Articles

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

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

Large-scale mitochondrial DNA analysis of native honey bee Apis mellifera populations reveals a new African subgroup private to the South West Indian Ocean islands

The South West Indian Ocean (SWIO) archipelagos and Madagascar constitute a hotspot of biodiversity with a high rate of endemism. In this area, the endemic subspecies A. m. unicolor has been described in Madagasc...

Authors: Maéva Angélique Techer, Johanna Clémencet, Christophe Simiand, Sookar Preeaduth, Hamza Abdou Azali, Bernard Reynaud and Delatte Hélène

In vivo screening reveals interactions between Drosophila Manf and genes involved in the mitochondria and the ubiquinone synthesis pathway

Mesencephalic Astrocyte-derived Neurotrophic Factor (MANF) and Cerebral Dopamine Neurotrophic Factor (CDNF) form an evolutionarily conserved family of neurotrophic factors. Orthologues for MANF/CDNF are the on...

Authors: Riitta Lindström, Päivi Lindholm, Mari Palgi, Mart Saarma and Tapio I. Heino

Genomic prediction in early selection stages using multi-year data in a hybrid rye breeding program

The use of multiple genetic backgrounds across years is appealing for genomic prediction (GP) because past years’ data provide valuable information on marker effects. Nonetheless, single-year GP models are les...

Authors: Angela-Maria Bernal-Vasquez, Andres Gordillo, Malthe Schmidt and Hans-Peter Piepho

Development of a SNP panel dedicated to parentage assignment in French sheep populations

The efficiency of breeding programs partly relies on the accuracy of the estimated breeding values which decreases when pedigrees are incomplete. Two reproduction techniques are mainly used by sheep breeders t...

Authors: F. Tortereau, C. R. Moreno, G. Tosser-Klopp, B. Servin and J. Raoul

The distribution of mitochondrial DNA haplogroup H in southern Iberia indicates ancient human genetic exchanges along the western edge of the Mediterranean

The structure of haplogroup H reveals significant differences between the western and eastern edges of the Mediterranean, as well as between the northern and southern regions. Human populations along the weste...

Authors: Candela L. Hernández, Jean M. Dugoujon, Andrea Novelletto, Juan N. Rodríguez, Pedro Cuesta and Rosario Calderón

Candidate gene based association mapping in Fusarium culmorum for field quantitative pathogenicity and mycotoxin production in wheat

Quantitative traits are common in nature, but quantitative pathogenicity has received only little attention in phytopathology. In this study, we used 100 Fusarium culmorum isolates collected from natural field en...

Authors: Valheria Castiblanco, Jose J. Marulanda, Tobias Würschum and Thomas Miedaner

Determination of genetic effects of ATF3 and CDKN1A genes on milk yield and compositions in Chinese Holstein population

Our previous RNA-sequencing study revealed that the ATF3 and CDKN1A genes were remarkably differentially expressed between the mammary glands of lactating Holstein cows with extremely high and low milk protein an...

Authors: Bo Han, Weijun Liang, Lin Liu, Yanhua Li and Dongxiao Sun

Genetic correlation of the plasma lipidome with type 2 diabetes, prediabetes and insulin resistance in Mexican American families

Differential plasma concentrations of circulating lipid species are associated with pathogenesis of type 2 diabetes (T2D). Whether the wide inter-individual variability in the plasma lipidome contributes to th...

Authors: Hemant Kulkarni, Manju Mamtani, Gerard Wong, Jacquelyn M. Weir, Christopher K. Barlow, Thomas D. Dyer, Laura Almasy, Michael C. Mahaney, Anthony G. Comuzzie, Ravindranath Duggirala, Peter J. Meikle, John Blangero and Joanne E. Curran

Effects of marker density and population structure on the genomic prediction accuracy for growth trait in Pacific white shrimp Litopenaeus vannamei

Due to the great advantages in selection accuracy and efficiency, genomic selection (GS) has been widely studied in livestock, crop and aquatic animals. Our previous study based on one full-sib family of Litopena...

Authors: Quanchao Wang, Yang Yu, Jianbo Yuan, Xiaojun Zhang, Hao Huang, Fuhua Li and Jianhai Xiang

Network-based regularization for high dimensional SNP data in the case–control study of Type 2 diabetes

Over the past decades, the prevalence of type 2 diabetes mellitus (T2D) has been steadily increasing around the world. Despite large efforts devoted to better understand the genetic basis of the disease, the i...

Authors: Jie Ren, Tao He, Ye Li, Sai Liu, Yinhao Du, Yu Jiang and Cen Wu

Sucrose non-ferment 1 related protein kinase 2 (SnRK2) genes could mediate the stress responses in potato (Solanum tuberosum L.)

The SnRKs (sucrose non-fermenting 1 related protein kinase) are a gene family coding for Ser/Thr protein kinases and play important roles in linking the tolerance and metabolic responses of plants to abiotic s...

Authors: Jiangping Bai, Juan Mao, Hongyu Yang, Awais Khan, Aqi Fan, Siyan Liu, Junlian Zhang, Di Wang, Huijuan Gao and Jinlin Zhang

A strategy to apply quantitative epistasis analysis on developmental traits

Genetic interactions are keys to understand complex traits and evolution. Epistasis analysis is an effective method to map genetic interactions. Large-scale quantitative epistasis analysis has been well establ...

Authors: Marta K. Labocha, Wang Yuan, Boanerges Aleman-Meza and Weiwei Zhong

FecX ^Bar a Novel BMP15 mutation responsible for prolificacy and female sterility in Tunisian Barbarine Sheep

Naturally occurring mutations in growth and differentiation factor 9 (GDF9) or bone morphogenetic protein 15 (BMP15) genes are associated with increased ovulation rate (OR) and litter size (LS) but also sterility...

Authors: Narjess Lassoued, Zohra Benkhlil, Florent Woloszyn, Ahmed Rejeb, Mohamed Aouina, Mourad Rekik, Stephane Fabre and Sonia Bedhiaf-Romdhani

High-content behavioral profiling reveals neuronal genetic network modulating Drosophila larval locomotor program

Two key questions in understanding the genetic control of behaviors are: what genes are involved and how these genes interact. To answer these questions at a systems level, we conducted high-content profiling of

Authors: Boanerges Aleman-Meza, Mario Loeza-Cabrera, Omar Peña-Ramos, Michael Stern and Weiwei Zhong

A novel nonsense mutation in the tyrosinase gene is related to the albinism in a capuchin monkey (Sapajus apella)

Oculocutaneous Albinism (OCA) is an autosomal recessive inherited condition that affects the pigmentation of eyes, hair and skin. The OCA phenotype may be caused by mutations in the tyrosinase gene (TYR), whic...

Authors: Felipe Tadeu Galante Rocha de Vasconcelos, Einat Hauzman, Leonardo Dutra Henriques, Paulo Roney Kilpp Goulart, Olavo de Faria Galvão, Ronaldo Yuiti Sano, Givago da Silva Souza, Jessica Lynch Alfaro, Luis Carlos de Lima Silveira, Dora Fix Ventura and Daniela Maria Oliveira Bonci

Detection and comparison of microRNAs in the caprine mammary gland tissues of colostrum and common milk stages

MicroRNAs (miRNAs) have a great influence on various physiological functions. A lot of high-throughput sequencing (HTS) research on miRNAs has been executed in the caprine mammary gland at different lactation ...

Authors: Jinxing Hou, Xiaopeng An, Yuxuan Song, Binyun Cao, Heping Yang, Zhou Zhang, Wenzheng Shen and Yunpu Li

Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication’s for germplasm utilization and conservation

The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining...

Authors: Maizura Ithnin, Chee-Keng Teh and Wickneswari Ratnam

Quantitative trait locus analysis of heterosis for plant height and ear height in an elite maize hybrid zhengdan 958 by design III

Plant height (PH) and ear height (EH) are two important agronomic traits in maize selection breeding. F₁ hybrid exhibit significant heterosis for PH and EH as compared to their parental inbred lines. To understan...

Authors: Hongjian Li, Qingsong Yang, Nannan Fan, Ming Zhang, Huijie Zhai, Zhongfu Ni and Yirong Zhang

Karyotype diversity and chromosomal organization of repetitive DNA in Tityus obscurus (Scorpiones, Buthidae)

Holocentric chromosomes occur in approximately 750 species of eukaryotes. Among them, the genus Tityus (Scorpiones, Buthidae) has a labile karyotype that shows complex multivalent associations during male meiosis...

Authors: Bruno Rafael Ribeiro de Almeida, Susana Suely Rodrigues Milhomem-Paixão, Renata Coelho Rodrigues Noronha, Cleusa Yoshiko Nagamachi, Marlyson Jeremias Rodrigues da Costa, Pedro Pereira de Oliveira Pardal, Johne Souza Coelho and Julio Cesar Pieczarka

Ploidy elicits a whole-genome dosage effect: growth of triploid Atlantic salmon is linked to the genetic origin of the second maternal chromosome set

The Atlantic salmon aquaculture industry is investigating the feasibility of using sterile triploids to mitigate genetic interactions with wild conspecifics, however, studies investigating diploid and triploid...

Authors: A. C. Harvey, P. G. Fjelldal, M. F. Solberg, T. Hansen and K. A. Glover

Genome-wide identification and expression analysis of ClLAX, ClPIN and ClABCB genes families in Citrullus lanatus under various abiotic stresses and grafting

Auxin plays an important role in regulating plant growth and development as well as in the response of plants to abiotic stresses. Auxin is transported by three kinds of major protein families, including the A...

Authors: Chenliang Yu, Wenqi Dong, Yihua Zhan, Zong-an Huang, Zhimiao Li, Il Seop Kim and Chenghao Zhang

Low-depth genotyping-by-sequencing (GBS) in a bovine population: strategies to maximize the selection of high quality genotypes and the accuracy of imputation

Genotyping-by-sequencing (GBS) has emerged as a powerful and cost-effective approach for discovering and genotyping single-nucleotide polymorphisms. The GBS technique was largely used in crop species where its...

Authors: Jean-Simon Brouard, Brian Boyle, Eveline M. Ibeagha-Awemu and Nathalie Bissonnette

Transcriptome profiling of Arabian horse blood during training regimens

Arabian horses are believed to be one of the oldest and most influential horse breeds in the world. Blood is the main tissue involved in maintaining body homeostasis, and it is considered a marker of the proce...

Authors: Katarzyna Ropka-Molik, Monika Stefaniuk-Szmukier, Kacper Żukowski, Katarzyna Piórkowska, Artur Gurgul and Monika Bugno-Poniewierska

A genome-wide association study reveals a locus for bilateral iridal hypopigmentation in Holstein Friesian cattle

Eye pigmentation abnormalities in cattle are often related to albinism, Chediak-Higashi or Tietz like syndrome. However, mutations only affecting pigmentation of coat color and eye have also been described. He...

Authors: Anne K. Hollmann, Martina Bleyer, Andrea Tipold, Jasmin N. Neßler, Wilhelm E. Wemheuer, Ekkehard Schütz and Bertram Brenig

A deletion in the intergenic region upstream of Ednrb causes head spot in the rat strain KFRS4/Kyo

Head spot is one of the phenotypes identified in the KFRS4/Kyo rat strain. Although previous linkage analysis suggested that Ednrb, which is frequently involved in coat color variations in various animals, could ...

Authors: Minako Yoshihara, Tetsuya Sato, Daisuke Saito, Osamu Ohara, Takashi Kuramoto and Mikita Suyama

Erratum to: Schrodinger’s scat: a critical review of the currently available tiger (Panthera Tigris) and leopard (Panthera pardus) specific primers in India, and a novel leopard specific primer

Authors: Pranay Amruth Maroju, Sonu Yadav, Vishnupriya Kolipakam, Shweta Singh, Qamar Qureshi and Yadvendradev Jhala

Genomic regions underlying susceptibility to bovine tuberculosis in Holstein-Friesian cattle

The significant social and economic loss as a result of bovine tuberculosis (bTB) presents a continuous challenge to cattle industries in the UK and worldwide. However, host genetic variation in cattle suscept...

Authors: Kethusegile Raphaka, Oswald Matika, Enrique Sánchez-Molano, Raphael Mrode, Mike Peter Coffey, Valentina Riggio, Elizabeth Janet Glass, John Arthur Woolliams, Stephen Christopher Bishop and Georgios Banos

The patterns of genomic variances and covariances across genome for milk production traits between Chinese and Nordic Holstein populations

With the development of SNP chips, SNP information provides an efficient approach to further disentangle different patterns of genomic variances and covariances across the genome for traits of interest. Due to...

Authors: Xiujin Li, Mogens Sandø Lund, Luc Janss, Chonglong Wang, Xiangdong Ding, Qin Zhang and Guosheng Su

Genetic diversity of a New Zealand multi-breed sheep population and composite breeds’ history revealed by a high-density SNP chip

Knowledge about the genetic diversity of a population is a crucial parameter for the implementation of successful genomic selection and conservation of genetic resources. The aim of this research was to establ...

Authors: Luiz F. Brito, John C. McEwan, Stephen P. Miller, Natalie K. Pickering, Wendy E. Bain, Ken G. Dodds, Flávio S. Schenkel and Shannon M. Clarke

Gain of power of the general regression model compared to Cochran-Armitage Trend tests: simulation study and application to bipolar disorder

Most genome-wide association studies assumed an additive model of inheritance which may result in significant loss of power when there is a strong departure from additivity. The General Regression Model (GRM),...

Authors: Marie-Hélène Dizier, Florence Demenais and Flavie Mathieu

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

Potato frying color is an agronomic trait influenced by the sugar content of tubers. The candidate gene approach was employed to elucidate the molecular basis of this trait in Solanum tuberosum Group Phureja, whi...

Authors: Diana Duarte-Delgado, Deissy Juyó, Christiane Gebhardt, Felipe Sarmiento and Teresa Mosquera-Vásquez

Genotypic background of the recipient plant is crucial for conferring RB gene mediated late blight resistance in potato

Late blight, caused by oomycetes pathogen Phytophthora infestans (Mont.) de Bary, is the most devastating potato disease in the world. RB gene from Solanum bulbocastanum has been shown to impart broad spectrum re...

Authors: Rajesh K. Shandil, Swarup K. Chakrabarti, Bir Pal Singh, Sanjeev Sharma, S. Sundaresha, Surinder K. Kaushik, Arvind K. Bhatt and Nitya Nand Sharma

Deciphering alternative splicing and nonsense-mediated decay modulate expression in primary lymphoid tissues of birds infected with avian pathogenic E. coli (APEC)

Avian pathogenic E. coli (APEC) can lead to a loss in millions of dollars in poultry annually because of mortality and produce contamination. Studies have verified that many immune-related genes undergo changes i...

Authors: Hongyan Sun

Genetic affinities among the historical provinces of Romania and Central Europe as revealed by an mtDNA analysis

As a major crossroads between Asia and Europe, Romania has experienced continuous migration and invasion episodes. The precise routes may have been shaped by the topology of the territory and had diverse impac...

Authors: Relu Cocoş, Sorina Schipor, Montserrat Hervella, Petru Cianga, Roxana Popescu, Claudia Bănescu, Mihai Constantinescu, Alina Martinescu and Florina Raicu

Molecular cytogenetic differentiation of paralogs of Hox paralogs in duplicated and re-diploidized genome of the North American paddlefish (Polyodon spathula)

Acipenseriformes is a basal lineage of ray-finned fishes and comprise 27 extant species of sturgeons and paddlefishes. They are characterized by several specific genomic features as broad ploidy variation, hig...

Authors: Radka Symonová, Miloš Havelka, Chris T. Amemiya, William Mike Howell, Tereza Kořínková, Martin Flajšhans, David Gela and Petr Ráb

Characterizing a region on BTA11 affecting β-lactoglobulin content of milk using high-density genotyping and haplotype grouping

Milk β-lactoglobulin (β-LG) content is of interest as it is associated with nutritional and manufacturing properties. It is known that milk β-LG content is strongly affected by genetic factors. In cattle, most...

Authors: Nicolas Bedere and Henk Bovenhuis

Comparative profiling of hepatopancreas transcriptomes in satiated and starving Pomacea canaliculata

Although Pomacea canaliculata is native to South and Central America, it has become one of the most abundant invasive species worldwide and causes extensive damage to agriculture and horticulture. Conventional ph...

Authors: Lei Yang, Tian-yin Cheng and Fei-yan Zhao

Identification of effector-like proteins in Trichoderma spp. and role of a hydrophobin in the plant-fungus interaction and mycoparasitism

Trichoderma spp. can establish beneficial interactions with plants by promoting plant growth and defense systems, as well as, antagonizing fungal phytopathogens in mycoparasitic intera...

Authors: Paulina Guzmán-Guzmán, Mario Iván Alemán-Duarte, Luis Delaye, Alfredo Herrera-Estrella and Vianey Olmedo-Monfil

Molecular characterization of MHC class IIB genes of sympatric Neotropical cichlids

The Major Histocompatibility Complex (MHC) is a key component of the adaptive immune system of all vertebrates and consists of the most polymorphic genes known to date. Due to this complexity, however, MHC rem...

Authors: Melinda J. Hofmann, Seraina E. Bracamonte, Christophe Eizaguirre and Marta Barluenga

Opportunities and challenges of whole-genome and -exome sequencing

Recent advances in the development of sequencing technologies provide researchers with unprecedented possibilities for genetic analyses. In this review, we will discuss the history of genetic studies and the p...

Authors: Britt-Sabina Petersen, Broder Fredrich, Marc P. Hoeppner, David Ellinghaus and Andre Franke

Whole-genome association analysis of pork meat pH revealed three significant regions and several potential genes in Finnish Yorkshire pigs

One of the most commonly used quality measurements of pork is pH measured 24 h after slaughter. The most probable mode of inheritance for this trait is oligogenic with several known major genes, such as PRKAG3. I...

Authors: Lucas L. Verardo, Marja-Liisa Sevón-Aimonen, Timo Serenius, Ville Hietakangas and Pekka Uimari