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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. Atractylodes DC is the basic original plant of the widely used herbal medicines “Baizhu” and “Cangzhu” and an endemic genus in East Asia. Species within the genus have minor morphological differences, and the uni...

    Authors: Yiheng Wang, Sheng Wang, Yanlei Liu, Qingjun Yuan, Jiahui Sun and Lanping Guo

    Citation: BMC Genomics 2021 22:103

    Content type: Research article

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  2. Availability of plant genome sequences has led to significant advances. However, with few exceptions, the great majority of existing genome assemblies are derived from short read sequencing technologies with h...

    Authors: Peipei Wang, Fanrui Meng, Bethany M. Moore and Shin-Han Shiu

    Citation: BMC Genomics 2021 22:99

    Content type: Research article

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  3. Paeonia lactiflora ‘Hangshao’ is widely cultivated in China as a traditional Chinese medicine ‘Radix Paeoniae Alba’. Due to the abundant unsaturated fatty acids in its seed, it can also be regarded as a new oilse...

    Authors: Jia-Song Meng, Yu-Han Tang, Jing Sun, Da-Qiu Zhao, Ke-Liang Zhang and Jun Tao

    Citation: BMC Genomics 2021 22:94

    Content type: Research article

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  4. The microRNAs(miRNA)-derived secondary phased small interfering RNAs (phasiRNAs) participate in post-transcriptional gene silencing and play important roles in various bio-processes in plants. In rice, two miR...

    Authors: Lan Yu, Rongkai Guo, Yeqin Jiang, Xinghuo Ye, Zhihong Yang, Yijun Meng and Chaogang Shao

    Citation: BMC Genomics 2021 22:93

    Content type: Research article

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  5. Rose (Rosa chinensis) is a traditional famous flower with valuable ornamental characteristics. However, drought stress restricts its growth and development, leading to an abnormal phenotype. One of the main trans...

    Authors: Wei Li, Ziwen Geng, Cuiping Zhang, Kuiling Wang and Xinqiang Jiang

    Citation: BMC Genomics 2021 22:90

    Content type: Research article

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  6. Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real...

    Authors: Jianqing Chen, Jinyu Zhou, Yanhong Hong, Zekun Li, Xiangyu Cheng, Aiying Zheng, Yilin Zhang, Juanjuan Song, Guifeng Xie, Changmei Chen, Meng Yuan, Tengyun Wang and Qingxi Chen

    Citation: BMC Genomics 2021 22:88

    Content type: Research article

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  7. The number of panicles per plant, number of grains per panicle, and 1000-grain weight are important factors contributing to the grain yield per plant in rice. The Rice Diversity Panel 1 (RDP1) contains a total...

    Authors: Hua Zhong, Shuai Liu, Xiaoxi Meng, Tong Sun, Yujuan Deng, Weilong Kong, Zhaohua Peng and Yangsheng Li

    Citation: BMC Genomics 2021 22:86

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2021 22:206

  8. Wall-associated kinases (WAK), one of the receptor-like kinases (RLK), function directly in the connection and communication between the plant cell wall and the cytoplasm. WAK genes are highly conserved and have ...

    Authors: Lingling Dou, Zhifang Li, Qian Shen, Huiran Shi, Huaizhu Li, Wenbo Wang, Changsong Zou, Haihong Shang, Hongbin Li and Guanghui Xiao

    Citation: BMC Genomics 2021 22:85

    Content type: Research article

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  9. Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here...

    Authors: Pan Zhang, Tianqi Duo, Fengdan Wang, Xunzhong Zhang, Zouzhuan Yang and Guofu Hu

    Citation: BMC Genomics 2021 22:82

    Content type: Research article

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  10. The genetic diversity and gene pool characteristics must be clarified for efficient genome-wide association studies, genomic selection, and hybrid breeding. The aim of this study was to evaluate the genetic st...

    Authors: Mirosław Tyrka, Monika Mokrzycka, Beata Bakera, Dorota Tyrka, Magdalena Szeliga, Stefan Stojałowski, Przemysław Matysik, Michał Rokicki, Monika Rakoczy-Trojanowska and Paweł Krajewski

    Citation: BMC Genomics 2021 22:81

    Content type: Research article

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  11. Mepiquat chloride (DPC) is a chemical that is extensively used to control internode growth and create compact canopies in cultured plants. Previous studies have suggested that DPC could also inhibit gibberelli...

    Authors: Rongfa Chen, Yegeng Fan, Huiwen Zhou, Shanping Mo, Zhongfeng Zhou, Haifeng Yan, Ting Luo, Xing Huang, Mengling Weng, Prakash Lakshmanan, Yangrui Li, Lihang Qiu and Jianming Wu

    Citation: BMC Genomics 2021 22:79

    Content type: Research article

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  12. Freezing injury, which is an important abiotic stress in horticultural crops, influences the growth and development and the production area of kiwifruit (Actinidia Lind1). Among Actinidia species, Actinidia argut...

    Authors: Miaomiao Lin, Shihang Sun, Jinbao Fang, Xiujuan Qi, Leiming Sun, Yunpeng Zhong, Yanxiang Sun, Gu Hong, Ran Wang and Yukuo Li

    Citation: BMC Genomics 2021 22:72

    Content type: Research article

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  13. Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 (Arabidopsis thaliana Activatio...

    Authors: Ambika Dudhate, Harshraj Shinde, Pei Yu, Daisuke Tsugama, Shashi Kumar Gupta, Shenkui Liu and Tetsuo Takano

    Citation: BMC Genomics 2021 22:70

    Content type: Research article

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  14. The wheat dwarfing gene increases lodging resistance, the grain number per spike and harvest index. Dwarf Polish wheat (Triticum polonicum L., 2n = 4x = 28, AABB, DPW), initially collected from Tulufan, Xinjiang,...

    Authors: Songyue Chai, Qin Yao, Xu Zhang, Xue Xiao, Xing Fan, Jian Zeng, Lina Sha, Houyang Kang, Haiqin Zhang, Jun Li, Yonghong Zhou and Yi Wang

    Citation: BMC Genomics 2021 22:63

    Content type: Research article

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  15. We have previously developed a rice-based oral vaccine against cholera diarrhea, MucoRice-CTB. Using Agrobacterium-mediated co-transformation, we produced the selection marker–free MucoRice-CTB line 51A, which ha...

    Authors: Ai Sasou, Yoshikazu Yuki, Ayaka Honma, Kotomi Sugiura, Koji Kashima, Hiroko Kozuka-Hata, Masanori Nojima, Masaaki Oyama, Shiho Kurokawa, Shinichi Maruyama, Masaharu Kuroda, Shinjiro Tanoue, Narushi Takamatsu, Kohtaro Fujihashi, Eiji Goto and Hiroshi Kiyono

    Citation: BMC Genomics 2021 22:59

    Content type: Research article

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  16. During the bread wheat speciation by polyploidization, a series of genome rearrangement and sequence recombination occurred. Simple sequence repeat (SSR) sequences, predominately located in heterochromatic reg...

    Authors: Yingxin Zhang, Chengming Fan, Yuhong Chen, Richard R.-C. Wang, Xiangqi Zhang, Fangpu Han and Zanmin Hu

    Citation: BMC Genomics 2021 22:55

    Content type: Research article

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  17. Genome-wide change of polyadenylation (polyA) sites (also known as alternative polyadenylation, APA) is emerging as an important strategy of gene regulation in response to stress in plants. But little is known...

    Authors: Chao Yan, Yupeng Wang, Tao Lyu, Zhikang Hu, Ning Ye, Weixin Liu, Jiyuan Li, Xiaohua Yao and Hengfu Yin

    Citation: BMC Genomics 2021 22:53

    Content type: Research article

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  18. Valsa canker is a serious disease in the stem of Malus sieversii, caused by Valsa mali. However, little is known about the global response mechanism in M. sieversii to V. mali infection.

    Authors: Xiaojie Liu, Xiaoshuang Li, Xuejing Wen, Yan Zhang, Yu Ding, Yiheng Zhang, Bei Gao and Daoyuan Zhang

    Citation: BMC Genomics 2021 22:52

    Content type: Research article

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  19. Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT acti...

    Authors: Shiqi Gao, Linzhi Li, Xiaolei Han, Tingting Liu, Peng Jin, Linna Cai, Miaoze Xu, Tianye Zhang, Fan Zhang, Jianping Chen, Jian Yang and Kaili Zhong

    Citation: BMC Genomics 2021 22:49

    Content type: Research article

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  20. Aspartic proteases (APs) are a class of aspartic peptidases belonging to nine proteolytic enzyme families whose members are widely distributed in biological organisms. APs play essential functions during plant...

    Authors: Xiaqin Wang, Xinyang Yan, Shubin Li, Yun Jing, Lianfeng Gu, Shuangquan Zou, Jin Zhang and Bobin Liu

    Citation: BMC Genomics 2021 22:45

    Content type: Research article

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  21. RNA interference (RNAi) regulates gene expression in most multicellular organisms through binding of small RNA effectors to target transcripts. Exploiting this process is a popular strategy for genetic manipul...

    Authors: Mosharrof Mondal, Jacob Peter, Obrie Scarbrough and Alex Flynt

    Citation: BMC Genomics 2021 22:42

    Content type: Methodology article

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  22. Apple (Malus domestica Borkh.) is a popular cultivated fruit crop with high economic value in China. Apple floral transition is an important process but liable to be affected by various environmental factors. The...

    Authors: Xiya Zuo, Shixiang Wang, Wen Xiang, Huiru Yang, Muhammad Mobeen Tahir, Shangong Zheng, Na An, Mingyu Han, Caiping Zhao and Dong Zhang

    Citation: BMC Genomics 2021 22:41

    Content type: Research article

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  23. Stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici (Pst), is a serious foliar disease of wheat. Identification of novel stripe rust resistance genes and cultivation of resistant cultiv...

    Authors: Yuqi Wang, Can Yu, Yukun Cheng, Fangjie Yao, Li Long, Yu Wu, Jing Li, Hao Li, Jirui Wang, Qiantao Jiang, Wei Li, Zhien Pu, Pengfei Qi, Jian Ma, Mei Deng, Yuming Wei…

    Citation: BMC Genomics 2021 22:34

    Content type: Research article

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  24. Cotton is more resistant to salt and drought stresses as compared to other field crops, which makes itself as a pioneer industrial crop in saline-alkali lands. However, abiotic stresses still negatively affect...

    Authors: Peng Xu, Qi Guo, Shan Meng, Xianggui Zhang, Zhenzhen Xu, Wangzhen Guo and Xinlian Shen

    Citation: BMC Genomics 2021 22:26

    Content type: Research article

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  25. Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 ...

    Authors: Juanjuan Feng, Xuexian Zhang, Meng Zhang, Liping Guo, Tingxiang Qi, Huini Tang, Haiyong Zhu, Hailin Wang, Xiuqin Qiao, Chaozhu Xing and Jianyong Wu

    Citation: BMC Genomics 2021 22:24

    Content type: Research article

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  26. Three-dimensional chromatin loop structures connect regulatory elements to their target genes in regions known as anchors. In complex plant genomes, such as maize, it has been proposed that loops span heteroch...

    Authors: Stéphane Deschamps, John A. Crow, Nadia Chaidir, Brooke Peterson-Burch, Sunil Kumar, Haining Lin, Gina Zastrow-Hayes and Gregory D. May

    Citation: BMC Genomics 2021 22:23

    Content type: Research article

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  27. The Gretchen Hagen 3 (GH3) genes encode acyl acid amido synthetases, many of which have been shown to modulate the amount of active plant hormones or their precursors. GH3 genes, especially Group III subgroup 6 G...

    Authors: Jiseong Jeong, Sunhee Park, Jeong Hui Im and Hankuil Yi

    Citation: BMC Genomics 2021 22:22

    Content type: Research article

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  28. Genetic improvement of root system architecture is essential to improve water and nutrient use efficiency of crops or to boost their productivity under stress or non-optimal soil conditions. One hundred ninety...

    Authors: Admas Alemu, Tileye Feyissa, Marco Maccaferri, Giuseppe Sciara, Roberto Tuberosa, Karim Ammar, Ayele Badebo, Maricelis Acevedo, Tesfaye Letta and Bekele Abeyo

    Citation: BMC Genomics 2021 22:20

    Content type: Research article

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  29. Several conventional genomic Bayesian (or no Bayesian) prediction methods have been proposed including the standard additive genetic effect model for which the variance components are estimated with mixed mode...

    Authors: Osval Antonio Montesinos-López, Abelardo Montesinos-López, Paulino Pérez-Rodríguez, José Alberto Barrón-López, Johannes W. R. Martini, Silvia Berenice Fajardo-Flores, Laura S. Gaytan-Lugo, Pedro C. Santana-Mancilla and José Crossa

    Citation: BMC Genomics 2021 22:19

    Content type: Review

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  30. Fruit ripening in Prunus persica melting varieties involves several physiological changes that have a direct impact on the fruit organoleptic quality and storage potential. By studying the proteomic differences b...

    Authors: Ricardo Nilo-Poyanco, Carol Moraga, Gianfranco Benedetto, Ariel Orellana and Andrea Miyasaka Almeida

    Citation: BMC Genomics 2021 22:17

    Content type: Research article

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  31. Asarum heterotropides Fr. Schmidt var. mandshuricum (Maxim.) Kitag. is an important medicinal and industrial plant, which is used in the treatment of various diseases. The main bioactive ingredient is the volatil...

    Authors: Zhiqing Wang, Haiqin Ma, Min Zhang, Ziqing Wang, Yixin Tian, Wei Li and Yingping Wang

    Citation: BMC Genomics 2021 22:16

    Content type: Research article

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  32. Improving grain yield in cereals especially in wheat is a main objective for plant breeders. One of the main constrains for improving this trait is the G × E interaction (GEI) which affects the performance of ...

    Authors: Shamseldeen Eltaher, P. Stephen Baenziger, Vikas Belamkar, Hamdy A. Emara, Ahmed A. Nower, Khaled F. M. Salem, Ahmad M. Alqudah and Ahmed Sallam

    Citation: BMC Genomics 2021 22:2

    Content type: Research article

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  33. Brassica nigra (BB), also called black mustard, is grown as a condiment crop in India. B. nigra represents the B genome of U’s triangle and is one of the progenitor species of B. juncea (AABB), an important oilse...

    Authors: Kumar Paritosh, Akshay Kumar Pradhan and Deepak Pental

    Citation: BMC Genomics 2020 21:887

    Content type: Research article

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  34. Calcineurin B-like protein (CBL)-interacting protein kinases (CIPKs) are the primary components of calcium sensors, and play crucial roles in plant developmental processes, hormone signaling transduction, and ...

    Authors: Weihua Su, Yongjuan Ren, Dongjiao Wang, Long Huang, Xueqin Fu, Hui Ling, Yachun Su, Ning Huang, Hanchen Tang, Liping Xu and Youxiong Que

    Citation: BMC Genomics 2020 21:868

    Content type: Research article

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  35. Ginkgo (Ginkgo biloba L.) is an excellent landscape species. Its yellow-green leaf mutants are ideal materials for research on pigment synthesis, but the regulatory mechanism of leaf coloration in these ginkgo mu...

    Authors: Yaqiong Wu, Jing Guo, Tongli Wang, Fuliang Cao and Guibin Wang

    Citation: BMC Genomics 2020 21:858

    Content type: Research article

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  36. The invasive species Xanthium spinosum has been used as a traditional Chinese medicine for many years. Unfortunately, no extensive molecular studies of this plant have been conducted.

    Authors: Gurusamy Raman, Kyu Tae Park, Joo-Hwan Kim and SeonJoo Park

    Citation: BMC Genomics 2020 21:855

    Content type: Research article

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    The Correction to this article has been published in BMC Genomics 2021 22:97

  37. Long noncoding RNAs (lncRNAs) have been reported to play critical roles in diverse growth and development processes in plants. However, the systematic identification and characterization of lncRNAs in foxtail ...

    Authors: Zilong Zhao, Dan Liu, Yanjiao Cui, Suying Li, Dan Liang, Daizhen Sun, Jianhe Wang and Zhengli Liu

    Citation: BMC Genomics 2020 21:853

    Content type: Research article

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  38. The root growth angle (RGA) typically determines plant rooting depth, which is significant for plant anchorage and abiotic stress tolerance. Several quantitative trait loci (QTLs) for RGA have been identified ...

    Authors: Caixia Zheng, Fei Shen, Yi Wang, Ting Wu, Xuefeng Xu, Xinzhong Zhang and Zhenhai Han

    Citation: BMC Genomics 2020 21:852

    Content type: Research article

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  39. Dioecious spinach (Spinacia oleracea L.), a commercial and nutritional vegetable crop, serves as a model for studying the mechanisms of sex determination and differentiation in plants. However, this mechanism is ...

    Authors: Ning Li, Ziwei Meng, Minjie Tao, Yueyuan Wang, Yulan Zhang, Shufen Li, Wujun Gao and Chuanliang Deng

    Citation: BMC Genomics 2020 21:850

    Content type: Research article

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  40. Loss of genetic variation negatively impacts breeding efforts and food security. Genebanks house over 7 million accessions representing vast allelic diversity that is a resource for sustainable breeding. Disco...

    Authors: Anna Hawliczek, Leszek Bolibok, Katarzyna Tofil, Ewa Borzęcka, Joanna Jankowicz-Cieślak, Piotr Gawroński, Adam Kral, Bradley J. Till and Hanna Bolibok-Brągoszewska

    Citation: BMC Genomics 2020 21:845

    Content type: Research article

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  41. Cotton (Gossypium hirsutum) is considered a fairly salt tolerant crop however, salinity can still cause significant economic losses by affecting the yield and deteriorating the fiber quality. We studied a salt-to...

    Authors: Delong Wang, Xuke Lu, Xiugui Chen, Shuai Wang, Junjuan Wang, Lixue Guo, Zujun Yin, Quanjia Chen and Wuwei Ye

    Citation: BMC Genomics 2020 21:838

    Content type: Research article

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  42. Barley scald, caused by the fungus Rhynchosporium commune, is distributed worldwide to all barley growing areas especially in cool and humid climates. Scald is an economically important leaf disease resulting in ...

    Authors: Bianca Büttner, Vera Draba, Klaus Pillen, Günther Schweizer and Andreas Maurer

    Citation: BMC Genomics 2020 21:837

    Content type: Research article

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  43. Male sterility is a simple and efficient pollination control system that is widely exploited in hybrid breeding. In upland cotton, CCRI9106, a photosensitive genetic male sterile (PGMS) mutant isolated from CC...

    Authors: Meng Zhang, Ji Liu, Qiang Ma, Yuan Qin, Hantao Wang, Pengyun Chen, Liang Ma, Xiaokang Fu, Longfu Zhu, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2020 21:825

    Content type: Research article

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  44. The NBS disease-related gene family coordinates the inherent immune system in plants in response to pathogen infections. Previous studies have identified NBS-encoding genes in Pyrus bretschneideri (‘Dangshansuli’...

    Authors: Manyi Sun, Mingyue Zhang, Jugpreet Singh, Bobo Song, Zikai Tang, Yueyuan Liu, Runze Wang, Mengfan Qin, Jiaming Li, Awais Khan and Jun Wu

    Citation: BMC Genomics 2020 21:809

    Content type: Research article

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  45. Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilita...

    Authors: Chia-Chi Hsu, Shu-Yun Chen, Pei-Han Lai, Yu-Yun Hsiao, Wen-Chieh Tsai, Zhong-Jian Liu, Mei-Chu Chung, Olivier Panaud and Hong-Hwa Chen

    Citation: BMC Genomics 2020 21:807

    Content type: Research article

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  46. The tRNAs act as a bridge between the coding mRNA and incoming amino acids during protein translation. The anti-codon of tRNA recognizes the codon of the mRNA and deliver the amino acid into the protein transl...

    Authors: Tapan Kumar Mohanta, Awdhesh Kumar Mishra, Abeer Hashem, Elsayed Fathi Abd_Allah, Abdul Latif Khan and Ahmed Al-Harrasi

    Citation: BMC Genomics 2020 21:804

    Content type: Research article

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  47. Eucalyptus, a highly diverse genus of the Myrtaceae family, is the most widely planted hardwood in the world due to its increasing importance for fiber and energy. Somatic embryogenesis (SE) is one large-scale me...

    Authors: Yufei Xiao, Junji Li, Ye Zhang, Xiaoning Zhang, Hailong Liu, Zihai Qin and Bowen Chen

    Citation: BMC Genomics 2020 21:803

    Content type: Research article

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  48. Common bean is an important staple crop in the tropics of Africa, Asia and the Americas. Particularly smallholder farmers rely on bean as a source for calories, protein and micronutrients. Drought is a major p...

    Authors: Santiago Diaz, Daniel Ariza-Suarez, Paulo Izquierdo, Juan David Lobaton, Juan Fernando de la Hoz, Fernando Acevedo, Jorge Duitama, Alberto F. Guerrero, Cesar Cajiao, Victor Mayor, Stephen E. Beebe and Bodo Raatz

    Citation: BMC Genomics 2020 21:799

    Content type: Research article

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  49. Genomic selection (GS) or genomic prediction is a promising approach for tree breeding to obtain higher genetic gains by shortening time of progeny testing in breeding programs. As proof-of-concept for Scots p...

    Authors: Ainhoa Calleja-Rodriguez, Jin Pan, Tomas Funda, Zhiqiang Chen, John Baison, Fikret Isik, Sara Abrahamsson and Harry X. Wu

    Citation: BMC Genomics 2020 21:796

    Content type: Research article

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  50. Valine-glutamine (VQ) motif-containing proteins play important roles in plant growth, development and abiotic stress response. For many plant species, the VQ genes have been identified and their functions have be...

    Authors: Pengyun Chen, Fei wei, Shuaishuai Cheng, Liang Ma, Hantao Wang, Meng Zhang, Guangzhi Mao, Jianhua Lu, Pengbo Hao, Adeel Ahmad, Lijiao Gu, Qiang Ma, Aimin Wu, Hengling Wei and Shuxun Yu

    Citation: BMC Genomics 2020 21:795

    Content type: Research article

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