Articles

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

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