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.

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  1. Research article

    Genome-wide analysis of UDP-glycosyltransferase super family in Brassica rapa and Brassica oleracea reveals its evolutionary history and functional characterization

    Glycosyltransferases comprise a highly divergent and polyphyletic multigene family that is involved in widespread modification of plant secondary metabolites in a process called glycosylation. According to con...

    Jingyin Yu, Fan Hu, Komivi Dossa, Zhaokai Wang and Tao Ke

    BMC Genomics 2017 18:474

    Published on: 23 June 2017

  2. Research article

    Transcriptomic dynamics in soybean near-isogenic lines differing in alleles for an aphid resistance gene, following infestation by soybean aphid biotype 2

    Genetic resistance of soybean [Glycine max (L.) Merr] against Aphis glycines provides effective management of this invasive pest, though the underlying molecular mechanisms are largely unknown. This study aimed t...

    Sungwoo Lee, Bryan J. Cassone, Asela Wijeratne, Tae-Hwan Jun, Andrew P. Michel and M.A. Rouf Mian

    BMC Genomics 2017 18:472

    Published on: 23 June 2017

  3. Research article

    Differential gene expression at different stages of mesocarp development in high- and low-yielding oil palm

    The oil yield trait of oil palm is expected to involve multiple genes, environmental influences and interactions. Many of the underlying mechanisms that contribute to oil yield are still poorly understood. In ...

    Yick Ching Wong, Huey Fang Teh, Katharina Mebus, Tony Eng Keong Ooi, Qi Bin Kwong, Ka Loo Koo, Chuang Kee Ong, Sean Mayes, Fook Tim Chew, David R. Appleton and Harikrishna Kulaveerasingam

    BMC Genomics 2017 18:470

    Published on: 21 June 2017

  4. Research article

    Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing

    One of the overarching goals of soybean breeding is to develop lines that combine increased yield with improved quality characteristics. High-density-marker QTL mapping can serve as an effective strategy to id...

    Nianxi Liu, Mu Li, Xiangbao Hu, Qibin Ma, Yinghui Mu, Zhiyuan Tan, Qiuju Xia, Gengyun Zhang and Hai Nian

    BMC Genomics 2017 18:466

    Published on: 19 June 2017

  5. Research article

    A reference genome for Nicotiana tabacum enables map-based cloning of homeologous loci implicated in nitrogen utilization efficiency

    Tobacco (Nicotiana tabacum) is an important plant model system that has played a key role in the early development of molecular plant biology. The tobacco genome is large and its characterisation challenging beca...

    K. D. Edwards, N. Fernandez-Pozo, K. Drake-Stowe, M. Humphry, A. D. Evans, A. Bombarely, F. Allen, R. Hurst, B. White, S. P. Kernodle, J. R. Bromley, J. P. Sanchez-Tamburrino, R. S. Lewis and L. A. Mueller

    BMC Genomics 2017 18:448

    Published on: 19 June 2017

  6. Research article

    The biocontrol agent Pseudomonas chlororaphis PA23 primes Brassica napus defenses through distinct gene networks

    The biological control agent Pseudomonas chlororaphis PA23 is capable of protecting Brassica napus (canola) from the necrotrophic fungus Sclerotinia sclerotiorum via direct antagonism. While we have elucidated ba...

    Kelly A. Duke, Michael G. Becker, Ian J. Girard, Jenna L. Millar, W. G. Dilantha Fernando, Mark F. Belmonte and Teresa R. de Kievit

    BMC Genomics 2017 18:467

    Published on: 19 June 2017

  7. Research article

    Genome and Transcriptome sequence of Finger millet (Eleusine coracana (L.) Gaertn.) provides insights into drought tolerance and nutraceutical properties

    Finger millet (Eleusine coracana (L.) Gaertn.) is an important staple food crop widely grown in Africa and South Asia. Among the millets, finger millet has high amount of calcium, methionine, tryptophan, fiber, a...

    Shailaja Hittalmani, H. B. Mahesh, Meghana Deepak Shirke, Hanamareddy Biradar, Govindareddy Uday, Y. R. Aruna, H. C. Lohithaswa and A. Mohanrao

    BMC Genomics 2017 18:465

    Published on: 15 June 2017

  8. Research article

    Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7

    Soybean (Glycine max L. Merr.) cyst nematode (SCN, Heterodera glycines I,) is a major pest of soybean worldwide. The most effective strategy to control this pest involves the use of resistant cultivars. The aim o...

    Xue Zhao, Weili Teng, Yinghui Li, Dongyuan Liu, Guanglu Cao, Dongmei Li, Lijuan Qiu, Hongkun Zheng, Yingpeng Han and Wenbin Li

    BMC Genomics 2017 18:462

    Published on: 14 June 2017

  9. Research article

    Integrated metabolome and transcriptome analysis of Magnolia champaca identifies biosynthetic pathways for floral volatile organic compounds

    Magnolia champaca, commonly known as champak is a well-known tree due to its highly fragrant flowers. Champak floral scent is attributed to a complex mix of volatile organic compounds ...

    Savitha Dhandapani, Jingjing Jin, Vishweshwaran Sridhar, Rajani Sarojam, Nam-Hai Chua and In-Cheol Jang

    BMC Genomics 2017 18:463

    Published on: 14 June 2017

  10. Research article

    Genome-wide comparative transcriptome analysis of CMS-D2 and its maintainer and restorer lines in upland cotton

    Cytoplasmic male sterility (CMS) conferred by the cytoplasm from Gossypium harknessii (D2) is an important system for hybrid seed production in Upland cotton (G. hirsutum). The male sterility of CMS-D2 (i.e., A l...

    Jianyong Wu, Meng Zhang, Bingbing Zhang, Xuexian Zhang, Liping Guo, Tingxiang Qi, Hailin Wang, Jinfa Zhang and Chaozhu Xing

    BMC Genomics 2017 18:454

    Published on: 8 June 2017

  11. Research article

    Integrated QTL detection for key breeding traits in multiple peach progenies

    Peach (Prunus persica (L.) Batsch) is a major temperate fruit crop with an intense breeding activity. Breeding is facilitated by knowledge of the inheritance of the key traits that are often of a quantitative nat...

    José R. Hernández Mora, Diego Micheletti, Marco Bink, Eric Van de Weg, Celia Cantín, Nelson Nazzicari, Andrea Caprera, Maria Teresa Dettori, Sabrina Micali, Elisa Banchi, José Antonio Campoy, Elisabeth Dirlewanger, Patrick Lambert, Thierry Pascal, Michela Troggio, Daniele Bassi…

    BMC Genomics 2017 18:404

    Published on: 6 June 2017

  12. Research Article

    Genome-enabled predictions for fruit weight and quality from repeated records in European peach progenies

    Highly polygenic traits such as fruit weight, sugar content and acidity strongly influence the agroeconomic value of peach varieties. Genomic Selection (GS) can accelerate peach yield and quality gain if predi...

    Filippo Biscarini, Nelson Nazzicari, Marco Bink, Pere Arús, Maria José Aranzana, Ignazio Verde, Sabrina Micali, Thierry Pascal, Benedicte Quilot-Turion, Patrick Lambert, Cassia da Silva Linge, Igor Pacheco, Daniele Bassi, Alessandra Stella and Laura Rossini

    BMC Genomics 2017 18:432

    Published on: 6 June 2017

  13. Research article

    Identification of candidate genes for fiber length quantitative trait loci through RNA-Seq and linkage and physical mapping in cotton

    Cotton (Gossypium spp.) fibers are single-celled elongated trichomes, the molecular aspects of genetic variation in fiber length (FL) among genotypes are currently unknown. In this study, two backcross inbred lin...

    Xihua Li, Man Wu, Guoyuan Liu, Wenfeng Pei, Honghong Zhai, Jiwen Yu, Jinfa Zhang and Shuxun Yu

    BMC Genomics 2017 18:427

    Published on: 31 May 2017

  14. Research article

    High-quality genetic mapping with ddRADseq in the non-model tree Quercus rubra

    Restriction site associated DNA sequencing (RADseq) has the potential to be a broadly applicable, low-cost approach for high-quality genetic linkage mapping in forest trees lacking a reference genome. The stat...

    Arpita Konar, Olivia Choudhury, Rebecca Bullis, Lauren Fiedler, Jacqueline M. Kruser, Melissa T. Stephens, Oliver Gailing, Scott Schlarbaum, Mark V. Coggeshall, Margaret E. Staton, John E. Carlson, Scott Emrich and Jeanne Romero-Severson

    BMC Genomics 2017 18:417

    Published on: 30 May 2017

  15. Research article

    In-depth genome characterization of a Brazilian common bean core collection using DArTseq high-density SNP genotyping

    Common bean is a legume of social and nutritional importance as a food crop, cultivated worldwide especially in developing countries, accounting for an important source of income for small farmers. The availab...

    Paula A. M. R. Valdisser, Wendell J. Pereira, Jâneo E. Almeida Filho, Bárbara S. F. Müller, Gesimária R. C. Coelho, Ivandilson P. P. de Menezes, João P. G. Vianna, Maria I. Zucchi, Anna C. Lanna, Alexandre S. G. Coelho, Jaison P. de Oliveira, Alessandra da Cunha Moraes, Claudio Brondani and Rosana P. Vianello

    BMC Genomics 2017 18:423

    Published on: 30 May 2017

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