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

    De novo transcriptome analysis and glucosinolate profiling in watercress (Nasturtium officinale R. Br.)

    Watercress (Nasturtium officinale R. Br.) is an aquatic herb species that is a rich source of secondary metabolites such as glucosinolates. Among these glucosinolates, watercress contains high amounts of gluconas...

    Jin Jeon, Sun Ju Bong, Jong Seok Park, Young-Kyu Park, Mariadhas Valan Arasu, Naif Abdullah Al-Dhabi and Sang Un Park

    BMC Genomics 2017 18:401

    Published on: 23 May 2017

  2. Research article

    A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing

    Despite the economic importance of sugarcane in sugar and bioenergy production, there is not yet a reference genome available. Most of the sugarcane transcriptomic studies have been based on Saccharum officinarum

    Nam V. Hoang, Agnelo Furtado, Patrick J. Mason, Annelie Marquardt, Lakshmi Kasirajan, Prathima P. Thirugnanasambandam, Frederik C. Botha and Robert J. Henry

    BMC Genomics 2017 18:395

    Published on: 22 May 2017

  3. Research article

    Discrimination of candidate subgenome-specific loci by linkage map construction with an S1 population of octoploid strawberry (Fragaria × ananassa)

    The strawberry, Fragaria × ananassa, is an allo-octoploid (2n = 8x = 56) and outcrossing species. Although it is the most widely consumed berry crop in the world, its complex genome structure has hindered its gen...

    Soichiro Nagano, Kenta Shirasawa, Hideki Hirakawa, Fumi Maeda, Masami Ishikawa and Sachiko N. Isobe

    BMC Genomics 2017 18:374

    Published on: 12 May 2017

  4. Research article

    Integrated mRNA and microRNA transcriptome variations in the multi-tepal mutant provide insights into the floral patterning of the orchid Cymbidium goeringii

    Cymbidium goeringii is a very famous traditional orchid plant in China, which is well known for its spectacular and diverse flower morphology. In particular, the multi-tepal mutants ha...

    Fengxi Yang, Genfa Zhu, Zhen Wang, Hailin Liu, Qingquan Xu, Dan huang and Chaoyi Zhao

    BMC Genomics 2017 18:367

    Published on: 11 May 2017

  5. Research article

    Transcriptome profiling of litchi leaves in response to low temperature reveals candidate regulatory genes and key metabolic events during floral induction

    Litchi (Litchi chinensis Sonn.) is an economically important evergreen fruit tree widely cultivated in subtropical areas. Low temperature is absolutely required for floral induction of litchi, but its molecular m...

    Hongna Zhang, Jiyuan Shen, Yongzan Wei and Houbin Chen

    BMC Genomics 2017 18:363

    Published on: 10 May 2017

  6. Research article

    Novel mutant alleles of the starch synthesis gene TaSSIVb-D result in the reduction of starch granule number per chloroplast in wheat

    Transient starch provides carbon and energy for plant growth, and its synthesis is regulated by the joint action of a series of enzymes. Starch synthesis IV (SSIV) is one of the important starch synthase isofo...

    Huijun Guo, Yunchuan Liu, Xiao Li, Zhihui Yan, Yongdun Xie, Hongchun Xiong, Linshu Zhao, Jiayu Gu, Shirong Zhao and Luxiang Liu

    BMC Genomics 2017 18:358

    Published on: 8 May 2017

  7. Research article

    High-density genetic map construction and QTLs identification for plant height in white jute (Corchorus capsularis L.) using specific locus amplified fragment (SLAF) sequencing

    Genetic mapping and quantitative trait locus (QTL) detection are powerful methodologies in plant improvement and breeding. White jute (Corchorus capsularis L.) is an important industrial raw material fiber crop b...

    Aifen Tao, Long Huang, Guifen Wu, Reza Keshavarz Afshar, Jianmin Qi, Jiantang Xu, Pingping Fang, Lihui Lin, Liwu Zhang and Peiqing Lin

    BMC Genomics 2017 18:355

    Published on: 8 May 2017

  8. Research article

    Footprints of domestication revealed by RAD-tag resequencing in loquat: SNP data reveals a non-significant domestication bottleneck and a single domestication event

    The process of crop domestication has long been a major area of research to gain insights into the history of human civilization and to understand the process of evolution. Loquat (Eriobotrya japonica Lindl.) is ...

    Yunsheng Wang, Muhammad Qasim Shahid, Shunquan Lin, Chengjie Chen and Chen Hu

    BMC Genomics 2017 18:354

    Published on: 6 May 2017

  9. Research article

    Genome-wide analysis and characterization of Aux/IAA family genes related to fruit ripening in papaya (Carica papaya L.)

    Auxin/indole-3-acetic acid (Aux/IAA) family genes encode short-lived nuclear proteins that mediate the responses of auxin-related genes and are involved in several plant developmental ...

    Kaidong Liu, Changchun Yuan, Shaoxian Feng, Shuting Zhong, Haili Li, Jundi Zhong, Chenjia Shen and Jinxiang Liu

    BMC Genomics 2017 18:351

    Published on: 5 May 2017

  10. Research article

    Factors affecting the accuracy of genomic selection for growth and wood quality traits in an advanced-breeding population of black spruce (Picea mariana)

    Genomic selection (GS) uses information from genomic signatures consisting of thousands of genetic markers to predict complex traits. As such, GS represents a promising approach to accelerate tree breeding, wh...

    Patrick R.N. Lenz, Jean Beaulieu, Shawn D. Mansfield, Sébastien Clément, Mireille Desponts and Jean Bousquet

    BMC Genomics 2017 18:335

    Published on: 28 April 2017

  11. Research article

    Small RNA sequencing reveals a role for sugarcane miRNAs and their targets in response to Sporisorium scitamineum infection

    Sugarcane smut caused by Sporisorium scitamineum leads to a significant reduction in cane yield and sucrose content. MicroRNAs (miRNAs) play an important role in regulating plant responses to biotic stress. The p...

    Yachun Su, Yuye Zhang, Ning Huang, Feng Liu, Weihua Su, Liping Xu, Waqar Ahmad, Qibin Wu, Jinlong Guo and Youxiong Que

    BMC Genomics 2017 18:325

    Published on: 24 April 2017

  12. Research article

    A reference floral transcriptome of sexual and apomictic Paspalum notatum

    Paspalum notatum Flügge is a subtropical grass native to South America, which includes sexual diploid and apomictic polyploid biotypes. In the past decade, a number of apomixis-associa...

    Juan Pablo A. Ortiz, Santiago Revale, Lorena A. Siena, Maricel Podio, Luciana Delgado, Juliana Stein, Olivier Leblanc and Silvina C. Pessino

    BMC Genomics 2017 18:318

    Published on: 21 April 2017

  13. Research article

    Global analysis of protein lysine succinylation profiles in common wheat

    Protein lysine succinylation is an important post-translational modification and plays a critical regulatory role in almost every aspects of cell metabolism in both eukaryotes and prokaryotes. Common wheat is ...

    Yumei Zhang, Guangyuan Wang, Limin Song, Ping Mu, Shu Wang, Wenxing Liang and Qi Lin

    BMC Genomics 2017 18:309

    Published on: 20 April 2017

  14. Research article

    Genetics and mapping of a new anthracnose resistance locus in Andean common bean Paloma

    The Andean cultivar Paloma is resistant to Mesoamerican and Andean races of Colletotrichum lindemuthianum, the fungal pathogen that causes the destructive anthracnose disease in common bean. Remarkably, Paloma is...

    Sandra Aparecida de Lima Castro, Maria Celeste Gonçalves-Vidigal, Thiago Alexandre Santana Gilio, Giselly Figueiredo Lacanallo, Giseli Valentini, Vanusa da Silva Ramos Martins, Qijian Song, Marta Zulema Galván, Oscar P. Hurtado-Gonzales and Marcial Antonio Pastor-Corrales

    BMC Genomics 2017 18:306

    Published on: 18 April 2017

  15. Research article

    Single-base resolution methylomes of upland cotton (Gossypium hirsutum L.) reveal epigenome modifications in response to drought stress

    DNA methylation, with a cryptic role in genome stability, gene transcription and expression, is involved in the drought response process in plants, but the complex regulatory mechanism is still largely unknown.

    Xuke Lu, Xiaoge Wang, Xiugui Chen, Na Shu, Junjuan Wang, Delong Wang, Shuai Wang, Weili Fan, Lixue Guo, Xiaoning Guo and Wuwei Ye

    BMC Genomics 2017 18:297

    Published on: 13 April 2017

  16. Research article

    QTL mapping for fruit quality in Citrus using DArTseq markers

    Citrus breeding programs have many limitations associated with the species biology and physiology, requiring the incorporation of new biotechnological tools to provide new breeding possibilities. Diversity Arr...

    Maiara Curtolo, Mariângela Cristofani-Yaly, Rodrigo Gazaffi, Marco Aurélio Takita, Antonio Figueira and Marcos Antonio Machado

    BMC Genomics 2017 18:289

    Published on: 12 April 2017

  17. Research article

    Divergent and convergent modes of interaction between wheat and Puccinia graminis f. sp. tritici isolates revealed by the comparative gene co-expression network and genome analyses

    Two opposing evolutionary constraints exert pressure on plant pathogens: one to diversify virulence factors in order to evade plant defenses, and the other to retain virulence factors critical for maintaining ...

    William B. Rutter, Andres Salcedo, Alina Akhunova, Fei He, Shichen Wang, Hanquan Liang, Robert L. Bowden and Eduard Akhunov

    BMC Genomics 2017 18:291

    Published on: 12 April 2017

  18. Research article

    Genome-wide comparative analysis of NBS-encoding genes in four Gossypium species

    Nucleotide binding site (NBS) genes encode a large family of disease resistance (R) proteins in plants. The availability of genomic data of the two diploid cotton species, Gossypium arboreum and Gossypium raimond...

    Liuxin Xiang, Jinggao Liu, Chaofeng Wu, Yushan Deng, Chaowei Cai, Xiao Zhang and Yingfan Cai

    BMC Genomics 2017 18:292

    Published on: 12 April 2017

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