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  1. Chicken skeletal muscle is an important economic product. The late stages of chicken development constitute the main period that affects meat production. LncRNAs play important roles in controlling the epigene...

    Authors: Yuanfang Li, Wenjiao Jin, Bin Zhai, Yi Chen, Guoxi Li, Yanhua Zhang, Yujie Guo, Guirong Sun, Ruili Han, Zhuanjian Li, Hong Li, Yadong Tian, Xiaojun Liu and Xiangtao Kang
    Citation: BMC Genomics 2021 22:44
    Content type: Research article Published on:

  2. Native cattle breeds are an important source of genetic variation because they might carry alleles that enable them to adapt to local environment and tough feeding conditions. Jiaxian Red, a Chinese native cat...

    Authors: Xiaoting Xia, Shunjin Zhang, Huaju Zhang, Zijing Zhang, Ningbo Chen, Zhigang Li, Hongxia Sun, Xian Liu, Shijie Lyu, Xianwei Wang, Zhiming Li, Peng Yang, Jiawei Xu, Xiaoting Ding, Qiaoting Shi, Eryao Wang…
    Citation: BMC Genomics 2021 22:43
    Content type: Research article Published on:

  3. 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 Published on:

  4. 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 Published on:

  5. Recently, pioneering expression quantitative trait loci (eQTL) studies on single cell RNA sequencing (scRNA-seq) data have revealed new and cell-specific regulatory single nucleotide variants (SNVs). Here, we ...

    Authors: Hongyu Liu, N. M. Prashant, Liam F. Spurr, Pavlos Bousounis, Nawaf Alomran, Helen Ibeawuchi, Justin Sein, Piotr Słowiński, Krasimira Tsaneva-Atanasova and Anelia Horvath
    Citation: BMC Genomics 2021 22:40
    Content type: Methodology article Published on:

  6. Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the P...

    Authors: Néhémie Nzoyikorera, Idrissa Diawara, Pablo Fresia, Fakhreddine Maaloum, Khalid Katfy, Kaotar Nayme, Mossaab Maaloum, Jennifer Cornick, Chrispin Chaguza, Mohammed Timinouni, Houria Belabess, Khalid Zerouali and Naima Elmdaghri
    Citation: BMC Genomics 2021 22:39
    Content type: Research article Published on:

  7. Atypical external genitalia are often a sign of reproductive organ pathologies and infertility with both environmental or genetic causes, including karyotypic abnormalities. Genome-wide association studies (GW...

    Authors: Gabriele Flossmann, Christine Wurmser, Hubert Pausch, Amabel Tenghe, Jörg Dodenhoff, Günther Dahinten, Kay-Uwe Götz, Ingolf Russ and Ruedi Fries
    Citation: BMC Genomics 2021 22:38
    Content type: Research article Published on:

  9. DNA methylation is likely a key mechanism regulating changes in gene transcription in traits that show temporal fluctuations in response to environmental conditions. To understand the transcriptional role of D...

    Authors: Melanie Lindner, Irene Verhagen, Heidi M. Viitaniemi, Veronika N. Laine, Marcel E. Visser, Arild Husby and Kees van Oers
    Citation: BMC Genomics 2021 22:36
    Content type: Research article Published on:

  11. 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 Published on:

  12. Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resol...

    Authors: Sonia Rey, Xingkun Jin, Børge Damsgård, Marie-Laure Bégout and Simon Mackenzie
    Citation: BMC Genomics 2021 22:33
    Content type: Research article Published on:

  13. The red sea urchin Mesocentrotus franciscanus is an ecologically important kelp forest herbivore and an economically valuable wild fishery species. To examine how M. franciscanus responds to its environment on a ...

    Authors: Juliet M. Wong and Gretchen E. Hofmann
    Citation: BMC Genomics 2021 22:32
    Content type: Research article Published on:

  15. The use of sex-sorted sperm in cattle assisted reproduction is constantly increasing. However, sperm fertility can substantially differ between unsorted (conventional) and sex-sorted semen batches of the same ...

    Authors: Esin Keles, Eleni Malama, Siyka Bozukova, Mathias Siuda, Sarah Wyck, Ulrich Witschi, Stefan Bauersachs and Heinrich Bollwein
    Citation: BMC Genomics 2021 22:30
    Content type: Research article Published on:

  16. Tomato plant growth is frequently hampered by a high susceptibility to pests and diseases. Traditional chemical control causes a serious impact on both the environment and human health. Therefore, seeking envi...

    Authors: Lu Zhou, Chunxu Song, Zhibo Li and Oscar P. Kuipers
    Citation: BMC Genomics 2021 22:29
    Content type: Research article Published on:

  17. Psychrotrophic lactic acid bacteria (LAB) species are the dominant species in the microbiota of cold-stored modified-atmosphere-packaged food products and are the main cause of food spoilage. Despite the impor...

    Authors: Ilhan Cem Duru, Anne Ylinen, Sergei Belanov, Alan Avila Pulido, Lars Paulin and Petri Auvinen
    Citation: BMC Genomics 2021 22:28
    Content type: Research article Published on:

  18. Exosomes are extracellular vesicles (EVs) derived from endocytic compartments of eukaryotic cells which contain various biomolecules like mRNAs or miRNAs. Exosomes influence the biologic behaviour and progress...

    Authors: Yao Dai, Yumeng Cao, Jens Köhler, Aiping Lu, Shaohua Xu and Haiyun Wang
    Citation: BMC Genomics 2021 22:27
    Content type: Research article Published on:

  19. 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 Published on:

  20. Olfactory systems take on important tasks to distinguish salient information from a complex olfactory environment, such as locating hosts, mating, aggression, selecting oviposition sites, and avoiding predator...

    Authors: Li Xu, Kai-Yue Tang, Xiao-Feng Chen, Yong Tao, Hong-Bo Jiang and Jin-Jun Wang
    Citation: BMC Genomics 2021 22:25
    Content type: Research article Published on:

  21. 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 Published on:

  22. 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 Published on:

  23. 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 Published on:

  24. Cadmium (Cd) is a nonessential heavy metal with potentially deleterious effects on different organisms. The organisms have evolved sophisticated defense system to alleviate heavy metal toxicity. Hydrogen sulfi...

    Authors: Hongrui Lv, Jing Xu, Tao Bo and Wei Wang
    Citation: BMC Genomics 2021 22:21
    Content type: Research article Published on:

  25. 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 Published on:

  26. 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 Published on:

  27. The pond snail Lymnaea stagnalis (L. stagnalis) has been widely used as a model organism in neurobiology, ecotoxicology, and parasitology due to the relative simplicity of its central nervous system (CNS). Howeve...

    Authors: Nancy Dong, Julia Bandura, Zhaolei Zhang, Yan Wang, Karine Labadie, Benjamin Noel, Angus Davison, Joris M. Koene, Hong-Shuo Sun, Marie-Agnès Coutellec and Zhong-Ping Feng
    Citation: BMC Genomics 2021 22:18
    Content type: Research article Published on:

  28. 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 Published on:

  29. 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 Published on:

  30. Walnut anthracnose caused by Colletotrichum gloeosporioides (Penz.) Penz. and Sacc. is an important walnut production problem in China. Although the long non-coding RNAs (lncRNAs) are important for plant disease ...

    Authors: Shan Feng, Hongcheng Fang, Xia Liu, Yuhui Dong, Qingpeng Wang and Ke Qiang Yang
    Citation: BMC Genomics 2021 22:15
    Content type: Research article Published on:

  31. Bovine Respiratory Syncytial Virus (BRSV) is a cause of Bovine Respiratory Disease (BRD). DNA-based biomarkers contributing to BRD resistance are potentially present in non-protein-coding regulatory regions of...

    Authors: Dayle Johnston, JaeWoo Kim, Jeremy F. Taylor, Bernadette Earley, Matthew S. McCabe, Ken Lemon, Catherine Duffy, Michael McMenamy, S. Louise Cosby and Sinéad M. Waters
    Citation: BMC Genomics 2021 22:14
    Content type: Research article Published on:

  32. Actinidia eriantha is a precious material to study the metabolism and regulation of ascorbic acid (AsA) because of its high AsA content. Although the pathway of AsA biosynthesis in kiwifruit has been identified, ...

    Authors: Guanglian Liao, Lu Chen, Yanqun He, Xishi Li, Zhengxin Lv, Shuyao Yi, Min Zhong, Chunhui Huang, Dongfeng Jia, Xueyan Qu and Xiaobiao Xu
    Citation: BMC Genomics 2021 22:13
    Content type: Research article Published on:

  33. Average daily gain (ADG) and lean meat percentage (LMP) are the main production performance indicators of pigs. Nevertheless, the genetic architecture of ADG and LMP is still elusive. Here, we conducted genome...

    Authors: Shenping Zhou, Rongrong Ding, Fanming Meng, Xingwang Wang, Zhanwei Zhuang, Jianping Quan, Qian Geng, Jie Wu, Enqin Zheng, Zhenfang Wu, Jianhui Yang and Jie Yang
    Citation: BMC Genomics 2021 22:12
    Content type: Research article Published on:

  34. The genus Ehrlichia consists of tick-borne obligatory intracellular bacteria that can cause deadly diseases of medical and agricultural importance. Ehrlichia sp. HF, isolated from Ixodes ovatus ticks in Japan [al...

    Authors: Mingqun Lin, Qingming Xiong, Matthew Chung, Sean C. Daugherty, Sushma Nagaraj, Naomi Sengamalay, Sandra Ott, Al Godinez, Luke J. Tallon, Lisa Sadzewicz, Claire Fraser, Julie C. Dunning Hotopp and Yasuko Rikihisa
    Citation: BMC Genomics 2021 22:11
    Content type: Research article Published on:

  37. DNA methylation, a biochemical modification of cytosine, has an important role in lipid metabolism. Fatty liver hemorrhagic syndrome (FLHS) is a serious disease and is tightly linked to lipid homeostasis. Here...

    Authors: Xiaodong Tan, Ranran Liu, Yonghong Zhang, Xicai Wang, Jie Wang, Hailong Wang, Guiping Zhao, Maiqing Zheng and Jie Wen
    Citation: BMC Genomics 2021 22:8
    Content type: Research article Published on:

  38. Population history, production system and within-breed selection pressure impacts the genome architecture resulting in reduced genetic diversity and increased frequency of runs of homozygosity islands. This st...

    Authors: E. F. Dzomba, M. Chimonyo, R. Pierneef and F. C. Muchadeyi
    Citation: BMC Genomics 2021 22:7
    Content type: Research article Published on:

  39. DNA methylation (DNAm) profiling has emerged as a powerful tool for characterizing the placental methylome. However, previous studies have focused primarily on whole placental tissue, which is a mixture of epi...

    Authors: Victor Yuan, Desmond Hui, Yifan Yin, Maria S. Peñaherrera, Alexander G. Beristain and Wendy P. Robinson
    Citation: BMC Genomics 2021 22:6
    Content type: Research article Published on:

  40. Single-cell (sc) sequencing performs unbiased profiling of individual cells and enables evaluation of less prevalent cellular populations, often missed using bulk sequencing. However, the scale and the complex...

    Authors: Namit Kumar, Ryan Golhar, Kriti Sen Sharma, James L. Holloway, Srikant Sarangi, Isaac Neuhaus, Alice M. Walsh and Zachary W. Pitluk
    Citation: BMC Genomics 2021 22:5
    Content type: Database Published on:

  41. Long noncoding RNAs (lncRNAs) have emerged as an important class of transcriptional regulators in cellular processes. The past decades have witnessed great progress in lncRNA studies in a variety of organisms....

    Authors: Longsheng Xing, Yu Xi, Xi Qiao, Cong Huang, Qiang Wu, Nianwan Yang, Jianyang Guo, Wanxue Liu, Wei Fan, Fanghao Wan and Wanqiang Qian
    Citation: BMC Genomics 2021 22:4
    Content type: Research article Published on:

  42. Studies on the airway microbiome have been performed using a wide range of laboratory protocols for high-throughput sequencing of the bacterial 16S ribosomal RNA (16S rRNA) gene. We sought to determine the imp...

    Authors: Christine Drengenes, Tomas M. L. Eagan, Ingvild Haaland, Harald G. Wiker and Rune Nielsen
    Citation: BMC Genomics 2021 22:3
    Content type: Research article Published on:

  43. 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 Published on:

  44. Bovine frontonasal dysplasias like arhinencephaly, synophthalmia, cyclopia and anophthalmia are sporadic congenital facial malformations. In this study, computed tomography, necropsy, histopathological examina...

    Authors: Marina Braun, Annika Lehmbecker, Deborah Eikelberg, Maren Hellige, Andreas Beineke, Julia Metzger and Ottmar Distl
    Citation: BMC Genomics 2021 22:1
    Content type: Research article Published on:

  46. Genome-wide association studies (GWAS) have identified many individual genes associated with brain imaging quantitative traits (QTs) in Alzheimer’s disease (AD). However single marker level association discove...

    Authors: Xianglian Meng, Jin Li, Qiushi Zhang, Feng Chen, Chenyuan Bian, Xiaohui Yao, Jingwen Yan, Zhe Xu, Shannon L. Risacher, Andrew J. Saykin, Hong Liang and Li Shen
    Citation: BMC Genomics 2020 21(Suppl 11):896
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  47. Accurate prediction of protein structure is fundamentally important to understand biological function of proteins. Template-based modeling, including protein threading and homology modeling, is a popular metho...

    Authors: Haicang Zhang and Yufeng Shen
    Citation: BMC Genomics 2020 21(Suppl 11):878
    Content type: Methodology Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  48. Abnormal metabolic pathways have been considered as one of the hallmarks of cancer. While numerous metabolic pathways have been studied in various cancers, the direct link between metabolic pathway gene expres...

    Authors: Dan Zhang, Yan Guo and Ni Xie
    Citation: BMC Genomics 2020 21(Suppl 11):860
    Content type: Research Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  49. In this introduction article, we summarize the 2020 International Conference on Intelligent Biology and Medicine (ICIBM 2020) conference which was held on August 9–10, 2020 (virtual conference). We then briefl...

    Authors: Wei Zhang, Zhongming Zhao, Kai Wang, Li Shen and Xinghua Shi
    Citation: BMC Genomics 2020 21(Suppl 11):831
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

  50. RNA-Seq, the high-throughput sequencing (HT-Seq) of mRNAs, has become an essential tool for characterizing gene expression differences between different cell types and conditions. Gene expression is regulated ...

    Authors: Yingying Cao, Simo Kitanovski and Daniel Hoffmann
    Citation: BMC Genomics 2020 21(Suppl 11):802
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 11

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BMC Genomics

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