P. Stephen Baenziger

    Citation: BMC Genomics 2018 19:591

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  7. Content type: Research article

    Allopolyploids require rapid genetic and epigenetic modifications to reconcile two or more sets of divergent genomes. To better understand the fate of duplicate genes following genomic mergers and doubling dur...

    Authors: Jian Wu, Li Lin, Meiling Xu, Peipei Chen, Dongxiao Liu, Qinfu Sun, Liping Ran and Youping Wang

    Citation: BMC Genomics 2018 19:586

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  8. Content type: Research article

    Meloidogyne incognita is a devastating nematode that causes significant losses in cucumber production worldwide. Although numerous studies have emphasized on the susceptible response of plants after nematode infe...

    Authors: Xing Wang, Chunyan Cheng, Kaijing Zhang, Zhen Tian, Jian Xu, Shuqiong Yang, Qunfeng Lou, Ji Li and Jin-Feng Chen

    Citation: BMC Genomics 2018 19:583

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  9. Content type: Research article

    Satellite DNA is a rapidly diverging, largely repetitive DNA component of many eukaryotic genomes. Here we analyse the evolutionary dynamics of a satellite DNA repeat in the genomes of a group of Asian subtrop...

    Authors: Yung-I Lee, Jing Wei Yap, Shairul Izan, Ilia J. Leitch, Michael F. Fay, Yi-Ching Lee, Oriane Hidalgo, Steven Dodsworth, Marinus J. M. Smulders, Barbara Gravendeel and Andrew R. Leitch

    Citation: BMC Genomics 2018 19:578

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  10. Content type: Research article

    The 14–3-3 family of ubiquitous proteins in eukaryotes plays important roles in the regulation of various plant biological processes. However, less information is known about this family in grape fruit.

    Authors: Cheng Cheng, Yi Wang, Fengmei Chai, Shaohua Li, Haiping Xin and Zhenchang Liang

    Citation: BMC Genomics 2018 19:579

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  11. Content type: Research article

    Multi-parent advanced generation intercross (MAGIC) populations are a newly established tool to dissect quantitative traits. We developed the high resolution MAGIC wheat population WM-800, consisting of 910 F4:6 ...

    Authors: Wiebke Sannemann, Antonia Lisker, Andreas Maurer, Jens Léon, Ebrahim Kazman, Hilmar Cöster, Josef Holzapfel, Hubert Kempf, Viktor Korzun, Erhard Ebmeyer and Klaus Pillen

    Citation: BMC Genomics 2018 19:559

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  12. Content type: Research article

    Flower morphology, a phenomenon regulated by a complex network, is one of the vital ornamental features in Nelumbo nucifera. Stamen petaloid is very prevalent in lotus flowers. However, the mechanism underlying t...

    Authors: Zhongyuan Lin, Rebecca Njeri Damaris, Tao Shi, Juanjuan Li and Pingfang Yang

    Citation: BMC Genomics 2018 19:554

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  13. Content type: Research article

    In flowering plants, the male gametophyte (pollen) is one of the most vulnerable cells to temperature stress. In Arabidopsis thaliana, a pollen-specific Cyclic Nucleotide-Gated cation Channel 16 (cngc16), is requ...

    Authors: Maryam Rahmati Ishka, Elizabeth Brown, Chrystle Weigand, Richard L. Tillett, Karen A. Schlauch, Gad Miller and Jeffrey F. Harper

    Citation: BMC Genomics 2018 19:549

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  14. Content type: Research article

    Cinnamomum camphora has been cultivated as an economically important tree for its medicinal and aromatic properties. Selective breeding has produced Cinnamomum plants for special uses, including spice strains wit...

    Authors: Caihui Chen, Yongjie Zheng, Yongda Zhong, Yangfang Wu, Zhiting Li, Li-An Xu and Meng Xu

    Citation: BMC Genomics 2018 19:550

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  15. Content type: Research article

    Since the proposal of Brachypodium distachyon as a model for the grasses, over 500 Bdi-miRNAs have been annotated in miRBase making Brachypodium second in number only to rice. Other monocots, such as switchgrass,...

    Authors: Karl R. Franke, Skye A. Schmidt, Sunhee Park, Dong-Hoon Jeong, Monica Accerbi and Pamela J. Green

    Citation: BMC Genomics 2018 19:547

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  16. Content type: Research article

    S. latifolia is a model organism for the study of sex chromosome evolution in plants. Its sex chromosomes include large regions in which recombination became gradually suppressed. The regions tend to expand over ...

    Authors: José Luis Rodríguez Lorenzo, Roman Hobza and Boris Vyskot

    Citation: BMC Genomics 2018 19:540

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  17. Content type: Research article

    Nitrogen (N) is a key macronutrient essential for plant growth, and its availability has a strong influence on crop development. The application of synthetic N fertilizers on crops has increased substantially ...

    Authors: Sang-Yoon Shin, Jin Seo Jeong, Jae Yun Lim, Taewook Kim, June Hyun Park, Ju-Kon Kim and Chanseok Shin

    Citation: BMC Genomics 2018 19:532

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  18. Content type: Research article

    Phytophthora nicotianae Breda de Haan (Phytophthora parasitica Dastur) causes severe damage to citrus crops worldwide. A population of citrandarins was created from the cross between the susceptible parent Citrus...

    Authors: Rômulo P. M. Lima, Maiara Curtolo, Marcus V. Merfa, Mariângela Cristofani-Yaly and Marcos A. Machado

    Citation: BMC Genomics 2018 19:516

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  19. Content type: Research article

    Flax (Linum usitatissimum. L) is an ancient oilseed and natural fiber crop. It could be divided into three categories by use, namely oil flax, fiber flax and oil-fiber dual purpose (OF). Cultivated flax is widely...

    Authors: Dongwei Xie, Zhigang Dai, Zemao Yang, Qing Tang, Jian Sun, Xue Yang, Xixia Song, Ying Lu, Debao Zhao, Liguo Zhang and Jianguang Su

    Citation: BMC Genomics 2018 19:512

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  20. Content type: Research article

    The medicinal plant, Catharanthus roseus (C. roseus), accumulates a wide range of terpenoid indole alkaloids (TIAs). Ethylene (ET) and methyl-jasmonate (MeJA) were previously reported as effective elicitors for t...

    Authors: Ya-jie Pan, Ying-chao Lin, Bo-fan Yu, Yuan-gang Zu, Fang Yu and Zhong-Hua Tang

    Citation: BMC Genomics 2018 19:508

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  22. Content type: Research article

    Genome scans based on outlier analyses have revolutionized detection of genes involved in adaptive processes, but reports of some forms of selection, such as balancing selection, are still limited. It is uncle...

    Authors: James Buckley, Eric B. Holub, Marcus A. Koch, Philippine Vergeer and Barbara K. Mable

    Citation: BMC Genomics 2018 19:496

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  23. Content type: Research article

    Simple sequence repeats (SSRs) are tandem repeats of DNA that have been used to develop robust genetic markers. These molecular markers are powerful tools for basic and applied studies such as molecular breedi...

    Authors: Xuewen Wang, Shuai Yang, Yongdui Chen, Shumeng Zhang, Qingshi Zhao, Meng Li, Yulong Gao, Long Yang and Jeffrey L. Bennetzen

    Citation: BMC Genomics 2018 19:500

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  24. Content type: Research article

    WRKY proteins comprise a large family of transcription factors that play important roles in many aspects of physiological processes and adaption to environment. However, little information was available about ...

    Authors: Tao Xie, Chengjie Chen, Chuhao Li, Jiarou Liu, Chaoyang Liu and Yehua He

    Citation: BMC Genomics 2018 19:490

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  25. Content type: Research article

    Gossypium barbadense (Sea Island, Egyptian or Pima cotton) cotton has high fiber quality, however, few studies have investigated the genetic basis of its traits using molecular markers. Genome complexity reductio...

    Authors: Liping Fan, Liping Wang, Xinyi Wang, Haiyan Zhang, Yanfei Zhu, Jiayan Guo, Wenwei Gao, Hongwei Geng, Quanjia Chen and Yanying Qu

    Citation: BMC Genomics 2018 19:489

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  26. Content type: Research article

    Advances in genomics technologies are making it increasingly feasible to characterize breeding lines that carry traits of agronomic interest. Tobacco germplasm lines that carry loci designated VAM and va have bee...

    Authors: Kurtis L. Dluge, Zhongbang Song, Bingwu Wang, W. Tyler Steede, Bingguang Xiao, Yong Liu and Ralph E. Dewey

    Citation: BMC Genomics 2018 19:484

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  27. Content type: Research article

    Sugarcane (Saccharum L. plant) is an important crop for sugar and bio-energy production around the world. Among sugarcane diseases, smut caused by Sporisorium scitamineum is one of the major fungal diseases causi...

    Authors: Ning Huang, Hui Ling, Feng Liu, Yachun Su, Weihua Su, Huaying Mao, Xu Zhang, Ling Wang, Rukai Chen and Youxiong Que

    Citation: BMC Genomics 2018 19:479

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  28. Content type: Research article

    Pear (Pyrus spp.) is an economically important temperate fruit tree worldwide. In the past decade, significant progress has been made in pear molecular genetics based on DNA research, but the number of molecular ...

    Authors: Huabai Xue, Pujuan Zhang, Ting Shi, Jian Yang, Long Wang, Suke Wang, Yanli Su, Huirong Zhang, Yushan Qiao and Xiugen Li

    Citation: BMC Genomics 2018 19:473

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  29. Content type: Research article

    Dryopteris fragrans (D. fragrans) is a potential medicinal fern distributed in volcanic magmatic rock areas under tough environmental condition. Sporangia are important organs for fern reproduction. This study wa...

    Authors: Zhen Lu, Qingyang Huang, Tong Zhang, Baozhong Hu and Ying Chang

    Citation: BMC Genomics 2018 19:471

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  30. Content type: Research article

    Long non-coding RNAs (lncRNAs) have been found to play a vital role in several gene regulatory networks involved in the various biological processes in plants related to stress response. However, systematic an...

    Authors: Liang Chen, Shilai Shi, Ninfei Jiang, Hira Khanzada, Ghulam Mustafa Wassan, Changlan Zhu, Xiaosong Peng, Jie Xu, Yujin Chen, Qiuying Yu, Xiaopeng He, Junru Fu, Xiaorong Chen, Lifang Hu, Linjuan Ouyang, Xiaotang Sun…

    Citation: BMC Genomics 2018 19:460

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  31. Content type: Research article

    Nitrogen (N) is a key macronutrient required for plant growth and development. In this study, watermelon plants were grown under hydroponic conditions at 0.2 mM N, 4.5 mM N, and 9 mM N for 14 days.

    Authors: Muhammad Azher Nawaz, Chen Chen, Fareeha Shireen, Zhuhua Zheng, Hamza Sohail, Muhammad Afzal, Muhammad Amjad Ali, Zhilong Bie and Yuan Huang

    Citation: BMC Genomics 2018 19:456

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  32. Content type: Research article

    Gene order and location in chromosomes of species are non-random. Neighboring gene pairs tend to display some similarities, such as co-expression and co-modification. However, the contribution of linear proxim...

    Authors: Shuaibin Lian, Tianliang Liu, Shengli Jing, Hongyu Yuan, Zaibao Zhang and Lin Cheng

    Citation: BMC Genomics 2018 19:455

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  33. Content type: Research article

    Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving ...

    Authors: Xiongming Du, Shouye Liu, Junling Sun, Gengyun Zhang, Yinhua Jia, Zhaoe Pan, Haitao Xiang, Shoupu He, Qiuju Xia, Songhua Xiao, Weijun Shi, Zhiwu Quan, Jianguang Liu, Jun Ma, Baoyin Pang, Liru Wang…

    Citation: BMC Genomics 2018 19:451

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  34. Content type: Research article

    Bananas (Musa spp.) are the most important fruit crops worldwide due to their high nutrition value. Fusarium wilt of banana, caused by fungal pathogen Fusarium oxysporum f. sp. cubense tropical race 4 (Foc 4), is...

    Authors: Zhihao Cheng, Xiang Yu, Shuxia Li and Qiong Wu

    Citation: BMC Genomics 2018 19:454

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  36. Content type: Methodology article

    Whole-genome bisulfite sequencing (WGBS) has become the standard method for interrogating plant methylomes at base resolution. However, deep WGBS measurements remain cost prohibitive for large, complex genomes...

    Authors: Aaron Taudt, David Roquis, Amaryllis Vidalis, René Wardenaar, Frank Johannes and Maria Colomé-Tatché

    Citation: BMC Genomics 2018 19:444

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  37. Content type: Research article

    Kudzu, Pueraria montana var. lobata, is a woody vine native to Southeast Asia that has been introduced globally for cattle forage and erosion control. The vine is highly invasive in its introduced areas, includin...

    Authors: Matthew S. Haynsen, Mohammad Vatanparast, Gouri Mahadwar, Dennis Zhu, Roy Z. Moger-Reischer, Jeff J. Doyle, Keith A. Crandall and Ashley N. Egan

    Citation: BMC Genomics 2018 19:439

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  38. Content type: Research article

    Aloe vera is a perennial, succulent, drought-resistant plant that exhibits many pharmacological characteristics such as wound healing ability against skin burns, anti-ulcer, anti-inflammatory, anti-tumor, anti-vi...

    Authors: Pragati Choudhri, Muniya Rani, Rajender S. Sangwan, Ravinder Kumar, Anil Kumar and Vinod Chhokar

    Citation: BMC Genomics 2018 19:427

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  39. Content type: Research article

    Chloroplasts have their own genomes, independent from nuclear genomes, that play vital roles in growth, which is a major targeted trait for genetic improvement in Populus. Angiosperm chloroplast genomes are mater...

    Authors: Sheng Zhu, Meng Xu, Haoran Wang, Huixin Pan, Guangping Wang and Minren Huang

    Citation: BMC Genomics 2018 19:411

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  40. Content type: Research article

    Mitogen-activated protein kinase (MAPK) cascades play critical functions in almost every aspect of plant growth and development, which regulates many physiological and biochemical processes. As a middle nodal ...

    Authors: Min Jiang and Zhaoqing Chu

    Citation: BMC Genomics 2018 19:407

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  41. Content type: Research article

    Understanding the genetic basis of frost tolerance (FT) in wheat (Triticum aestivum L.) is essential for preventing yield losses caused by frost due to cellular damage, dehydration and reduced metabolism. FT is a...

    Authors: Steve Babben, Edgar Schliephake, Philipp Janitza, Thomas Berner, Jens Keilwagen, Michael Koch, Fernando Alberto Arana-Ceballos, Sven Eduard Templer, Yuriy Chesnokov, Tatyana Pshenichnikova, Jörg Schondelmaier, Andreas Börner, Klaus Pillen, Frank Ordon and Dragan Perovic

    Citation: BMC Genomics 2018 19:409

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  42. Content type: Research article

    Meiotic recombination events include crossovers and non-crossovers or gene conversions. Although the rate of crossovers is often used for genetic mapping, the gene conversion events are not well studied especi...

    Authors: Shentong Tao, Jiyan Wu, Dan Yao, Yuhua Chen, Wenguo Yang and Chunfa Tong

    Citation: BMC Genomics 2018 19:398

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  43. Content type: Research article

    Plant P-type II Ca2+ATPases are formed by two distinct groups of proteins (ACAs and ECAs) that perform pumping of Ca2+ outside the cytoplasm during homeostasis, and play vital functions during development and str...

    Authors: Mehak Taneja and Santosh Kumar Upadhyay

    Citation: BMC Genomics 2018 19:389

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  44. Content type: Research article

    Sacha Inchi (Plukenetia volubilis L.), which belongs to the Euphorbiaceae, has been considered a new potential oil crop because of its high content of polyunsaturated fatty acids in its seed oil. The seed oil esp...

    Authors: Xiao-Di Hu, Bang-Zhen Pan, Qiantang Fu, Longjian Niu, Mao-Sheng Chen and Zeng-Fu Xu

    Citation: BMC Genomics 2018 19:380

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  45. Content type: Research article

    Euryale ferox Salisb., an annual aquatic plant, is the only species in the genus Euryale in the Nymphaeaceae. Seeds of E. ferox are a nutritious food and also used in traditional Chinese medicine (Qian Shi in Man...

    Authors: Xian Liu, Zhen He, Yulai Yin, Xu Xu, Weiwen Wu and Liangjun Li

    Citation: BMC Genomics 2018 19:343

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  46. Content type: Research article

    Cotton is a major fiber and oil crop worldwide. Cotton production, however, is often threatened by abiotic environmental stresses. GRAS family proteins are among the most abundant transcription factors in plan...

    Authors: Bin Zhang, J. Liu, Zhao E. Yang, Er Y. Chen, Chao J. Zhang, Xue Y. Zhang and Fu G. Li

    Citation: BMC Genomics 2018 19:348

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  47. Content type: Methodology article

    In plants, long non-protein coding RNAs are believed to have essential roles in development and stress responses. However, relative to advances on discerning biological roles for long non-protein coding RNAs i...

    Authors: Caitlin M. A. Simopoulos, Elizabeth A. Weretilnyk and G. Brian Golding

    Citation: BMC Genomics 2018 19:316

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  48. Content type: Research article

    Chrysanthemum is one kind of ornamental plant well-known and widely used in the world. However, its quality and production were severely affected by low temperature conditions in winter and early spring period...

    Authors: Ke Wang, Zhen-yu Bai, Qian-yu Liang, Qing-lin Liu, Lei Zhang, Yuan-zhi Pan, Guang-li Liu, Bei-bei Jiang, Fan Zhang and Yin Jia

    Citation: BMC Genomics 2018 19:319

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  49. Content type: Research article

    The wild relatives of crop species represent a potentially valuable source of novel genetic variation, particularly in the context of improving the crop’s level of tolerance to abiotic stress. The mechanistic ...

    Authors: Anna Janská, Pavel Svoboda, Vojtěch Spiwok, Ladislav Kučera and Jaroslava Ovesná

    Citation: BMC Genomics 2018 19:317

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