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Genomics and evolution

Section edited by David Alvarez-Ponce and Z Jeffrey Chen 

This section considers studies in the evolution of plants as well as comparative genomics in relation to plant biology.

Page 5 of 7

  1. Content type: Research article

    In plant, non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that have been reported to be involved in numerous biological processes such as transfer of phospholipids, reproductive develop...

    Authors: Kaifa Wei and Xiaojun Zhong

    Citation: BMC Plant Biology 2014 14:281

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  2. Content type: Research article

    Domestication and selection of crops have notably reshaped fruit morphology. With its large phenotypic diversity, tomato (Solanum lycopersicum) illustrates this evolutive trend. Genes involved in flower meristem ...

    Authors: Guillaume Bauchet, Stéphane Munos, Christopher Sauvage, Julien Bonnet, Laurent Grivet and Mathilde Causse

    Citation: BMC Plant Biology 2014 14:279

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  3. Content type: Research article

    An allopolyploid formation consists of the two processes of hybridisation and chromosome doubling. Hybridisation makes a different genome combined in the same cell, and genome "shock" and instability occur dur...

    Authors: Muhammad Awais Ghani, Junxing Li, Linli Rao, Muhammad Ammar Raza, Liwen Cao, Ningning Yu, Xiaoxia Zou and Liping Chen

    Citation: BMC Plant Biology 2014 14:272

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  4. Content type: Research article

    Evolutionary theory suggests that males and females may evolve sexually dimorphic phenotypic and biochemical traits concordant with each sex having different optimal strategies of resource investment to maximi...

    Authors: Kathryn M Robinson, Nicolas Delhomme, Niklas Mähler, Bastian Schiffthaler, Jenny Önskog, Benedicte R Albrectsen, Pär K Ingvarsson, Torgeir R Hvidsten, Stefan Jansson and Nathaniel R Street

    Citation: BMC Plant Biology 2014 14:276

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  5. Content type: Research article

    Tea is a popular natural non-alcoholic beverage consumed worldwide due to its bioactive ingredients, particularly catechins (flavan-3-ols). Catechins not only contribute to tea quality but also serve important...

    Authors: Zhi-Jun Wu, Xing-Hui Li, Zhi-Wei Liu, Zhi-Sheng Xu and Jing Zhuang

    Citation: BMC Plant Biology 2014 14:277

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  6. Content type: Research article

    Members of the ancient land-plant-specific transcription factor AT-Hook Motif Nuclear Localized (AHL) gene family regulate various biological processes. However, the relationships among the AHL genes, as well as ...

    Authors: Jianfei Zhao, David S Favero, Jiwen Qiu, Eric H Roalson and Michael M Neff

    Citation: BMC Plant Biology 2014 14:266

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  7. Content type: Research article

    New SNP marker platforms offer the opportunity to investigate the relationships between wheat cultivars from different regions and assess the mechanism and processes that have led to adaptation to particular p...

    Authors: Yuri Shavrukov, Radoslaw Suchecki, Serik Eliby, Aigul Abugalieva, Serik Kenebayev and Peter Langridge

    Citation: BMC Plant Biology 2014 14:258

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  8. Content type: Research article

    Cultivated soybean (Glycine max) experienced a severe genetic bottleneck during its domestication and a further loss in diversity during its subsequent selection. Here, a panel of 65 wild (G. soja) and 353 cultiv...

    Authors: Ying-Hui Li, Jochen C Reif, Scott A Jackson, Yan-Song Ma, Ru-Zhen Chang and Li-Juan Qiu

    Citation: BMC Plant Biology 2014 14:251

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  9. Content type: Research article

    The R2R3-MYB genes comprise one of the largest transcription factor gene families in plants, playing regulatory roles in plant-specific developmental processes, metabolite accumulation and defense responses. Alth...

    Authors: Ralf Stracke, Daniela Holtgräwe, Jessica Schneider, Boas Pucker, Thomas Rosleff Sörensen and Bernd Weisshaar

    Citation: BMC Plant Biology 2014 14:249

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  10. Content type: Research article

    Many previous studies have shown that soybean WRKY transcription factors are involved in the plant response to biotic and abiotic stresses. Phakopsora pachyrhizi is the causal agent of Asian Soybean Rust, one of ...

    Authors: Marta Bencke-Malato, Caroline Cabreira, Beatriz Wiebke-Strohm, Lauro Bücker-Neto, Estefania Mancini, Marina B Osorio, Milena S Homrich, Andreia Carina Turchetto-Zolet, Mayra CCG De Carvalho, Renata Stolf, Ricardo LM Weber, Gastón Westergaard, Atílio P Castagnaro, Ricardo V Abdelnoor, Francismar C Marcelino-Guimarães, Márcia Margis-Pinheiro…

    Citation: BMC Plant Biology 2014 14:236

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  11. Content type: Research article

    In Vitis vinifera L., domestication induced a dramatic change in flower morphology: the wild sylvestris subspecies is dioecious while hermaphroditism is largely predominant in the domesticated subsp. V. v. vinife...

    Authors: Sandrine Picq, Sylvain Santoni, Thierry Lacombe, Muriel Latreille, Audrey Weber, Morgane Ardisson, Sarah Ivorra, David Maghradze, Rosa Arroyo-Garcia, Philippe Chatelet, Patrice This, Jean-Frédéric Terral and Roberto Bacilieri

    Citation: BMC Plant Biology 2014 14:229

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  12. Content type: Research article

    MicroRNAs (miRNAs) are a new class of endogenous regulators of a broad range of physiological processes, which act by regulating gene expression post-transcriptionally. The brassica vegetable, broccoli (Brassica ...

    Authors: Yunhong Tian, Yunming Tian, Xiaojun Luo, Tao Zhou, Zuoping Huang, Ying Liu, Yihan Qiu, Bing Hou, Dan Sun, Hongyu Deng, Shen Qian and Kaitai Yao

    Citation: BMC Plant Biology 2014 14:226

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  13. Content type: Research article

    Mitogen-activated protein kinase kinase kinases (MAPKKKs; MAP3Ks) are important components of MAPK cascades, which are highly conserved signal transduction pathways in animals, yeast and plants, play important...

    Authors: Gang Wang, Arianna Lovato, Annalisa Polverari, Min Wang, Ying-Hai Liang, Yuan-Chun Ma and Zong-Ming Cheng

    Citation: BMC Plant Biology 2014 14:219

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  14. Content type: Research article

    Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and m...

    Authors: Sonali Sachin Ranade, Yao-Cheng Lin, Andrea Zuccolo, Yves Van de Peer and María del Rosario García-Gil

    Citation: BMC Plant Biology 2014 14:220

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  15. Content type: Research article

    The paper mulberry (Broussonetia papyifera) is one of the multifunctional tree species in agroforestry system and is also commonly utilized in traditional medicine in China and other Asian countries. To identify ...

    Authors: Xianjun Peng, Yucheng Wang, Ruiping He, Meiling Zhao and Shihua Shen

    Citation: BMC Plant Biology 2014 14:194

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  16. Content type: Research article

    Sweet orange (Citrus sinensis) is one of the most important fruits world-wide. Because it is a woody plant with a long growth cycle, genetic studies of sweet orange are lagging behind those of other species.

    Authors: Yu-Duan Ding, Ji-Wei Chang, Jing Guo, DiJun Chen, Sen Li, Qiang Xu, Xiu-Xin Deng, Yun-Jiang Cheng and Ling-Ling Chen

    Citation: BMC Plant Biology 2014 14:213

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  17. Content type: Research article

    The Maternally expressed gene (Meg) family is a locally-duplicated gene family of maize which encodes cysteine-rich proteins (CRPs). The founding member of the family, Meg1, is required for normal development of ...

    Authors: Yuqing Xiong, Wenbin Mei, Eun-Deok Kim, Krishanu Mukherjee, Hatem Hassanein, William Brad Barbazuk, Sibum Sung, Bryan Kolaczkowski and Byung-Ho Kang

    Citation: BMC Plant Biology 2014 14:204

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  18. Content type: Research article

    The understanding of sugarcane genetics has lagged behind that of other members of the Poaceae family such as wheat, rice, barley and sorghum mainly due to the complexity, size and polyploidization of the geno...

    Authors: Karen S Aitken, Meredith D McNeil, Paul J Berkman, Scott Hermann, Andrzej Kilian, Peter C Bundock and Jingchuan Li

    Citation: BMC Plant Biology 2014 14:190

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  19. Content type: Research article

    Taxodium is renowned for its strong tolerance to waterlogging stress, thus it has great ecological and economic potential. However, the scant genomic resources in genus Taxodium have greatly hindered further expl...

    Authors: Baiyan Qi, Ying Yang, Yunlong Yin, Meng Xu and Huogen Li

    Citation: BMC Plant Biology 2014 14:201

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  20. Content type: Research article

    In angiosperms, the endosperm plays a crucial placenta-like role in that not only is it necessary for nurturing the embryo, but also regulating embryogenesis through complicated genetic and epigenetic interact...

    Authors: Mingming Xin, Ruolin Yang, Yingyin Yao, Chuang Ma, Huiru Peng, Qixin Sun, Xiangfeng Wang and Zhongfu Ni

    Citation: BMC Plant Biology 2014 14:192

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  21. Content type: Research article

    Polygalacturonase-inhibiting proteins (PGIPs) are leucine-rich repeat (LRR) plant cell wall glycoproteins involved in plant immunity. They are typically encoded by gene families with a small number of gene cop...

    Authors: Raviraj M Kalunke, Alberto Cenci, Chiara Volpi, Donal M O’Sullivan, Luca Sella, Francesco Favaron, Felice Cervone, Giulia De Lorenzo and Renato D’Ovidio

    Citation: BMC Plant Biology 2014 14:189

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  22. Content type: Research article

    Theobroma cacao L. is a tropical fruit tree, the seeds of which are used to create chocolate. In vitro somatic embryogenesis (SE) of cacao is a propagation system useful for rapid mass-multiplication to accelerat...

    Authors: Siela N Maximova, Sergio Florez, Xiangling Shen, Nicolas Niemenak, Yufan Zhang, Wayne Curtis and Mark J Guiltinan

    Citation: BMC Plant Biology 2014 14:185

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  23. Content type: Research article

    The genus Citrus encompasses major cultivated plants such as sweet orange, mandarin, lemon and grapefruit, among the world’s most economically important fruit crops. With increasing volumes of transcriptomics dat...

    Authors: Darren CJ Wong, Crystal Sweetman and Christopher M Ford

    Citation: BMC Plant Biology 2014 14:186

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  24. Content type: Research article

    Endogenous small (sm) RNAs (primarily si- and miRNAs) are important trans/cis-acting regulators involved in diverse cellular functions. In plants, the RNA-dependent RNA polymerases (RDRs) are essential for smRNA ...

    Authors: Ningning Wang, Di Zhang, Zhenhui Wang, Hongwei Xun, Jian Ma, Hui Wang, Wei Huang, Ying Liu, Xiuyun Lin, Ning Li, Xiufang Ou, Chunyu Zhang, Ming-Bo Wang and Bao Liu

    Citation: BMC Plant Biology 2014 14:177

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  25. Content type: Research article

    Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model...

    Authors: Lei Wang, Chenlong Cao, Qibin Ma, Qiaoying Zeng, Haifeng Wang, Zhihao Cheng, Genfeng Zhu, Ji Qi, Hong Ma, Hai Nian and Yingxiang Wang

    Citation: BMC Plant Biology 2014 14:169

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  26. Content type: Research article

    The American cranberry (Vaccinium macrocarpon Ait.) is one of only three widely-cultivated fruit crops native to North America- the other two are blueberry (Vaccinium spp.) and native grape (Vitis spp.). In terms...

    Authors: James Polashock, Ehud Zelzion, Diego Fajardo, Juan Zalapa, Laura Georgi, Debashish Bhattacharya and Nicholi Vorsa

    Citation: BMC Plant Biology 2014 14:165

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  27. Content type: Research article

    Cultivated rice consists of two important ecotypes, upland and irrigated, that have respectively adapted to either dry land or irrigated cultivation. Upland rice, widely adopted in rainfed upland areas in virt...

    Authors: Jun Lyu, Baoye Li, Weiming He, Shilai Zhang, Zhiheng Gou, Jing Zhang, Liyun Meng, Xin Li, Dayun Tao, Wangqi Huang, Fengyi Hu and Wen Wang

    Citation: BMC Plant Biology 2014 14:160

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  28. Content type: Research article

    Recurrent gene duplication and retention played an important role in angiosperm genome evolution. It has been hypothesized that these processes contribute significantly to plant adaptation but so far this hypo...

    Authors: Iris Fischer, Jacques Dainat, Vincent Ranwez, Sylvain Glémin, Jean-François Dufayard and Nathalie Chantret

    Citation: BMC Plant Biology 2014 14:151

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  29. Content type: Research article

    Plant ALDH10 enzymes are aminoaldehyde dehydrogenases (AMADHs) that oxidize different ω-amino or trimethylammonium aldehydes, but only some of them have betaine aldehyde dehydrogenase (BADH) activity and produ...

    Authors: Rosario A Muñoz-Clares, Héctor Riveros-Rosas, Georgina Garza-Ramos, Lilian González-Segura, Carlos Mújica-Jiménez and Adriana Julián-Sánchez

    Citation: BMC Plant Biology 2014 14:149

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  30. Content type: Research article

    Pre-exposing plants to diverse abiotic stresses may alter their physiological and transcriptional responses to a subsequent stress, suggesting a form of “stress memory”. Arabidopsis thaliana plants that have e...

    Authors: Yong Ding, Laetitia Virlouvet, Ning Liu, Jean-Jack Riethoven, Michael Fromm and Zoya Avramova

    Citation: BMC Plant Biology 2014 14:141

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  31. Content type: Research article

    R2R3 MYB proteins constitute one of the largest plant transcription factor clades and regulate diverse plant-specific processes. Several R2R3 MYB proteins act as regulators of secondary cell wall (SCW) biosynt...

    Authors: Kangmei Zhao and Laura E Bartley

    Citation: BMC Plant Biology 2014 14:135

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  32. Content type: Research article

    Miscanthus is a promising biomass crop for temperate regions. Despite the increasing interest in this plant, limited sequence information has constrained research into its biology, physiology, and breeding. The w...

    Authors: Changsoo Kim, Tae-Ho Lee, Hui Guo, Sung Jin Chung, Andrew H Paterson, Do-Soon Kim and Geung-Joo Lee

    Citation: BMC Plant Biology 2014 14:134

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  33. Content type: Research article

    The availability of draft crop plant genomes allows the prediction of the full complement of genes that encode NB-LRR resistance gene homologs, enabling a more targeted breeding for disease resistance. Recentl...

    Authors: Giuseppe Andolfo, Florian Jupe, Kamil Witek, Graham J Etherington, Maria R Ercolano and Jonathan D G Jones

    Citation: BMC Plant Biology 2014 14:120

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  34. Content type: Research article

    A major step in the higher plant life cycle is the decision to leave the mitotic cell cycle and begin the progression through the meiotic cell cycle that leads to the formation of gametes. The molecular mechan...

    Authors: Stefanie Dukowic-Schulze, Anitha Sundararajan, Joann Mudge, Thiruvarangan Ramaraj, Andrew D Farmer, Minghui Wang, Qi Sun, Jaroslaw Pillardy, Shahryar Kianian, Ernest F Retzel, Wojciech P Pawlowski and Changbin Chen

    Citation: BMC Plant Biology 2014 14:118

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  35. Content type: Research article

    Alternative splicing (AS) significantly enhances transcriptome complexity. It is differentially regulated in a wide variety of cell types and plays a role in several cellular processes. Here we describe a deta...

    Authors: Nicola Vitulo, Claudio Forcato, Elisa Corteggiani Carpinelli, Andrea Telatin, Davide Campagna, Michela D'Angelo, Rosanna Zimbello, Massimiliano Corso, Alessandro Vannozzi, Claudio Bonghi, Margherita Lucchin and Giorgio Valle

    Citation: BMC Plant Biology 2014 14:99

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  36. Content type: Research article

    Expansins are plant cell wall loosening proteins that are involved in cell enlargement and a variety of other developmental processes. The expansin superfamily contains four subfamilies; namely, α-expansin (EX...

    Authors: Yan Zhu, Ningning Wu, Wanlu Song, Guangjun Yin, Yajuan Qin, Yueming Yan and Yingkao Hu

    Citation: BMC Plant Biology 2014 14:93

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  37. Content type: Research article

    Pectins are acidic sugar-containing polysaccharides that are universally conserved components of the primary cell walls of plants and modulate both tip and diffuse cell growth. However, many of their specific ...

    Authors: Thomas W McCarthy, Joshua P Der, Loren A Honaas, Claude W dePamphilis and Charles T Anderson

    Citation: BMC Plant Biology 2014 14:79

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  38. Content type: Research article

    Genetic improvement of shrub willow (Salix), a perennial energy crop common to temperate climates, has led to the development of new cultivars with improved biomass yield, pest and disease resistance, and biomass...

    Authors: Michelle J Serapiglia, Fred E Gouker and Lawrence B Smart

    Citation: BMC Plant Biology 2014 14:74

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  39. Content type: Research article

    The genomes of non-heading Chinese cabbage (Brassica rapa ssp. chinensis), heading Chinese cabbage (Brassica rapa ssp. pekinensis) and their close relative Arabidopsis thaliana have provided important resources f...

    Authors: Xiaoming Song, Ying Li, Tongkun Liu, Weike Duan, Zhinan Huang, Li Wang, Huawei Tan and Xilin Hou

    Citation: BMC Plant Biology 2014 14:71

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  40. Content type: Research article

    Phosphorus (P) deficiency is one of the major nutrient stresses limiting plant growth. The uptake of P by plants is well considered to be mediated by a number of high-affinity phosphate (Pi) transporters belon...

    Authors: Aiqun Chen, Xiao Chen, Huimin Wang, Dehua Liao, Mian Gu, Hongye Qu, Shubin Sun and Guohua Xu

    Citation: BMC Plant Biology 2014 14:61

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  41. Content type: Research article

    Breeders in the allo-octoploid strawberry currently make little use of molecular marker tools. As a first step of a QTL discovery project on fruit quality traits and resistance to soil-borne pathogens such as Phy...

    Authors: Thijs van Dijk, Giulia Pagliarani, Anna Pikunova, Yolanda Noordijk, Hulya Yilmaz-Temel, Bert Meulenbroek, Richard GF Visser and Eric van de Weg

    Citation: BMC Plant Biology 2014 14:55

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  42. Content type: Research article

    There is a rapidly growing awareness that plant peptide signalling molecules are numerous and varied and they are known to play fundamental roles in angiosperm plant growth and development. Two closely related...

    Authors: Timothy J Strabala, Lorelle Phillips, Mark West and Lisa Stanbra

    Citation: BMC Plant Biology 2014 14:47

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  43. Content type: Research article

    The rhizome, the original stem of land plants, enables species to invade new territory and is a critical component of perenniality, especially in grasses. Red rice (Oryza longistaminata) is a perennial wild rice ...

    Authors: Ruifeng He, Fernanda Salvato, Jeong-Jin Park, Min-Jeong Kim, William Nelson, Tiago S Balbuena, Mark Willer, John A Crow, Greg D May, Carol A Soderlund, Jay J Thelen and David R Gang

    Citation: BMC Plant Biology 2014 14:46

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  44. Content type: Research article

    The rubber tree, Hevea brasiliensis, is an important plant species that is commercially grown to produce latex rubber in many countries. The rubber tree variety BPM 24 exhibits cytoplasmic male sterility, inherit...

    Authors: Jeremy R Shearman, Duangjai Sangsrakru, Panthita Ruang-areerate, Chutima Sonthirod, Pichahpuk Uthaipaisanwong, Thippawan Yoocha, Supannee Poopear, Kanikar Theerawattanasuk, Somvong Tragoonrung and Sithichoke Tangphatsornruang

    Citation: BMC Plant Biology 2014 14:45

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  45. Content type: Research article

    Safflower (Carthamus tinctorius L.) is an oilseed crop in the Compositae (a.k.a. Asteraceae) that is valued for its oils rich in unsaturated fatty acids. Here, we present an analysis of the genetic architecture o...

    Authors: Stephanie A Pearl, John E Bowers, Sebastian Reyes-Chin-Wo, Richard W Michelmore and John M Burke

    Citation: BMC Plant Biology 2014 14:43

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  46. Content type: Research article

    Reconstruction of the parental origins of cultivated plants from wild relatives, especially after long periods of domestication, is not a trivial task. However, recent advances in molecular phylogenetics, amon...

    Authors: Željana Fredotović, Ivica Šamanić, Hanna Weiss-Schneeweiss, Juraj Kamenjarin, Tae-Soo Jang and Jasna Puizina

    Citation: BMC Plant Biology 2014 14:24

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  47. Content type: Research article

    Wheat seed germination directly affects wheat yield and quality. Although transcriptome and proteome analyses during seed germination have been reported in some crop plant species, dynamic transcriptome charac...

    Authors: Yonglong Yu, Guangfang Guo, Dongwen Lv, Yingkao Hu, Jiarui Li, Xiaohui Li and Yueming Yan

    Citation: BMC Plant Biology 2014 14:20

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  48. Content type: Research article

    Besides gene duplication and de novo gene generation, horizontal gene transfer (HGT) is another important way of acquiring new genes. HGT may endow the recipients with novel phenotypic traits that are important f...

    Authors: Dale Zhang, Jinfeng Qi, Jipei Yue, Jinling Huang, Ting Sun, Suoping Li, Jian-Fan Wen, Christian Hettenhausen, Jinsong Wu, Lei Wang, Huifu Zhuang, Jianqiang Wu and Guiling Sun

    Citation: BMC Plant Biology 2014 14:19

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  49. Content type: Research article

    In Arabidopsis thaliana (A. thaliana) the WD40 protein TRANSPARENT TESTA GLABRA1 (TTG1) controls five traits relevant for the adaptation of plants to environmental changes including the production of proanthocyan...

    Authors: Divykriti Chopra, Heike Wolff, Johannes Span, Swen Schellmann, George Coupland, Maria C Albani, Andrea Schrader and Martin Hülskamp

    Citation: BMC Plant Biology 2014 14:16

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