Skip to main content

Plant genomics

This section covers all aspects of the genome structure and function of plants, including crop species.

Page 1 of 38

  1. Dendrobium officinale, an endangered Chinese herb, possesses extensive therapeutic effects and contains bioactive ingredients such as major polysaccharides, alkaloids, and minimal flavonoids. We first obtained th...

    Authors: Zhaojian Wang, Weimin Jiang, Yingying Liu, Xiaoxi Meng, Xinglong Su, Mengyang Cao, Liping Wu, Nianjun Yu, Shihai Xing and Daiyin Peng

    Citation: BMC Genomics 2021 22:579

    Content type: Research article

    Published on:

  2. Blueberry (Vaccinium corymbosum L.) is an important species with a high content of flavonoids in fruits. As a perennial shrub, blueberry is characterized by shallow-rooted property and susceptible to drought stre...

    Authors: Aibin Wang, Kehao Liang, Shiwen Yang, Yibo Cao, Lei Wang, Ming Zhang, Jing Zhou and Lingyun Zhang

    Citation: BMC Genomics 2021 22:565

    Content type: Research article

    Published on:

  3. Breeding for new maize varieties with propitious root systems has tremendous potential in improving water and nutrients use efficiency and plant adaptation under suboptimal conditions. To date, most of the pre...

    Authors: Abdourazak Alio Moussa, Ajmal Mandozai, Yukun Jin, Jing Qu, Qi Zhang, He Zhao, Gulaqa Anwari, Mohamed Abdelsamiaa Sayed Khalifa, Abraham Lamboro, Muhammad Noman, Yacoubou Bakasso, Mo Zhang, Shuyan Guan and Piwu Wang

    Citation: BMC Genomics 2021 22:558

    Content type: Research article

    Published on:

  5. Theobroma cacao is a major source of flavonoids such as catechins and their monomers proanthocyanidins (PAs), widely studied for their potential benefits in cardiovascular diseases. Light has been shown to promot...

    Authors: Adriana M. Gallego, Luisa F. Rojas, Wilmar G. Valencia, Lucía Atehortúa, Aura I. Urrea, Andrew S. Fister, Mark J. Guiltinan, Siela N. Maximova and Natalia Pabón-Mora

    Citation: BMC Genomics 2021 22:551

    Content type: Research article

    Published on:

  6. Whole genome duplication (WGD) events are common in the evolutionary history of many living organisms. For decades, researchers have been trying to understand the genetic and epigenetic impact of WGD and its u...

    Authors: Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro K. Shimizu, Rie Shimizu-Inatsugi and Mark D. Robinson

    Citation: BMC Genomics 2021 22:547

    Content type: Software

    Published on:

  7. Most plants rely on photosynthesis; therefore, albinism in plants with leaves that are white instead of green causes slow growth, dwarfing, and even death. Although albinism has been characterized in annual mo...

    Authors: Xiangxu Meng, Jiahong Xu, Maoning Zhang, Ruyue Du, Wenxiu Zhao, Qing Zeng, Zhihua Tu, Jinhui Chen and Beibei Chen

    Citation: BMC Genomics 2021 22:543

    Content type: Research article

    Published on:

  9. The Orchidaceae family is one of the most diverse among flowering plants and serves as an important research model for plant evolution, especially “evo-devo” study on floral organs. Recently, sequencing of sev...

    Authors: Weixiong Zhang, Guoqiang Zhang, Peng Zeng, Yongqiang Zhang, Hao Hu, Zhongjian Liu and Jing Cai

    Citation: BMC Genomics 2021 22:536

    Content type: Research article

    Published on:

  10. In soybean, some circadian clock genes have been identified as loci for maturity traits. However, the effects of these genes on soybean circadian rhythmicity and their impacts on maturity are unclear.

    Authors: Yanlei Yue, Ze Jiang, Enoch Sapey, Tingting Wu, Shi Sun, Mengxue Cao, Tianfu Han, Tao Li, Hai Nian and Bingjun Jiang

    Citation: BMC Genomics 2021 22:529

    Content type: Research article

    Published on:

  11. Chrysanthemum (Chrysanthemum morifolium) black spot disease caused by Alternaria alternata is one of the plant’s most destructive diseases. Dual RNA-seq was performed to simultaneously assess their transcriptomes...

    Authors: Lina Liu, Fadi Chen, Sumei Chen, Weimin Fang, Ye Liu and Zhiyong Guan

    Citation: BMC Genomics 2021 22:523

    Content type: Research article

    Published on:

  12. Amino acid transporters (AATs) plays an essential roles in growth and development of plants, including amino acids long-range transport, seed germination, quality formation, responsiveness to pathogenic bacter...

    Authors: Yang Yang, Yongmao Chai, Jiayi Liu, Jie Zheng, Zhangchen Zhao, Aduragbemi Amo, Chunge Cui, Qiumei Lu, Liang Chen and Yin-Gang Hu

    Citation: BMC Genomics 2021 22:519

    Content type: Research article

    Published on:

  13. Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil prope...

    Authors: Alina I. Chernova, Rim F. Gubaev, Anupam Singh, Katrina Sherbina, Svetlana V. Goryunova, Elena U. Martynova, Denis V. Goryunov, Stepan V. Boldyrev, Anna A. Vanyushkina, Nikolay A. Anikanov, Elena A. Stekolshchikova, Ekaterina A. Yushina, Yakov N. Demurin, Zhanna M. Mukhina, Vera A. Gavrilova, Irina N. Anisimova…

    Citation: BMC Genomics 2021 22:505

    Content type: Research article

    Published on:

  14. Gmelina arborea Roxb is a fast-growing tree species of commercial importance for tropical countries due to multiple industrial uses of its wood. Wood is primarily composed of thick secondary cell walls of xylem c...

    Authors: Mary Luz Yaya Lancheros, Krishan Mohan Rai, Vimal Kumar Balasubramanian, Lavanya Dampanaboina, Venugopal Mendu and Wilson Terán

    Citation: BMC Genomics 2021 22:494

    Content type: Research article

    Published on:

  15. Genomic information for Allium cepa L. is limited as it is heterozygous and its genome is very large. To elucidate potential SNP markers obtained by NGS, we used a complete set of A. fistulosum L.-A. cepa monosom...

    Authors: Satoshi Fujito, Turgut Yigit Akyol, Takuya Mukae, Tadayuki Wako, Ken-ichiro Yamashita, Hikaru Tsukazaki, Hideki Hirakawa, Keisuke Tanaka, Yoko Mine, Shusei Sato and Masayoshi Shigyo

    Citation: BMC Genomics 2021 22:481

    Content type: Research article

    Published on:

  16. Downy mildew, the most devastating disease of spinach (Spinacia oleracea L.), is caused by the oomycete Peronospora effusa [=P. farinosa f. sp. spinaciae]. The P. effusa shows race specificities to the resistant ...

    Authors: Gehendra Bhattarai, Wei Yang, Ainong Shi, Chunda Feng, Braham Dhillon, James C. Correll and Beiquan Mou

    Citation: BMC Genomics 2021 22:478

    Content type: Research article

    Published on:

  17. Wheat is one of the most widely planted crops worldwide. The heading date is important for wheat environmental adaptability, as it not only controls flowering time but also determines the yield component in te...

    Authors: Yuxin Yang, Xueying Zhang, Lifen Wu, Lichao Zhang, Guoxiang Liu, Chuan Xia, Xu Liu and Xiuying Kong

    Citation: BMC Genomics 2021 22:468

    Content type: Research article

    Published on:

  18. Amber-like compounds form in tobacco (Nicotiana tabacum) during leaf curing and impact aromatic quality. In particular, cis-abienol, a polycyclic labdane-related diterpenoid, is of research interest as a precurso...

    Authors: Lingxiao He, Huabing Liu, Changhe Cheng, Min Xu, Lei He, Lihua Li, Jian Yao, Wenjun Zhang, Zhengguang Zhai, Qinzhan Luo, Jutao Sun, Tiezhao Yang and Shixiao Xu

    Citation: BMC Genomics 2021 22:467

    Content type: Research article

    Published on:

  19. Brassinosteroid (BR) signaling regulates plant growth and development in concert with other signaling pathways. Although many genes have been identified that play a role in BR signaling, the biological and fun...

    Authors: Razgar Seyed Rahmani, Tao Shi, Dongzhi Zhang, Xiaoping Gou, Jing Yi, Giles Miclotte, Kathleen Marchal and Jia Li

    Citation: BMC Genomics 2021 22:465

    Content type: Research article

    Published on:

  20. The amino acid/auxin permease (AAAP) family represents a class of proteins that transport amino acids across cell membranes. Members of this family are widely distributed in different organisms and participate...

    Authors: Xiaoxue Pan, Mingyu Hu, Zhongwei Wang, Ling Guan, Xiaoying Jiang, Wenqin Bai, Hong Wu and Kairong Lei

    Citation: BMC Genomics 2021 22:463

    Content type: Research article

    Published on:

  21. Seeds are the economic basis of oilseed crops, especially soybeans, the most widely cultivated oilseed crop worldwide. Seed development is accompanied by a multitude of diverse cellular processes, and revealin...

    Authors: Hengyou Zhang, Zhenbin Hu, Yuming Yang, Xiaoqian Liu, Haiyan Lv, Bao-Hua Song, Yong-qiang Charles An, Zhimin Li and Dan Zhang

    Citation: BMC Genomics 2021 22:453

    Content type: Research article

    Published on:

  22. An evolutionary model using diploid and allotetraploid cotton species identified 80 % of non-coding transcripts in allotetraploid cotton as being uniquely activated in comparison with its diploid ancestors. Th...

    Authors: Luyao Wang, Jin Han, Kening Lu, Menglin Li, Mengtao Gao, Zeyi Cao, Ting Zhao, Xue Chen, Xiaoyuan Tao, Quanjia Chen and Xueying Guan

    Citation: BMC Genomics 2021 22:443

    Content type: Research article

    Published on:

  24. Phosphorus (P) is essential for plant growth and development, and low-phosphorus (LP) stress is a major factor limiting the growth and yield of soybean. Long noncoding RNAs (lncRNAs) have recently been reporte...

    Authors: Jinyu Zhang, Huanqing Xu, Yuming Yang, Xiangqian Zhang, Zhongwen Huang and Dan Zhang

    Citation: BMC Genomics 2021 22:433

    Content type: Research article

    Published on:

  25. Domain of unknown function 668 (DUF668) may play a crucial role in the plant growth and developmental response to adverse stress. However, our knowledge of the function of the DUF668 gene family is limited.

    Authors: Jieyin Zhao, Peng Wang, Wenju Gao, Yilei Long, Yuxiang Wang, Shiwei Geng, Xuening Su, Yang Jiao, Quanjia Chen and Yanying Qu

    Citation: BMC Genomics 2021 22:395

    Content type: Research article

    Published on:

  26. Leaf color is an important ornamental trait of colored-leaf plants. The change of leaf color is closely related to the synthesis and accumulation of anthocyanins in leaves. Acer pseudosieboldianum is a colored-le...

    Authors: Yu-Fu Gao, Dong-Hui Zhao, Jia-Qi Zhang, Jia-Shuo Chen, Jia-Lin Li, Zhuo Weng and Li-Ping Rong

    Citation: BMC Genomics 2021 22:383

    Content type: Research article

    Published on:

  27. The genus Rhododendron L. has been widely cultivated for hundreds of years around the world. Members of this genus are known for great ornamental and medicinal value. Owing to advances in sequencing technology, g...

    Authors: Ningyawen Liu, Lu Zhang, Yanli Zhou, Mengling Tu, Zhenzhen Wu, Daping Gui, Yongpeng Ma, Jihua Wang and Chengjun Zhang

    Citation: BMC Genomics 2021 22:376

    Content type: Database

    Published on:

  28. Members of the WRKY protein family, one of the largest transcription factor families in plants, are involved in plant growth and development, signal transduction, senescence, and stress resistance. However, li...

    Authors: Hongmei Yuan, Wendong Guo, Lijuan Zhao, Ying Yu, Si Chen, Lei Tao, Lili Cheng, Qinghua Kang, Xixia Song, Jianzhong Wu, Yubo Yao, Wengong Huang, Ying Wu, Yan Liu, Xue Yang and Guangwen Wu

    Citation: BMC Genomics 2021 22:375

    Content type: Research article

    Published on:

  29. Improving yield prediction and selection efficiency is critical for tree breeding. This is vital for macadamia trees with the time from crossing to production of new cultivars being almost a quarter of a centu...

    Authors: Katie M. O’Connor, Ben J. Hayes, Craig M. Hardner, Mobashwer Alam, Robert J. Henry and Bruce L. Topp

    Citation: BMC Genomics 2021 22:370

    Content type: Research article

    Published on:

  30. Polygonum cuspidatum Sieb. et Zucc. is a well-known medicinal plant whose pharmacological effects derive mainly from its stilbenes, anthraquinones, and flavonoids. These compounds accumulate differentially in the...

    Authors: Xiaowei Wang, Hongyan Hu, Zhijun Wu, Haili Fan, Guowei Wang, Tuanyao Chai and Hong Wang

    Citation: BMC Genomics 2021 22:353

    Content type: Research article

    Published on:

  32. Curculigo latifolia is a perennial plant endogenous to Southeast Asia whose fruits contain the taste-modifying protein neoculin, which binds to sweet receptors and makes sour fruits taste sweet. Although similar ...

    Authors: Satoshi Okubo, Kaede Terauchi, Shinji Okada, Yoshikazu Saito, Takao Yamaura, Takumi Misaka, Ken-ichiro Nakajima, Keiko Abe and Tomiko Asakura

    Citation: BMC Genomics 2021 22:347

    Content type: Research article

    Published on:

  33. Ananas comosus var. bracteatus is a colorful plant used as a cut flower or landscape ornamental. The unique foliage color of this plant includes both green and red leaves and, as a trait of interest, deserves inv...

    Authors: Xuzixin Zhou, Yanbin Xue, Meiqin Mao, Yehua He, Mark Owusu Adjei, Wei Yang, Hao Hu, Jiawen Liu, Lijun Feng, Huiling Zhang, Jiaheng Luo, Xi Li, Lingxia Sun, Zhuo Huang and Jun Ma

    Citation: BMC Genomics 2021 22:331

    Content type: Research article

    Published on:

  34. The molecular characterization information of T-DNA integration is not only required by public risk assessors and regulators, but is also closely related to the expression of exogenous and endogenous genes. At...

    Authors: Xinghao Chen, Yan Dong, Yali Huang, Jianmin Fan, Minsheng Yang and Jun Zhang

    Citation: BMC Genomics 2021 22:329

    Content type: Research article

    Published on:

  35. HAK/KUP/KT (High-affinity K+ transporters/K+ uptake permeases/K+ transporters) is the largest potassium transporter family in plants, and plays pivotal roles in K+ uptake and transport, as well as biotic and abio...

    Authors: Kangfeng Cai, Fanrong Zeng, Junmei Wang and Guoping Zhang

    Citation: BMC Genomics 2021 22:317

    Content type: Research article

    Published on:

  36. Ginseng is an important medicinal herb in Asia and Northern America. The basic leucine zipper (bZIP) transcription factor genes play important roles in many biological processes and plant responses to abiotic and...

    Authors: Hongjie Li, Jing Chen, Qi Zhao, Yilai Han, Li Li, Chunyu Sun, Kangyu Wang, Yanfang Wang, Mingzhu Zhao, Ping Chen, Jun Lei, Yi Wang and Meiping Zhang

    Citation: BMC Genomics 2021 22:316

    Content type: Research article

    Published on:

  37. ATP-binding cassette (ABC) transporters have been found to play important roles in metabolic transport in plant cells, influencing subcellular compartmentalisation and tissue distribution of these metabolic co...

    Authors: Li Yan, Jianhong Zhang, Hongyu Chen and Hongmei Luo

    Citation: BMC Genomics 2021 22:315

    Content type: Research article

    Published on:

  39. DNA methyltransferase (DMT) genes contribute to plant stress responses and development by de novo establishment and subsequent maintenance of DNA methylation during replication. The photoperiod and/or temperat...

    Authors: Dan Li, Bian-E Feng, Yong-Jie Liu, Jie Gong, Yi-Miao Tang, Li-Ping Zhang, Bin-Shuang Pang, Ren-Wei Sun, Feng-Ting Zhang, Zhao-Bo Chen, Yong-Bo Wang, Xian-Chao Chen, Ai-Ping Wang, Chang-Ping Zhao and Shi-Qing Gao

    Citation: BMC Genomics 2021 22:310

    Content type: Research article

    Published on:

  40. Cotton fibers provide a powerful model for studying cell differentiation and elongation. Each cotton fiber is a singular and elongated cell derived from epidermal-layer cells of a cotton seed. Efforts to under...

    Authors: Atsumi Ando, Ryan C. Kirkbride, Don C. Jones, Jane Grimwood and Z. Jeffrey Chen

    Citation: BMC Genomics 2021 22:309

    Content type: Research article

    Published on:

  41. Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signa...

    Authors: Zhiwei Chen, Longhua Zhou, Panpan Jiang, Ruiju Lu, Nigel G. Halford and Chenghong Liu

    Citation: BMC Genomics 2021 22:300

    Content type: Research article

    Published on:

  42. Tribenuron methyl (TBM) is an herbicide that inhibits sulfonylurea acetolactate synthase (ALS) and is one of the most widely used broad-leaved herbicides for crop production. However, soil residues or drifting...

    Authors: Liuyan Wang, Ruili Wang, Wei Lei, Jiayi Wu, Chenyang Li, Hongsong Shi, Lijiao Meng, Fang Yuan, Qingyuan Zhou and Cui Cui

    Citation: BMC Genomics 2021 22:299

    Content type: Research article

    Published on:

  43. Chloroplasts are important semi-autonomous organelles in plants and algae. Unlike higher plants, the chloroplast genomes of green algal linage have distinct features both in organization and expression. Despit...

    Authors: Xiaoxiao Zou, Heroen Verbruggen, Tianjingwei Li, Jun Zhu, Zou Chen, Henqi He, Shixiang Bao and Jinhua Sun

    Citation: BMC Genomics 2021 22:298

    Content type: Research article

    Published on:

  44. Most Distylium species are endangered. Distylium species mostly display homoplasy in their flowers and fruits, and are classified primarily based on leaf morphology. However, leaf size, shape, and serration vary ...

    Authors: Wenpan Dong, Yanlei Liu, Chao Xu, Yongwei Gao, Qingjun Yuan, Zhili Suo, Zhixiang Zhang and Jiahui Sun

    Citation: BMC Genomics 2021 22:293

    Content type: Research article

    Published on:

  45. Chickpea, pigeonpea, and groundnut are the primary legume crops of semi-arid tropics (SAT) and their global productivity is severely affected by drought stress. The plant-specific NAC (NAM - no apical meristem...

    Authors: Sadhana Singh, Himabindu Kudapa, Vanika Garg and Rajeev K. Varshney

    Citation: BMC Genomics 2021 22:289

    Content type: Research article

    Published on:

  46. Heterosis has been exploited for decades in different crops due to resulting in dramatic increases in yield, but relatively little molecular evidence on this topic was reported in cotton.

    Authors: Yuanhao Ding, Rui Zhang, Longfu Zhu, Maojun Wang, Yizan Ma, Daojun Yuan, Nian Liu, Haiyan Hu, Ling Min and Xianlong Zhang

    Citation: BMC Genomics 2021 22:277

    Content type: Research article

    Published on:

  47. Fertilization in flowering plants depends on the early contact and acceptance of pollen grains by the receptive papilla cells of the stigma. Deciphering the specific transcriptomic response of both pollen and ...

    Authors: Chie Kodera, Jérémy Just, Martine Da Rocha, Antoine Larrieu, Lucie Riglet, Jonathan Legrand, Frédérique Rozier, Thierry Gaude and Isabelle Fobis-Loisy

    Citation: BMC Genomics 2021 22:268

    Content type: Research article

    Published on:

  48. Single nucleotide polymorphism (SNP) array technology has been increasingly used to generate large quantities of SNP data for use in genetic studies. As new arrays are developed to take advantage of new techno...

    Authors: Nicholas P. Howard, Michela Troggio, Charles-Eric Durel, Hélène Muranty, Caroline Denancé, Luca Bianco, John Tillman and Eric van de Weg

    Citation: BMC Genomics 2021 22:246

    Content type: Research article

    Published on:

  49. Vernalization is a type of low temperature stress used to promote rapid bolting and flowering in plants. Although rapid bolting and flowering promote the reproduction of Chinese cabbages (Brassica rapa L. ssp. pe...

    Authors: Yun Dai, Xiao Sun, Chenggang Wang, Fei Li, Shifan Zhang, Hui Zhang, Guoliang Li, Lingyun Yuan, Guohu Chen, Rifei Sun and Shujiang Zhang

    Citation: BMC Genomics 2021 22:236

    Content type: Research article

    Published on:

  50. Barley is one of the founder crops of Neolithic agriculture and is among the most-grown cereals today. The only trait that universally differentiates the cultivated and wild subspecies is ‘non-brittleness’ of ...

    Authors: Peter Civáň, Konstantina Drosou, David Armisen-Gimenez, Wandrille Duchemin, Jérôme Salse and Terence A. Brown

    Citation: BMC Genomics 2021 22:227

    Content type: Research article

    Published on:

Submit manuscript

Annual Journal Metrics

Follow

Peerage of Science logo

Portable peer review

The editors of BMC Genomics support initiatives that expedite the peer review process and are happy to consider manuscripts that have been reviewed in Peerage of Science. Please indicate in your cover letter if this applies to your manuscript.

Space creator

BMC Genomics

ISSN: 1471-2164

Contact us