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  1. Content type: Research article

    Insights into the genetic capacities of species to adapt to future climate change can be gained by using comparative genomic and transcriptomic data to reconstruct the genetic changes associated with such adap...

    Authors: Rahul V. Rane, Stephen L. Pearce, Fang Li, Chris Coppin, Michele Schiffer, Jennifer Shirriffs, Carla M. Sgrò, Philippa C. Griffin, Goujie Zhang, Siu F. Lee, Ary A. Hoffmann and John G. Oakeshott

    Citation: BMC Genomics 2019 20:52

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  2. Content type: Research article

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

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

    Citation: BMC Genomics 2019 20:51

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  3. Content type: Research article

    Aging is accompanied with loss of tissue homeostasis and accumulation of cellular damages. As one of the important metabolic centers, liver shows age-related dysregulation of lipid metabolism, impaired detoxif...

    Authors: Kerui Huang, Wenhao Chen, Fang Zhu, Patrick Wai-Lun Li, Pankaj Kapahi and Hua Bai

    Citation: BMC Genomics 2019 20:50

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  4. Content type: Research article

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

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

    Citation: BMC Genomics 2019 20:49

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  5. Content type: Research article

    Being critically important to the ecosystem, the stability of coral reefs is directly related to the marine and surrounding terrestrial environments. However, coral reefs are now undergoing massive and acceler...

    Authors: Chen Huang, Dongliang Leng, Shixue Sun and Xiaohua Douglas Zhang

    Citation: BMC Genomics 2019 20:48

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  6. Content type: Research article

    Bloodstream malaria parasites require Ca++ for their development, but the sites and mechanisms of Ca++ utilization are not well understood. We hypothesized that there may be differences in Ca++ uptake or utilizat...

    Authors: Liana Apolis, Joanna Olivas, Prakash Srinivasan, Ambuj K. Kushwaha and Sanjay A. Desai

    Citation: BMC Genomics 2019 20:47

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  7. Content type: Research article

    The mechanism of latency and the ability of the cyprinid herpesvirus 3 (CyHV-3) to establish life-long infections in carp remains poorly understood. To explain the role of miRNAs in this process we applied a r...

    Authors: Michal Reichert, Anna Lukasik, Piotr Zielenkiewicz, Marek Matras, Joanna Maj-Paluch, Magdalena Stachnik and Ewa Borzym

    Citation: BMC Genomics 2019 20:46

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  8. Content type: Research article

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

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

    Citation: BMC Genomics 2019 20:45

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  9. Content type: Correction

    Following the publication of this article [1], the authors informed us of the following typographical errors in the Results section (the changes are marked in bold).

    Authors: Thomas J. F. Pranzatelli, Drew G. Michae and John A. Chiorini

    Citation: BMC Genomics 2019 20:44

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    The original article was published in BMC Genomics 2018 19:563

  10. Content type: Research article

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

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

    Citation: BMC Genomics 2019 20:43

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  11. Content type: Research article

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

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

    Citation: BMC Genomics 2019 20:41

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  12. Content type: Software

    Target enrichment combined with chromosome conformation capturing methodologies such as capture Hi-C (CHC) can be used to investigate spatial layouts of genomic regions with high resolution and at scalable cos...

    Authors: Peter Hansen, Salaheddine Ali, Hannah Blau, Daniel Danis, Jochen Hecht, Uwe Kornak, Darío G. Lupiáñez, Stefan Mundlos, Robin Steinhaus and Peter N. Robinson

    Citation: BMC Genomics 2019 20:40

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  13. Content type: Research article

    Differential gene expression can be translated into differing phenotypic traits. Especially during embryogenesis, specific gene expression networks regulate the development of different body structures. Cichli...

    Authors: Athimed El Taher, Nicolás Lichilín, Walter Salzburger and Astrid Böhne

    Citation: BMC Genomics 2019 20:39

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  14. Content type: Review

    The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protei...

    Authors: Shannon J. Sibbald, Julia F. Hopkins, Gina V. Filloramo and John M. Archibald

    Citation: BMC Genomics 2019 20:38

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  15. Content type: Research article

    Cryptosporidium parvum is an important zoonotic parasitic disease worldwide, but the molecular mechanisms of the host–parasite interaction are not fully understood. Noncoding microRNAs (miRNAs) are considered key...

    Authors: Chenrong Wang, Limin Liu, Huili Zhu, Lu Zhang, Rongjun Wang, Zhenjie Zhang, Jianying Huang, Sumei Zhang, Fuchun Jian, Changshen Ning and Longxian Zhang

    Citation: BMC Genomics 2019 20:37

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  16. Content type: Research article

    Long non-coding RNAs (lncRNAs) are important component of mammalian genomes, where their numbers are even larger than that of protein-coding genes. For example, human (Homo sapiens) (96,308 vs. 20,376) and mouse

    Authors: Chang Lu, Yanling Xing, Han Cai, Yirong Shi, Jinhua Liu and Yinhua Huang

    Citation: BMC Genomics 2019 20:36

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  17. Content type: Research article

    The Dickeya genus is part of the Pectobacteriaceae family that is included in the newly described enterobacterales order. It comprises a group of aggressive soft rot pathogens with wide geographic distribution an...

    Authors: Špela Alič, Jacques Pédron, Tanja Dreo and Frédérique Van Gijsegem

    Citation: BMC Genomics 2019 20:34

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  18. Content type: Research article

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

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

    Citation: BMC Genomics 2019 20:33

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  19. Content type: Research article

    Positively correlated with carcass weight and animal growth, the ribeye area (REA) and the backfat thickness (BFT) are economic important carcass traits, which impact directly on producer’s payment. The select...

    Authors: Bárbara Silva-Vignato, Luiz L. Coutinho, Mirele D. Poleti, Aline S. M. Cesar, Cristina T. Moncau, Luciana C. A. Regitano and Júlio C. C. Balieiro

    Citation: BMC Genomics 2019 20:32

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  20. Content type: Research article

    Average daily gain (ADG) is an important trait that contributes to the production efficiency and economic benefits in the beef cattle industry. The molecular mechanisms of ADG have not yet been fully explored ...

    Authors: Lingyang Xu, Liu Yang, Lei Wang, Bo Zhu, Yan Chen, Huijiang Gao, Xue Gao, Lupei Zhang, George E. Liu and Junya Li

    Citation: BMC Genomics 2019 20:31

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  21. Content type: Research article

    Co-colonization by Pseudomonas aeruginosa and Staphylococcus aureus is frequent in cystic fibrosis patients. Polymicrobial infections involve both detrimental and beneficial interactions between different bacteri...

    Authors: Mikaël Tognon, Thilo Köhler, Alexandre Luscher and Christian van Delden

    Citation: BMC Genomics 2019 20:30

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  22. Content type: Research article

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

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

    Citation: BMC Genomics 2019 20:29

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  23. Content type: Research article

    The prevalence of azole resistance in clinical and environmental Aspergillus fumigatus isolates is rising over the past decades, but the molecular basis of the development of antifungal drug resistance is not wel...

    Authors: Margriet W. J. Hokken, Jan Zoll, Jordy P. M. Coolen, Bas J. Zwaan, Paul E. Verweij and Willem J. G. Melchers

    Citation: BMC Genomics 2019 20:28

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  24. Content type: Research article

    B-box (BBX) proteins play important roles in plant growth regulation and development including photomorphogenesis, photoperiodic regulation of flowering, and responses to biotic and abiotic stresses.

    Authors: Abdullah Shalmani, Xiu-Qing Jing, Yi Shi, Izhar Muhammad, Meng-Ru Zhou, Xiao-Yong Wei, Qiong-Qiong Chen, Wen-Qiang Li, Wen-Ting Liu and Kun-Ming Chen

    Citation: BMC Genomics 2019 20:27

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  25. Content type: Research article

    Orchids produce a colorless protocorm by symbiosis with fungi upon seed germination. For mass production of orchids, the prevailing approaches are both generation of protocorm-like bodies (PLBs) from callus an...

    Authors: Chia-Chi Hsu, Pei-Han Lai, Tien-Chih Chen, Wen-Chieh Tsai, Jui-Lin Hsu, Yu-Yun Hsiao, Wen-Luan Wu, Ching-Hsiu Tsai, Wen-Huei Chen and Hong-Hwa Chen

    Citation: BMC Genomics 2019 20:25

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  26. Content type: Research article

    Euscaphis konishii Hayata, a member of the Staphyleaceae Family, is a plant that has been widely used in Traditional Chinese Medicine and it has been the source for several types of flavonoids. To identify candid...

    Authors: Wenxian Liang, Lin Ni, Rebeca Carballar-Lejarazú, Xiaoxing Zou, Weihong Sun, Lingjiao Wu, Xueyuan Yuan, Yanling Mao, Wei Huang and Shuangquan Zou

    Citation: BMC Genomics 2019 20:24

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  27. Content type: Research article

    Short-read sequencing technologies have made microbial genome sequencing cheap and accessible. However, closing genomes is often costly and assembling short reads from genomes that are repetitive and/or have e...

    Authors: Sarah Goldstein, Lidia Beka, Joerg Graf and Jonathan L. Klassen

    Citation: BMC Genomics 2019 20:23

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  28. Content type: Research article

    Aging is affected by genetic and environmental factors, and cigarette smoking is strongly associated with accumulation of senescent cells. In this study, we wanted to identify genes that may potentially be ben...

    Authors: Hannah Voic, Xiuying Li, Jun-Ho Jang, Chunbin Zou, Prithu Sundd, Jonathan Alder, Mauricio Rojas, Divay Chandra, Scott Randell, Rama K. Mallampalli, Yohannes Tesfaigzi, Tyrone Ryba and Toru Nyunoya

    Citation: BMC Genomics 2019 20:22

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  29. Content type: Research article

    Optimum flowering time is a key agronomic trait in Brassica napus. To investigate the genetic architecture and genetic regulation of flowering time in this important crop, we conducted quantitative trait loci (QT...

    Authors: Hongju Jian, Aoxiang Zhang, Jinqi Ma, Tengyue Wang, Bo Yang, Lan Shuan Shuang, Min Liu, Jiana Li, Xinfu Xu, Andrew H. Paterson and Liezhao Liu

    Citation: BMC Genomics 2019 20:21

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  30. Content type: Research article

    Salmonella enterica subspecies enterica is an animal and zoonotic pathogen of global importance. Cattle are a significant reservoir of human non-typhoidal salmonellosis and can suffer enteric and systemic disease...

    Authors: Prerna Vohra, Roy R. Chaudhuri, Matthew Mayho, Christina Vrettou, Cosmin Chintoan-Uta, Nicholas R. Thomson, Jayne C. Hope, John Hopkins and Mark P. Stevens

    Citation: BMC Genomics 2019 20:20

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  31. Content type: Research article

    A widely used approach in next-generation sequencing projects is the alignment of reads to a reference genome. Despite methodological and hardware improvements which have enhanced the efficiency and accuracy o...

    Authors: Veronika N. Laine, Toni I. Gossmann, Kees van Oers, Marcel E. Visser and Martien A. M. Groenen

    Citation: BMC Genomics 2019 20:19

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  32. Content type: Research article

    Research on the submergence stress of rice has concentrated on the quiescence strategy to survive in long-term flooding conditions based on Submergence-1A (SUB1A). In the case of the ripening period, it is imp...

    Authors: Hyeon Seok Lee, Woon Ha Hwang, Jae Hyeok Jeong, Seung Hyeon Ahn, Jeong Seon Baek, Han Yong Jeong, Hong Kyu Park, Bon Il Ku, Jong Tak Yun, Geon Hwi Lee and Kyung Jin Choi

    Citation: BMC Genomics 2019 20:18

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  33. Content type: Research article

    Spalax, the blind mole rat, developed an extraordinary cancer resistance during 40 million years of evolution in a subterranean, hypoxic, thus DNA damaging, habitat. In 50 years of Spalax research, no spontaneous...

    Authors: Robert Altwasser, Arnon Paz, Abraham Korol, Irena Manov, Aaron Avivi and Imad Shams

    Citation: BMC Genomics 2019 20:17

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  34. Content type: Research article

    Transcription factors (TFs) specifically bind to DNA sequences and control the expression of target genes. AoXlnR is a key TF involved in the expression of xylanolytic and cellulolytic enzymes in the filamento...

    Authors: Hiroya Oka, Takaaki Kojima, Kunio Ihara, Tetsuo Kobayashi and Hideo Nakano

    Citation: BMC Genomics 2019 20:16

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  35. Content type: Research article

    Pathogens stimulate immune functions of macrophages. Macrophages are a key sentinel cell regulating the response to pathogenic ligands and orchestrating the direction of the immune response. Our study aimed at...

    Authors: Felix N. Toka, Kiera Dunaway, Felicia Smaltz, Lidia Szulc-Dąbrowska, Jenny Drnevich, Matylda Barbara Mielcarska, Magdalena Bossowska-Nowicka and Matthias Schweizer

    Citation: BMC Genomics 2019 20:15

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  36. Content type: Research article

    Circadian clocks are found in nearly all organisms, from bacteria to mammals, and ensure that behavioral and physiological processes occur at optimal times of day and in the correct temporal order. It is becom...

    Authors: Alex C. Boomgarden, Gabriel D. Sagewalker, Aashaka C. Shah, Sarah D. Haider, Pramathini Patel, Heather E. Wheeler, Christine M. Dubowy and Daniel J. Cavanaugh

    Citation: BMC Genomics 2019 20:14

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  37. Content type: Research article

    Duck species are known to have different susceptibility to fatty liver production in response to overfeeding. In order to better describe mechanisms involved in the development of hepatic steatosis and differe...

    Authors: Frédéric Hérault, Magalie Houée-Bigot, Elisabeth Baéza, Olivier Bouchez, Diane Esquerré, Christophe Klopp and Christian Diot

    Citation: BMC Genomics 2019 20:13

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  38. Content type: Research article

    It has become clear in recent years that many genes in a given species may not be found in a single genotype thus using sequences from a single genotype as reference may not be adequate for various applications.

    Authors: Yanling Ma, Miao Liu, Jiri Stiller and Chunji Liu

    Citation: BMC Genomics 2019 20:12

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  39. Content type: Research article

    Streptococcus agalactiae (GBS) is a major pathogen of Nile tilapia, a global commodity of the aquaculture sector. The aims of this study were to evaluate protein expression in the main genotypes of GBS isolated f...

    Authors: Guilherme Campos Tavares, Felipe Luiz Pereira, Gustavo Morais Barony, Cristiana Perdigão Rezende, Wanderson Marques da Silva, Gustavo Henrique Martins Ferreira de Souza, Thiago Verano-Braga, Vasco Ariston de Carvalho Azevedo, Carlos Augusto Gomes Leal and Henrique César Pereira Figueiredo

    Citation: BMC Genomics 2019 20:11

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  40. Content type: Research article

    Canker disease caused by Neoscytalidium dimidiatum is the most serious disease that attacks the pitaya industry. One pathogenic fungus, referred to as ND8, was isolated from the wild-type red-fleshed pitaya (Hylo...

    Authors: Min Xu, Cheng-Li Liu, Juan Luo, Zhao Qi, Zhen Yan, Yu Fu, Shuang-Shuang Wei and Hua Tang

    Citation: BMC Genomics 2019 20:10

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  41. Content type: Research article

    3’ RNA sequencing provides an alternative to whole transcript analysis. However, we do not know a priori the relative advantage of each method. Thus, a comprehensive comparison between the whole transcript and...

    Authors: Feiyang Ma, Brie K. Fuqua, Yehudit Hasin, Clara Yukhtman, Chris D. Vulpe, Aldons J. Lusis and Matteo Pellegrini

    Citation: BMC Genomics 2019 20:9

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  42. Content type: Research article

    Ruminants play a great role in sustainable livestock since they transform pastures, silage, and crop residues into high-quality human food (i.e. milk and beef). Animals with better ability to convert food into...

    Authors: Francisco José Novais, Pedro Ratto Lisboa Pires, Pâmela Almeida Alexandre, Robert A Dromms, Amadeu Hoshi Iglesias, José Bento Sterman Ferraz, Mark Philip-Walter Styczynski and Heidge Fukumasu

    Citation: BMC Genomics 2019 20:8

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  43. Content type: Research article

    Celastrus angulatus Maxim is a kind of crucial and traditional insecticidal plant widely distributed in the mountains of southwest China. Celangulin V is the efficient insecticidal sesquiterpenoid of C. angulatus

    Authors: Weiguo Li, Ranran Xu, Xiaoguang Yan, Dongmei Liang, Lei Zhang, Xiaoyu Qin, Qinggele Caiyin, Guangrong Zhao, Wenhai Xiao, Zhaonong Hu and Jianjun Qiao

    Citation: BMC Genomics 2019 20:7

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  44. Content type: Software

    Sequencing data has become a standard measure of diverse cellular activities. For example, gene expression is accurately measured by RNA sequencing (RNA-Seq) libraries, protein-DNA interactions are captured by...

    Authors: Alper Kucukural, Onur Yukselen, Deniz M. Ozata, Melissa J. Moore and Manuel Garber

    Citation: BMC Genomics 2019 20:6

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  45. Content type: Research article

    Innate immunity provides the core recognition system in animals for preventing infection, but also plays an important role in managing the relationship between an animal host and its symbiont. Most of our know...

    Authors: Kai Kamm, Bernd Schierwater and Rob DeSalle

    Citation: BMC Genomics 2019 20:5

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  46. Content type: Research article

    Argument remains as to whether birds have lost genes compared with mammals and non-avian vertebrates during speciation. High quality-reference gene sets are necessary for precisely evaluating gene gain and los...

    Authors: Zhong-Tao Yin, Feng Zhu, Fang-Bin Lin, Ting Jia, Zhen Wang, Dong-Ting Sun, Guang-Shen Li, Cheng-Lin Zhang, Jacqueline Smith, Ning Yang and Zhuo-Cheng Hou

    Citation: BMC Genomics 2019 20:4

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  47. Content type: Research article

    Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This stud...

    Authors: Meng-Ting Deng, Feng Zhu, Yu-Ze Yang, Fang-Xi Yang, Jin-ping Hao, Si-Rui Chen and Zhuo-Cheng Hou

    Citation: BMC Genomics 2019 20:1

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