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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. Tartary buckwheat (Fagopyrum tataricum), an important pseudocereal crop, has high economic value due to its nutritional and medicinal properties. However, dehulling of Tartary buckwheat is difficult owing to its ...

    Authors: Tao-Xiong Shi, Rui-Yuan Li, Ran Zheng, Qing-Fu Chen, Hong-You Li, Juan Huang, Li-Wei Zhu and Cheng-Gang Liang

    Citation: BMC Genomics 2021 22:142

    Content type: Research article

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  2. Sweetpotato (Ipomoea batatas (L.) Lam.) serves as an important food source for human beings. β-galactosidase (bgal) is a glycosyl hydrolase involved in cell wall modification, which plays essential roles in plant...

    Authors: Fuyun Hou, Taifeng Du, Zhen Qin, Tao Xu, Aixian Li, Shunxu Dong, Daifu Ma, Zongyun Li, Qingmei Wang and Liming Zhang

    Citation: BMC Genomics 2021 22:140

    Content type: Research article

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  3. Mitochondrial transcription termination factor (mTERF) is a large gene family which plays a significant role during plant growth under various environmental stresses. However, knowledge of mTERF genes in grape...

    Authors: Xiangjing Yin, Yu Gao, Shiren Song, Danial Hassani and Jiang Lu

    Citation: BMC Genomics 2021 22:136

    Content type: Research article

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  4. The root system provides nutrient absorption and is closely related to abiotic stress tolerance, but it is difficult to study the roots under field conditions. This study was conducted to identify quantitative...

    Authors: Huatao Chen, Giriraj Kumawat, Yongliang Yan, Baojie Fan and Donghe Xu

    Citation: BMC Genomics 2021 22:132

    Content type: Research article

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  5. 2-Oxoglutarate and Fe(II)-dependent dioxygenases (2ODDs) belong to the 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily and are involved in various vital metabolic pathways of plants at different develo...

    Authors: Shuo Wei, Wen Zhang, Rao Fu and Yang Zhang

    Citation: BMC Genomics 2021 22:126

    Content type: Research article

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  6. Heterosis has been extensively utilized in different crops and made a significant contribution to global food security. Genetic distance (GD) is one of the valuable criteria for selecting parents in hybrid bre...

    Authors: Xiaoli Geng, Yujie Qu, Yinhua Jia, Shoupu He, Zhaoe Pan, Liru Wang and Xiongming Du

    Citation: BMC Genomics 2021 22:123

    Content type: Research article

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  7. Autophagy, meaning ‘self-eating’, is required for the degradation and recycling of cytoplasmic constituents under stressful and non-stressful conditions, which helps to maintain cellular homeostasis and delay ...

    Authors: Huan Wang, Zhaotang Ding, Mengjie Gou, Jianhui Hu, Yu Wang, Lu Wang, Yuchun Wang, Taimei Di, Xinfu Zhang, Xinyuan Hao, Xinchao Wang, Yajun Yang and Wenjun Qian

    Citation: BMC Genomics 2021 22:121

    Content type: Research article

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  8. Legume species are an important plant model because of their protein-rich physiology. The adaptability and productivity of legumes are limited by major biotic and abiotic stresses. Responses to these stresses ...

    Authors: Daniel Restrepo-Montoya, Phillip E. McClean and Juan M. Osorno

    Citation: BMC Genomics 2021 22:113

    Content type: Research article

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  9. Oil flax (linseed, Linum usitatissimum L.) is one of the most important oil crops., However, the increases in drought resulting from climate change have dramatically reduces linseed yield and quality, but very li...

    Authors: Wei Wang, Lei Wang, Ling Wang, Meilian Tan, Collins O. Ogutu, Ziyan Yin, Jian Zhou, Jiaomei Wang, Lijun Wang and Xingchu Yan

    Citation: BMC Genomics 2021 22:109

    Content type: Research article

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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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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  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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  34. 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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  35. 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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  36. 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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  37. 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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  38. 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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  39. 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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  40. 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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  41. 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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  42. 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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  43. 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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  44. 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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  45. 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

    Published on:

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

  46. 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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  47. 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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  48. 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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  49. 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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