Articles

Genome-wide identification and expression analysis of HSP90 gene family in Nicotiana tabacum

Heat shock proteins 90 (HSP90s) are a highly conserved protein family of cellular chaperones widely found in plants; they play a fundamental role in response to biotic and abiotic stresses. The genome-wide ana...

Authors: Zhaopeng Song, Feilong Pan, Chao Yang, Hongfang Jia, Houlong Jiang, Fan He, Najia Li, Xiaochong Lu and Hongying Zhang

Favorable alleles mining for gelatinization temperature, gel consistency and amylose content in Oryza sativa by association mapping

Improving the gelatinization temperature (GT), gel consistency (GC) and amylose content (AC) for parental grain eating and cooking qualities (ECQs) are key factors for enhancing average grain ECQs for hybrid j...

Authors: Hui Wang, Shangshang Zhu, Xiaojing Dang, Erbao Liu, Xiaoxiao Hu, Moaz Salah Eltahawy, Imdad Ullah Zaid and Delin Hong

A toolset to study functions of Cytosolic non-specific dipeptidase 2 (CNDP2) using Drosophila as a model organism

Expression of the CNDP2 gene is frequently up- or down-regulated in different types of human cancers. However, how the product of this gene is involved in cell growth and proliferation is poorly understood. Moreo...

Authors: Evgeniya N. Andreyeva, Anna A. Ogienko, Tatiana D. Dubatolova, Anastasiya L. Oshchepkova, Elena N. Kozhevnikova, Anton V. Ivankin, Gera A. Pavlova, Sergei A. Kopyl and Alexey V. Pindyurin

Organization and evolution of the chalcone synthase gene family in bread wheat and relative species

Flavonoid compounds are secondary plant metabolites, having a functional importance in plant development, protection from pathogens and unfavorable environmental factors. Chalcone synthase (CHS) is a key enzym...

Authors: Anastasia Y. Glagoleva, Nikita V. Ivanisenko and Elena K. Khlestkina

Starch phosphorylation associated SNPs found by genome-wide association studies in the potato (Solanum tuberosum L.)

The natural variation of starch phosphate content in potatoes has been previously reported. It is known that, in contrast to raw starch, commercially phosphorylated starch is more stable at high temperatures a...

Authors: Vadim K. Khlestkin, Irina V. Rozanova, Vadim M. Efimov and Elena K. Khlestkina

Computational models in genetics at BGRS-2018

Authors: Yuriy L. Orlov, Tatiana V. Tatarinova and Alex V. Kochetov

Genetic control of anthocyanin pigmentation of potato tissues

The cultivated potato Solanum tuberosum L. is the fourth most important crop worldwide. Anthocyanins synthesis and accumulation in potato tissues are considered as one of important traits related to stress resist...

Authors: Ksenia V. Strygina, Alex V. Kochetov and Elena K. Khlestkina

Genome-wide association study and scan for signatures of selection point to candidate genes for body temperature maintenance under the cold stress in Siberian cattle populations

Design of new highly productive livestock breeds, well-adapted to local climatic conditions is one of the aims of modern agriculture and breeding. The genetics underlying economically important traits in cattl...

Authors: Alexander V. Igoshin, Andrey A. Yurchenko, Nadezhda M. Belonogova, Dmitry V. Petrovsky, Ruslan B. Aitnazarov, Vladimir A. Soloshenko, Nikolay S. Yudin and Denis M. Larkin

Interspecific delimitation and relationships among four Ostrya species based on plastomes

The genus Ostrya (Betulaceae) contains eight species and four of them are distributed in China. However, studies based on limited informative sites of several chloroplast markers failed to resolve interspecific d...

Authors: Yanyou Jiang, Yongzhi Yang, Zhiqiang Lu, Dongshi Wan and Guangpeng Ren

Identification of genomic regions and diagnostic markers for resistance to aflatoxin contamination in peanut (Arachis hypogaea L.)

Aflatoxin contamination caused by Aspergillus flavus is a major constraint to peanut industry worldwide due to its toxicological effects to human and animals. Developing peanut varieties with resistance to seed i...

Authors: Bolun Yu, Dongxin Huai, Li Huang, Yanping Kang, Xiaoping Ren, Yuning Chen, Xiaojing Zhou, Huaiyong Luo, Nian Liu, Weigang Chen, Yong Lei, Manish K. Pandey, Hari Sudini, Rajeev K. Varshney, Boshou Liao and Huifang Jiang

Structural organization and functional divergence of high isoelectric point α-amylase genes in bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

High isoelectric point α-amylase genes (Amy1) play major roles during cereal seed germination, and are associated with unacceptable high residual α-amylase activities in ripe wheat grains. However, in wheat and b...

Authors: Liangliang Ju, Guangbing Deng, Junjun Liang, Haili Zhang, Qiao Li, Zhifen Pan, Maoqun Yu and Hai Long

Inheritance of coat colour in the cane Corso Italiano dog

The inheritance of different coat colours in the Cane Corso Italiano dog has not been described thus far. We analysed data from 23,271 dogs and bitches using the Cane Corso Italiano Pedigree Database. We are d...

Authors: Evžen Korec, Matyáš Hančl, Marie Bydžovská, Ondřej Chalupa and Jana Korcová

QTL for spike-layer uniformity and their influence on yield-related traits in wheat

Common wheat (Triticum aestivum L.) is one of the most important food crops worldwide. Wheat spike-layer uniformity related traits (SLURTs) were complex traits that directly affect yield potential and appearance....

Authors: Chunhua Zhao, Na Zhang, Yongzhen Wu, Han Sun, Cheng Liu, Xiaoli Fan, Xuemei Yan, Hongxing Xu, Jun Ji and Fa Cui

Evaluation of fecal samples as a valid source of DNA by comparing paired blood and fecal samples from American bison (Bison bison)

The collection and analysis of fecal DNA is a common practice, especially when dealing with wildlife species that are difficult to track or capture. While fecal DNA is known to be lower quality than traditiona...

Authors: David Forgacs, Rick L. Wallen, Amy L. Boedeker and James N. Derr

Increasing accuracy of genomic selection in presence of high density marker panels through the prioritization of relevant polymorphisms

It becomes clear that the increase in the density of marker panels and even the use of sequence data didn’t result in any meaningful increase in the accuracy of genomic selection (GS) using either regression (...

Authors: Ling-Yun Chang, Sajjad Toghiani, Samuel E. Aggrey and Romdhane Rekaya

No genetic erosion after five generations for Impatiens glandulifera populations across the invaded range in Europe

The observation that many alien species become invasive despite low genetic diversity has long been considered the ‘genetic paradox’ in invasion biology. This paradox is often resolved through the temporal bui...

Authors: Kenny Helsen, Jenny Hagenblad, Kamal P. Acharya, Jörg Brunet, Sara A. O. Cousins, Guillaume Decocq, Pieter De Frenne, Adam Kimberley, Annette Kolb, Jana Michaelis, Jan Plue, Kris Verheyen, James D. M. Speed and Bente J. Graae

Subcongenic analysis of a quantitative trait locus affecting body weight and glucose metabolism in zinc transporter 7 (znt7)-knockout mice

A genome-wide mapping study using male F₂ zinc transporter 7-knockout mice (znt7-KO) and their wild type littermates in a mixed 129P1/ReJ (129P1) and C57BL/6J (B6) background identified a quantitative trait locus...

Authors: L. Huang, S. Tepaamorndech, C. P. Kirschke, Y. Cai, J. Zhao, Xiaohan Cao and Andrew Rao

Characterization of the extra copy of TPOX locus with tri-allelic pattern

An STR locus with tri-allelic pattern is occasionally observed in routine forensic casework. The extra copy of TPOX locus with tri-allelic pattern in populations has been assumed to be inserted into an X chrom...

Authors: Qinrui Yang, Baonian Liu, Chengchen Shao, Yuxiang Zhou, Yining Yao, Yuyin Pan, Kuan Sun, Hongmei Xu, Chengtao Li, Ting Wei, Yueqin Zhou, Qiqun Tang and Jianhui Xie

The epigenetic regulation of HsMar1, a human DNA transposon

Both classes of transposable elements (DNA and RNA) are tightly regulated at the transcriptional level leading to the inactivation of transposition via epigenetic mechanisms. Due to the high copies number of t...

Authors: Sylvaine Renault, Murielle Genty, Alison Gabori, Catherine Boisneau, Charles Esnault, Thomas Dugé de Bernonville and Corinne Augé-Gouillou

Uncovering a multitude of human glucocorticoid receptor variants: an expansive survey of a single gene

Glucocorticoids are commonly used in the clinical setting for their potent anti-inflammatory effects; however, significant variations in response to treatment have been demonstrated. Although the underlying m...

Authors: Stacey M. Leventhal, Debora Lim, Tajia L. Green, Anna E. Cantrell, Kiho Cho and David G. Greenhalgh

Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

Genome-wide association studies (GWAS) have been successfully implemented in cattle research and breeding. However, moving from the associations to identify the causal variants and reveal underlying mechanisms...

Authors: Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund and Goutam Sahana

The main WAP isoform usually found in camel milk arises from the usage of an improbable intron cryptic splice site in the precursor to mRNA in which a GC-AG intron occurs

Whey acidic protein (WAP) is a major protein identified in the milk of several mammalian species with cysteine-rich domains known as four-disulfide cores (4-DSC). The organization of the eutherian WAP genes is...

Authors: Alma Ryskaliyeva, Céline Henry, Guy Miranda, Bernard Faye, Gaukhar Konuspayeva and Patrice Martin

Genetic diversity and structure in Arapaima gigas populations from Amazon and Araguaia-Tocantins river basins

Arapaima gigas (Schinz, 1822) is the largest freshwater scaled fish in the world, and an emerging species for tropical aquaculture development. Conservation of the species, and the expansion of aquaculture requir...

Authors: Lucas Simon Torati, John Bernard Taggart, Eduardo Sousa Varela, Juliana Araripe, Stefanie Wehner and Hervé Migaud

Tissue expression profiles unveil the gene interaction of hepatopancreas, eyestalk, and ovary in the precocious female Chinese mitten crab, Eriocheir sinensis

Sexual precocity is a common biological phenomenon in animal species. A large number of precocity individuals were identified in Chinese mitten crab Eriocheir sinensis, which caused huge economic loss annually. H...

Authors: Xiaowen Chen, Jun Wang, Xin Hou, Wucheng Yue, Shu Huang and Chenghui Wang

Dispersal route of the Asian house rat (Rattus tanezumi) on mainland China: insights from microsatellite and mitochondrial DNA

Rattus tanezumi is a common commensal rat and an important host animal of bubonic plague in South China and Southeast Asia. The northward dispersal of this species in mainland China has been reported in recent de...

Authors: Song Guo, Guichang Li, Jinli Liu, Jun Wang, Liang Lu and Qiyong Liu

p.E95K mutation in Indian hedgehog causing brachydactyly type A1 impairs IHH/Gli1 downstream transcriptional regulation

Brachydactyly type A1 (BDA1, OMIM 112500) is a rare inherited malformation characterized primarily by shortness or absence of middle bones of fingers and toes. It is the first recorded disorder of the autosoma...

Authors: Lu Shen, Gang Ma, Ye Shi, Yunfeng Ruan, Xuhan Yang, Xi Wu, Yuyu Xiong, Chunling Wan, Chao Yang, Lei Cai, Likuan Xiong, Xueli Gong, Lin He and Shengying Qin

Comparative transcriptome analysis of two selenium-accumulating genotypes of Aegilops tauschii Coss. in response to selenium

Selenium (Se), an essential micronutrient in both animals and humans, has various biological functions, and its deficiency can lead to various diseases. The most common method for increasing Se uptake is the c...

Authors: Lijun Wu, Tao Liu, Yongsheng Xu, Wenjie Chen, Baolong Liu, Lianquan Zhang, Dengcai Liu, Huaigang Zhang and Bo Zhang

Sliding window haplotype approaches overcome single SNP analysis limitations in identifying genes for meat tenderness in Nelore cattle

Traditional single nucleotide polymorphism (SNP) genome-wide association analysis (GWAA) can be inefficient because single SNPs provide limited genetic information about genomic regions. On the other hand, usi...

Authors: Camila U. Braz, Jeremy F. Taylor, Tiago Bresolin, Rafael Espigolan, Fabieli L. B. Feitosa, Roberto Carvalheiro, Fernando Baldi, Lucia G. de Albuquerque and Henrique N. de Oliveira

Vps4b heterozygous mice do not develop tooth defects that replicate human dentin dysplasia I

Vacuolar protein sorting-associated protein 4B (VPS4B) is a member of the ATP enzyme AAA protein family, and is mainly involved in protein degradation and cell membrane fusion. Recently, a dominant mutation in...

Authors: Aiqin Hu, Ting Lu, Danna Chen, Jin Huang, Weiwei Feng, Yanjun Li, Dan Guo, Xiangmin Xu, Dong Chen and Fu Xiong

Genome-wide association study for response to vaccination in Angus calves¹

Bovine respiratory disease complex (BRDC) is one of the most important sources of loss within the beef cattle industry in the USA. Steps have been taken to reduce the incidence of BRDC through vaccination. Des...

Authors: L. M. Kramer, M. S. Mayes, E. D. Downey, R. G. Tait Jr, A. Woolums, C. Chase and J. M. Reecy

A panel of 32 AIMs suitable for population stratification correction and global ancestry estimation in Mexican mestizos

Association studies are useful to unravel the genetic basis of common human diseases. However, the presence of undetected population structure can lead to both false positive results and failures to detect gen...

Authors: Alicia Huerta-Chagoya, Hortensia Moreno-Macías, Juan Carlos Fernández-López, María Luisa Ordóñez-Sánchez, Rosario Rodríguez-Guillén, Alejandra Contreras, Alfredo Hidalgo-Miranda, Luis Alberto Alfaro-Ruíz, Edgar Pavel Salazar-Fernandez, Andrés Moreno-Estrada, Carlos Alberto Aguilar-Salinas and Teresa Tusié-Luna

A genome wide association study for the number of animals born dead in domestic pigs

The number of animals born dead, which includes the number of mummified (NM) and stillborn (NS) animals, is the most important trait to directly quantify the reproductive loss in domestic pigs. In this study, ...

Authors: Pingxian Wu, Kai Wang, Jie Zhou, Qiang Yang, Xidi Yang, Anan Jiang, Yanzhi Jiang, Mingzhou Li, Li Zhu, Lin Bai, Xuewei Li and Guoqing Tang

Evidence for paternal DNA transmission to gynogenetic grass carp

Grass carp (Ctenopharyngodon idellus, GC), as the highest-output fish in China, is economically important. The production of gynogenetic grass carp (GGC) will provide important germplasm resource for producing im...

Authors: Zhuangwen Mao, Yeqing Fu, Yude Wang, Shi Wang, Minghe Zhang, Xin Gao, Kaikun Luo, Qinbo Qin, Chun Zhang, Min Tao, Zhanzhou Yao and Shaojun Liu

funbarRF: DNA barcode-based fungal species prediction using multiclass Random Forest supervised learning model

Identification of unknown fungal species aids to the conservation of fungal diversity. As many fungal species cannot be cultured, morphological identification of those species is almost impossible. But, DNA ba...

Authors: Prabina Kumar Meher, Tanmaya Kumar Sahu, Shachi Gahoi, Ruchi Tomar and Atmakuri Ramakrishna Rao

Methylation of the first exon in the erythropoietin receptor gene does not correlate with its mRNA and protein level in cancer cells

Erythropoietin receptor (EPOR) is a functional membrane-bound cytokine receptor. Erythropoietin (EPO) represents an important hematopoietic factor for production, maturation and differentiation of erythroid pr...

Authors: Barbora Fecková, Patrícia Kimáková, Lenka Ilkovičová, Erika Szentpéteriová, Mária Macejová, Ján Košuth, Anthony Zulli, Nataša Debeljak, Petra Hudler, Karin Jašek, Ivana Kašubová, Peter Kubatka and Peter Solár

Characterization and functional analyses of the human HTR1A gene: 5’ regulatory region modulates gene expression in vitro

The serotonin neurotransmitter (5-HT) and its receptors have important roles in neuropsychiatric disorders such as schizophrenia. The aim of this study was to investigate the functional sequences of the 5′ reg...

Authors: Xue Wu, Feng-ling Xu, Mei Ding, Jing-jing Zhang, Jun Yao and Bao-jie Wang

Genome-wide assessment of genetic diversity and population structure insights into admixture and introgression in Chinese indigenous cattle

China exhibits a great diversity of ecosystems and abundant cattle resources, with nearly 30 million cattle from 53 indigenous breeds reared in specific geographic regions. To explore the genetic diversity and...

Authors: Wengang Zhang, Xue Gao, Yang Zhang, Yumin Zhao, Jiabao Zhang, Yutang Jia, Bo Zhu, Lingyang Xu, Lupei Zhang, Huijiang Gao, Junya Li and Yan Chen

Associations of sex hormone-binding globulin and testosterone with genome-wide DNA methylation

Levels of sex hormone-binding globulin (SHBG) and the androgen testosterone have been associated with risk of diseases throughout the lifecourse. Although both SHBG and testosterone have been shown to be highl...

Authors: Ryan Arathimos, Gemma C. Sharp, Raquel Granell, Kate Tilling and Caroline L. Relton

The transcription factor PRO44 and the histone chaperone ASF1 regulate distinct aspects of multicellular development in the filamentous fungus Sordaria macrospora

Fungal fruiting bodies are complex three-dimensional structures that are formed to protect and disperse the sexual spores. Their morphogenesis requires the concerted action of numerous genes; however, at the m...

Authors: David Immanuel Schumacher, Ramona Lütkenhaus, Florian Altegoer, Ines Teichert, Ulrich Kück and Minou Nowrousian

Retraction Note: Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

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Authors: Zexi Cai, Bernt Guldbrandtsen, Mogens Sandø Lund and Goutam Sahana

Polymorphisms of HOMER1 gene are associated with piglet splay leg syndrome and one significant SNP can affect its intronic promoter activity in vitro

In our previous genome-wide association study (GWAS) on the piglet splay leg (PSL) syndrome, the homer scaffolding protein 1 (HOMER1) was detected as a candidate gene. The aim of this work was to further verify t...

Authors: Sutong Xu, Xingjie Hao, Min Zhang, Kai Wang, Shuaifeng Li, Xing Chen, Liaohan Yang, Lin Hu and Shujun Zhang

A statistical measure for the skewness of X chromosome inactivation based on family trios

X chromosome inactivation (XCI) is an important gene regulation mechanism in females to equalize the expression levels of X chromosome between two sexes. Generally, one of two X chromosomes in females is rando...

Authors: Si-Qi Xu, Yu Zhang, Peng Wang, Wei Liu, Xian-Bo Wu and Ji-Yuan Zhou

Design of low density SNP chips for genotype imputation in layer chicken

The main goal of selection is to achieve genetic gain for a population by choosing the best breeders among a set of selection candidates. Since 2013, the use of a high density genotyping chip (600K Affymetrix®...

Authors: Florian Herry, Frédéric Hérault, David Picard Druet, Amandine Varenne, Thierry Burlot, Pascale Le Roy and Sophie Allais

Investigation of allele-specific expression of genes involved in adipogenesis and lipid metabolism suggests complex regulatory mechanisms of PPARGC1A expression in porcine fat tissues

The expression of genes involved in regulating adipogenesis and lipid metabolism may affect economically important fatness traits in pigs. Allele-specific expression (ASE) reflects imbalance between allelic tr...

Authors: Monika Stachowiak, Izabela Szczerbal and Krzysztof Flisikowski

Seedless mutant ‘Wuzi Ougan’ (Citrus suavissima Hort. ex Tanaka ‘seedless’) and the wild type were compared by iTRAQ-based quantitative proteomics and integratedly analyzed with transcriptome to improve understanding of male sterility

Bud mutation is a vital method of citrus. ‘Wuzi Ougan’ (mutant type, MT) as a bud variant of ‘Ougan’ (wild type, WT) was first found in 1996 and has become popular because of its male sterility and seedless ch...

Authors: Chi Zhang, Dihu Yu, Fuzhi Ke, Mimi Zhu, Jianguo Xu and Min Zhang

Quantifying the genetic parameters of feed efficiency in juvenile Nile tilapia Oreochromis niloticus

Improving feed efficiency in fish is crucial at the economic, social and environmental levels with respect to developing a more sustainable aquaculture. The important contribution of genetic improvement to ach...

Authors: Hugues de Verdal, Marc Vandeputte, Wagdy Mekkawy, Béatrice Chatain and John A. H. Benzie

A preliminary integrated genetic map distinguishes every chromosome pair and locates essential genes related to abiotic adaptation of Crassostrea angulata/gigas

The re-sequencing of C. angulata has revealed many polymorphisms in candidate genes related to adaptation to abiotic stress that are not present in C. gigas; these genes, therefore, are probably related to the ab...

Authors: Ismael Cross, Silvia Portela-Bens, Aglaya García-Angulo, Manuel A. Merlo, María E. Rodríguez, Thomas Liehr and Laureana Rebordinos

SNP markers associated with body size and pelt length in American mink (Neovison vison)

Identification of genes underlying production traits is a key aim of the mink research community. Recent availability of genomic tools have opened the possibility for faster genetic progress in mink breeding. ...

Authors: Zexi Cai, Trine Michelle Villumsen, Torben Asp, Bernt Guldbrandtsen, Goutam Sahana and Mogens Sandø Lund

Identification and validation of QTL and their associated genes for pre-emergent metribuzin tolerance in hexaploid wheat (Triticum aestivum L.)

Herbicide tolerance is an important trait that allows effective weed management in wheat crops. Genetic knowledge of metribuzin tolerance in wheat is needed to develop new cultivars for the industry. Here, we ...

Authors: Roopali Bhoite, Ifeyinwa Onyemaobi, Ping Si, Kadambot H. M. Siddique and Guijun Yan

Unexpected patterns of segregation distortion at a selfish supergene in the fire ant Solenopsis invicta

The Sb supergene in the fire ant Solenopsis invicta determines the form of colony social organization, with colonies whose inhabitants bear the element containing multiple reproductive queens and colonies lacking...

Authors: Kenneth G. Ross and DeWayne Shoemaker