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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 29

  1. Content type: Research article

    Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots...

    Authors: Wenbin Li, Xiaolin Wang, Chunqiang Li, Jianbo Sun, Shuxia Li and Ming Peng

    Citation: BMC Genomics 2019 20:519

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  2. Content type: Research article

    Polyploidization, pervasive among higher plant species, enhances adaptation to water deficit, but the physiological and molecular advantages need to be investigated widely. Long non-coding RNAs (lncRNAs) are i...

    Authors: Liang Xiao, Xiao-Hong Shang, Sheng Cao, Xiang-Yu Xie, Wen-Dan Zeng, Liu-Ying Lu, Song-Bi Chen and Hua-Bing Yan

    Citation: BMC Genomics 2019 20:514

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  3. Content type: Research article

    DNA methylation is an important epigenetic modification. Recently the developed single-molecule real-time (SMRT) sequencing technology provided an efficient way to detect DNA N6-methyladenine (6mA) modificatio...

    Authors: Mei-Wei Luan, Wei Chen, Jian-Feng Xing, Chuan-Le Xiao, Ying Chen and Shang-Qian Xie

    Citation: BMC Genomics 2019 20:508

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  4. Content type: Research article

    Seed aging in soybean is a serious challenge for agronomic production and germplasm preservation. However, its genetic basis remains largely unclear in soybean. Unraveling the genetic mechanism involved in see...

    Authors: Xi Zhang, Aiman Hina, Shiyu Song, Jiejie Kong, Javaid Akhter Bhat and Tuanjie Zhao

    Citation: BMC Genomics 2019 20:499

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  5. Content type: Research article

    The date palm is one of the oldest cultivated fruit trees. The tree can withstand high temperatures and low water and the fruit can be stored dry offering nutrition across the year. The first region of cultiva...

    Authors: Yasmin A. Mohamoud, Lisa S. Mathew, Maria F. Torres, Shameem Younuskunju, Robert Krueger, Karsten Suhre and Joel A. Malek

    Citation: BMC Genomics 2019 20:498

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  6. Content type: Research article

    Puccinia graminis f. sp. tritici (Pgt) race TTKSK and its lineage pose a threat to barley production world-wide justifying the extensive efforts to identify, clone, and characterize the rpg4-mediated resistance l...

    Authors: Shyam Solanki, Jonathan Richards, Gazala Ameen, Xue Wang, Atiya Khan, Harris Ali, Alex Stangel, Prabin Tamang, Thomas Gross, Patrick Gross, Thomas G. Fetch and Robert S. Brueggeman

    Citation: BMC Genomics 2019 20:495

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  7. Content type: Research article

    Juncus effusus L. (family: Juncaceae; order: Poales) is a helophytic rush growing in temperate damp or wet terrestrial habitats and is of almost cosmopolitan distribution. The species has been studied intensively...

    Authors: Muhammad Arslan, Upendra Kumar Devisetty, Martin Porsch, Ivo Große, Jochen A. Müller and Stefan G. Michalski

    Citation: BMC Genomics 2019 20:489

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  8. Content type: Research article

    With rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post...

    Authors: Sridhar Ravichandran, Raja Ragupathy, Tara Edwards, Michael Domaratzki and Sylvie Cloutier

    Citation: BMC Genomics 2019 20:488

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  9. Content type: Research article

    Apomixis is considered an evolutionary deviation of the sexual reproductive pathway leading to the generation of clonal maternal progenies by seeds. Recent evidence from model and non-model species suggested t...

    Authors: Juan Pablo A. Ortiz, Olivier Leblanc, Cristian Rohr, Mauricio Grisolia, Lorena A. Siena, Maricel Podio, Carolina Colono, Celeste Azzaro and Silvina C. Pessino

    Citation: BMC Genomics 2019 20:487

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  10. Content type: Research article

    In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein,...

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

    Citation: BMC Genomics 2019 20:483

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  11. Content type: Research article

    Due to the recent domestication of peanut from a single tetraploidization event, relatively little genetic diversity underlies the extensive morphological and agronomic diversity in peanut cultivars today. To ...

    Authors: Paul I. Otyama, Andrew Wilkey, Roshan Kulkarni, Teshale Assefa, Ye Chu, Josh Clevenger, Dan J. O’Connor, Graeme C. Wright, Stanley W. Dezern, Gregory E. MacDonald, Noelle L. Anglin, Ethalinda K. S. Cannon, Peggy Ozias-Akins and Steven B. Cannon

    Citation: BMC Genomics 2019 20:481

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  12. Content type: Research article

    The redundancy of genomic resources, including transcript and molecular markers, and their uncertain position in the genome have dramatically hindered the study of traits in ramie, an important natural fiber c...

    Authors: Yanzhou Wang, Zheng Zeng, Fu Li, Xiufeng Yang, Xinyue Gao, Yonghong Ma, Jing Rao, Hengyun Wang and Touming Liu

    Citation: BMC Genomics 2019 20:476

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  13. Content type: Research article

    Reliable indicators for the onset of flowering are not available for most perennial monocarpic species, representing a drawback for crops such as bamboo, agave and banana. The ability to predict and control th...

    Authors: Emmanuel Avila de Dios, Luis Delaye and June Simpson

    Citation: BMC Genomics 2019 20:473

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  14. Content type: Research article

    Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from ...

    Authors: Sushil Raj Subedi, Nitika Sandhu, Vikas Kumar Singh, Pallavi Sinha, Santosh Kumar, S. P. Singh, Surya Kant Ghimire, Madhav Pandey, Ram Baran Yadaw, Rajeev K. Varshney and Arvind Kumar

    Citation: BMC Genomics 2019 20:471

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  15. Content type: Research article

    The WRKY gene family is one of the most important families in higher plants. As transcription factors, they actively respond to biotic and abiotic stress and are also involved in plant development. Chinese juj...

    Authors: Chaoling Xue, Hongtai Li, Zhiguo Liu, Lili Wang, Yitong Zhao, Ximeng Wei, Hu Fang, Mengjun Liu and Jin Zhao

    Citation: BMC Genomics 2019 20:464

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  16. Content type: Research article

    Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an economically important fruit tree characterized by its juicy fruits rich in antioxidant compounds. Elucidating the genetic basis of the biosynthesis of active a...

    Authors: Haiying Ren, Haiyan Yu, Shuwen Zhang, Senmiao Liang, Xiliang Zheng, Shujian Zhang, Pu Yao, Hongkun Zheng and Xingjiang Qi

    Citation: BMC Genomics 2019 20:458

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  17. Content type: Research article

    Ricinus communis is a highly economically valuable oil crop plant from the spurge family, Euphorbiaceae. However, the available reference genomes are incomplete and to date studies on ricinoleic acid biosynthesis...

    Authors: Lijun Wang, Xiaoling Jiang, Lei Wang, Wei Wang, Chunling Fu, Xingchu Yan and Xinxin Geng

    Citation: BMC Genomics 2019 20:456

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  18. Content type: Research article

    Natural rubber, an indispensable commodity used in approximately 40,000 products, is fundamental to the tire industry. The rubber tree species Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell-Arg., which is nat...

    Authors: Camila Campos Mantello, Lucas Boatwright, Carla Cristina da Silva, Erivaldo Jose Scaloppi Jr, Paulo de Souza Goncalves, W. Brad Barbazuk and Anete Pereira de Souza

    Citation: BMC Genomics 2019 20:455

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  19. Content type: Research article

    The importance of Indian germplasm as origin and primary center of diversity of cultivated melon is widely accepted. Genetic diversity of several collections from Indian has been studied previously, although a...

    Authors: Maria José Gonzalo, Aurora Díaz, Narinder P. S. Dhillon, Umesh K. Reddy, Belén Picó and Antonio J. Monforte

    Citation: BMC Genomics 2019 20:448

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  20. Content type: Database

    Trait ontology (TO) analysis is a powerful system for functional annotation and enrichment analysis of genes. However, given the complexity of the molecular mechanisms underlying phenomes, only a few hundred g...

    Authors: Qingchun Pan, Junfeng Wei, Feng Guo, Suiyong Huang, Yong Gong, Hao Liu, Jianxiao Liu and Lin Li

    Citation: BMC Genomics 2019 20:443

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  21. Content type: Research article

    For spring-type Chinese cabbage production, premature bolting refers to the excessive elongation of dwarf stems before harvesting. Although quantitative trait loci (QTL) mapping for bolting-related traits have...

    Authors: Shuantao Liu, Ronghua Wang, Zhigang Zhang, Qiaoyun Li, Lihua Wang, Yongqiang Wang and Zhizhong Zhao

    Citation: BMC Genomics 2019 20:437

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  22. Content type: Research article

    Cotton is the most essential textile crop worldwide, and phytohormones are critical for cotton fiber development. One example is the role of auxin in fiber initiation, but we know little molecular basis. Micro...

    Authors: Tianlun Zhao, Xiaojian Xu, Min Wang, Cheng Li, Cong Li, Rubing Zhao, Shuijin Zhu, Qiuling He and Jinhong Chen

    Citation: BMC Genomics 2019 20:421

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  23. Content type: Research article

    The process of crop domestication often consists of two stages: initial domestication, where the wild species is first cultivated by humans, followed by diversification, when the domesticated species are subse...

    Authors: Elizabeth A. Cooper, Zachary W. Brenton, Barry S. Flinn, Jerry Jenkins, Shengqiang Shu, Dave Flowers, Feng Luo, Yunsheng Wang, Penny Xia, Kerrie Barry, Chris Daum, Anna Lipzen, Yuko Yoshinaga, Jeremy Schmutz, Christopher Saski, Wilfred Vermerris…

    Citation: BMC Genomics 2019 20:420

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  24. Content type: Research article

    Cotton (Gossypium spp.) is the most important natural fiber crop worldwide, and cottonseed oil is its most important byproduct. Phospholipid: diacylglycerol acyltransferase (PDAT) is important in TAG biosynthesis...

    Authors: Xinshan Zang, Xiaoli Geng, Lei Ma, Nuohan Wang, Wenfeng Pei, Man Wu, Jinfa Zhang and Jiwen Yu

    Citation: BMC Genomics 2019 20:402

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  25. Content type: Research article

    Peanut embryo development is a complex process involving a series of gene regulatory pathways and is easily affected by various elements in the soil. Calcium deficiency in the soil induces early embryo abortio...

    Authors: Hua Chen, Qiang Yang, Kun Chen, Shanshan Zhao, Chong Zhang, Ronglong Pan, Tiecheng Cai, Ye Deng, Xingjun Wang, Yuting Chen, Wenting Chu, Wenping Xie and Weijian Zhuang

    Citation: BMC Genomics 2019 20:392

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  26. Content type: Research article

    Phytohormones are key regulators of plant growth, development, and signalling networks involved in responses to diverse biotic and abiotic stresses. Transcriptional reference maps of hormone responses have bee...

    Authors: Peng-Fei Qi, Yun-Feng Jiang, Zhen-Ru Guo, Qing Chen, Thérèse Ouellet, Lu-Juan Zong, Zhen-Zhen Wei, Yan Wang, Ya-Zhou Zhang, Bin-Jie Xu, Li Kong, Mei Deng, Ji-Rui Wang, Guo-Yue Chen, Qian-Tao Jiang, Xiu-Jin Lan…

    Citation: BMC Genomics 2019 20:390

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  27. Content type: Research article

    Panax ginseng C. A. Mey is one of famous medicinal herb plant species. Its major bioactive compounds are various ginsenosides in roots and rhizomes. It is commonly accepted that ginsenosides are synthesized from ...

    Authors: Le Xue, Zilong He, Xiaochun Bi, Wei Xu, Ting Wei, Shuangxiu Wu and Songnian Hu

    Citation: BMC Genomics 2019 20:383

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  28. Content type: Research article

    Discovering a genome-wide set of avocado (Persea americana Mill.) single nucleotide polymorphisms and characterizing the diversity of germplasm collection is a powerful tool for breeding. However, discovery is a ...

    Authors: Mor Rubinstein, Ravit Eshed, Ada Rozen, Tali Zviran, David N. Kuhn, Vered Irihimovitch, Amir Sherman and Ron Ophir

    Citation: BMC Genomics 2019 20:379

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  29. Content type: Research article

    Banana is one of the most important crops in tropical and sub-tropical regions. To meet the demands of international markets, banana plantations require high amounts of chemical fertilizers which translate int...

    Authors: Rocío M. Gamez, Fernando Rodríguez, Newton Medeiros Vidal, Sandra Ramirez, Roberto Vera Alvarez, David Landsman and Leonardo Mariño-Ramírez

    Citation: BMC Genomics 2019 20:378

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  30. Content type: Research article

    Plant non-specific lipid transfer proteins (nsLTPs) are small, basic proteins that are abundant in higher plants. They have been reported to play an important role in various plant physiological processes, suc...

    Authors: Guojun Li, Menglu Hou, Yaxue Liu, Yue Pei, Minghui Ye, Yao Zhou, Chenxi Huang, Yaqi Zhao and Haoli Ma

    Citation: BMC Genomics 2019 20:375

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  31. Content type: Research article

    Legumes can establish on nitrogen-deprived soils a symbiotic interaction with Rhizobia bacteria, leading to the formation of nitrogen-fixing root nodules. Cytokinin phytohormones are critical for triggering ro...

    Authors: Sovanna Tan, Frédéric Debellé, Pascal Gamas, Florian Frugier and Mathias Brault

    Citation: BMC Genomics 2019 20:373

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  32. Content type: Research article

    Barbarea vulgaris is a wild cruciferous plant and include two distinct types: the G- and P-types named after their glabrous and pubescent leaves, respectively. The types differ significantly in resistance to a ra...

    Authors: Tong-jin Liu, You-jun Zhang, Niels Agerbirk, Hai-ping Wang, Xiao-chun Wei, Jiang-ping Song, Hong-ju He, Xue-zhi Zhao, Xiao-hui Zhang and Xi-xiang Li

    Citation: BMC Genomics 2019 20:371

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  33. Content type: Research article

    Heat shock proteins have important functions in regulating plant growth and response to abiotic stress. HSP70 family genes have been described in several plant species, but a comprehensive analysis of the HSP70 f...

    Authors: Henan Su, Miaomiao Xing, Xing Liu, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang, Yong Wang and Honghao Lv

    Citation: BMC Genomics 2019 20:369

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  34. Content type: Research article

    Species of the Festuca and Lolium genera, as well as intergeneric Festuca × Lolium (Festulolium) hybrids, are valuable fodder and turf grasses for agricultural and amenity purposes worldwide. Festulolium hybrids ...

    Authors: Joanna Majka, Katarzyna Bzdęga, Agnieszka Janiak, Hanna Ćwiek-Kupczyńska, Paweł Krajewski, Tomasz Książczyk and Zbigniew Zwierzykowski

    Citation: BMC Genomics 2019 20:367

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  35. Content type: Research article

    The glyoxalase system usually comprises two enzymes, glyoxalase I (GLYI) and glyoxalase II (GLYII). This system converts cytotoxic methylglyoxal (MG) into non-toxic D-lactate in the presence of reduced glutath...

    Authors: Tiemei Li, Xin Cheng, Yuting Wang, Xiao Yin, Zhiqian Li, Ruiqi Liu, Guotian Liu, Yuejin Wang and Yan Xu

    Citation: BMC Genomics 2019 20:362

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  36. Content type: Research article

    Anaerobic germination tolerance is an important trait for direct-seeded rice varieties. Understanding the genetic basis of anaerobic germination is a key for breeding direct-seeded rice varieties.

    Authors: Jing Yang, Kai Sun, Dongxiu Li, Lixin Luo, Yongzhu Liu, Ming Huang, Guili Yang, Hong Liu, Hui Wang, Zhiqiang Chen and Tao Guo

    Citation: BMC Genomics 2019 20:355

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  37. Content type: Research article

    Bagging is commonly used to enhance red pigmentation and thereby improve fruit quality of apples (Malus domestica). The green-skinned apple cultivar ‘Granny Smith’ develops red pigmentation after bagging removal,...

    Authors: Changqing Ma, Bowen Liang, Bo Chang, Jiuying Yan, Li Liu, Ying Wang, Yazhou Yang and Zhengyang Zhao

    Citation: BMC Genomics 2019 20:353

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  38. Content type: Research article

    Alloplasmic lines, in which the nuclear genome is combined with wild cytoplasm, are often characterized by cytoplasmic male sterility (CMS), regardless of whether it was derived from sexual or somatic hybridiz...

    Authors: Zengxiang Wu, Kaining Hu, Mengjiao Yan, Liping Song, Jing Wen, Chaozhi Ma, Jinxiong Shen, Tingdong Fu, Bin Yi and Jinxing Tu

    Citation: BMC Genomics 2019 20:348

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  39. Content type: Research article

    Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part ...

    Authors: Gui-Hua Li, Han-Cai Chen, Jia-Li Liu, Wen-Long Luo, Da-Sen Xie, Shao-Bo Luo, Ting-Quan Wu, Waheed Akram and Yu-Juan Zhong

    Citation: BMC Genomics 2019 20:343

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  40. Content type: Research article

    Both a source of diversity and the development of genomic tools, such as reference genomes and molecular markers, are equally important to enable faster progress in plant breeding. Pear (Pyrus spp.) lags far behi...

    Authors: Sara Montanari, Luca Bianco, Brian J. Allen, Pedro J. Martínez-García, Nahla V. Bassil, Joseph Postman, Mareike Knäbel, Biff Kitson, Cecilia H. Deng, David Chagné, Marc W. Crepeau, Charles H. Langley, Kate Evans, Amit Dhingra, Michela Troggio and David B. Neale

    Citation: BMC Genomics 2019 20:331

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  41. Content type: Research article

    Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. E3 ligases play a central role in subj...

    Authors: Moon Young Ryu, Seok Keun Cho, Yourae Hong, Jinho Kim, Jong Hum Kim, Gu Min Kim, Yan-Jun Chen, Eva Knoch, Birger Lindberg Møller, Woo Taek Kim, Michael Foged Lyngkjær and Seong Wook Yang

    Citation: BMC Genomics 2019 20:326

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  42. Content type: Research article

    Water deficit and soil salinity substantially influence plant growth and productivity. When occurring individually, plants often exhibit reduced growth resulting in yield losses. The simultaneous occurrence of...

    Authors: Alina Osthoff, Petra Donà dalle Rose, Jutta A. Baldauf, Hans-Peter Piepho and Frank Hochholdinger

    Citation: BMC Genomics 2019 20:325

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  43. Content type: Research article

    Crocins are soluble apocarotenoids that mainly accumulate in the stigma tissue of Crocus sativus and provide the characteristic red color to saffron spice, in addition to being responsible for many of the medicin...

    Authors: Oussama Ahrazem, Javier Argandoña, Alessia Fiore, Andrea Rujas, Ángela Rubio-Moraga, Raquel Castillo and Lourdes Gómez-Gómez

    Citation: BMC Genomics 2019 20:320

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  44. Content type: Research article

    Salinity is an abiotic stress that negatively affects soybean [Glycine max (L.) Merr.] seed yield. Although a major gene for salt tolerance was identified and consistently mapped to chromosome (Chr.) 3 by linkage...

    Authors: Tuyen D. Do, Tri D. Vuong, David Dunn, Michael Clubb, Babu Valliyodan, Gunvant Patil, Pengyin Chen, Dong Xu, Henry T. Nguyen and J. Grover Shannon

    Citation: BMC Genomics 2019 20:318

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  45. Content type: Research article

    Climate change models predict more frequent incidents of heat stress worldwide. This trend will contribute to food insecurity, particularly for some of the most vulnerable regions, by limiting the productivity...

    Authors: Ali Soltani, Sarathi M. Weraduwage, Thomas D. Sharkey and David B. Lowry

    Citation: BMC Genomics 2019 20:312

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  46. Content type: Research article

    Integration of T-DNA into plant genomes via Agrobacterium may interrupt gene structure and generate numerous mutants. The T-DNA caused mutants are valuable materials for understanding T-DNA integration model in p...

    Authors: Huixin Gang, Guifeng Liu, Manman Zhang, Yuming Zhao, Jing Jiang and Su Chen

    Citation: BMC Genomics 2019 20:311

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  47. Content type: Research article

    Although rapeseed (Brassica napus L.) mutant forming multiple siliques was morphologically described and considered to increase the silique number per plant, an important agronomic trait in this crop, the molecul...

    Authors: Liang Chai, Jinfang Zhang, Kun Lu, Haojie Li, Lintao Wu, Hongshen Wan, Benchuan Zheng, Cheng Cui, Jun Jiang and Liangcai Jiang

    Citation: BMC Genomics 2019 20:304

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  48. 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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  49. 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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