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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 26

  1. Content type: Research article

    Cold temperatures and their alleviation affect many plant traits including the abundance of protein coding gene transcripts. Transcript level changes that occur in response to cold temperatures and their allev...

    Authors: Luis M Avila, Wisam Obeidat, Hugh Earl, Xiaomu Niu, William Hargreaves and Lewis Lukens

    Citation: BMC Genomics 2018 19:761

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  2. Content type: Research article

    In diverse plant taxa, whole-genome duplication (WGD) events are major sources of phenotypic novelty. Studies of gene expression in synthetic polyploids have shown immediate expression and functional partition...

    Authors: Long Zhao, Lei Han, Chaoxia Xiao, Xiuyun Lin, Chunming Xu and Chunwu Yang

    Citation: BMC Genomics 2018 19:756

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  3. Content type: Research article

    COI (CORONATINE INSENSITIVE), an F-box component of the Skp1-Cullin-F-box protein (SCFCOI1) ubiquitin E3 ligase, plays important roles in the regulation of plant growth and development. Recent studies have shown ...

    Authors: Jian-fang Bai, Yu-kun Wang, Peng Wang, Shao-hua Yuan, Jian-gang Gao, Wen-jing Duan, Na Wang, Feng-ting Zhang, Wen-jie Zhang, Meng-ying Qin, Chang-ping Zhao and Li-ping Zhang

    Citation: BMC Genomics 2018 19:754

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  5. Content type: Research article

    Transgenerational plasticity occurs when the environmental experience of an organism modifies the growth and development of its progeny. Leaf damage in Mimulus guttatus exhibits transgenerational plasticity media...

    Authors: Jack M Colicchio, John K Kelly and Lena C Hileman

    Citation: BMC Genomics 2018 19:746

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  6. Content type: Research article

    Long noncoding RNAs (lncRNAs) are transcripts longer than 200 bp that do not encode proteins but nonetheless have been shown to play important roles in various biological processes in plants. Brassica napus is an...

    Authors: Enhui Shen, Xintian Zhu, Shuijin Hua, Hongyu Chen, Chuyu Ye, Longhua Zhou, Qing Liu, Qian-Hao Zhu, Longjiang Fan and Xi Chen

    Citation: BMC Genomics 2018 19:745

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  7. Content type: Research article

    The hop plant (Humulus lupulus L.) is a valuable source of several secondary metabolites, such as flavonoids, bitter acids, and essential oils. These compounds are widely implicated in the beer brewing industry a...

    Authors: Ajay Kumar Mishra, Ganesh Selvaraj Duraisamy, Mudra Khare, Tomáš Kocábek, Jernej Jakse, Jindřich Bříza, Josef Patzak, Teruo Sano and Jaroslav Matoušek

    Citation: BMC Genomics 2018 19:739

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  8. Content type: Research article

    The majority of eukaryote genomes can be actively transcribed into non-coding RNAs (ncRNAs), which are functionally important in development and evolution. In the study of maize, an important crop for both hum...

    Authors: Dandan Li, Huili Qiao, Wujie Qiu, Xin Xu, Tiemei Liu, Qianling Jiang, Renyi Liu, Zhujin Jiao, Kun Zhang, Lijun Bi, Runsheng Chen and Yunchao Kan

    Citation: BMC Genomics 2018 19:730

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  9. Content type: Research article

    Flowering is a critical reproductive process in higher plants. Timing of optimal flowering depends upon the coordination among seasonal environmental cues. For cool season grasses, such as Dactylis glomerata, ver...

    Authors: Guangyan Feng, Lei Xu, Jianping Wang, Gang Nie, Bradley Shaun Bushman, Wengang Xie, Haidong Yan, Zhongfu Yang, Hao Guan, Linkai Huang and Xinquan Zhang

    Citation: BMC Genomics 2018 19:727

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  10. Content type: Research article

    MADS-box genes encode transcription factors that are known to be involved in several aspects of plant growth and development, especially in floral organ specification. To date, the comprehensive analysis of po...

    Authors: Huhu Gao, Ziming Wang, Silu Li, Menglu Hou, Yao Zhou, Yaqi Zhao, Guojun Li, Hua Zhao and Haoli Ma

    Citation: BMC Genomics 2018 19:726

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  11. Content type: Research article

    Cytokinin is a classical phytohormone that plays important roles in numerous plant growth and development processes. In plants, cytokinin signals are transduced by a two-component system, which involves many g...

    Authors: Lijun Kong, Kun Zhao, Yingying Gao, Liming Miao, Chaoquan Chen, Hang Deng, Zhenning Liu and Xiaolin Yu

    Citation: BMC Genomics 2018 19:728

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  12. Content type: Research article

    Pentatricopeptide-repeat proteins (PPRs) are characterized by tandem arrays of a degenerate 35-amino-acid (PPR motifs), which can bind RNA strands and participate in post-transcription. PPR proteins family is ...

    Authors: Guanglong Chen, Yu Zou, Jihong Hu and Yi Ding

    Citation: BMC Genomics 2018 19:720

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  13. Content type: Research article

    Arabidopsis pumila is native to the desert region of northwest China and it is extraordinarily well adapted to the local semi-desert saline soil, thus providing a candidate plant system for environmental adaptati...

    Authors: Lifei Yang, Yuhuan Jin, Wei Huang, Qi Sun, Fang Liu and Xianzhong Huang

    Citation: BMC Genomics 2018 19:717

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  14. Content type: Research article

    Metal tolerance is often an integrative result of metal uptake and distribution, which are fine-tuned by a network of signaling cascades and metal transporters. Thus, with the goal of advancing the molecular u...

    Authors: Dan Cheng, Mingpu Tan, Haijuan Yu, Liang Li, Dandan Zhu, Yahua Chen and Mingyi Jiang

    Citation: BMC Genomics 2018 19:709

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  15. Content type: Research article

    VQ motif-containing (VQ) proteins are plant-specific proteins that interact with WRKY transcription factors and play important roles in plant growth, development and stress response. To date, VQ gene families hav...

    Authors: Junhong Guo, Jiangfei Chen, Jiankun Yang, Youben Yu, Yajun Yang and Weidong Wang

    Citation: BMC Genomics 2018 19:710

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  16. Content type: Research article

    Rice plants are sensitive to the agro-climate conditions, being photoperiod one of main factor contributing to their adaptation to the region where they are grown. Dissecting the genetic bases underlying diver...

    Authors: Juan L Reig-Valiente, Luis Marqués, Manuel Talón and Concha Domingo

    Citation: BMC Genomics 2018 19:706

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  17. Content type: Research article

    The FK506-binding proteins (FKBPs) play diverse roles in numerous critical processes for plant growth, development, and abiotic stress responses. However, the FKBP gene family in the important fruit crop apple (M...

    Authors: Qinglong Dong, Ke Mao, Dingyue Duan, Shuang Zhao, Yanpeng Wang, Qian Wang, Dong Huang, Chao Li, Changhai Liu, Xiaoqing Gong and Fengwang Ma

    Citation: BMC Genomics 2018 19:707

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  18. Content type: Research article

    Sorghum bicolor is the fifth most commonly grown cereal worldwide and is remarkable for its drought and abiotic stress tolerance. For these reasons and the large size of biomass varieties, it has been proposed as...

    Authors: Jennifer E. Spindel, Jeffery Dahlberg, Matthew Colgan, Joy Hollingsworth, Julie Sievert, Scott H. Staggenborg, Robert Hutmacher, Christer Jansson and John P. Vogel

    Citation: BMC Genomics 2018 19:679

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  19. Content type: Research article

    Cytoplasmic male sterility (CMS) is a natural phenomenon of pollen abortion caused by the interaction between cytoplasmic genes and nuclear genes. CMS is a simple and effective pollination control system, and ...

    Authors: Linfeng Chen, Xianlong Ding, Hao Zhang, Tingting He, Yanwei Li, Tanliu Wang, Xiaoqiang Li, Ling Jin, Qijian Song, Shouping Yang and Junyi Gai

    Citation: BMC Genomics 2018 19:663

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  20. Content type: Research article

    Pectin is a major component and structural polysaccharide of the primary cell walls and middle lamella of higher plants. Pectate lyase (PEL, EC 4.2.2.2), a cell wall modification enzyme, degrades de-esterified...

    Authors: Huiru Sun, Pengbo Hao, Qiang Ma, Meng Zhang, Yuan Qin, Hengling Wei, Junji Su, Hantao Wang, Lijiao Gu, Nuohan Wang, Guoyuan Liu and Shuxun Yu

    Citation: BMC Genomics 2018 19:661

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  21. Content type: Research article

    Short read DNA sequencing technologies have revolutionized genome assembly by providing high accuracy and throughput data at low cost. But it remains challenging to assemble short read data, particularly for l...

    Authors: Alina Ott, James C. Schnable, Cheng-Ting Yeh, Linjiang Wu, Chao Liu, Heng-Cheng Hu, Clifton L. Dalgard, Soumik Sarkar and Patrick S. Schnable

    Citation: BMC Genomics 2018 19:651

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  22. Content type: Research article

    Soybean is not only an important oil crop, but also an important source of edible protein and industrial raw material. Yield-traits and quality-traits are increasingly attracting the attention of breeders. The...

    Authors: Yanwei Zhang, Wei Li, Yanhui Lin, Lifeng Zhang, Caijie Wang and Ran Xu

    Citation: BMC Genomics 2018 19:641

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  23. Content type: Research article

    Fusarium head blight (FHB) of wheat in North America is caused mostly by the fungal pathogen Fusarium graminearum (Fg). Upon exposure to Fg, wheat initiates a series of cellular responses involving massive transc...

    Authors: Youlian Pan, Ziying Liu, Hélène Rocheleau, François Fauteux, Yunli Wang, Curt McCartney and Thérèse Ouellet

    Citation: BMC Genomics 2018 19:642

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  24. Content type: Research article

    Fusarium circinatum is a pressing threat to the cultivation of many economically important pine tree species. Efforts to develop effective disease management strategies can be aided by investigating the molecular...

    Authors: Erik A. Visser, Jill L. Wegrzyn, Alexander A. Myburg and Sanushka Naidoo

    Citation: BMC Genomics 2018 19:632

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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  46. 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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  47. 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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  48. 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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  49. 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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  50. 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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