Articles

Functional analysis of bovine interleukin-10 receptor alpha in response to Mycobacterium avium subsp. paratuberculosis lysate using CRISPR/Cas9

The interleukin-10 receptor alpha (IL10RA) gene codes for the alpha chain of the IL-10 receptor which binds the cytokine IL-10. IL-10 is an anti-inflammatory cytokine with immunoregulatory function during the pat...

Authors: Sanjay Mallikarjunappa, Umesh K. Shandilya, Ankita Sharma, Kristen Lamers, Nathalie Bissonnette, Niel A. Karrow and Kieran G. Meade

The story of the lost twins: decoding the genetic identities of the Kumhar and Kurcha populations from the Indian subcontinent

The population structure of the Indian subcontinent is a tapestry of extraordinary diversity characterized by the amalgamation of autochthonous and immigrant ancestries and rigid enforcement of sociocultural s...

Authors: Ranajit Das, Vladimir A. Ivanisenko, Anastasia A. Anashkina and Priyanka Upadhyai

Studying polymorphic variants of the NAT2 gene (NAT2*5 and NAT2*7) in Nenets populations of Northern Siberia

N-acetyltransferase 2 plays a crucial role in the metabolism of a wide range of xenobiotics, including many drugs, carcinogens, and other chemicals in the human environment. The article presents for the first ...

Authors: Roza Pavlovna Tiis, Ludmila Pavlovna Osipova, Daria Veniaminovna Lichman, Elena Nikolaevna Voronina and Maxim Leonidovich Filipenko

Genetics research at the "Centenary of human population genetics" conference and SBB-2019

Authors: Tatiana V. Tatarinova, Ludmila E. Tabikhanova, Gilda Eslami, Haihua Bai and Yuriy L. Orlov

Positive selection in admixed populations from Ethiopia

In the process of adaptation of humans to their environment, positive or adaptive selection has played a main role. Positive selection has, however, been under-studied in African populations, despite their div...

Authors: Sandra Walsh, Luca Pagani, Yali Xue, Hafid Laayouni, Chris Tyler-Smith and Jaume Bertranpetit

Molecular and cytological analysis of widely-used Gal4 driver lines for Drosophila neurobiology

The Drosophila central nervous system (CNS) is a convenient model system for the study of the molecular mechanisms of conserved neurobiological processes. The manipulation of gene activity in specific cell types ...

Authors: Anna A. Ogienko, Evgeniya N. Andreyeva, Evgeniya S. Omelina, Anastasiya L. Oshchepkova and Alexey V. Pindyurin

Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome

In population ecology, the concept of reproductive potential denotes the most vital indicator of chances to produce and sustain a healthy descendant until his/her reproductive maturity under the best condition...

Authors: Mikhail Ponomarenko, Maxim Kleshchev, Petr Ponomarenko, Irina Chadaeva, Ekaterina Sharypova, Dmitry Rasskazov, Semyon Kolmykov, Irina Drachkova, Gennady Vasiliev, Natalia Gutorova, Elena Ignatieva, Ludmila Savinkova, Anton Bogomolov, Ludmila Osadchuk, Alexandr Osadchuk and Dmitry Oshchepkov

The medieval Mongolian roots of Y-chromosomal lineages from South Kazakhstan

The majority of the Kazakhs from South Kazakhstan belongs to the 12 clans of the Senior Zhuz. According to traditional genealogy, nine of these clans have a common ancestor and constitute the Uissun tribe. The...

Authors: Maxat Zhabagin, Zhaxylyk Sabitov, Pavel Tarlykov, Inkar Tazhigulova, Zukhra Junissova, Dauren Yerezhepov, Rakhmetolla Akilzhanov, Elena Zholdybayeva, Lan-Hai Wei, Ainur Akilzhanova, Oleg Balanovsky and Elena Balanovska

Analyzing a putative enhancer of optic disc morphology

Genome-wide association studies have identified the CDC7-TGFBR3 intergenic region on chromosome 1 to be strongly associated with optic disc area size. The mechanism of its function remained unclear until new data...

Authors: Vladimir Babenko, Roman Babenko and Yuri Orlov

Genotypes diversity of env gene of Bovine leukemia virus in Western Siberia

This study describes the biodiversity and properties of Bovine leukemia virus in Western Siberia. This paper explores the effect of different genotypes of the env gene of the cattle leukemia virus on hematologica...

Authors: Natalia Blazhko, Sultan Vyshegurov, Alexander Donchenko, Kirill Shatokhin, Valeria Ryabinina, Kirill Plotnikov, Alevtina Khodakova and Sergey Pashkovskiy

Amyloid-β peptides slightly affect lifespan or antimicrobial peptide gene expression in Drosophila melanogaster

Beta-amyloid peptide (Aβ) is the key protein in the pathogenesis of Alzheimer’s disease, the most common age-related neurodegenerative disorder in humans. Aβ peptide induced pathological phenotypes in differen...

Authors: Mikhail V. Shaposhnikov, Nadezhda V. Zemskaya, Lyubov А. Koval, Natalya R. Minnikhanova, Olga I. Kechko, Vladimir A. Mitkevich, Alexander A. Makarov and Alexey А. Moskalev

DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

Our previous study found that chicken KLF7 was an important regulator in formation of adipose tissue. In the present study, we analyzed the association for DNA methylation in chicken KLF7 with its transcripts of ...

Authors: Zhiwei Zhang, Cunxi Nie, Yuechan Chen, Yanzhe Dong and Tao Lin

Genetic dissection of eating and cooking qualities in different subpopulations of cultivated rice (Oryza sativa L.) through association mapping

Eating and cooking qualities (ECQs) of rice (Oryza sativa L.) determine consumer acceptance and the economic value of rice varieties. The starch physicochemical properties, i.e. amylose content, gel consistency, ...

Authors: Chunfang Zhao, Ling Zhao, Qingyong Zhao, Tao Chen, Shu Yao, Zhen Zhu, Lihui Zhou, Altafhusian B. Nadaf, Wenhua Liang, Kai Lu, Yadong Zhang and Cailin Wang

Genome wide analysis reveals genetic divergence between Goldsinny wrasse populations

Marine fish populations are often characterized by high levels of gene flow and correspondingly low genetic divergence. This presents a challenge to define management units. Goldsinny wrasse (Ctenolabrus rupestri...

Authors: Eeva Jansson, Francois Besnier, Ketil Malde, Carl André, Geir Dahle and Kevin A. Glover

Breeding strategies for animal resilience to weather variation in meat sheep

The alteration in weather patterns expected due to climate change will affect farm animal performance, probably resulting in lower quantity and quality of available products. A potential mitigation strategy wo...

Authors: Enrique Sánchez-Molano, Vanessa V. Kapsona, Stavroula Oikonomou, Ann McLaren, Nicola Lambe, Joanne Conington and Georgios Banos

Meta-analyses of genome wide association studies in lines of laying hens divergently selected for feather pecking using imputed sequence level genotypes

Feather pecking (FP) is damaging behavior in laying hens leading to global economic losses in the layer industry and massive impairments of animal welfare. The objective of the study was to discover genetic va...

Authors: Clemens Falker-Gieske, Hanna Iffland, Siegfried Preuß, Werner Bessei, Cord Drögemüller, Jörn Bennewitz and Jens Tetens

Bioinformatic screening for candidate biomarkers and their prognostic values in endometrial cancer

Endometrial cancer is a common gynecological cancer with annually increasing incidence worldwide. However, the biomarkers that provide prognosis and progression for this disease remain elusive.

Authors: Yaowei Li and Li Li

Multi-omics profiling highlights lipid metabolism alterations in pigs fed low-dose antibiotics

In order to study the relations of hepatocellular functions, weight gain and metabolic imbalance caused by low-dose antibiotics (LDA) via epigenetic regulation of gene transcription, 32 weaned piglets were emp...

Authors: Yue Hu, Yihe Zhang, Cong Liu, Rui Qin, Desheng Gong, Ru Wang, Du Zhang, Lianqiang Che, Daiwen Chen, Guizhong Xin, Fei Gao and Qi Hu

Identification of single nucleotide variants in the Moroccan population by whole-genome sequencing

Large-scale human sequencing projects have described around a hundred-million single nucleotide variants (SNVs). These studies have predominately involved individuals with European ancestry despite the fact th...

Authors: Lucy Crooks, Johnathan Cooper-Knock, Paul R. Heath, Ahmed Bouhouche, Mostafa Elfahime, Mimoun Azzouz, Youssef Bakri, Mohammed Adnaoui, Azeddine Ibrahimi, Saaïd Amzazi and Rachid Tazi-Ahnini

Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers

Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to ...

Authors: Nelia Nkhoma, Hussein Shimelis, Mark D. Laing, Admire Shayanowako and Isack Mathew

Optimal reference genes for gene expression analysis in polyploid of Cyprinus carpio and Carassius auratus

Reference genes are usually stably expressed in various cells and tissues. However, it was reported that the expression of some reference genes may be distinct in different species. In this study, we intend to...

Authors: Wenbin Liu, Xiudan Yuan, Shuli Yuan, Liuye Dai, Shenghua Dong, Jinhui Liu, Liangyue Peng, Minmeng Wang, Yi Tang and Yamei Xiao

Molecular basis of a new ovine model for human 3M syndrome-2

Brachygnathia, cardiomegaly and renal hypoplasia syndrome (BCRHS, OMIA 001595–9940) is a previously reported recessively inherited disorder in Australian Poll Merino/Merino sheep. Affected lambs are stillborn ...

Authors: S. A. Woolley, S. E. Hayes, M. R. Shariflou, F. W. Nicholas, C. E. Willet, B. A. O’Rourke and I. Tammen

Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) gene family in wheat (Triticum aestivum L.)

Plant calmodulin-binding transcription activator (CAMTA) proteins play important roles in hormone signal transduction, developmental regulation, and environmental stress tolerance. However, in wheat, the CAMTA ge...

Authors: Fan Yang, Fu-shuang Dong, Fang-hui Hu, Yong-wei Liu, Jian-fang Chai, He Zhao, Meng-yu Lv and Shuo Zhou

Pedigree analysis of pre-breeding efforts in Trifolium spp. germplasm in New Zealand

Prebreeding in plants is the activity designed to identify useful characteristics from wild germplasm and its integration in breeding programs. Prebreeding aims to introduce new variation into the populations ...

Authors: L. M. Egan, R. W. Hofmann, P. Seguin, K. Ghamkhar and V. Hoyos-Villegas

Overexpression of transcription factor SlWRKY28 improved the tolerance of Populus davidiana × P. bolleana to alkaline salt stress

WRKY transcription factors (TFs) have been suggested to play crucial roles in the response to biotic and abiotic stresses. This study is the first to report the alkaline salt regulation of the WRKY gene.

Authors: Xin Wang, Zainab Ajab, Chenxi Liu, Songmiao Hu, Jiali Liu and Qingjie Guan

Genetic diversity and population structure of Amorphophallus albus, a plant species with extremely small populations (PSESP) endemic to dry-hot valley of Jinsha River

Amorphophallus albus P. Y. Liu & J. F. Chen (Araceae) is a plant species with extremely small populations (PSESP) and an important economic crop endemic to dry-hot valleys along the Jinsha River. In order to gain...

Authors: Rong Tang, Erxi Liu, Yazhou Zhang, Johann Schinnerl, Weibang Sun and Gao Chen

A novel mouse model expressing human forms for complement receptors CR1 and CR2

The complement cascade is increasingly implicated in development of a variety of diseases with strong immune contributions such as Alzheimer’s disease and Systemic Lupus Erythematosus. Mouse models have been u...

Authors: Harriet M. Jackson, Kate E. Foley, Rita O’Rourke, Timothy M. Stearns, Dina Fathalla, B. Paul Morgan and Gareth R. Howell

A LINE-1 insertion situated in the promoter of IMPG2 is associated with autosomal recessive progressive retinal atrophy in Lhasa Apso dogs

Canine progressive retinal atrophies are a group of hereditary retinal degenerations in dogs characterised by depletion of photoreceptor cells in the retina, which ultimately leads to blindness. PRA in the Lha...

Authors: Rebekkah J. Hitti-Malin, Louise M. Burmeister, Sally L. Ricketts, Thomas W. Lewis, Louise Pettitt, Mike Boursnell, Ellen C. Schofield, David Sargan and Cathryn S. Mellersh

Statistically efficient association analysis of quantitative traits with haplotypes and untyped SNPs in family studies

Associations between haplotypes and quantitative traits provide valuable information about the genetic basis of complex human diseases. Haplotypes also provide an effective way to deal with untyped SNPs. Two m...

Authors: Guoqing Diao and Dan-yu Lin

Systematic analysis reveals cis and trans determinants affecting C-to-U RNA editing in Arabidopsis thaliana

C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The biological functions of a fraction of C-to-U editing sites are continuously discovered by case studies. However, at gen...

Authors: Duan Chu and Lai Wei

mbend: an R package for bending non-positive-definite symmetric matrices to positive-definite

R package mbend was developed for bending symmetric non-positive-definite matrices to positive-definite (PD). Bending is a procedure of transforming non-PD matrices to PD. The covariance matrices used in multi...

Authors: Mohammad Ali Nilforooshan

Characterization of bovine MHC DRB3 diversity in global cattle breeds, with a focus on cattle in Myanmar

Myanmar cattle populations predominantly consist of native cattle breeds (Pyer Sein and Shwe), characterized by their geographical location and coat color, and the Holstein-Friesian crossbreed, which is highly...

Authors: Guillermo Giovambattista, Kyaw Kyaw Moe, Meripet Polat, Liushiqi Borjigin, Si Thu Hein, Hla Hla Moe, Shin-Nosuke Takeshima and Yoko Aida

Predicting the most deleterious missense nsSNPs of the protein isoforms of the human HLA-G gene and in silico evaluation of their structural and functional consequences

The Human Leukocyte Antigen G (HLA-G) protein is an immune tolerogenic molecule with 7 isoforms. The change of expression level and some polymorphisms of the HLA-G gene are involved in various pathologies. The...

Authors: Elaheh Emadi, Fatemeh Akhoundi, Seyed Mehdi Kalantar and Modjtaba Emadi-Baygi

Transcriptomic and anatomic profiling reveal the germination process of different wheat varieties in response to waterlogging stress

Waterlogging is one of the most serious abiotic stresses affecting wheat-growing regions in China. Considerable differences in waterlogging tolerance have been found among different wheat varieties, and the me...

Authors: Changwei Shen, Jingping Yuan, Hong Qiao, Zijuan Wang, Yuanhai Liu, Xiujuan Ren, Fei Wang, Xing Liu, Ying Zhang, Xiling Chen and Xingqi Ou

Microsatellite variation revealed panmictic pattern for Triatoma brasiliensis (Triatominae: Reduviidae) in rural northeastern Brazil: the control measures implications

Triatoma brasiliensis Neiva, 1911 is the main vector of Trypanosoma cruzi in the caatinga of Northeastern Brazil. Despite of its epidemiological relevance, there are few studies on its genetic variability. Using ...

Authors: Claudia Mendonça Bezerra, Carlota Josefovicz Belisário, Grasielle Caldas D’Ávilla Pessoa, Aline Cristine Luiz Rosa, Carla Patrícia Barezani, Flávio Campos Ferreira, Alberto Novaes Ramos Jr, Ricardo Esteban Gürtler and Liléia Diotaiuti

A 31-bp indel in the 5′ UTR region of GNB1L is significantly associated with chicken body weight and carcass traits

G-protein subunit beta 1 like (GNB1L) encodes a G-protein beta-subunit-like polypeptide. Chicken GNB1L is upregulated in the breast muscle of high feed efficiency chickens, and its expression is 1.52-fold that in...

Authors: Tuanhui Ren, Ying Yang, Wujian Lin, Wangyu Li, Mingjian Xian, Rong Fu, Zihao Zhang, Guodong Mo, Wen Luo and Xiquan Zhang

MCC-SP: a powerful integration method for identification of causal pathways from genetic variants to complex disease

Genome-wide association studies (GWAS) have successfully identified genetic susceptible variants for complex diseases. However, the underlying mechanism of such association remains largely unknown. Most diseas...

Authors: Yuchen Zhu, Jiadong Ji, Weiqiang Lin, Mingzhuo Li, Lu Liu, Huanhuan Zhu, Fuzhong Xue, Xiujun Li, Xiang Zhou and Zhongshang Yuan

Identification and genetic analysis of EMS-mutagenized wheat mutants conferring lesion-mimic premature aging

Lesion-mimic and premature aging (lmpa) mutant lmpa1 was identified from the ethyl methane sulfonate (EMS) mutant library in the bread wheat variety Keda 527 (KD527) background. To reveal the genetic basis of lmp...

Authors: Weiwei Kong, Liming Wang, Pei Cao, Xingfeng Li, Jingjing Ji, Puhui Dong, Xuefang Yan, Chunping Wang, Honggang Wang and Jiaqiang Sun

Phenotypic and molecular marker analysis uncovers the genetic diversity of the grass Stenotaphrum secundatum

Stenotaphrum secundatum is an important grass with a rich variety of accessions and great potential for development as an economically valuable crop. However, little is known about the genetic diversity of S. sec...

Authors: Ying Luo, Xiujie Zhang, Jiahong Xu, Yao Zheng, Shouqin Pu, Zhizhen Duan, Zhihao Li, Guodao Liu, Jinhui Chen and Zhiyong Wang

A novel path-specific effect statistic for identifying the differential specific paths in systems epidemiology

Biological pathways play an important role in the occurrence, development and recovery of complex diseases, such as cancers, which are multifactorial complex diseases that are generally caused by mutation of m...

Authors: Hongkai Li, Zhi Geng, Xiaoru Sun, Yuanyuan Yu and Fuzhong Xue

CGGBP1-regulated cytosine methylation at CTCF-binding motifs resists stochasticity

The human CGGBP1 binds to GC-rich regions and interspersed repeats, maintains homeostasis of stochastic cytosine methylation and determines DNA-binding of CTCF. Interdependence between regulation of cytosine m...

Authors: Manthan Patel, Divyesh Patel, Subhamoy Datta and Umashankar Singh

Characterization of two MHC II genes (DOB, DRB) in white-tailed deer (Odocoileus virginianus)

The major histocompatibility complex (MHC) is responsible for detecting and addressing foreign pathogens inside the body. While the general structure of MHC genes is relatively well conserved among mammalian s...

Authors: Natascha M. D. Ivy-Israel, Carolyn E. Moore, Tonia S. Schwartz and Stephen S. Ditchkoff

The molecular effect of a polymorphic microRNA binding site of Wolfram syndrome 1 gene in dogs

Although the molecular function of wolframin remains unclear, the lack of this protein is known to cause stress in the endoplasmic reticulum. Some variants in the Wolfram Syndrome 1 gene (WFS1) were associated wi...

Authors: Dora Koller, Eniko Kubinyi, Zsuzsanna Elek, Helga Nemeth, Adam Miklosi, Maria Sasvari-Szekely and Zsolt Ronai

Type 2 diabetes susceptibility genes on mouse chromosome 11 under high sucrose environment

Both genetic and environmental factors contribute to type 2 diabetes development. We used consomic mice established from an animal type 2 diabetes model to identify susceptibility genes that contribute to type...

Authors: Misato Kobayashi, Hironori Ueda, Naru Babaya, Michiko Itoi-Babaya, Shinsuke Noso, Tomomi Fujisawa, Fumihiko Horio and Hiroshi Ikegami

Characterization, identification and expression profiling of genome-wide R-genes in melon and their putative roles in bacterial fruit blotch resistance

Bacterial fruit blotch (BFB), a disease caused by Acidovorax citrulli, results in significant economic losses in melon. The causal QTLs and genes for resistance to this disease have yet to be identified. Resistan...

Authors: Md. Rafiqul Islam, Mohammad Rashed Hossain, Denison Michael Immanuel Jesse, Hee-Jeong Jung, Hoy-Taek Kim, Jong-In Park and Ill-Sup Nou

Effects of HTR1B 3′ region polymorphisms and functional regions on gene expression regulation

The HTR1B gene encodes the 5-hydroxytryptamine (5-HT1B) receptor, which is involved in a variety of brain activities and mental disorders. The regulatory effects of non-coding regions on genomic DNA are one of ma...

Authors: Xi Xia, Mei Ding, Jin-feng Xuan, Jia-xin Xing, Hao Pang, Jun Yao, Xue Wu and Bao-jie Wang

Genetic diversity among early provitamin A quality protein maize inbred lines and the performance of derived hybrids under contrasting nitrogen environments

Information on population structure and genetic diversity of germplasm in a breeding programme is useful because it enhances judicious utilisation of genetic resources to achieve breeding objectives. Seventy e...

Authors: Ebenezer Obeng-Bio, Baffour Badu-Apraku, Beatrice Elohor Ifie, Agyemang Danquah, Essie Takyiwaa Blay, Mustapha Abu Dadzie, Gilbert Tchala Noudifoulè and Abidemi Olutayo Talabi

Genome-wide characterization of copy number variations in the host genome in genetic resistance to Marek’s disease using next generation sequencing

Marek’s disease (MD) is a highly neoplastic disease primarily affecting chickens, and remains as a chronic infectious disease that threatens the poultry industry. Copy number variation (CNV) has been examined ...

Authors: Hao Bai, Yanghua He, Yi Ding, Qin Chu, Ling Lian, Eliyahu M. Heifetz, Ning Yang, Hans H. Cheng, Huanmin Zhang, Jilan Chen and Jiuzhou Song

Genetic mapping of physiological traits associated with terminal stage drought tolerance in rice

Drought during reproductive stage is among the main abiotic stresses responsible for drastic reduction of grain yield in rainfed rice. The genetic mechanism of reproductive stage drought tolerance is very comp...

Authors: Saumya Ranjan Barik, Elssa Pandit, Shakti Prakash Mohanty, Deepak Kumar Nayak and Sharat Kumar Pradhan

A database for ITS2 sequences from nematodes

Marker gene surveys have a wide variety of applications in species identification, population genetics, and molecular epidemiology. As these methods expand to new types of organisms and additional markers beyo...

Authors: Matthew L. Workentine, Rebecca Chen, Shawna Zhu, Stefan Gavriliuc, Nicolette Shaw, Jill de Rijke, Elizabeth M. Redman, Russell W. Avramenko, Janneke Wit, Jocelyn Poissant and John S. Gilleard