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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 24 of 34

  1. (1,3;1,4)-β-Glucan is an important component of the cell walls of barley grain as it affects processability during the production of alcoholic beverages and has significant human health benefits when consumed ...

    Authors: Kelly Houston, Joanne Russell, Miriam Schreiber, Claire Halpin, Helena Oakey, Jennifer M Washington, Allan Booth, Neil Shirley, Rachel A Burton, Geoffrey B Fincher and Robbie Waugh

    Citation: BMC Genomics 2014 15:907

    Content type: Research article

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  2. Common bean was one of the first crops that benefited from the development and utilization of molecular marker-assisted selection (MAS) for major disease resistance genes. Efficiency of MAS for breeding common...

    Authors: Marco H Bello, Samira M Moghaddam, Mark Massoudi, Phillip E McClean, Perry B Cregan and Phillip N Miklas

    Citation: BMC Genomics 2014 15:903

    Content type: Research article

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  3. Stripe rust (Puccinia striiformis f. sp. tritici; Pst) and powdery mildew (Blumeria graminis f. sp. tritici; Bgt) are important diseases of wheat (Triticum aestivum) worldwide. Similar mechanisms and gene transcr...

    Authors: Hong Zhang, Yongzheng Yang, Changyou Wang, Min Liu, Hao Li, Ying Fu, Yajuan Wang, Yingbin Nie, Xinlun Liu and Wanquan Ji

    Citation: BMC Genomics 2014 15:898

    Content type: Research article

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  4. The genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the ...

    Authors: Fabio Cericola, Ezio Portis, Sergio Lanteri, Laura Toppino, Lorenzo Barchi, Nazzareno Acciarri, Laura Pulcini, Tea Sala and Giuseppe Leonardo Rotino

    Citation: BMC Genomics 2014 15:896

    Content type: Research article

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  5. Understanding the molecular basis of domestication can provide insights into the processes of rapid evolution and crop improvement. Here we demonstrated the processes of carrot domestication and identified gen...

    Authors: Jun Rong, Youri Lammers, Jared L Strasburg, Natasha S Schidlo, Yavuz Ariyurek, Tom J de Jong, Peter G L Klinkhamer, Marinus J M Smulders and Klaas Vrieling

    Citation: BMC Genomics 2014 15:895

    Content type: Research article

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  6. Citrus shoot tips abscise at an anatomically distinct abscission zone (AZ) that separates the top part of the shoots into basal and apical portions (citrus self-pruning). Cell separation occurs only at the AZ,...

    Authors: Jin-Zhi Zhang, Kun Zhao, Xiao-Yan Ai and Chun-Gen Hu

    Citation: BMC Genomics 2014 15:892

    Content type: Research article

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  7. Durum wheat (Triticum durum Desf.) is a tetraploid cereal grown in the medium to low-precipitation areas of the Mediterranean Basin, North America and South-West Asia. Genomics applications in durum wheat have th...

    Authors: Marco Maccaferri, Maria Angela Cane’, Maria C Sanguineti, Silvio Salvi, Maria C Colalongo, Andrea Massi, Fran Clarke, Ron Knox, Curtis J Pozniak, John M Clarke, Tzion Fahima, Jorge Dubcovsky, Steven Xu, Karim Ammar, Ildikó Karsai, Gyula Vida…

    Citation: BMC Genomics 2014 15:873

    Content type: Research article

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  8. Sand rice (Agriophyllum squarrosum) is an annual desert plant adapted to mobile sand dunes in arid and semi-arid regions of Central Asia. The sand rice seeds have excellent nutrition value and have been historica...

    Authors: Pengshan Zhao, Salvador Capella-Gutiérrez, Yong Shi, Xin Zhao, Guoxiong Chen, Toni Gabaldón and Xiao-Fei Ma

    Citation: BMC Genomics 2014 15:872

    Content type: Research article

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  9. Sinopodophyllum hexandrum is an endangered medicinal herb, which is commonly present in elevations ranging between 2,400–4,500 m and is sensitive to temperature. Medicinal property of the species is attributed to...

    Authors: Anita Kumari, Heikham Russiachand Singh, Ashwani Jha, Mohit Kumar Swarnkar, Ravi Shankar and Sanjay Kumar

    Citation: BMC Genomics 2014 15:871

    Content type: Research article

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  10. Small, secreted signaling peptides work in parallel with phytohormones to control important aspects of plant growth and development. Genes from the C-TERMINALLY ENCODED PEPTIDE (CEP) family produce such peptid...

    Authors: Huw A Ogilvie, Nijat Imin and Michael A Djordjevic

    Citation: BMC Genomics 2014 15:870

    Content type: Research article

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  11. Common bean (Phaseolus vulgaris) is grown throughout the world and comprises roughly 50% of the grain legumes consumed worldwide. Despite this, genetic resources for common beans have been lacking. Next generatio...

    Authors: Jamie A O’Rourke, Luis P Iniguez, Fengli Fu, Bruna Bucciarelli, Susan S Miller, Scott A Jackson, Philip E McClean, Jun Li, Xinbin Dai, Patrick X Zhao, Georgina Hernandez and Carroll P Vance

    Citation: BMC Genomics 2014 15:866

    Content type: Research article

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  12. Cotton is a major fibre crop grown worldwide that suffers extensive damage from chewing insects, including the cotton boll weevil larvae (Anthonomus grandis). Transcriptome analysis was performed to understand th...

    Authors: Sinara Artico, Marcelo Ribeiro-Alves, Osmundo Brilhante Oliveira-Neto, Leonardo Lima Pepino de Macedo, Sylvia Silveira, Maria Fátima Grossi-de-Sa, Adriana Pinheiro Martinelli and Marcio Alves-Ferreira

    Citation: BMC Genomics 2014 15:854

    Content type: Research article

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  13. Cyclic nucleotide-gated channels (CNGCs) are Ca2+-permeable cation transport channels, which are present in both animal and plant systems. They have been implicated in the uptake of both essential and toxic catio...

    Authors: Zarqa Nawaz, Kaleem Ullah Kakar, Mumtaz A Saand and Qing-Yao Shu

    Citation: BMC Genomics 2014 15:853

    Content type: Research article

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  14. A major constraint affecting the quality and productivity of chrysanthemum is the unusual period of low temperature occurring during early spring, late autumn, and winter. Yet, there has been no systematic inv...

    Authors: Liping Ren, Jing Sun, Sumei Chen, Jiaojiao Gao, Bin Dong, Yanan Liu, Xiaolong Xia, Yinjie Wang, Yuan Liao, Nianjun Teng, Weimin Fang, Zhiyong Guan, Fadi Chen and Jiafu Jiang

    Citation: BMC Genomics 2014 15:844

    Content type: Research article

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  15. Cotton fiber, a highly elongated, thickened single cell of the seed epidermis, is a powerful cell wall research model. Fiber length, largely determined during the elongation stage, is a key property of fiber q...

    Authors: Lei Fang, Ruiping Tian, Xinghe Li, Jiedan Chen, Sen Wang, Peng Wang and Tianzhen Zhang

    Citation: BMC Genomics 2014 15:838

    Content type: Research article

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  16. Independent transcriptome profile analyses of miRNAs or mRNAs under conditions of cadmium (Cd) stress have been widely reported in plants. However, a combined analysis of sRNA sequencing expression data with m...

    Authors: Mingfeng Tang, Donghai Mao, Liwei Xu, Dayong Li, Shuhui Song and Caiyan Chen

    Citation: BMC Genomics 2014 15:835

    Content type: Research article

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  17. Intronless genes are a feature of prokaryotes; however, they are widespread and unequally distributed among eukaryotes and represent an important resource to study the evolution of gene architecture. Although ...

    Authors: Hanwei Yan, Cuiping Jiang, Xiaoyu Li, Lei Sheng, Qing Dong, Xiaojian Peng, Qian Li, Yang Zhao, Haiyang Jiang and Beijiu Cheng

    Citation: BMC Genomics 2014 15:832

    Content type: Database

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  18. The ability to form adventitious roots (AR) is an economically important trait that is lost during the juvenile-to-mature phase change in woody plants. Auxin treatment, which generally promotes rooting in juve...

    Authors: Mohamad Abu-Abied, David Szwerdszarf, Inna Mordehaev, Yossi Yaniv, Saar Levinkron, Mor Rubinstein, Joseph Riov, Ron Ophir and Einat Sadot

    Citation: BMC Genomics 2014 15:826

    Content type: Research article

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  19. High density genotyping data are indispensable for genomic analyses of complex traits in animal and crop species. Maize is one of the most important crop plants worldwide, however a high density SNP genotyping...

    Authors: Sandra Unterseer, Eva Bauer, Georg Haberer, Michael Seidel, Carsten Knaak, Milena Ouzunova, Thomas Meitinger, Tim M Strom, Ruedi Fries, Hubert Pausch, Christofer Bertani, Alessandro Davassi, Klaus FX Mayer and Chris-Carolin Schön

    Citation: BMC Genomics 2014 15:823

    Content type: Research article

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  20. The passion fruit (Passiflora edulis) is a tropical crop of economic importance both for juice production and consumption as fresh fruit. The juice is also used in concentrate blends that are consumed worldwide. ...

    Authors: Anselmo Azevedo Santos, Helen Alves Penha, Arnaud Bellec, Carla de Freitas Munhoz, Andrea Pedrosa-Harand, Hélène Bergès and Maria Lucia Carneiro Vieira

    Citation: BMC Genomics 2014 15:816

    Content type: Research article

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  21. Sudden death syndrome (SDS) is a serious threat to soybean production that can be managed with host plant resistance. To dissect the genetic architecture of quantitative resistance to the disease in soybean, t...

    Authors: Zixiang Wen, Ruijuan Tan, Jiazheng Yuan, Carmille Bales, Wenyan Du, Shichen Zhang, Martin I Chilvers, Cathy Schmidt, Qijian Song, Perry B Cregan and Dechun Wang

    Citation: BMC Genomics 2014 15:809

    Content type: Research article

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  22. Growth regulating factors (GRFs) have been shown to play important roles in plant growth and development. GRF genes represent a large multigene family in plants. Recently, genome-wide structural and evolutiona...

    Authors: Fengde Wang, Nianwei Qiu, Qian Ding, Jingjuan Li, Yihui Zhang, Huayin Li and Jianwei Gao

    Citation: BMC Genomics 2014 15:807

    Content type: Research article

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  23. Litchi is an evergreen woody tree widely cultivated in subtropical and tropical regions. Defective flowering is a major challenge for litchi production in time of climate change and global warming. Previous st...

    Authors: Xingyu Lu, Hyeji Kim, Silin Zhong, Houbin Chen, Zhiqun Hu and Biyan Zhou

    Citation: BMC Genomics 2014 15:805

    Content type: Research article

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  24. The local environment plays a major role in the spatial distribution of plant populations. Natural plant populations have an extremely poor displacing capacity, so their continued survival in a given environme...

    Authors: Matteo Dell’Acqua, Andrea Zuccolo, Metin Tuna, Luca Gianfranceschi and Mario Enrico Pè

    Citation: BMC Genomics 2014 15:801

    Content type: Research article

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  25. Introgression populations are used to make the genetic variation of unadapted germplasm or wild relatives of crops available for plant breeding. They consist of introgression lines that carry small chromosome ...

    Authors: Karen Christin Falke, Gregory S Mahone, Eva Bauer, Grit Haseneyer, Thomas Miedaner, Frank Breuer and Matthias Frisch

    Citation: BMC Genomics 2014 15:782

    Content type: Research article

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  26. Wood formation in tree species is regulated by multiple factors at various layers. Alternative splicing (AS) occurs within a large number of genes in wood formation. However, the functional implications and co...

    Authors: Peng Xu, Yimeng Kong, Dongliang Song, Cheng Huang, Xuan Li and Laigeng Li

    Citation: BMC Genomics 2014 15:780

    Content type: Research article

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  27. A large single nucleotide polymorphism (SNP) dataset was used to analyze genome-wide diversity in a diverse collection of watermelon cultivars representing globally cultivated, watermelon genetic diversity. Th...

    Authors: Padma Nimmakayala, Amnon Levi, Lavanya Abburi, Venkata Lakshmi Abburi, Yan R Tomason, Thangasamy Saminathan, Venkata Gopinath Vajja, Sridhar Malkaram, Rishi Reddy, Todd C Wehner, Sharon E Mitchell and Umesh K Reddy

    Citation: BMC Genomics 2014 15:767

    Content type: Research article

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  28. Small RNA (sRNA) has been described as a regulator of gene expression. In order to understand the role of maize sRNA (Zea mays – hybrid UENF 506-8) during association with endophytic nitrogen-fixing bacteria, we ...

    Authors: Flávia Thiebaut, Cristian A Rojas, Clícia Grativol, Mariana Romeiro Motta, Tauan Vieira, Michael Regulski, Robert A Martienssen, Laurent Farinelli, Adriana S Hemerly and Paulo CG Ferreira

    Citation: BMC Genomics 2014 15:766

    Content type: Research article

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  29. Cotton (Gossypium spp.) is one of the major fibre crops of the world. Although it is classified as salt tolerant crop, cotton growth and productivity are adversely affected by high salinity, especially at germina...

    Authors: Zhen Peng, Shoupu He, Wenfang Gong, Junling Sun, Zhaoe Pan, Feifei Xu, Yanli Lu and Xiongming Du

    Citation: BMC Genomics 2014 15:760

    Content type: Research article

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  30. Bacterial panicle blight caused by the bacterium Burkholderia glumae is an emerging disease of rice in the United States. Not much is known about this disease, the disease cycle or any source of disease resistanc...

    Authors: Zenaida V Magbanua, Mark Arick II, Teresia Buza, Chuan-Yu Hsu, Kurt C Showmaker, Philippe Chouvarine, Peng Deng, Daniel G Peterson and Shien Lu

    Citation: BMC Genomics 2014 15:755

    Content type: Research article

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  31. The Orchidaceae is one of the largest families in the plant kingdom and orchid mycorrhizae (OM) are indispensable in the life cycle of all orchids under natural conditions. In spite of this, little is known co...

    Authors: Xiaolan Zhao, Jianxia Zhang, Chunli Chen, Jingze Yang, Haiyan Zhu, Min Liu and Fubing Lv

    Citation: BMC Genomics 2014 15:747

    Content type: Research article

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  32. Saponins are mainly amphipathic glycosides that posses many biological activities and confer potential health benefits to humans. Inspite of its medicinal attributes most of the triterpenes and enzymes involve...

    Authors: Swati Upadhyay, Ujjal J Phukan, Sonal Mishra and Rakesh Kumar Shukla

    Citation: BMC Genomics 2014 15:746

    Content type: Research article

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  33. Widespread and more frequently occurring drought conditions are a consequence of global warming and increase the demand for tolerant crop varieties to feed the growing world population. A better understanding ...

    Authors: Nina Opitz, Anja Paschold, Caroline Marcon, Waqas Ahmed Malik, Christa Lanz, Hans-Peter Piepho and Frank Hochholdinger

    Citation: BMC Genomics 2014 15:741

    Content type: Research article

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  34. Advances in genotyping technology, such as genotyping by sequencing (GBS), are making genomic prediction more attractive to reduce breeding cycle times and costs associated with phenotyping. Genomic prediction...

    Authors: Diego Jarquín, Kyle Kocak, Luis Posadas, Katie Hyma, Joseph Jedlicka, George Graef and Aaron Lorenz

    Citation: BMC Genomics 2014 15:740

    Content type: Research article

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  35. Legumes form root nodules to house nitrogen fixing bacteria of the rhizobium family. The rhizobia are located intracellularly in the symbiotic nodule cells. In the legume Medicago truncatula these cells produce h...

    Authors: Ibtissem Guefrachi, Marianna Nagymihaly, Catalina I Pislariu, Willem Van de Velde, Pascal Ratet, Mohamed Mars, Michael K Udvardi, Eva Kondorosi, Peter Mergaert and Benoît Alunni

    Citation: BMC Genomics 2014 15:712

    Content type: Research article

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  36. Fusarium verticillioides causes ear rot in maize (Zea mays L.) and accumulation of mycotoxins, that affect human and animal health. Currently, chemical and agronomic measures to control Fusarium ear rot are not v...

    Authors: Alessandra Lanubile, Alberto Ferrarini, Valentina Maschietto, Massimo Delledonne, Adriano Marocco and Diana Bellin

    Citation: BMC Genomics 2014 15:710

    Content type: Research article

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  37. In the whole genome sequencing, genetic map provides an essential framework for accurate and efficient genome assembly and validation. The main objectives of this study were to develop a high-density genetic m...

    Authors: Amit A Deokar, Larissa Ramsay, Andrew G Sharpe, Marwan Diapari, Anoop Sindhu, Kirstin Bett, Thomas D Warkentin and Bunyamin Tar’an

    Citation: BMC Genomics 2014 15:708

    Content type: Research article

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  38. Magnolia sprengeri Pamp is one of the most highly valuable medicinal and ornamental plants of the Magnolia Family. The natural color of M. sprengeri is variable. The complete genome sequence of M. sprengeri is no...

    Authors: Shou-Guo Shi, Mei Yang, Min Zhang, Ping Wang, Yong-Xiang Kang and Jian-Jun Liu

    Citation: BMC Genomics 2014 15:706

    Content type: Research article

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  39. Iron is an essential micronutrient for all living things, required in plants for photosynthesis, respiration and metabolism. A lack of bioavailable iron in soil leads to iron deficiency chlorosis (IDC), causin...

    Authors: Adrienne N Moran Lauter, Gregory A Peiffer, Tengfei Yin, Steven A Whitham, Dianne Cook, Randy C Shoemaker and Michelle A Graham

    Citation: BMC Genomics 2014 15:702

    Content type: Research article

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  40. Hybridization coupled with whole-genome duplication (allopolyploidy) leads to a variety of genetic and epigenetic modifications in the resultant merged genomes. In particular, gene loss and gene silencing are ...

    Authors: Tina Sehrish, V Vaughan Symonds, Douglas E Soltis, Pamela S Soltis and Jennifer A Tate

    Citation: BMC Genomics 2014 15:701

    Content type: Research article

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  41. In plants, microRNAs (miRNAs) regulate gene expression mainly at the post-transcriptional level. Previous studies have demonstrated that miRNA-mediated gene silencing pathways play vital roles in plant develop...

    Authors: Yuanlong Liu, Lun Wang, Dijun Chen, Xiaomeng Wu, Ding Huang, Lingling Chen, Li Li, Xiuxin Deng and Qiang Xu

    Citation: BMC Genomics 2014 15:695

    Content type: Research article

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  42. Herbaceous peony (Paeonia lactiflora Pall.) is a traditional flower in China and a wedding attractive flower in worldwide. In its flower colour, yellow is the rarest which is ten times the price of the other colo...

    Authors: Daqiu Zhao, Yao Jiang, Chuanlong Ning, Jiasong Meng, Shasha Lin, Wen Ding and Jun Tao

    Citation: BMC Genomics 2014 15:689

    Content type: Research article

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  43. High density stress, also known as intraspecies competition, causes significant yield losses in a wide variety of crop plants. At the same time, increases in density tolerance through selective breeding and th...

    Authors: Maksym Misyura, David Guevara, Sanjeena Subedi, Darryl Hudson, Paul D McNicholas, Joseph Colasanti and Steven J Rothstein

    Citation: BMC Genomics 2014 15:681

    Content type: Research article

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  44. Mapping expression quantitative trait loci (eQTL) of targeted genes represents a powerful and widely adopted approach to identify putative regulatory variants. Linking regulation differences to specific genes ...

    Authors: Yan Wang, Yingpeng Han, Weili Teng, Xue Zhao, Yongguang Li, Lin Wu, Dongmei Li and Wenbin Li

    Citation: BMC Genomics 2014 15:680

    Content type: Research article

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  45. The major medicinal alkaloids isolated from Uncaria rhynchophylla (gouteng in chinese) capsules are rhynchophylline (RIN) and isorhynchophylline (IRN). Extracts containing these terpene indole alkaloids (TIAs) ca...

    Authors: Qianqian Guo, Xiaojun Ma, Shugen Wei, Deyou Qiu, Iain W Wilson, Peng Wu, Qi Tang, Lijun Liu, Shoukun Dong and Wei Zu

    Citation: BMC Genomics 2014 15:676

    Content type: Research article

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  46. The molecular mechanisms involved in plant tolerance to either drought or cold have been extensively studied in many plant species. However, few studies have focused on their comparisons especially using non-m...

    Authors: Yaqi Wu, Wei Wei, Xinyue Pang, Xuefeng Wang, Huiling Zhang, Bo Dong, Yanping Xing, Xinguo Li and Maoyan Wang

    Citation: BMC Genomics 2014 15:671

    Content type: Research article

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  47. Genomic prediction is becoming a daily tool for plant breeders. It makes use of genotypic information to make predictions used for selection decisions. The accuracy of the predictions depends on the number of ...

    Authors: Angela-Maria Bernal-Vasquez, Jens Möhring, Malthe Schmidt, Manfred Schönleben, Chris-Carolin Schön and Hans-Peter Piepho

    Citation: BMC Genomics 2014 15:646

    Content type: Research article

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