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Plant genomics

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

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  1. SPL (SQUAMOSA-promoter binding protein-like) proteins form a large family of plant-specific transcription factors that play essential roles in various aspects of plant growth and development. They are potentia...

    Authors: Niu Yu, Jin-Chang Yang, Guang-Tian Yin, Rong-Sheng Li and Wen-Tao Zou

    Citation: BMC Genomics 2020 21:368

    Content type: Research article

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  2. Sweetpotato root rot is a devastating disease caused by Fusarium solani that seriously endangers the yield of sweetpotato in China. Although there is currently no effective method to control the disease, breeding...

    Authors: Zhimin Ma, Wenchuan Gao, Lanfu Liu, Minghui Liu, Ning Zhao, Meikun Han, Zhao Wang, Weijing Jiao, Zhiyuan Gao, Yaya Hu and Qingchang Liu

    Citation: BMC Genomics 2020 21:366

    Content type: Research article

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  3. Pumpkins (Cucurbita moschata; Cucurbitaceae) are valued for their fruits and seeds and are rich in nutrients. Carotenoids and sugar contents, as main feature of pumpkin pulp, are used to determine the fruit quali...

    Authors: Hafiz Muhammad Khalid Abbas, He-Xun Huang, An-Jun Wang, Ting-Quan Wu, Shu-Dan Xue, Aqeel Ahmad, Da-Sen Xie, Jun-Xing Li and Yu-Juan Zhong

    Citation: BMC Genomics 2020 21:365

    Content type: Research article

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  4. Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cl...

    Authors: Yabin Wu, Zijian Zhou, Chaopei Dong, Jiafa Chen, Junqiang Ding, Xuecai Zhang, Cong Mu, Yuna Chen, Xiaopeng Li, Huimin Li, Yanan Han, Ruixia Wang, Xiaodong Sun, Jingjing Li, Xiaodong Dai, Weibin Song…

    Citation: BMC Genomics 2020 21:357

    Content type: Research article

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  5. The fluctuation of nitrogen (N) contents profoundly affects the root growth and architecture in maize by altering the expression of thousands of genes. The differentially expressed genes (DEGs) in response to ...

    Authors: Yuancong Wang, Jinyan Xu, Min Ge, Lihua Ning, Mengmei Hu and Han Zhao

    Citation: BMC Genomics 2020 21:353

    Content type: Research article

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  6. The narrow genetic base of elite germplasm compromises long-term genetic gain and increases the vulnerability to biotic and abiotic stresses in unpredictable environmental conditions. Therefore, an efficient s...

    Authors: Antoine Allier, Simon Teyssèdre, Christina Lehermeier, Laurence Moreau and Alain Charcosset

    Citation: BMC Genomics 2020 21:349

    Content type: Research article

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  7. Heavy metal cadmium (Cd) is a common environmental pollutant in soils, which has an negative impacts on crop growth and development. At present, cadmium has become a major soil and water heavy metal pollutant,...

    Authors: Mingyang Jian, Dazhong Zhang, Xiaoying Wang, Shuwei Wei, Yue Zhao, Qin Ding, Yucui Han and Lingjian Ma

    Citation: BMC Genomics 2020 21:343

    Content type: Research article

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  8. Root systems are critical for plant growth and development. The Casparian strip in root systems is involved in stress resistance and maintaining homeostasis. Casparian strip membrane domain proteins (CASPs) ar...

    Authors: Xiaoyang Wang, Yuanming Zhang, Liyuan Wang, Zhaoe Pan, Shoupu He, Qiong Gao, Baojun Chen, Wenfang Gong and Xiongming Du

    Citation: BMC Genomics 2020 21:340

    Content type: Research article

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  9. Schizaphis graminum is one of the most important and devastating cereal aphids worldwide, and its feeding can cause chlorosis and necrosis in wheat. However, little information is available on the wheat defence r...

    Authors: Yong Zhang, Yu Fu, Qian Wang, Xiaobei Liu, Qian Li and Julian Chen

    Citation: BMC Genomics 2020 21:339

    Content type: Research article

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  10. Norway spruce trees in subalpine forests frequently face infections by the needle rust fungus Chrysomyxa rhododendri, which causes significant growth decline and increased mortality of young trees. Yet, it is unk...

    Authors: Carlos Trujillo-Moya, Andrea Ganthaler, Wolfgang Stöggl, Ilse Kranner, Silvio Schüler, Reinhard Ertl, Sarah Schlosser, Jan-Peter George and Stefan Mayr

    Citation: BMC Genomics 2020 21:336

    Content type: Research article

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  11. Recombination plays an important evolutionary role by breaking up haplotypes and shuffling genetic variation. This process impacts the ability of selection to eliminate deleterious mutations or increase the fr...

    Authors: Enrique J. Schwarzkopf, Juan C. Motamayor and Omar E. Cornejo

    Citation: BMC Genomics 2020 21:332

    Content type: Research article

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  12. Pitayas are currently attracting considerable interest as a tropical fruit with numerous health benefits. However, as a long-day plant, pitaya plants cannot flower in the winter season from November to April i...

    Authors: Rui Xiong, Chengli Liu, Min Xu, Shuang-shuang Wei, Jia-quan Huang and Hua Tang

    Citation: BMC Genomics 2020 21:329

    Content type: Research article

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  13. Physic nut (Jatropha curcas), an inedible oilseed plant, is among the most promising alternative energy sources because of its high oil content, rapid growth and extensive adaptability. Proteins encoded by MADS-b...

    Authors: Yuehui Tang, Jian Wang, Xinxin Bao, Qian Wu, Tongwen Yang, Han Li, Wenxia Wang, Yizhen Zhang, Nannan Bai, Yaxin Guan, Jiaxi Dai, Yanjie Xie, Shen Li, Rui Huo and Wei Cheng

    Citation: BMC Genomics 2020 21:325

    Content type: Research article

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  14. Genomic selection (GS) or genomic prediction is considered as a promising approach to accelerate tree breeding and increase genetic gain by shortening breeding cycle, but the efforts to develop routines for op...

    Authors: Linghua Zhou, Zhiqiang Chen, Lars Olsson, Thomas Grahn, Bo Karlsson, Harry X. Wu, Sven-Olof Lundqvist and María Rosario García-Gil

    Citation: BMC Genomics 2020 21:323

    Content type: Research article

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  15. Strong artificial and natural selection causes the formation of highly conserved haplotypes that harbor agronomically important genes. GWAS combination with haplotype analysis has evolved as an effective metho...

    Authors: Min Yao, Mei Guan, Zhenqian Zhang, Qiuping Zhang, Yixin Cui, Hao Chen, Wei Liu, Habib U. Jan, Kai P. Voss-Fels, Christian R. Werner, Xin He, Zhongsong Liu, Chunyun Guan, Rod J. Snowdon, Wei Hua and Lunwen Qian

    Citation: BMC Genomics 2020 21:320

    Content type: Research article

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  16. Climate change, including higher temperatures (HT) has a detrimental impact on wheat productivity and modeling studies predict more frequent heat waves in the future. Wheat growth can be impaired by high dayti...

    Authors: Sumit Pradhan, Md Ali Babar, Guihua Bai, Jahangir Khan, Dipendra Shahi, Muhsin Avci, Jia Guo, Jordan McBreen, Senthold Asseng, Salvador Gezan, Byung-Kee Baik, Ann Blount, Stephen Harrison, Suraj Sapkota, Paul St. Amand and Sanju Kunwar

    Citation: BMC Genomics 2020 21:315

    Content type: Research article

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  17. Puccinellia tenuiflora, a forage grass, is considered a model halophyte given its strong tolerance for multiple stress conditions and its close genetic relationship with cereals. This halophyte has enormous value...

    Authors: Rui Guo, Long Zhao, Kaijian Zhang, Dan Gao and Chunwu Yang

    Citation: BMC Genomics 2020 21:311

    Content type: Database

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  18. In citrus, genetic improvement via biotechnology is hindered by the obstacle of in vitro regeneration via somatic embryogenesis (SE). Although a few B3 transcription factors are reported to regulate embryogene...

    Authors: Zheng Liu, Xiao-Xia Ge, Xiao-Meng Wu, Qiang Xu, Ross G. Atkinson and Wen-Wu Guo

    Citation: BMC Genomics 2020 21:305

    Content type: Research article

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  19. Low temperatures decrease the capacity for biomass production and lead to growth retardation up to irreversible cellular damage in modern maize cultivars. European flint landraces are an untapped genetic resou...

    Authors: Felix P. Frey, Marion Pitz, Chris-Carolin Schön and Frank Hochholdinger

    Citation: BMC Genomics 2020 21:300

    Content type: Research article

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  20. Walnut kernels contain a large amount of unsaturated fatty acids, such as linoleic acid and linolenic acid, which are essential fatty acids for humans and have important effects on growth and health. The main ...

    Authors: Kai Liu, Shugang Zhao, Shuang Wang, Hongxia Wang and Zhihua Zhang

    Citation: BMC Genomics 2020 21:299

    Content type: Research article

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  21. Lycium barbarum and L. ruthenicum have been used as traditional medicinal plants in China and other Asian counties for centuries. However, the molecular mechanisms underlying fruit development and ripening, as we...

    Authors: Cuiping Wang, Yan Dong, Lizhen Zhu, Libin Wang, Li Yan, Mengze Wang, Qiang Zhu, Xiongxiong Nan, Yonghua Li and Jian Li

    Citation: BMC Genomics 2020 21:295

    Content type: Research article

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  22. Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Meta-QTL (MQTL) analysis discovers the most stable QTLs regardless of populations genetic background and field tr...

    Authors: Bahman Khahani, Elahe Tavakol, Vahid Shariati and Fabio Fornara

    Citation: BMC Genomics 2020 21:294

    Content type: Research article

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  23. Jatropha curcas, a tropical shrub, is a promising biofuel crop, which produces seeds with high content of oil and protein. To better understand the maturation process of J. curcas seeds and to improve its agronom...

    Authors: Fatemeh Maghuly, Tamás Deák, Klemens Vierlinger, Stephan Pabinger, Hakim Tafer and Margit Laimer

    Citation: BMC Genomics 2020 21:290

    Content type: Research article

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  24. Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares sign...

    Authors: Patrick J. Monnahan, Jean-Michel Michno, Christine O’Connor, Alex B. Brohammer, Nathan M. Springer, Suzanne E. McGaugh and Candice N. Hirsch

    Citation: BMC Genomics 2020 21:281

    Content type: Methodology article

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  25. The family of NAC proteins (NAM, ATAF1/2, and CUC2) represent a class of large plant-specific transcription factors. However, identification and functional surveys of NAC genes of tomato (Solanum lycopersicum) re...

    Authors: Jian Feng Jin, Zhan Qi Wang, Qi Yu He, Jia Yi Wang, Peng Fei Li, Ji Ming Xu, Shao Jian Zheng, Wei Fan and Jian Li Yang

    Citation: BMC Genomics 2020 21:288

    Content type: Research article

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  26. Ascorbic acid (Vitamin C, AsA) is an antioxidant metabolite involved in plant development and environmental stimuli. AsA biosynthesis has been well studied in plants, and MIOX is a critical enzyme in plants As...

    Authors: Shoaib Munir, Muhammad Ali Mumtaz, John Kojo Ahiakpa, Genzhong Liu, Weifang Chen, Guolin Zhou, Wei Zheng, Zhibiao Ye and Yuyang Zhang

    Citation: BMC Genomics 2020 21:284

    Content type: Research article

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  27. Phytophthora root rot (PRR) caused by Phytophthora sojae (P. sojae) is one of the most serious limitations to soybean production worldwide. The identification of resistance gene(s) and their incorporation into el...

    Authors: Bingzhi Jiang, Yanbo Cheng, Zhandong Cai, Mu Li, Ze Jiang, Ruirui Ma, Yeshan Yuan, Qiuju Xia and Hai Nian

    Citation: BMC Genomics 2020 21:280

    Content type: Research article

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  28. The non-climacteric ‘Yellow’ melon (Cucumis melo, inodorus group) is an economically important crop and its quality is mainly determined by the sugar content. Thus, knowledge of sugar metabolism and its related p...

    Authors: Michelle Orane Schemberger, Marília Aparecida Stroka, Letícia Reis, Kamila Karoline de Souza Los, Gillize Aparecida Telles de Araujo, Michelle Zibetti Tadra Sfeir, Carolina Weigert Galvão, Rafael Mazer Etto, Amanda Regina Godoy Baptistão and Ricardo Antonio Ayub

    Citation: BMC Genomics 2020 21:262

    Content type: Research article

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  29. The Mi-1 gene was the first identified and cloned gene that provides resistance to root-knot nematodes (RKNs) in cultivated tomato. However, owing to its temperature sensitivity, this gene does not meet the need ...

    Authors: Chong Du, Jingbin Jiang, He Zhang, Tingting Zhao, Huanhuan Yang, Dongye Zhang, Zhentong Zhao, Xiangyang Xu and Jingfu Li

    Citation: BMC Genomics 2020 21:250

    Content type: Research article

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  30. Sheath blight (SB), caused by Rhizoctonia solani, is a common rice disease worldwide. Currently, rice cultivars with robust resistance to R. solani are still lacking. To provide theoretic basis for molecular bree...

    Authors: Wei Shi, Shao-Lu Zhao, Kai Liu, Yi-Biao Sun, Zheng-Bin Ni, Gui-Yun Zhang, Hong-Sheng Tang, Jing-Wen Zhu, Bai-Jie Wan, Hong-Qin Sun, Jin-Ying Dai, Ming-Fa Sun, Guo-Hong Yan, Ai-Min Wang and Guo-Yong Zhu

    Citation: BMC Genomics 2020 21:245

    Content type: Research article

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  31. Glyphosate has become the most widely used herbicide in the world. Therefore, the development of new varieties of glyphosate-tolerant crops is a research focus of seed companies and researchers. The glyphosate...

    Authors: Rongrong Zhai, Shenghai Ye, Guofu Zhu, Yanting Lu, Jing Ye, Faming Yu, Qiren Chu and Xiaoming Zhang

    Citation: BMC Genomics 2020 21:238

    Content type: Research article

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  32. Plant genomes are rich in repetitive sequences, and transposable elements (TEs) are the most accumulated of them. This mobile fraction can be distinguished as Class I (retrotransposons) and Class II (transposo...

    Authors: Rafael de Assis, Viviane Yumi Baba, Leonardo Adabo Cintra, Leandro Simões Azeredo Gonçalves, Rosana Rodrigues and André Luís Laforga Vanzela

    Citation: BMC Genomics 2020 21:237

    Content type: Research article

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  33. Iron (Fe) deficiency is a common problem in citrus production. As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins have been shown to participate in the...

    Authors: Xiao-Yong Zhang, Jie-Ya Qiu, Qiu-Ling Hui, Yuan-Yuan Xu, Yi-Zhong He, Liang-Zhi Peng and Xing-Zheng Fu

    Citation: BMC Genomics 2020 21:233

    Content type: Research article

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  34. Plant miRNAs play crucial roles in responses to drought and developmental processes. It is essential to understand the association of miRNAs with drought-tolerance (DT), as well as their impacts on growth, dev...

    Authors: Hui Xia, Shunwu Yu, Deyan Kong, Jie Xiong, Xiaosong Ma, Liang Chen and Lijun Luo

    Citation: BMC Genomics 2020 21:232

    Content type: Research article

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  35. Plants have developed various sophisticated mechanisms to cope up with climate extremes and different stress conditions, especially by involving specific transcription factors (TFs). The members of the WRKY TF...

    Authors: Jeky Chanwala, Suresh Satpati, Anshuman Dixit, Ajay Parida, Mrunmay Kumar Giri and Nrisingha Dey

    Citation: BMC Genomics 2020 21:231

    Content type: Research article

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  36. The U-box gene encodes a ubiquitin ligase that contain U-box domain. The plant U-box gene (PUB) plays an important role in the response to stresses, but few reports about PUBs in cotton were available. Therefo...

    Authors: Xuke Lu, Na Shu, Delong Wang, Junjuan Wang, Xiugui Chen, Binglei Zhang, Shuai Wang, Lixue Guo, Chao Chen and Wuwei Ye

    Citation: BMC Genomics 2020 21:213

    Content type: Research article

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  37. Salt significantly depresses the growth and development of the greater duckweed, Spirodela polyrhiza, a model species of floating aquatic plants. Physiological responses of this plant to salt stress have been cha...

    Authors: Lili Fu, Zehong Ding, Deguan Tan, Bingying Han, Xuepiao Sun and Jiaming Zhang

    Citation: BMC Genomics 2020 21:212

    Content type: Research article

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  38. Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular...

    Authors: Fengdan Guo, Junjie Ma, Lei Hou, Suhua Shi, Jinbo Sun, Guanghui Li, Chuanzhi Zhao, Han Xia, Shuzhen Zhao, Xingjun Wang and Yanxiu Zhao

    Citation: BMC Genomics 2020 21:211

    Content type: Research article

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  39. Rye (Secale cereale L., 2n = 2x = 14, RR), a relative of common wheat, is a large gene resource pool for wheat improvement. Accurate and convenient identification of the rye chromatin in wheat background will fac...

    Authors: Guohao Han, Shiyu Liu, Yuli Jin, Mengshu Jia, Pengtao Ma, Hong Liu, Jing Wang and Diaoguo An

    Citation: BMC Genomics 2020 21:206

    Content type: Research article

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  40. Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS...

    Authors: Anthony Bernard, Annarita Marrano, Armel Donkpegan, Patrick J. Brown, Charles A. Leslie, David B. Neale, Fabrice Lheureux and Elisabeth Dirlewanger

    Citation: BMC Genomics 2020 21:203

    Content type: Research article

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  41. Breeding for new macadamia cultivars with high nut yield is expensive in terms of time, labour and cost. Most trees set nuts after four to five years, and candidate varieties for breeding are evaluated for at ...

    Authors: Katie O’Connor, Ben Hayes, Craig Hardner, Catherine Nock, Abdul Baten, Mobashwer Alam, Robert Henry and Bruce Topp

    Citation: BMC Genomics 2020 21:199

    Content type: Research article

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  42. Purple-fleshed sweetpotato (PFSP) is one of the most important crops in the word which helps to bridge the food gap and contribute to solve the malnutrition problem especially in developing countries. Salt str...

    Authors: Mohamed Hamed Arisha, Hesham Aboelnasr, Muhammad Qadir Ahmad, Yaju Liu, Wei Tang, Runfei Gao, Hui Yan, Meng Kou, Xin Wang, Yungang Zhang and Qiang Li

    Citation: BMC Genomics 2020 21:197

    Content type: Research article

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  43. Genome assemblies are foundational for understanding the biology of a species. They provide a physical framework for mapping additional sequences, thereby enabling characterization of, for example, genomic div...

    Authors: Nancy Manchanda, John L. Portwood II, Margaret R. Woodhouse, Arun S. Seetharam, Carolyn J. Lawrence-Dill, Carson M. Andorf and Matthew B. Hufford

    Citation: BMC Genomics 2020 21:193

    Content type: Software

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  44. Cyclic nucleotide gated channels (CNGCs) play multifaceted roles in plant physiological processes, especially with respect to signalling processes, plant development, and responses to environmental stresses. H...

    Authors: Lixin Wang, Min Li, Zhiguo Liu, Li Dai, Mengling Zhang, Lili Wang, Jin Zhao and Mengjun Liu

    Citation: BMC Genomics 2020 21:191

    Content type: Research article

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  45. MicroRNAs (miRNAs), a class of small regulatory RNAs, have been proven to play important roles in plant growth, development and stress responses. Sweet potato (Ipomoea batatas L.) is an important food and industr...

    Authors: Zhengmei Yang, Panpan Zhu, Hunseung Kang, Lin Liu, Qinghe Cao, Jian Sun, Tingting Dong, Mingku Zhu, Zongyun Li and Tao Xu

    Citation: BMC Genomics 2020 21:164

    Content type: Research article

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  46. Climate plays an essential role in forest health, and climate change may increase forest productivity losses due to abiotic and biotic stress. Increased temperature leads to the increased formation of ozone (O3)....

    Authors: Nourolah Soltani, Teo Best, Dantria Grace, Christen Nelms, Ketia Shumaker, Jeanne Romero-Severson, Daniela Moses, Stephan Schuster, Margaret Staton, John Carlson and Kimberly Gwinn

    Citation: BMC Genomics 2020 21:160

    Content type: Research article

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  47. Haplotypes combine the effects of several single nucleotide polymorphisms (SNPs) with high linkage disequilibrium, which benefit the genome-wide association analysis (GWAS). In the haplotype association analys...

    Authors: Heli Chen, Zhiyu Hao, Yunfeng Zhao and Runqing Yang

    Citation: BMC Genomics 2020 21:151

    Content type: Research article

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  48. Lotus (Nelumbo nucifera) is an aquatic plant with important agronomic, horticulture, art and religion values. It was the basal eudicot species occupying a critical phylogenetic position in flowering plants. After...

    Authors: Ye Li, Feng-Lin Zhu, Xing-Wen Zheng, Man-Li Hu, Chen Dong, Ying Diao, You-Wei Wang, Ke-Qiang Xie and Zhong-Li Hu

    Citation: BMC Genomics 2020 21:146

    Content type: Research article

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