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Genomics and evolution

Section edited by Z Jeffrey Chen and Jim Leebens-Mack

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

Page 2 of 6

  1. Content type: Research article

    The B-BOX (BBX) proteins have important functions in regulating plant growth and development. In plants, the BBX gene family has been identified in several plants, such as rice, Arabidopsis and tomato. However, t...

    Authors: Yunpeng Cao, Yahui Han, Dandan Meng, Dahui Li, Chunyan Jiao, Qing Jin, Yi Lin and Yongping Cai

    Citation: BMC Plant Biology 2017 17:156

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  2. Content type: Research article

    Methyl anthranilate (MA) contributes an attractive fruity note to the complex flavor and aroma of strawberry (Fragaria spp.), yet it is rare in modern cultivars. The genetic basis for its biosynthesis has not bee...

    Authors: Jeremy Pillet, Alan H. Chambers, Christopher Barbey, Zhilong Bao, Anne Plotto, Jinhe Bai, Michael Schwieterman, Timothy Johnson, Benjamin Harrison, Vance M. Whitaker, Thomas A. Colquhoun and Kevin M. Folta

    Citation: BMC Plant Biology 2017 17:147

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  3. Content type: Research article

    Abscisic acid (ABA) signaling plays a crucial role in developmental and environmental adaptation processes of plants. However, the PYL-PP2C-SnRK2 families that function as the core components of ABA signaling ...

    Authors: Wei Hu, Yan Yan, Haitao Shi, Juhua Liu, Hongxia Miao, Weiwei Tie, Zehong Ding, XuPo Ding, Chunlai Wu, Yang Liu, Jiashui Wang, Biyu Xu and Zhiqiang Jin

    Citation: BMC Plant Biology 2017 17:145

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  4. Content type: Research article

    Garden asparagus (Asparagus officinalis) is a highly valuable vegetable crop of commercial and nutritional interest. It is also commonly used to investigate the mechanisms of sex determination and differentiation...

    Authors: Shu-Fen Li, Guo-Jun Zhang, Xue-Jin Zhang, Jin-Hong Yuan, Chuan-Liang Deng and Wu-Jun Gao

    Citation: BMC Plant Biology 2017 17:143

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  5. Content type: Research article

    The mechanism of winter survival for perennials involves multiple levels of gene regulation, especially cold resistance. Agropyron mongolicum is one important perennial grass species, but there is little informat...

    Authors: Jiancai Du, Xiaoquan Li, Tingting Li, Dongyang Yu and Bing Han

    Citation: BMC Plant Biology 2017 17:138

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  6. Content type: Research article

    The advent of big data in biology offers opportunities while poses challenges to derive biological insights. For maize, a large amount of publicly available transcriptome datasets have been generated but a com...

    Authors: Shisong Ma, Zehong Ding and Pinghua Li

    Citation: BMC Plant Biology 2017 17:131

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  7. Content type: Research article

    Among CESA-like gene superfamily, the cellulose synthase-like D (CSLD) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, t...

    Authors: Yanpeng Li, Tiegang Yang, Dandan Dai, Ying Hu, Xiaoyang Guo and Hongxia Guo

    Citation: BMC Plant Biology 2017 17:119

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  8. Content type: Research article

    WUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published co...

    Authors: Zhaoen Yang, Qian Gong, Wenqiang Qin, Zuoren Yang, Yuan Cheng, Lili Lu, Xiaoyang Ge, Chaojun Zhang, Zhixia Wu and Fuguang Li

    Citation: BMC Plant Biology 2017 17:113

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  9. Content type: Research article

    Genomic prediction is a genomics assisted breeding methodology that can increase genetic gains by accelerating the breeding cycle and potentially improving the accuracy of breeding values. In this study, we us...

    Authors: Biyue Tan, Dario Grattapaglia, Gustavo Salgado Martins, Karina Zamprogno Ferreira, Björn Sundberg and Pär K. Ingvarsson

    Citation: BMC Plant Biology 2017 17:110

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  10. Content type: Research article

    Invertases (INVs) are key enzymes regulating sucrose metabolism and are here revealed to be involved in responses to environmental stress in plants. To date, individual members of the invertase gene family and...

    Authors: Liming Wang, Yuexia Zheng, Shihui Ding, Qing Zhang, Youqiang Chen and Jisen Zhang

    Citation: BMC Plant Biology 2017 17:109

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  11. Content type: Database

    Cotton (Gossypium spp.) is the most important fiber and oil crop in the world. With the emergence of huge -omics data sets, it is essential to have an integrated functional genomics database that allows worldwide...

    Authors: Tao Zhu, Chengzhen Liang, Zhigang Meng, Guoqing Sun, Zhaoghong Meng, Sandui Guo and Rui Zhang

    Citation: BMC Plant Biology 2017 17:101

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  12. Content type: Research article

    A complete and hardened endocarp is a typical trait of drupe fruits. However, the ‘Liehe’ (LE) apricot cultivar has a thin, soft, cleavable endocarp that represents 60.39% and 63.76% of the thickness and ligni...

    Authors: Xiao Zhang, Lijie Zhang, Qiuping Zhang, Jiayu Xu, Weisheng Liu and Wenxuan Dong

    Citation: BMC Plant Biology 2017 17:72

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  13. Content type: Research article

    The environment has a profound influence on the organoleptic quality of tomato (Solanum lycopersicum) fruit, the extent of which depends on a well-regulated and dynamic interplay among genes, metabolites and sens...

    Authors: Daniela D’Esposito, Francesca Ferriello, Alessandra Dal Molin, Gianfranco Diretto, Adriana Sacco, Andrea Minio, Amalia Barone, Rossella Di Monaco, Silvana Cavella, Luca Tardella, Giovanni Giuliano, Massimo Delledonne, Luigi Frusciante and Maria Raffaella Ercolano

    Citation: BMC Plant Biology 2017 17:66

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  14. Content type: Research article

    Long non-coding RNA (lncRNA) is a class of non-coding RNA with important regulatory roles in biological process of organisms. The systematic comparison of lncRNAs with protein coding mRNAs in population expres...

    Authors: Qin Xu, Zhihong Song, Caiyun Zhu, Chengcheng Tao, Lifang Kang, Wei Liu, Fei He, Juan Yan and Tao Sang

    Citation: BMC Plant Biology 2017 17:42

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  15. Content type: Research article

    Ca2+ ion is a versatile second messenger that operate in a wide ranges of cellular processes that impact nearly every aspect of life. Ca2+ regulates gene expression and biotic and abiotic stress responses in orga...

    Authors: Tapan Kumar Mohanta, Pradeep Kumar and Hanhong Bae

    Citation: BMC Plant Biology 2017 17:38

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  16. Content type: Research article

    Rubber dandelion (Taraxacum kok-saghyz, TK) is being developed as a domestic source of natural rubber to meet increasing global demand. However, the domestication of TK is complicated by its colocation with two w...

    Authors: Yingxiao Zhang, Brian J. Iaffaldano, Xiaofeng Zhuang, John Cardina and Katrina Cornish

    Citation: BMC Plant Biology 2017 17:34

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  17. Content type: Research article

    microRNA166 (miR166) is a highly conserved family of miRNAs implicated in a wide range of cellular and physiological processes in plants. miR166 family generally comprises multiple miR166 members in plants, wh...

    Authors: Xuyan Li, Xin Xie, Ji Li, Yuhai Cui, Yanming Hou, Lulu Zhai, Xiao Wang, Yanli Fu, Ranran Liu and Shaomin Bian

    Citation: BMC Plant Biology 2017 17:32

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  18. Content type: Research article

    Members of the amino acid/auxin permease (AAAP) gene family play indispensable roles in various plant metabolism and biosynthesis processes. Comprehensive analysis of AAAP genes has been conducted in Arabidops...

    Authors: Huanlong Liu, Min Wu, Dongyue Zhu, Feng Pan, Yujiao Wang, Yue Wang and Yan Xiang

    Citation: BMC Plant Biology 2017 17:29

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  19. Content type: Research article

    Polyploid hybrids represent a rich natural resource to study molecular evolution of plant genes and genomes. Here, we applied a combination of karyological and molecular methods to investigate chromosomal stru...

    Authors: Roman A. Volkov, Irina I. Panchuk, Nikolai V. Borisjuk, Marta Hosiawa-Baranska, Jolanta Maluszynska and Vera Hemleben

    Citation: BMC Plant Biology 2017 17:21

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  20. Content type: Research article

    The complex process of formation of storage roots (SRs) from adventitious roots affects sweetpotato yield. Identifying the genes that are uniquely expressed in the SR forming cultivated species, Ipomoea batatas (

    Authors: Sathish K. Ponniah, Jyothi Thimmapuram, Ketaki Bhide, Venu (Kal) Kalavacharla and Muthusamy Manoharan

    Citation: BMC Plant Biology 2017 17:9

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  21. Content type: Research article

    Polyploidy is well studied from a genetic and genomic perspective, but the morphological, anatomical, and physiological consequences of polyploidy remain relatively uncharacterized. Whether these potential cha...

    Authors: Robert L. Baker, Yulia Yarkhunova, Katherine Vidal, Brent E. Ewers and Cynthia Weinig

    Citation: BMC Plant Biology 2017 17:3

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  22. Content type: Research article

    Naturally growing populations of olive trees are found in the Mediterranean garrigue and maquis in Israel. Here, we used the Simple Sequence Repeat (SSR) genetic marker technique to investigate whether these r...

    Authors: Oz Barazani, Alexandra Keren-Keiserman, Erik Westberg, Nir Hanin, Arnon Dag, Giora Ben-Ari, Ori Fragman-Sapir, Yizhar Tugendhaft, Zohar Kerem and Joachim W. Kadereit

    Citation: BMC Plant Biology 2016 16:261

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  23. Content type: Research article

    Cytokinin activates transcriptional cascades important for development and the responses to biotic and abiotic stresses. Most of what is known regarding cytokinin-regulated gene expression comes from studies o...

    Authors: Tracy Raines, Ivory C. Blakley, Yu-Chang Tsai, Jennifer M. Worthen, José Manuel Franco-Zorrilla, Roberto Solano, G. Eric Schaller, Ann E. Loraine and Joseph J. Kieber

    Citation: BMC Plant Biology 2016 16:260

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  24. Content type: Research article

    RNA editing is a posttranscriptional modification process that alters the RNA sequence so that it deviates from the genomic DNA sequence. RNA editing mainly occurs in chloroplasts and mitochondrial genomes, an...

    Authors: Peng He, Sheng Huang, Guanghui Xiao, Yuzhou Zhang and Jianing Yu

    Citation: BMC Plant Biology 2016 16:257

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  25. Content type: Research article

    Climate change is predicted to be a serious threat to agriculture due to the need for crops to be able to tolerate increased heat stress. Desert plants have already adapted to high levels of heat stress so the...

    Authors: Abdullah Y. Obaid, Jamal S. M. Sabir, Ahmed Atef, Xuan Liu, Sherif Edris, Fotouh M. El-Domyati, Mohammed Z. Mutwakil, Nour O. Gadalla, Nahid H. Hajrah, Magdy A. Al-Kordy, Neil Hall, Ahmed Bahieldin and Robert K. Jansen

    Citation: BMC Plant Biology 2016 16:252

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  26. Content type: Research article

    Divergent phenotypes and genotypes are key signals for identifying the targets of natural selection in locally adapted populations. Here, we used a combination of common garden phenotyping for a variety of gro...

    Authors: Edward V. McAssey, Jonathan Corbi and John M. Burke

    Citation: BMC Plant Biology 2016 16:249

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  27. Content type: Research article

    Hydroxyproline-rich glycoproteins (HRGPs) constitute a plant cell wall protein superfamily that functions in diverse aspects of growth and development. This superfamily contains three members: the highly glyco...

    Authors: Allan M. Showalter, Brian D. Keppler, Xiao Liu, Jens Lichtenberg and Lonnie R. Welch

    Citation: BMC Plant Biology 2016 16:229

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  28. Content type: Research article

    Blueberry is an economically important fruit crop in Ericaceae family. The substantial quantities of flavonoids in blueberry have been implicated in a broad range of health benefits. However, the information r...

    Authors: Lingli Li, Hehua Zhang, Zhongshuai Liu, Xiaoyue Cui, Tong Zhang, Yanfang Li and Lingyun Zhang

    Citation: BMC Plant Biology 2016 16:223

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  29. Content type: Research article

    Environmental stress puts organisms at risk and requires specific stress-tailored responses to maximize survival. Long-term exposure to stress necessitates a global reprogramming of the cellular activities at ...

    Authors: Radoslaw Lukoszek, Peter Feist and Zoya Ignatova

    Citation: BMC Plant Biology 2016 16:221

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  30. Content type: Research article

    Phosphorus (P), an essential macronutrient, is often limiting in soils and affects plant growth and development. In Arabidopsis thaliana, Low Phosphate Root1 (LPR1) and its close paralog LPR2 encode multicopper o...

    Authors: Yue Cao, Hao Ai, Ajay Jain, Xueneng Wu, Liang Zhang, Wenxia Pei, Aiqun Chen, Guohua Xu and Shubin Sun

    Citation: BMC Plant Biology 2016 16:210

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  31. Content type: Research article

    Multidrug and toxic compound extrusion (MATE) transporter proteins are present in all organisms. Although the functions of some MATE gene family members have been studied in plants, few studies have investigat...

    Authors: Lihui Wang, Xiujuan Bei, Jiansheng Gao, Yaxuan Li, Yueming Yan and Yingkao Hu

    Citation: BMC Plant Biology 2016 16:207

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  32. Content type: Research article

    Avocado (Persea americana Mill.) is a commercially important fruit crop worldwide. A major limitation to production is the oomycete Phytophthora cinnamomi, which causes root rot leading to branch-dieback and tree...

    Authors: B. J. Reeksting, N. A. Olivier and N. van den Berg

    Citation: BMC Plant Biology 2016 16:205

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  33. Content type: Research article

    The new shoots of the albino tea cultivar ‘Anji Baicha’ are yellow or white at low temperatures and turn green as the environmental temperatures increase during the early spring. ‘Anji Baicha’ metabolite profi...

    Authors: Chun-Fang Li, Yan-Xia Xu, Jian-Qiang Ma, Ji-Qiang Jin, Dan-Juan Huang, Ming-Zhe Yao, Chun-Lei Ma and Liang Chen

    Citation: BMC Plant Biology 2016 16:195

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  34. Content type: Research article

    SBP-box genes belong to one of the largest families of transcription factors. Though members of this family have been characterized to be important regulators of diverse biological pro...

    Authors: Hongtao Cheng, Mengyu Hao, Wenxiang Wang, Desheng Mei, Chaobo Tong, Hui Wang, Jia Liu, Li Fu and Qiong Hu

    Citation: BMC Plant Biology 2016 16:196

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  35. Content type: Research article

    Some plants develop a breeding system that produces both chasmogamous (CH) and cleistogamous (CL) flowers. However, the underlying molecular mechanism remains elusive.

    Authors: Qiaoxia Li, Qingdi Huo, Juan Wang, Jing Zhao, Kun Sun and Chaoying He

    Citation: BMC Plant Biology 2016 16:151

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  36. Content type: Research article

    In cereal crops such as wheat, an optimal timing of developmental transitions is required to maximize grain yield. Many of these developmental changes are precisely regulated by changes in the duration, intens...

    Authors: Stephen Pearce, Nestor Kippes, Andrew Chen, Juan Manuel Debernardi and Jorge Dubcovsky

    Citation: BMC Plant Biology 2016 16:141

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  37. Content type: Research article

    Panicoideae are the second largest subfamily in Poaceae (grass family), with 212 genera and approximately 3316 species. Previous studies have begun to reveal relationships within the subfamily, but largely lac...

    Authors: Sean V. Burke, William P. Wysocki, Fernando O. Zuloaga, Joseph M. Craine, J. Chris Pires, Patrick P. Edger, Dustin Mayfield-Jones, Lynn G. Clark, Scot A. Kelchner and Melvin R. Duvall

    Citation: BMC Plant Biology 2016 16:140

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  38. Content type: Research article

    Dwarfism is one of the most valuable traits in banana breeding because semi-dwarf cultivars show good resistance to damage by wind and rain. Moreover, these cultivars present advantages of convenient cultivati...

    Authors: Jingjing Chen, Jianghui Xie, Yajie Duan, Huigang Hu, Yulin Hu and Weiming Li

    Citation: BMC Plant Biology 2016 16:123

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  39. Content type: Research article

    MicroRNAs (miRNAs), a class of small non-coding endogenous RNAs that regulate gene expression post-transcriptionally, play multiple key roles in plant growth and development and in biotic and abiotic stress re...

    Authors: Thangasamy Saminathan, Abiodun Bodunrin, Nripendra V. Singh, Ramajayam Devarajan, Padma Nimmakayala, Moersfelder Jeff, Mallikarjuna Aradhya and Umesh K. Reddy

    Citation: BMC Plant Biology 2016 16:122

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  40. Content type: Research article

    Sugar beet (Beta vulgaris) is an important crop of temperate climate zones, which provides nearly 30 % of the world’s annual sugar needs. From the total genome size of 758 Mb, only 567 Mb were incorporated in the...

    Authors: Teresa Kowar, Falk Zakrzewski, Jiří Macas, Andrea Kobližková, Prisca Viehoever, Bernd Weisshaar and Thomas Schmidt

    Citation: BMC Plant Biology 2016 16:120

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  41. Content type: Research article

    It is widely accepted that cultivated rice (Oryza sativa L.) was domesticated from common wild rice (Oryza rufipogon Griff.). Compared to other studies which concentrate on rice origin, this study is to genetical...

    Authors: Fantao Zhang, Tao Xu, Linyong Mao, Shuangyong Yan, Xiwen Chen, Zhenfeng Wu, Rui Chen, Xiangdong Luo, Jiankun Xie and Shan Gao

    Citation: BMC Plant Biology 2016 16:103

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  42. Content type: Research article

    The ability to grow in phosphorus-depleted soils is an important trait for rice cultivation in many world regions, especially in the tropics. The Phosphorus Starvation Tolerance 1 (PSTOL1) gene has been identifie...

    Authors: Cynthia C. Vigueira, Linda L. Small and Kenneth M. Olsen

    Citation: BMC Plant Biology 2016 16:101

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  43. Content type: Research article

    CRISPR/Cas9 has been recently demonstrated as an effective and popular genome editing tool for modifying genomes of humans, animals, microorganisms, and plants. Success of such genome editing is highly depende...

    Authors: Yi Wang, Xianju Liu, Chong Ren, Gan-Yuan Zhong, Long Yang, Shaohua Li and Zhenchang Liang

    Citation: BMC Plant Biology 2016 16:96

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  44. Content type: Research article

    Glyoxalase pathway consists of two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII) which detoxifies a highly cytotoxic metabolite methylglyoxal (MG) to its non-toxic form. MG may form advanced glycation...

    Authors: Ajit Ghosh and Tahmina Islam

    Citation: BMC Plant Biology 2016 16:87

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  45. Content type: Research article

    Dove tree (Davidia involucrata Baill.) is a rare and endangered species. Natural reproduction of dove tree is extremely difficult due to its low fecundity. Serious seed abortion is one of the key factors restrain...

    Authors: Meng Li, Xujie Dong, Jiqing Peng, Wen Xu, Rui Ren, Jane Liu, Fuxiang Cao and Zhiming Liu

    Citation: BMC Plant Biology 2016 16:82

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  46. Content type: Research article

    Leucine-rich repeat receptor-like kinases (LRR-RLKs) constitute the largest subfamily of receptor-like kinases in plant. A number of reports have demonstrated that plant LRR-RLKs play important roles in growth, d...

    Authors: Fulai Zhou, Yong Guo and Li-Juan Qiu

    Citation: BMC Plant Biology 2016 16:58

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  47. Content type: Research article

    MicroRNAs (miRNAs) are important regulatory elements of gene expression. Similarly to coding genes, miRNA genes follow a birth and death pattern of evolution likely reflecting functional relevance and divergen...

    Authors: Edna Gicela Ortiz Morea, Eder Marques da Silva, Geraldo Felipe Ferreira e Silva, Guilherme Targino Valente, Carlos Hernan Barrera Rojas, Michel Vincentz and Fabio Tebaldi Silveira Nogueira

    Citation: BMC Plant Biology 2016 16:40

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    The Erratum to this article has been published in BMC Plant Biology 2016 16:153

  48. Content type: Research article

    Eragrostis tef is an allotetraploid (2n = 4 × = 40) annual, C4 grass with an estimated nuclear genome size of 730 Mbp. It is widely grown in Ethiopia, where it provides basic nutrition...

    Authors: Yohannes Gedamu Gebre, Edoardo Bertolini, Mario Enrico Pè and Andrea Zuccolo

    Citation: BMC Plant Biology 2016 16:39

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  49. Content type: Research article

    Individual fiber strength is an important quality attribute that greatly influences the strength of the yarn spun from cotton fibers. Fiber strength is usually measured from bundles of fibers due to the diffic...

    Authors: Md S. Islam, David D. Fang, Gregory N. Thyssen, Chris D. Delhom, Yongliang Liu and Hee Jin Kim

    Citation: BMC Plant Biology 2016 16:36

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