Articles

Maternal variant in the upstream of FOXP3 gene on the X chromosome is associated with recurrent infertility in Japanese Black cattle

Repeat breeding, which is defined as cattle failure to conceive after three or more inseminations in the absence of clinical abnormalities, is a substantial problem in cattle breeding. To identify maternal gen...

Authors: Taichi Arishima, Shinji Sasaki, Tomohiro Isobe, Yoshihisa Ikebata, Shinichi Shimbara, Shogo Ikeda, Keisuke Kawashima, Yutaka Suzuki, Manabu Watanabe, Sumio Sugano, Kazunori Mizoshita and Yoshikazu Sugimoto

On the impact of relatedness on SNP association analysis

When testing for SNP (single nucleotide polymorphism) associations in related individuals, observations are not independent. Simple linear regression assuming independent normally distributed residuals results...

Authors: Arnd Gross, Anke Tönjes and Markus Scholz

IntroMap: a signal analysis based method for the detection of genomic introgressions

Breeding programs often rely on marker-assisted tests or variant calling of next generation sequence (NGS) data to identify regions of genomic introgression arising from the hybridization of two plant species....

Authors: Daniel J. Shea, Motoki Shimizu, Namiko Nishida, Eigo Fukai, Takashi Abe, Ryo Fujimoto and Keiichi Okazaki

Identification and integrated analysis of differentially expressed lncRNAs and circRNAs reveal the potential ceRNA networks during PDLSC osteogenic differentiation

Researchers have been exploring the molecular mechanisms underlying the control of periodontal ligament stem cell (PDLSC) osteogenic differentiation. Recently, long noncoding RNAs (lncRNAs) and circular RNAs (...

Authors: Xiuge Gu, Mengying Li, Ye Jin, Dongxu Liu and Fulan Wei

Evaluating genetic ancestry and self-reported ethnicity in the context of carrier screening

Current professional society guidelines recommend genetic carrier screening be offered on the basis of ethnicity, or when using expanded carrier screening panels, they recommend to compute residual risk based ...

Authors: Roman Shraga, Sarah Yarnall, Sonya Elango, Arun Manoharan, Sally Ann Rodriguez, Sara L. Bristow, Neha Kumar, Mohammad Niknazar, David Hoffman, Shahin Ghadir, Rita Vassena, Serena H. Chen, Avner Hershlag, Jamie Grifo and Oscar Puig

Genetic variation in populations of the earthworm, Lumbricus rubellus, across contaminated mine sites

Populations of the earthworm, Lumbricus rubellus, are commonly found across highly contaminated former mine sites and are considered to have under-gone selection for mitigating metal toxicity. Comparison of adapt...

Authors: Craig Anderson, Luis Cunha, Pierfrancesco Sechi, Peter Kille and David Spurgeon

Assessment of genetic diversity in Vigna unguiculata L. (Walp) accessions using inter-simple sequence repeat (ISSR) and start codon targeted (SCoT) polymorphic markers

Assessment of genetic diversity of Vigna unguiculata (L.) Walp (cowpea) accessions using informative molecular markers is imperative for their genetic improvement and conservation. Use of efficacious molecular ma...

Authors: David Okeh Igwe, Celestine Azubike Afiukwa, Benjamin Ewa Ubi, Kenneth Idika Ogbu, Omena Bernard Ojuederie and George Nkem Ude

Association between ß2-adrenergic receptor gene polymorphisms and adverse events of ritodrine in the treatment of preterm labor: a prospective observational study

Ritodrine, a tocolytic β2-agonist, has been used extensively in Europe and Asia despite its safety concerns. This study was designed to identify associations between β2-adrenergic receptor (ADRB2) polymorphisms a...

Authors: Jee Eun Chung, Soo An Choi, Han Sung Hwang, Jin Young Park, Kyung Eun Lee, Jeong Yee, Young Ju Kim and Hye Sun Gwak

Comparative Transcriptome and DNA methylation analyses of the molecular mechanisms underlying skin color variations in Crucian carp (Carassius carassius L.)

Crucian carp is a popular ornamental strain in Asia with variants in body color. To further explore the genetic mechanisms underlying gray and red body color formation in crucian carp, the skin transcriptomes ...

Authors: Yongqin Zhang, Jinhui Liu, Wen Fu, Wenting Xu, Huiqin Zhang, Shujuan Chen, Wenbin Liu, Liangyue Peng and Yamei Xiao

Detection of QTLs for seedling characteristics in barley (Hordeum vulgare L.) grown under hydroponic culture condition

Seedling characteristics play significant roles in the growth and development of barley (Hordeum vulgare L.), including stable stand establishment, water and nutrients uptake, biotic resistance and abiotic stress...

Authors: Qifei Wang, Genlou Sun, Xifeng Ren, Jibin Wang, Binbin Du, Chengdao Li and Dongfa Sun

Network analysis for count data with excess zeros

Undirected graphical models or Markov random fields have been a popular class of models for representing conditional dependence relationships between nodes. In particular, Markov networks help us to understand...

Authors: Hosik Choi, Jungsoo Gim, Sungho Won, You Jin Kim, Sunghoon Kwon and Changyi Park

Genetic variability in Italian populations of Drosophila suzukii

Drosophila suzukii is a highly destructive pest species, causing substantial economic losses in soft fruit production. To better understand migration patterns, gene flow and adaptation...

Authors: Gabriella Tait, Silvia Vezzulli, Fabiana Sassù, Gloria Antonini, Antonio Biondi, Nuray Baser, Giorgia Sollai, Alessandro Cini, Lorenzo Tonina, Lino Ometto and Gianfranco Anfora

Whole genome population genetics analysis of Sudanese goats identifies regions harboring genes associated with major traits

Sudan is endowed with a variety of indigenous goat breeds which are used for meat and milk production and which are well adapted to the local environment. The aim of the present study was to determine the gene...

Authors: Siham A. Rahmatalla, Danny Arends, Monika Reissmann, Ammar Said Ahmed, Klaus Wimmers, Henry Reyer and Gudrun A. Brockmann

Correction to: Novel SNP markers in InvGE and SssI genes are associated with natural variation of sugar contents and frying color in Solanum tuberosum Group Phureja

Authors: D. Duarte-Delgado, D. Juyó, C. Gebhardt, F. Sarmiento and T. Mosquera-Vásquez

Generalized disequilibrium test for association in qualitative traits incorporating imprinting effects based on extended pedigrees

For dichotomous traits, the generalized disequilibrium test with the moment estimate of the variance (GDT-ME) is a powerful family-based association method. Genomic imprinting is an important epigenetic phenom...

Authors: Jian-Long Li, Peng Wang, Wing Kam Fung and Ji-Yuan Zhou

Identification of putative markers linked to grain plumpness in rice (Oryza sativa L.) via association mapping

Poor grain plumpness (GP) is one of the main constraints to reaching the yield potential of hybrid rice.

Authors: Erbao Liu, Siyuan Zeng, Xiangong Chen, Xiaojing Dang, Lijun Liang, Hui Wang, Zhiyao Dong, Yang Liu and Delin Hong

Genetic evidence of multiple invasions and a small number of founders of Asian Palmyra palm (Borassus flabellifer) in Thailand

Borassus flabellifer or Asian Palmyra palm is an important crop for local economies in the South and Southeast Asia for its fruit and palm sugar production. Archeological and historica...

Authors: Kwanjai Pipatchartlearnwong, Akarapong Swatdipong, Supachai Vuttipongchaikij and Somsak Apisitwanich

Fine mapping of a QTL affecting levels of skatole on pig chromosome 7

Previous studies in the Norwegian pig breeds Landrace and Duroc have revealed a QTL for levels of skatole located in the region 74.7–80.5 Mb on SSC7. Skatole is one of the main components causing boar taint, w...

Authors: Maren van Son, Matthew P. Kent, Harald Grove, Rahul Agarwal, Hanne Hamland, Sigbjørn Lien and Eli Grindflek

Hox genes reveal genomic DNA variation in tetraploid hybrids derived from Carassius auratus red var. (female) × Megalobrama amblycephala (male)

Allotetraploid F₁ hybrids (4nF₁) (AABB, 4n = 148) were generated from the distant hybridization of Carassius auratus red var. (RCC) (AA, 2n = 100) (♀) × Megalobrama amblycephala (BSB) (BB, 2n = 48) (♂). It has be...

Authors: Y. D. Wang, Q. B. Qin, R. Yang, W. Z. Sun, Q. W. Liu, Y. Y. Huo, X. Huang, M. Tao, C. Zhang, T. Li and S. J. Liu

Quantitative trait loci associated with different polar metabolites in perennial ryegrass - providing scope for breeding towards increasing certain polar metabolites

Recent advances in the mapping of biochemical traits have been reported in Lolium perenne. Although the mapped traits, including individual sugars and fatty acids, contribute greatly towards ruminant productivity...

Authors: Alexandre Foito, Christine Anne Hackett, Derek Stewart, Janaki Velmurugan, Dan Milbourne, Stephen L. Byrne and Susanne Barth

LAIT: a local ancestry inference toolkit

Inferring local ancestry in individuals of mixed ancestry has many applications, most notably in identifying disease-susceptible loci that vary among different ethnic groups. Many software packages are availab...

Authors: Daniel Hui, Zhou Fang, Jerome Lin, Qing Duan, Yun Li, Ming Hu and Wei Chen

Refining the South Asian Origin of the Romani people

 Recent genetic studies based on genome-wide Single Nucleotide Polymorphism (SNP) data further investigated the history of Roma and suggested that the source of South Asian ancestry in Roma originates most lik...

Authors: Bela I. Melegh, Zsolt Banfai, Kinga Hadzsiev, Attila Miseta and Bela Melegh

The satellite DNA AflaSAT-1 in the A and B chromosomes of the grasshopper Abracris flavolineata

Satellite DNAs (satDNAs) are organized in repetitions directly contiguous to one another, forming long arrays and composing a large portion of eukaryote genomes. These sequences evolve according to the concert...

Authors: Diogo Milani, Érica Ramos, Vilma Loreto, Dardo Andrea Martí, Adauto Lima Cardoso, Karen Cristiane Martinez de Moraes, Cesar Martins and Diogo Cavalcanti Cabral-de-Mello

Identifying highly informative genetic markers for quantification of ancestry proportions in crossbred sheep populations: implications for choosing optimum levels of admixture

Understanding the relationship between genetic admixture and performances is crucial for the success of crossbreeding programs. Use of small sets of ancestry informative markers (AIMs) is a cost effective opti...

Authors: Tesfaye Getachew, Heather J. Huson, Maria Wurzinger, Jörg Burgstaller, Solomon Gizaw, Aynalem Haile, Barbara Rischkowsky, Gottfried Brem, Solomon Antwi Boison, Gábor Mészáros, Ally Okeyo Mwai and Johann Sölkner

A major QTL on chromosome 7HS controls the response of barley seedling to salt stress in the Nure × Tremois population

Seedling establishment is a crucial and vulnerable stage in the crop life cycle which determines further plant growth. While many studies are available on salt tolerance at the vegetative stage, the mechanisms...

Authors: Wentao Xue, Jun Yan, Gang Zhao, Yan Jiang, Jianping Cheng, Luigi Cattivelli and Alessandro Tondelli

Prenatal caloric restriction alters lipid metabolism but not hepatic Fasn gene expression and methylation profiles in rats

Undernutrition is an increasingly common problem. Insufficient calorie intake and nutrient deficiencies during pregnancy may have an impact not only on the mother, but may also alter metabolism in the infant. ...

Authors: Joanna Nowacka-Woszuk, Zofia E. Madeja and Agata Chmurzynska

Investigating knockdown resistance (kdr) mechanism against pyrethroids/DDT in the malaria vector Anopheles funestus across Africa

Understanding the molecular basis of insecticide resistance is key to improve the surveillance and monitoring of malaria vector populations under control. In the major malaria vector Anopheles funestus, little is...

Authors: Helen Irving and Charles S. Wondji

Mapping of leptin and its syntenic genes to chicken chromosome 1p

Misidentification of the chicken leptin gene has hampered research of leptin signaling in this species for almost two decades. Recently, the genuine leptin gene with a GC-rich (~70%) repetitive-sequence content w...

Authors: Eyal Seroussi, Frédérique Pitel, Sophie Leroux, Mireille Morisson, Susanne Bornelöv, Shoval Miyara, Sara Yosefi, Larry A. Cogburn, David W. Burt, Leif Anderson and Miriam Friedman-Einat

Variations in 5S rDNAs in diploid and tetraploid offspring of red crucian carp × common carp

The allotetraploid hybrid fish (4nAT) that was created in a previous study through an intergeneric cross between red crucian carp (Carassius auratus red var., ♀) and common carp (Cyprinus carpio L., ♂) provided a...

Authors: Lihai Ye, Chun Zhang, Xiaojun Tang, Yiyi Chen and Shaojun Liu

A de novo missense mutation of FGFR2 causes facial dysplasia syndrome in Holstein cattle

Surveillance for bovine genetic diseases in Denmark identified a hitherto unreported congenital syndrome occurring among progeny of a Holstein sire used for artificial breeding. A genetic aetiology due to a do...

Authors: Jørgen S. Agerholm, Fintan J. McEvoy, Steffen Heegaard, Carole Charlier, Vidhya Jagannathan and Cord Drögemüller

Genetic structure and relationships within and between cultivated and wild korarima [Aframomum corrorima (Braun) P.C.M. Jansen] in Ethiopia as revealed by simple sequence repeat (SSR) markers

Korarima [Aframomum corrorima (Braun) P.C.M. Jansen] is a spice crop native to Ethiopia. Understanding the extent and partitioning of diversity within and among crop landraces and their wild relatives is among th...

Authors: Dagmawit Chombe, Endashaw Bekele, Tomas Bryngelsson, Abel Teshome and Mulatu Geleta

Erratum to: Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression

Authors: Anke Hüls, Katja Ickstadt, Tamara Schikowski and Ursula Krämer

Association between serotonin transporter gene polymorphisms and increased suicidal risk among HIV positive patients in Uganda

Persons living with HIV/AIDS (PLWHA) are at an increased risk of suicide. Increased suicidal risk is a predictor of future attempted and completed suicides and has been associated with poor quality of life and...

Authors: Allan Kalungi, Soraya Seedat, Sian M. J. Hemmings, Lize van der Merwe, Moses L. Joloba, Ann Nanteza, Noeline Nakassujja, Harriet Birabwa, Jennifer Serwanga, Pontiano Kaleebu and Eugene Kinyanda

Resampling-based tests for Lasso in genome-wide association studies

Genome-wide association studies involve detecting association between millions of genetic variants and a trait, which typically use univariate regression to test association between each single variant and the...

Authors: Jaron Arbet, Matt McGue, Snigdhansu Chatterjee and Saonli Basu

Gene expression patterns of chicken neuregulin 3 in association with copy number variation and frameshift deletion

Neuregulin 3 (NRG3) plays a key role in central nervous system development and is a strong candidate for human mental disorders. Thus, genetic variation in NRG3 may have some impact on a variety of phenotypes in ...

Authors: Hideaki Abe, Daiki Aoya, Hiro-aki Takeuchi and Miho Inoue-Murayama

Estimation of linkage disequilibrium and effective population size in New Zealand sheep using three different methods to create genetic maps

Investments in genetic selection have played a major role in the New Zealand sheep industry competitiveness. Selection may erode genetic diversity, which is a crucial factor for the success of breeding program...

Authors: Vincent Prieur, Shannon M. Clarke, Luiz F. Brito, John C. McEwan, Michael A. Lee, Rudiger Brauning, Ken G. Dodds and Benoît Auvray

Dynamics in multiplicity of Plasmodium falciparum infection among children with asymptomatic malaria in central Ghana

The determinants of malaria parasite virulence is not entirely known, but the outcome of malaria infection (asymptomatic or symptomatic) has been associated with carriage of distinct parasite genotypes. Allele...

Authors: Akua Kyerewaa Botwe, Kwaku Poku Asante, George Adjei, Samuel Assafuah, David Dosoo and Seth Owusu-Agyei

Karyotype differentiation in tellin shells (Bivalvia: Tellinidae)

Although Tellinidae is one of the largest and most diverse families of bivalves, its taxonomy is utterly chaotic. This is mainly due to the morphological diversity and homoplasy displayed by their shells and t...

Authors: Daniel García-Souto, Gonzalo Ríos and Juan J. Pasantes

De novo transcriptomic analysis of cowpea (Vigna unguiculata L. Walp.) for genic SSR marker development

Cowpea [Vigna unguiculata (L.) Walp.] is one of the most important legumes in tropical and semi-arid regions. However, there is relatively little genomic information available for genetic research on and breeding...

Authors: Honglin Chen, Lixia Wang, Xiaoyan Liu, Liangliang Hu, Suhua Wang and Xuzhen Cheng

Genome-wide association study identifies candidate genes for piglet splay leg syndrome in different populations

Piglet splay leg syndrome (PSL) is one of the most frequent genetic defects, and can cause considerable economic loss in pig production. The present understanding of etiology and pathogenesis of PSL is poor. T...

Authors: Xingjie Hao, Graham Plastow, Chunyan Zhang, Sutong Xu, Zhiqiu Hu, Tianfu Yang, Kai Wang, Huawei Yang, Xiaoxue Yin, Shili Liu, Zhenghua Wang, Zhiquan Wang and Shujun Zhang

Genetic effects of PDGFRB and MARCH1 identified in GWAS revealing strong associations with semen production traits in Chinese Holstein bulls

Using a genome-wide association study strategy, our previous study discovered 19 significant single-nucleotide polymorphisms (SNPs) related to semen production traits in Chinese Holstein bulls. Among them, thr...

Authors: Shuli Liu, Hongwei Yin, Cong Li, Chunhua Qin, Wentao Cai, Mingyue Cao and Shengli Zhang

Genomic variability in Mexican chicken population using copy number variants

Copy number variations are genome polymorphism that influence phenotypic variation and are an important source of genetic variation in populations. The aim of this study was to investigate genetic variability ...

Authors: E. Gorla, M. C. Cozzi, S. I. Román-Ponce, F. J. Ruiz López, V. E. Vega-Murillo, S. Cerolini, A. Bagnato and M. G. Strillacci

Gene expression variations in high-altitude adaptation: a case study of the Asiatic toad (Bufo gargarizans)

Genome-wide investigation of molecular mechanisms for high-altitude adaptation has attracted great attention in the last few years. In order to understand the contribution of gene expression level variations t...

Authors: Weizhao Yang, Yin Qi, Bin Lu, Liang Qiao, Yayong Wu and Jinzhong Fu

Cattle phenotypes can disguise their maternal ancestry

Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually conside...

Authors: Kanokwan Srirattana, Kieren McCosker, Tim Schatz and Justin C. St. John

Canis mtDNA HV1 database: a web-based tool for collecting and surveying Canis mtDNA HV1 haplotype in public database

Canine and wolf mitochondrial DNA haplotypes, which can be used for forensic or phylogenetic analyses, have been defined in various schemes depending on the region analyzed. In recent studies, the 582 bp fragm...

Authors: Quan Ke Thai, Dung Anh Chung and Hoang-Dung Tran

Circadian CLOCK gene polymorphisms in relation to sleep patterns and obesity in African Americans: findings from the Jackson heart study

Circadian rhythms regulate key biological processes and the dysregulation of the intrinsic clock mechanism affects sleep patterns and obesity onset. The CLOCK (circadian locomotor output cycles protein kaput) gen...

Authors: Pia Riestra, Samson Y Gebreab, Ruihua Xu, Rumana J Khan, Amadou Gaye, Adolfo Correa, Nancy Min, Mario Sims and Sharon K Davis

The relation between DNA methylation patterns and serum cytokine levels in community-dwelling adults: a preliminary study

The levels of circulating cytokines fluctuate with age, acute illness, and chronic disease, and are predictive of mortality; this is also true for patterns of DNA (CpG) methylation. Given that immune cells are...

Authors: Chris P. Verschoor, Lisa M. McEwen, Vikas Kohli, Christina Wolfson, Dawn ME. Bowdish, Parminder Raina, Michael S. Kobor and Cynthia Balion

Effects of selection for fast growth on survival rate during grow-out phase in giant freshwater prawn (Macrobrachium rosenbergii)

Correlated genetic response in survival to selection for high growth has not been reported in giant freshwater prawn (GFP) (Macrobrachium rosenbergii). The main aim of this study was to measure genetic changes an...

Authors: Nguyen Thanh Vu, Trinh Quoc Trong and Nguyen Hong Nguyen

Genome-wide identification and characterization of SnRK2 gene family in cotton (Gossypium hirsutum L.)

Sucrose non-fermenting-1-related protein kinase 2 (SnRK2) is a plant-specific serine/threonine kinase family involved in the abscisic acid (ABA) signaling pathway and responds to osmotic stress. A genome-wide ...

Authors: Zhao Liu, Xiaoyang Ge, Zuoren Yang, Chaojun Zhang, Ge Zhao, Eryong Chen, Ji Liu, Xueyan Zhang and Fuguang Li

Detection of gene-environment interactions in the presence of linkage disequilibrium and noise by using genetic risk scores with internal weights from elastic net regression

For the analysis of gene-environment (GxE) interactions commonly single nucleotide polymorphisms (SNPs) are used to characterize genetic susceptibility, an approach that mostly lacks power and has poor reprodu...

Authors: Anke Hüls, Katja Ickstadt, Tamara Schikowski and Ursula Krämer