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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 28

  1. Content type: Research article

    Genomic selection accuracy increases with the use of high SNP (single nucleotide polymorphism) coverage. However, such gains in coverage come at high costs, preventing their prompt operational implementation b...

    Authors: Marie Pégard, Odile Rogier, Aurélie Bérard, Patricia Faivre-Rampant, Marie-Christine Le Paslier, Catherine Bastien, Véronique Jorge and Leopoldo Sánchez

    Citation: BMC Genomics 2019 20:302

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  2. Content type: Research article

    Dasypyrum villosum is an important wild species of wheat (Triticum aestivum L.) and harbors many desirable genes that can be used to improve various traits of wheat. Compared with other D. villosum accessions, D....

    Authors: Shijin Li, Jing Wang, Kunyang Wang, Jingnan Chen, Ke Wang, Lipu Du, Zhongfu Ni, Zhishan Lin and Xingguo Ye

    Citation: BMC Genomics 2019 20:289

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  3. Content type: Research article

    The trihelix gene family is a plant-specific transcription factor family that plays important roles in plant growth, development, and responses to abiotic stresses. However, to date, no systemic characterization ...

    Authors: Jie Xiao, Rui Hu, Ting Gu, Jiapeng Han, Ding Qiu, Peipei Su, Jialu Feng, Junli Chang, Guangxiao Yang and Guangyuan He

    Citation: BMC Genomics 2019 20:287

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  4. Content type: Research article

    The tetraploid durum wheat (Triticum turgidum L. ssp. durum Desf. Husnot) is an important crop which provides the raw material for pasta production and a valuable source of genetic diversity for breeding hexaploi...

    Authors: Vera Vendramin, Danara Ormanbekova, Simone Scalabrin, Davide Scaglione, Marco Maccaferri, Pierluigi Martelli, Silvio Salvi, Irena Jurman, Rita Casadio, Federica Cattonaro, Roberto Tuberosa, Andrea Massi and Michele Morgante

    Citation: BMC Genomics 2019 20:278

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  5. Content type: Research article

    Chinese kale (Brassica alboglabra) contains high nutritional elements and functional molecules, especially anticarcinogenic and antioxidant glucosinolates (GS), which was highly affected by environment temperatur...

    Authors: Rongfang Guo, Xingru Wang, Xiaoyun Han, Wenjing Li, Tao Liu, Bingxing Chen, Xiaodong Chen and Gefu Wang-Pruski

    Citation: BMC Genomics 2019 20:269

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  6. Content type: Research article

    The two original plants of the oolong tea cultivar (‘Tieguanyin’) are “Wei shuo” ‘Tieguanyin’—TGY (Wei) and “Wang shuo” ‘Tieguanyin’—TGY (Wang). Another cultivar, ‘Benshan’ (BS), is similar to TGY in its aroma...

    Authors: Yuqiong Guo, Chen Zhu, Shanshan Zhao, Shuting Zhang, Wenjian Wang, Haifeng Fu, Xiaozhen Li, Chengzhe Zhou, Lan Chen, Yuling Lin and Zhongxiong Lai

    Citation: BMC Genomics 2019 20:265

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  7. Content type: Research article

    Genic male sterility (GMS) line is an important approach to utilize heterosis in Brassica rapa, one of the most widely cultivated vegetable crops in Northeast Asia. However, the molecular genetic mechanisms of GM...

    Authors: Xiuping Shen, Liai Xu, Yanhong Liu, Heng Dong, Dong Zhou, Yuzhi Zhang, Sue Lin, Jiashu Cao and Li Huang

    Citation: BMC Genomics 2019 20:264

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  8. Content type: Research article

    The different leaf type associated traits of soybean (Glycine max L.) including leaf area, leaf length, leaf width, leaf shape and petiole length are considered to be associated with seed yield. In order to ident...

    Authors: Liang Wang, Yanbo Cheng, Qibin Ma, Yinghui Mu, Zhifeng Huang, Qiuju Xia, Gengyun Zhang and Hai Nian

    Citation: BMC Genomics 2019 20:260

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  9. Content type: Research article

    Histone methylation mainly occurs on the lysine residues and plays a crucial role during flowering and stress responses of plants, through changing the methylation status or ratio of lysine residues. Histone l...

    Authors: Yexiong Qian, Changle Chen, Lingyu Jiang, Jing Zhang and Qiaoyu Ren

    Citation: BMC Genomics 2019 20:256

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  10. Content type: Research article

    Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, f...

    Authors: Alberto Cenci, Yann Hueber, Yasmin Zorrilla-Fontanesi, Jelle van Wesemael, Ewaut Kissel, Marie Gislard, Julie Sardos, Rony Swennen, Nicolas Roux, Sebastien Christian Carpentier and Mathieu Rouard

    Citation: BMC Genomics 2019 20:244

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  11. Content type: Research article

    Brassica oleracea exhibits extensive phenotypic diversity. As an important trait, petal color varies among different B. oleracea cultivars, enabling the study of the genetic basis of this trait. In a previous stu...

    Authors: Fengqing Han, Huilin Cui, Bin Zhang, Xiaoping Liu, Limei Yang, Mu Zhuang, Honghao Lv, Zhansheng Li, Yong Wang, Zhiyuan Fang, Jianghua Song and Yangyong Zhang

    Citation: BMC Genomics 2019 20:242

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  12. Content type: Research article

    Common cutworm (CCW) is highly responsible for destabilizing soybean productivity. Wild soybean is a resource used by breeders to discover elite defensive genes.

    Authors: Haiping Du, Xiao Li, Lihua Ning, Rui Qin, Qing Du, Qing Wang, Haina Song, Fang Huang, Hui Wang and Deyue Yu

    Citation: BMC Genomics 2019 20:237

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  13. Content type: Research article

    Pigeonpea has considerable extent of insect-aided natural out-crossing that impedes genetic purity of seeds. Pre-anthesis cleistogamy in pigeonpea promotes self-pollination which helps in maintaining genetic p...

    Authors: Pooja Yadav, K. B. Saxena, Anupama Hingane, C. V. Sameer Kumar, V. S. Kandalkar, Rajeev K. Varshney and Rachit K. Saxena

    Citation: BMC Genomics 2019 20:235

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  14. Content type: Research article

    Flowering time and maturity are among the most important adaptive traits in soybean (Glycine max (L.) Merill). Flowering Locus T (FT) family genes function as key flowering integrators, with flowering-promoting m...

    Authors: Bingjun Jiang, Shouwei Zhang, Wenwen Song, Mohammad Abdul Awal Khan, Shi Sun, Chengsheng Zhang, Tingting Wu, Cunxiang Wu and Tianfu Han

    Citation: BMC Genomics 2019 20:230

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  15. Content type: Research article

    Abiotic stresses like drought, heat, cold and salinity cause major productivity loss in the rapeseed-mustard crops (Brassica). Major efforts have been made in the past to identify genes that provide resistance ag...

    Authors: Deepika Verma, Neha Lakhanpal and Kashmir Singh

    Citation: BMC Genomics 2019 20:227

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  16. Content type: Research article

    Aquaporins (AQPs) facilitate transport of water and small solutes across cell membranes and play an important role in different physiological processes in plants. Despite their importance, limited data is avai...

    Authors: S. M. Shivaraj, Rupesh Deshmukh, Humira Sonah and Richard R. Bélanger

    Citation: BMC Genomics 2019 20:222

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  17. Content type: Research article

    Long noncoding RNAs (lncRNAs) have emerged as playing crucial roles in abiotic stress responsive regulation, however, the mechanism of lncRNAs underlying drought-tolerance remains largely unknown in cassava, a...

    Authors: Zehong Ding, Weiwei Tie, Lili Fu, Yan Yan, Guanghua Liu, Wei Yan, Yanan Li, Chunlai Wu, Jiaming Zhang and Wei Hu

    Citation: BMC Genomics 2019 20:214

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  18. Content type: Research article

    The SnRK2s (Plant specific protein kinase) are involved in various biological processes, such as plant defense and environmental challenges. In Arabidopsis, AtSnRK2s regulate the expression of some metal transpor...

    Authors: Ruijiao Wang, Chao Wang, Qin Yao, Xue Xiao, Xing Fan, Lina Sha, Jian Zeng, Houyang Kang, Haiqin Zhang, Yonghong Zhou and Yi Wang

    Citation: BMC Genomics 2019 20:210

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  19. Content type: Research article

    Plants adapted to diverse environments on Earth throughout their evolutionary history, and developed mechanisms to thrive in a variety of terrestrial habitats. When plants are grown in the novel environment of...

    Authors: Mingqi Zhou, Natasha J. Sng, Collin E. LeFrois, Anna-Lisa Paul and Robert J. Ferl

    Citation: BMC Genomics 2019 20:205

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  20. Content type: Research article

    Glyceollins are isoflavonoid-derived pathogen-inducible defense metabolites (phytoalexins) from soybean (Glycine max L. Merr) that have important roles in providing defense against pathogens. They also have impre...

    Authors: Md Asraful Jahan, Brianna Harris, Matthew Lowery, Katie Coburn, Aniello M. Infante, Ryan J. Percifield, Amanda G. Ammer and Nik Kovinich

    Citation: BMC Genomics 2019 20:149

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  21. Content type: Research article

    Trichoderma spp. are effective biocontrol agents for many plant pathogens, thus the mechanism of Trichoderma-induced plant resistance is not fully understood. In this study, a novel Trichoderma strain was identif...

    Authors: Min Yuan, Yuanyuan Huang, Weina Ge, Zhenhua Jia, Shuishan Song, Lan Zhang and Yali Huang

    Citation: BMC Genomics 2019 20:144

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  22. Content type: Research article

    Carbonic anhydrase (CA) catalyzes the hydration of CO2 in the first biochemical step of C4 photosynthesis, and has been considered a potentially rate-limiting step when CO2 availability within a leaf is low. Prev...

    Authors: Allison R. Kolbe, Anthony J. Studer, Omar E. Cornejo and Asaph B. Cousins

    Citation: BMC Genomics 2019 20:138

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  23. Content type: Research article

    Potassium (K) is essential to plant growth and development. Foxtail millet (Setaria italic L.) is an important fodder grain crop in arid and semi-arid regions of Asia and Africa because of its strong tolerance to...

    Authors: Xinyou Cao, Liqin Hu, Xueyan Chen, Rongzhi Zhang, Dungong Cheng, Haosheng Li, Zhaoshi Xu, Liancheng Li, Yongbin Zhou, Aifeng Liu, Jianming Song, Cheng Liu, Jianjun Liu, Zhendong Zhao, Ming Chen and Youzhi Ma

    Citation: BMC Genomics 2019 20:136

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  24. Content type: Research article

    Whilst information regarding small RNAs within agricultural crops is increasing, the miRNA composition of the nutritionally valuable pulse narrow-leafed lupin (Lupinus angustifolius) remains unknown.

    Authors: Kathleen DeBoer, Su Melser, Jana Sperschneider, Lars G. Kamphuis, Gagan Garg, Ling-Ling Gao, Karen Frick and Karam B. Singh

    Citation: BMC Genomics 2019 20:135

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  25. Content type: Software

    MicroRNAs (miRNAs) constitute a well-known small RNA (sRNA) species with important regulatory roles. To date, several bioinformatics tools have been developed for large-scale prediction of miRNAs based on high...

    Authors: Dongliang Yu, Ying Wan, Hidetaka Ito, Xiaoxia Ma, Tian Xie, Tingzhang Wang, Chaogang Shao and Yijun Meng

    Citation: BMC Genomics 2019 20:133

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  26. Content type: Research article

    Land plant organellar genomes have significant impact on metabolism and adaptation, and as such, accurate assembly and annotation of plant organellar genomes is an important tool in understanding the evolution...

    Authors: Desre Pinard, Alexander A. Myburg and Eshchar Mizrachi

    Citation: BMC Genomics 2019 20:132

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  27. Content type: Research article

    Warm winter and hot spring attributed to global warming affected floral development and may induce floral abortion, resulted in poor flowering in litchi. To identify genes potentially involved in litchi floral...

    Authors: Hao Liu, Congcong Wang, Houbin Chen and Biyan Zhou

    Citation: BMC Genomics 2019 20:127

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  28. Content type: Research article

    Cymbidium faberi, one of the most famous oriental orchids, has a distinct flower scent, which increases its economic value. However, the molecular mechanism of the flower scent biosynthesis was unclear prior to t...

    Authors: Qi Xu, Songtai Wang, Huazhu Hong and Yin Zhou

    Citation: BMC Genomics 2019 20:125

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  29. Content type: Research article

    Fruit peel colour is an important agronomic trait for fruit quality. Cytosine methylation plays an important role in gene regulation. Although the DNA methylation level of a single gene is important to affect ...

    Authors: Sheng-Hui Jiang, Qing-Guo Sun, Min Chen, Nan Wang, Hai-Feng Xu, Hong-Cheng Fang, Yi-Cheng Wang, Zong-Ying Zhang and Xue-Sen Chen

    Citation: BMC Genomics 2019 20:117

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  30. Content type: Research article

    The NAC (NAM, ATAF1/2, and CUC2) transcription factor family represents a group of large plant-specific transcriptional regulators, participating in plant development and response to external stress. However, the...

    Authors: Moyang Liu, Zhaotang Ma, Wenjun Sun, Li Huang, Qi Wu, Zizhong Tang, Tongliang Bu, Chenglei Li and Hui Chen

    Citation: BMC Genomics 2019 20:113

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  31. Content type: Research article

    Improving cotton fiber length without reducing yield is one of the major goals of cotton breeding. However, genetic improvement of cotton fiber length by breeding has been a challenge due to the narrow genetic...

    Authors: Marina Naoumkina, Gregory N. Thyssen, David D. Fang, Johnie N. Jenkins, Jack C. McCarty and Christopher B. Florane

    Citation: BMC Genomics 2019 20:112

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  32. Content type: Research article

    Citrus plants are commercially propagated by grafting, with the rootstock variety influencing a number of horticultural traits, including drought tolerance. Among the different rootstock varieties available fo...

    Authors: Luana P. Gonçalves, Raquel L. Boscariol Camargo, Marco Aurélio Takita, Marcos A. Machado, Walter S. dos Soares Filho and Marcio G. C. Costa

    Citation: BMC Genomics 2019 20:110

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  33. Content type: Research article

    Avocado (Persea americana Mill.) is a basal angiosperm from the Lauraceae family. This species has a diploid genome with an approximated size of ~ 920 Mbp and produces a climacteric, fleshy and oily fruit. The fl...

    Authors: Cristian Vergara-Pulgar, Karin Rothkegel, Mauricio González-Agüero, Romina Pedreschi, Reinaldo Campos-Vargas, Bruno G. Defilippi and Claudio Meneses

    Citation: BMC Genomics 2019 20:108

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  34. Content type: Research article

    Expansin loosens plant cell walls and involves in cell enlargement and various abiotic stresses. Plant expansin superfamily contains four subfamilies: α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXL...

    Authors: Zhisheng Han, Yanlin Liu, Xiong Deng, Dongmiao Liu, Yue Liu, Yingkao Hu and Yueming Yan

    Citation: BMC Genomics 2019 20:101

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  35. Content type: Research article

    RNA-sequencing analysis is increasingly utilized to study gene expression in non-model organisms without sequenced genomes. Aethionema arabicum (Brassicaceae) exhibits seed dimorphism as a bet-hedging strategy – ...

    Authors: Per K. I. Wilhelmsson, Jake O. Chandler, Noe Fernandez-Pozo, Kai Graeber, Kristian K. Ullrich, Waheed Arshad, Safina Khan, Johannes A. Hofberger, Karl Buchta, Patrick P. Edger, J. Chris Pires, M. Eric Schranz, Gerhard Leubner-Metzger and Stefan A. Rensing

    Citation: BMC Genomics 2019 20:95

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  36. Content type: Research article

    As important female reproductive tissues, the rice (Oryza sativa L.) ovule and female gametophyte is significant in terms of their fertility. Long noncoding RNAs (lncRNAs) play important and wide-ranging roles in...

    Authors: Helian Liu, Ruihua Wang, Bigang Mao, Bingran Zhao and Jianbo Wang

    Citation: BMC Genomics 2019 20:90

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  37. Content type: Research article

    Salt stress, a major plant environmental stress, is a critical constraint for rice productivity. Dissecting the genetic loci controlling salt tolerance in rice for improving productivity, especially at the flo...

    Authors: Chakkree Lekklar, Monnat Pongpanich, Duangjai Suriya-arunroj, Aumnart Chinpongpanich, Helen Tsai, Luca Comai, Supachitra Chadchawan and Teerapong Buaboocha

    Citation: BMC Genomics 2019 20:76

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  38. Content type: Research article

    The nutritional value of soybean oil is largely influenced by the proportions of unsaturated fatty acids (FAs), including oleic acid (OA, 18:1), linoleic acid (LLA, 18:2), and linolenic acid (LNA, 18:3). Genom...

    Authors: Xue Zhao, Haipeng Jiang, Lei Feng, Yingfan Qu, Weili Teng, Lijuan Qiu, Hongkun Zheng, Yingpeng Han and Wenbin Li

    Citation: BMC Genomics 2019 20:68

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  39. Content type: Research article

    Sugarcane smut is a fungal disease caused by Sporisorium scitamineum. Cultivation of smut-resistant sugarcane varieties is the most effective way to control this disease. The interaction between sugarcane and S. ...

    Authors: Yachun Su, Xinhuan Xiao, Hui Ling, Ning Huang, Feng Liu, Weihua Su, Yuye Zhang, Liping Xu, Khushi Muhammad and Youxiong Que

    Citation: BMC Genomics 2019 20:57

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  40. Content type: Research article

    Cymbidium goeringii is one of the most horticulturally important and popular ornamental plants in the orchid family (Orchidaceae). It blooms in winter during January–March and a period of low temperature is neces...

    Authors: Fengxi Yang, Genfa Zhu, Yonglu Wei, Jie Gao, Gang Liang, Lingyuan Peng, Chuqiao Lu and Jianpeng Jin

    Citation: BMC Genomics 2019 20:53

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  41. Content type: Research article

    Plant basic leucine zipper (bZIP) transcription factors play crucial roles in plant growth, development, and abiotic stress responses. However, systematic investigation and analyses of the bZIP gene family in pea...

    Authors: Zhihui Wang, Liying Yan, Liyun Wan, Dongxin Huai, Yanping Kang, Lei Shi, Huifang Jiang, Yong Lei and Boshou Liao

    Citation: BMC Genomics 2019 20:51

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  42. Content type: Research article

    Red-fleshed papaya is a good material to study the different carotenoids accumulation mechanism in the peel and flesh. Although the peel and flesh of papaya closely integrated into one body, the flesh colorati...

    Authors: Yan Hong Shen, Fei Ying Yang, Bing Guo Lu, Wan Wan Zhao, Tao Jiang, Li Feng, Xiao Jing Chen and Ray Ming

    Citation: BMC Genomics 2019 20:49

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  43. Content type: Research article

    Taste and aroma, which are important organoleptic qualities of apricot (Prunus armeniaca L.) fruit, undergo rapid and substantial changes during ripening. However, the associated molecular mechanisms remain uncle...

    Authors: Qiuyun Zhang, Chao Feng, Wenhui Li, Zehui Qu, Ming Zeng and Wanpeng Xi

    Citation: BMC Genomics 2019 20:45

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  44. Content type: Research article

    Tomato is an economically important crop with fruits that are a significant source of bioactive compounds such as ascorbic acid and phenolics. Nowadays, the majority of the enzymes of the biosynthetic pathways...

    Authors: Adriana Sacco, Assunta Raiola, Roberta Calafiore, Amalia Barone and Maria Manuela Rigano

    Citation: BMC Genomics 2019 20:43

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  45. Content type: Research article

    The apomictic reproductive mode of Brachiaria (syn. Urochloa) forage species allows breeders to faithfully propagate heterozygous genotypes through seed over multiple generations. In Brachiaria, reproductive mode...

    Authors: Margaret Worthington, Masumi Ebina, Naoki Yamanaka, Christopher Heffelfinger, Constanza Quintero, Yeny Patricia Zapata, Juan Guillermo Perez, Michael Selvaraj, Manabu Ishitani, Jorge Duitama, Juan Fernando de la Hoz, Idupulapati Rao, Stephen Dellaporta, Joe Tohme and Jacobo Arango

    Citation: BMC Genomics 2019 20:41

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  46. Content type: Research article

    Temperature stress is a major environmental factor affecting not only plant growth and development, but also fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that pla...

    Authors: Hong Zhu, Yu Zhang, Ruifang Tang, Hongxia Qu, Xuewu Duan and Yueming Jiang

    Citation: BMC Genomics 2019 20:33

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  47. Content type: Research article

    Hexaploid bread wheat (Triticum aestivum L) arose by two polyploidisation events from three diploid species with homoeologous genomes. Nullisomic-tetrasomic (nulli-tetra or NT) lines are aneuploid wheat plants la...

    Authors: Rongzhi Zhang, Shuaifeng Geng, Zhengrui Qin, Zongxiang Tang, Cheng Liu, Dongfeng Liu, Guoqi Song, Yulian Li, Shujuan Zhang, Wei Li, Jie Gao, Xiaodong Han and Genying Li

    Citation: BMC Genomics 2019 20:29

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