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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.

Page 1 of 35

  1. Different soybean (Glycine max L.) leaf chlorophyll-content traits are considered to be significantly linked to soybean yield. To map the quantitative trait loci (QTLs) of soybean leaf chlorophyll-content traits,...

    Authors: Liang Wang, Brima Conteh, Linzhi Fang, Qiuju Xia and Hai Nian

    Citation: BMC Genomics 2020 21:739

    Content type: Research article

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  2. Transcription factors (TFs) are essential regulators of growth and development in eukaryotes. Basic-helix-loop-helix (bHLHs) is one of the most significant TFs families involved in several critical regulatory ...

    Authors: Mohammad Aslam, Bello Hassan Jakada, Beenish Fakher, Joseph G. Greaves, Xiaoping Niu, Zhenxia Su, Yan Cheng, Shijiang Cao, Xiaomei Wang and Yuan Qin

    Citation: BMC Genomics 2020 21:735

    Content type: Research article

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  3. Elucidating the candidate genes and key metabolites responsible for pulp and peel coloration is essential for breeding pitaya fruit with new and improved appeal and high nutritional value. Here, we used transc...

    Authors: Zhaoxi Zhou, Hongmao Gao, Jianhong Ming, Zheli Ding, Xing’e Lin and Rulin Zhan

    Citation: BMC Genomics 2020 21:734

    Content type: Research article

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  4. The ray floret shapes referred to as petal types on the chrysanthemum (Chrysanthemum × morifolium Ramat.) capitulum is extremely abundant, which is one of the most important ornamental traits of chrysanthemum. Ho...

    Authors: Ya Pu, He Huang, Xiaohui Wen, Chenfei Lu, Bohan Zhang, Xueqi Gu, Shuai Qi, Guangxun Fan, Wenkui Wang and Silan Dai

    Citation: BMC Genomics 2020 21:728

    Content type: Research article

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  5. Phosphorus (P) is an essential element in maintaining high biomass and yield in crops. Soybean [Glycine max (L.) Merr.] requires a large amount of P during growth and development. Improvement of P efficiency and ...

    Authors: Wenkai Du, Lihua Ning, Yongshun Liu, Shixi Zhang, Yuming Yang, Qing Wang, Shengqian Chao, Hui Yang, Fang Huang, Hao Cheng and Deyue Yu

    Citation: BMC Genomics 2020 21:725

    Content type: Research article

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  6. The recent release of the reference genome sequence assembly of flax, a self-pollinated crop with 15 chromosome pairs, into chromosome-scale pseudomolecules enables the characterization of gene families. The A...

    Authors: Nadeem Khan, Frank M. You, Raju Datla, Sridhar Ravichandran, Bosen Jia and Sylvie Cloutier

    Citation: BMC Genomics 2020 21:722

    Content type: Research article

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  7. We previously reported on the interplay between miR156/SPL13 and WD40–1/DFR to improve response to drought stress in alfalfa (Medicago sativa L.). Here we aimed to investigate whether the role of miR156/SPL13 mod...

    Authors: Biruk A. Feyissa, Justin Renaud, Vida Nasrollahi, Susanne E. Kohalmi and Abdelali Hannoufa

    Citation: BMC Genomics 2020 21:721

    Content type: Research article

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  8. To elucidate features of seed development, we investigated the transcriptome of a soybean isoline from the germplasm collection that contained an introgressed allele known as minute hilum (mi) which confers a sma...

    Authors: Gracia Zabala, Anupreet Kour and Lila O. Vodkin

    Citation: BMC Genomics 2020 21:716

    Content type: Research article

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  9. As global warming continues, heat stress (HS) is becoming an increasingly significant factor limiting plant growth and reproduction, especially for cool-season grass species. The objective of this study was to...

    Authors: Qi Yan, Xifang Zong, Fan Wu, Jie Li, Tiantian Ma, Yufeng Zhao, Qian Ma, Penglei Wang, Yanrong Wang and Jiyu Zhang

    Citation: BMC Genomics 2020 21:715

    Content type: Research article

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  10. The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CL...

    Authors: Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi and Bo Zheng

    Citation: BMC Genomics 2020 21:709

    Content type: Methodology article

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  11. Lotus is an aquatic horticultural crop that is widely cultivated in most regions of China and is used as an important off-season vegetable. The principal root of lotus is degenerated, and adventitious roots (A...

    Authors: Cheng Libao, Han Yuyan, Zhao Minrong, Xu Xiaoyong, Shen Zhiguang, Wang Chunfei, Li Shuyan and Hu Zhubing

    Citation: BMC Genomics 2020 21:707

    Content type: Research article

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  12. Tall fescue (Festuca arundinacea Schreb.) is a major cool-season forage and turfgrass species. The low tiller density and size dramatically limits its turf performance and forage yield. MicroRNAs (miRNA)-genes mo...

    Authors: Tao Hu, Tao Wang, Huiying Li, Misganaw Wassie, Huawei Xu and Liang Chen

    Citation: BMC Genomics 2020 21:696

    Content type: Research article

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  14. MiRNAs play essential roles in plant development and response to biotic and abiotic stresses through interaction with their target genes. The expression level of miRNAs shows great variations among different p...

    Authors: Shu-Yun Chen, Mei-Hsiu Su, Karl A. Kremling, Nicholas K. Lepak, M. Cinta Romay, Qi Sun, Peter J. Bradbury, Edward S. Buckler and Hsin-Mei Ku

    Citation: BMC Genomics 2020 21:689

    Content type: Research article

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  15. APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) transcription factors play essential roles in plant growth, development, metabolism, and responses to biotic and abiotic stresses. However, few studies concerning AP2...

    Authors: Peiting Li, Zhe Chai, Pingping Lin, Chaohua Huang, Guoqiang Huang, Liangnian Xu, Zuhu Deng, Muqing Zhang, Yu Zhang and Xinwang Zhao

    Citation: BMC Genomics 2020 21:685

    Content type: Research article

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  16. Abscisic acid (ABA), a key phytohormone that controls plant growth and stress responses, is sensed by the pyrabactin resistance 1(PYR1)/PYR1-like (PYL)/regulatory components of the ABA receptor (RCAR) family o...

    Authors: Shashank Kumar Yadav, Vinjamuri Venkata Santosh Kumar, Rakesh Kumar Verma, Pragya Yadav, Ankit Saroha, Dhammaprakash Pandhari Wankhede, Bhupendra Chaudhary and Viswanathan Chinnusamy

    Citation: BMC Genomics 2020 21:676

    Content type: Research article

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  17. The development of biomass crops aims to meet industrial yield demands, in order to optimize profitability and sustainability. Achieving these goals in an energy crop like sugarcane relies on breeding for sucr...

    Authors: Fernando Henrique Correr, Guilherme Kenichi Hosaka, Fernanda Zatti Barreto, Isabella Barros Valadão, Thiago Willian Almeida Balsalobre, Agnelo Furtado, Robert James Henry, Monalisa Sampaio Carneiro and Gabriel Rodrigues Alves Margarido

    Citation: BMC Genomics 2020 21:673

    Content type: Research article

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  18. The banana (Musa sp., AAA) genome is constantly increasing due to high-frequency of somaclonal variations. Due to its large diversity, a conventional numerical and morphological based taxonomic identification of ...

    Authors: S. Dhivya, S. Ashutosh, I. Gowtham, V. Baskar, A. Baala Harini, S. Mukunthakumar and R. Sathishkumar

    Citation: BMC Genomics 2020 21:659

    Content type: Research article

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  19. Plant mitochondrial genomes (mitogenomes) can be structurally complex while their size can vary from ~ 222 Kbp in Brassica napus to 11.3 Mbp in Silene conica. To date, in comparison with the number of plant speci...

    Authors: Yuliya A. Putintseva, Eugeniya I. Bondar, Evgeniy P. Simonov, Vadim V. Sharov, Natalya V. Oreshkova, Dmitry A. Kuzmin, Yuri M. Konstantinov, Vladimir N. Shmakov, Vadim I. Belkov, Michael G. Sadovsky, Olivier Keech and Konstantin V. Krutovsky

    Citation: BMC Genomics 2020 21:654

    Content type: Research article

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  20. In China, lotus is an important cultivated crop with multiple applications in ornaments, food, and environmental purification. Adventitious roots (ARs), a secondary root is necessary for the uptake of nutritio...

    Authors: Cheng libao, Zhao minrong, Hu Zhubing, Liu huiying and Li Shuyan

    Citation: BMC Genomics 2020 21:653

    Content type: Research article

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  21. The lateral organ boundaries domain (LBD) gene is a plant-specific transcription factor that plays a critical role in diverse biological processes. However, the evolution and functional divergence of the LBD gene...

    Authors: Bobo Song, Zikai Tang, Xiaolong Li, Jiaming Li, Mingyue Zhang, Kejiao Zhao, Hainan Liu, Shaoling Zhang and Jun Wu

    Citation: BMC Genomics 2020 21:644

    Content type: Research article

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  22. Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is...

    Authors: Jingjing Zhang, Aimin Wu, Hengling Wei, Pengbo Hao, Qi Zhang, Miaomiao Tian, Xu Yang, Shuaishuai Cheng, Xiaokang Fu, Liang Ma, Hantao Wang and Shuxun Yu

    Citation: BMC Genomics 2020 21:643

    Content type: Research article

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  23. Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness an...

    Authors: Weifang Liao, Zhinan Mei, Lihong Miao, Pulin Liu and Ruijie Gao

    Citation: BMC Genomics 2020 21:639

    Content type: Research article

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  24. Protein kinases (PKs) play an important role in signaling cascades and are one of the largest and most conserved protein super families in plants. Despite their importance, the woodland strawberry (Fragaria vesca

    Authors: Hui Liu, Wei Qu, Kaikai Zhu and Zong-Ming ( Max) Cheng

    Citation: BMC Genomics 2020 21:635

    Content type: Research article

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  25. The contribution of mitogen-activated protein kinase (MAPK) cascades to plant growth and development has been widely studied, but this knowledge has not yet been extended to the medicinal plant Salvia miltiorrhiz...

    Authors: Yongfeng Xie, Meiling Ding, Bin Zhang, Jie Yang, Tianlin Pei, Pengda Ma and Juane Dong

    Citation: BMC Genomics 2020 21:630

    Content type: Research article

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  26. Age-related resistance (ARR) is a developmentally regulated phenomenon conferring resistance to pathogens or pests. Although ARR has been observed in several host-pathogen systems, the underlying mechanisms ar...

    Authors: Ben N. Mansfeld, Marivi Colle, Chunqiu Zhang, Ying-Chen Lin and Rebecca Grumet

    Citation: BMC Genomics 2020 21:628

    Content type: Research article

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  27. Mitogen Activated Protein Kinase (MAPK) cascade is a fundamental pathway in organisms for signal transduction. Though it is well characterized in various plants, there is no systematic study of this cascade in...

    Authors: Archita Chatterjee, Abhirup Paul, G. Meher Unnati, Ruchika Rajput, Trisha Biswas, Tamalika Kar, Srijita Basak, Neelam Mishra, Ashutosh Pandey and Anurag Prakash Srivastava

    Citation: BMC Genomics 2020 21:613

    Content type: Research article

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  28. Anthocyanins determinate the flower color of many plants. Tobacco is a model plant for studying the molecular regulation of flower coloration. We investigated the mechanism underlying flower coloration in toba...

    Authors: Fangchan Jiao, Lu Zhao, Xingfu Wu, Zhongbang Song and Yongping Li

    Citation: BMC Genomics 2020 21:611

    Content type: Research article

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  29. Phytohormones are the key factors regulating vascular development in plants, and they are also involved in tension wood (TW) formation. Although the theory of hormone distribution in TW formation is widely sup...

    Authors: Yao Xiao, Fei Yi, Juanjuan Ling, Guijuan Yang, Na Lu, Zirui Jia, Junchen Wang, Kun Zhao, Junhui Wang and Wenjun Ma

    Citation: BMC Genomics 2020 21:609

    Content type: Research article

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  30. Seed germination and young seedling growth are important agricultural traits for developing populations of both irrigated and directly seeded rice. Previous studies have focused on the identification of QTLs. ...

    Authors: Jing Yang, Ling Su, Dandan Li, Lixin Luo, Kai Sun, Meng Yang, Fengwei Gu, Aoyun Xia, Yongzhu Liu, Hui Wang, Zhiqiang Chen and Tao Guo

    Citation: BMC Genomics 2020 21:603

    Content type: Research article

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  31. It has been reported that nitric oxide (NO) could ameliorate cadmium (Cd) toxicity in tall fescue; however, the underlying mechanisms of NO mediated Cd detoxification are largely unknown. In this study, we inv...

    Authors: Huihui Zhu, Honglian Ai, Zhengrong Hu, Dongyun Du, Jie Sun, Ke Chen and Liang Chen

    Citation: BMC Genomics 2020 21:601

    Content type: Research article

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  32. Transcription factor (TF) GAMYB, belonging to MYB family (named after the gene of the avian myeloblastosis virus) is a master gibberellin (GA)-induced regulatory protein that is crucial for development and germin...

    Authors: Anna Bienias, Magdalena Góralska, Piotr Masojć, Paweł Milczarski and Beata Myśków

    Citation: BMC Genomics 2020 21:578

    Content type: Research article

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  33. Drought is one of the most adverse environmental factors limiting crop productions and it is important to identify key genetic determinants for food safety. Calcium-dependent protein kinases (CPKs) are known t...

    Authors: Ge-Zi Li, Han-Xiao Li, Meng-Jun Xu, Peng-Fei Wang, Xiang-Hong Xiao and Guo-Zhang Kang

    Citation: BMC Genomics 2020 21:577

    Content type: Research article

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  34. ERF transcription factors (TFs) belong to the Apetala2/Ethylene responsive Factor (AP2/ERF) TF family and play a vital role in plant growth and development processes. Capsorubin and capsaicinoids have relative...

    Authors: Jiali Song, Changming Chen, Shuanglin Zhang, Juntao Wang, Zhubing Huang, Muxi Chen, Bihao Cao, Zhangsheng Zhu and Jianjun Lei

    Citation: BMC Genomics 2020 21:573

    Content type: Research article

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  35. As air temperatures increase globally, more and more plants are exposed to heat-stress conditions. Although many studies have explored regulation networks in plants with the aim of improving their heat-stress ...

    Authors: Jiahong Xu, Yao Zheng, Shouqin Pu, Xiujie Zhang, Zhihao Li and Jinhui Chen

    Citation: BMC Genomics 2020 21:572

    Content type: Research article

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  36. The investigation of transcriptome profiles using short reads in non-model organisms, which lack of well-annotated genomes, is limited by partial gene reconstruction and isoform detection. In contrast, long-re...

    Authors: Giuseppe D. Puglia, Andrey D. Prjibelski, Domenico Vitale, Elena Bushmanova, Karl J. Schmid and Salvatore A. Raccuia

    Citation: BMC Genomics 2020 21:317

    Content type: Research article

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  37. Common bacterial blight (CBB) caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans is one of the major threats to common bean crops (Phaseolus vulgaris L.). Resistance to CBB is particula...

    Authors: Justine Foucher, Mylène Ruh, Anne Préveaux, Sébastien Carrère, Sandra Pelletier, Martial Briand, Rémy-Félix Serre, Marie-Agnès Jacques and Nicolas W. G. Chen

    Citation: BMC Genomics 2020 21:566

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2020 21:657

  38. GGPP (geranylgeranyl diphosphate) is produced in the isoprenoid pathway and mediates the function of various plant metabolites, which is synthesized by GGPPS (GGPP synthases) in plants. GGPPS characterization has...

    Authors: Faiza Ali, Ghulam Qanmber, Zhenzhen Wei, Daoqian Yu, Yong hui Li, Lei Gan, Fuguang Li and Zhi Wang

    Citation: BMC Genomics 2020 21:561

    Content type: Research article

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  39. High temperatures, particularly at night, decrease rice yield and quality. As high nighttime temperatures (HNTs) become increasingly frequent due to climate change, it is imperative to develop rice crops that ...

    Authors: Chao He, Hong-Yu Zhang, Yong-Xin Zhang, Pei Fu, Li-Li You, Wen-Bo Xiao, Zhao-Hai Wang, Hai-Yan Song, Ying-Jin Huang and Jiang-Lin Liao

    Citation: BMC Genomics 2020 21:560

    Content type: Research article

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  41. Tea plant is one of the most important non-alcoholic beverage crops worldwide. While potassium (K+) is an essential macronutrient and greatly affects the growth and development of plants, the molecular mechanism ...

    Authors: Tianyuan Yang, Xin Lu, Yan Wang, Yunxia Xie, Jingzhen Ma, Xunmin Cheng, Enhua Xia, Xiaochun Wan and Zhaoliang Zhang

    Citation: BMC Genomics 2020 21:556

    Content type: Research article

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  42. The reblooming bearded iris (Iris germanica) can bloom twice a year, in spring and autumn. The extended ornamental period makes it more popular and brings additional commercial values. However, little is known ab...

    Authors: Zhuping Fan, Yike Gao, Yi Ren, Chunjing Guan, Rong Liu and Qixiang Zhang

    Citation: BMC Genomics 2020 21:553

    Content type: Research article

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  43. Saline, alkaline, and saline-alkaline stress severely affect plant growth and development. The tolerance of plants to these stressors has long been important breeding objectives, especially for woody perennial...

    Authors: Jing Liu, Fei Shen, Yao Xiao, Hongcheng Fang, Changpeng Qiu, Wei Li, Ting Wu, Xuefeng Xu, Yi Wang, Xinzhong Zhang and Zhenhai Han

    Citation: BMC Genomics 2020 21:550

    Content type: Research article

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  44. Full chloroplast genomes provide high resolution taxonomic discrimination between closely related plant species and are quickly replacing single and multi-locus barcoding regions as reference materials of choi...

    Authors: Jorge Villacrés-Vallejo, José Aranda-Ventura, Anna Wallis, Robin Cagle, Sara M. Handy, Jeffery Davis, Elizabeth Reed, Shu Zhang, Errol Strain, Monica Pava-Ripoll, David Erickson, Padmini Ramachandran and Andrea Ottesen

    Citation: BMC Genomics 2020 21:544

    Content type: Research article

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  45. Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. Quantitative ...

    Authors: Sana Beji, Véronique Fontaine, Rosemonde Devaux, Martine Thomas, Sandra Silvia Negro, Nasser Bahrman, Mathieu Siol, Grégoire Aubert, Judith Burstin, Jean-Louis Hilbert, Bruno Delbreil and Isabelle Lejeune-Hénaut

    Citation: BMC Genomics 2020 21:536

    Content type: Research article

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  46. Water spinach (Ipomoea aquatica) is an important heat-resistant leafy vegetable that can survive under long-time heat stress condition. However, the physiological characteristics and molecular changes in its resp...

    Authors: Rongfang Guo, Xingru Wang, Xiaoyun Han, Xiaodong Chen and Gefu Wang-Pruski

    Citation: BMC Genomics 2020 21:533

    Content type: Research article

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  47. Alternanthera philoxeroides (alligator weed) is a highly invasive alien plant that has continuously and successfully expanded from the tropical to the temperate regions of China via asexual reproduction. During t...

    Authors: Landi Luo, Xiangxiang Kong, Zean Gao, Yan Zheng, Yunqiang Yang, Xiong Li, Danni Yang, Yupeng Geng and Yongping Yang

    Citation: BMC Genomics 2020 21:532

    Content type: Research article

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  48. Studies of leaf shape development and plant stature have made important contributions to the fields of plant breeding and developmental biology. The optimization of leaf morphology and plant height to improve ...

    Authors: Chengwei Huang, Mao Yang, Danlei Shao, Yangming Wang, Shubei Wan, Jianbo He, Zuqing Meng and Rongzhan Guan

    Citation: BMC Genomics 2020 21:530

    Content type: Research article

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  49. Paphiopedilum is an important genus of the orchid family Orchidaceae and has high horticultural value. The wild populations are under threat of extinction because of overcollection and habitat destruction. Mature...

    Authors: Lin Fang, Xin Xu, Ji Li, Feng Zheng, Mingzhi Li, Jingwei Yan, Yuan Li, Xinhua Zhang, Lin Li, Guohua Ma, Aying Zhang, Fubing Lv, Kunlin Wu and Songjun Zeng

    Citation: BMC Genomics 2020 21:524

    Content type: Research article

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  50. Fruit quality traits have a significant effect on consumer acceptance and subsequently on peach (Prunus persica (L.) Batsch) consumption. Determining the genetic bases of key fruit quality traits is essential for...

    Authors: Zena J. Rawandoozi, Timothy P. Hartmann, Silvia Carpenedo, Ksenija Gasic, Cassia da Silva Linge, Lichun Cai, Eric Van de Weg and David H. Byrne

    Citation: BMC Genomics 2020 21:522

    Content type: Research article

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