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BMC Genetics

Christine A Hackett, Linda Milne, Kay Smith, Pete Hedley, Jenny Morris, Craig G Simpson, Katharine Preedy, Julie Graham
BACKGROUND: The changing climate is altering timing of key fruit ripening processes and increasing the occurrence of fruit defects. To improve our understanding of the genetic control of raspberry fruit development an enhanced genetic linkage map was developed and used to examine ripening phenotypic data. RESULTS: In this study we developed an enhanced genetic linkage map for the raspberry cvs. Glen Moy x Latham reference mapping population using genotyping by sequencing (GbS)...
August 15, 2018: BMC Genetics
Md Tarikul Islam, Suprovath Kumar Sarker, Shezote Talukder, Golam Sarower Bhuyan, Asifuzzaman Rahat, Nafisa Nawal Islam, Hasan Mahmud, Mohammad Amir Hossain, A K M Muraduzzaman, Jakia Rahman, Syeda Kashfi Qadri, Mohammod Shahidullah, Mohammad Abdul Mannan, Sarabon Tahura, Manzoor Hussain, Narayan Saha, Shahida Akhter, Nazmun Nahar, Firoza Begum, Tahmina Shirin, Sharif Akhteruzzaman, Syed Saleheen Qadri, Firdausi Qadri, Kaiissar Mannoor
BACKGROUND: Like glucose-6-phosphate dehydrogenase (G6PD) deficient hemizygous males and homozygous females, heterozygous females could also manifest hemolytic crisis, neonatal hyperbilirubinemia or kernicterus upon exposure to oxidative stress induced by certain foods such as fava beans, drugs or infections. Although hemizygous males and homozygous females are easily detected by conventional G6PD enzyme assay method, the heterozygous state could be missed by the conventional methods as the mosaic population of both normal and deficient RBCs circulates in the blood...
August 10, 2018: BMC Genetics
Jun He, Yage Guo, Jiaqi Xu, Hao Li, Anna Fuller, Richard G Tait, Xiao-Lin Wu, Stewart Bauck
BACKGROUND: SNPs are informative to estimate genomic breed composition (GBC) of individual animals, but selected SNPs for this purpose were not made available in the commercial bovine SNP chips prior to the present study. The primary objective of the present study was to select five common SNP panels for estimating GBC of individual animals initially involving 10 cattle breeds (two dairy breeds and eight beef breeds). The performance of the five common SNP panels was evaluated based on admixture model and linear regression model, respectively...
August 9, 2018: BMC Genetics
Beata Myśków, Magdalena Góralska, Natalia Lenarczyk, Ilona Czyczyło-Mysza, Stefan Stojałowski
BACKGROUND: Rolling of leaves (RL) is a phenomenon commonly found in grasses. Morphology of the leaf is an important agronomic trait in field crops especially in rice; therefore, majority of the rice breeders are interested in RL. There are only few studies with respect to RL of wheat and barley; however, the information regarding the genetic base of RL with respect to the shape of leaf in rye is lacking. To the best of our knowledge, this is the first study on the localization of loci controlling RL on high density consensus genetic map of rye...
August 9, 2018: BMC Genetics
I-Hsuan Lin, Junn-Liang Chang, Kate Hua, Wan-Chen Huang, Ming-Ta Hsu, Yi-Fan Chen
BACKGROUND: Aging leads to decreased skeletal muscle function in mammals and is associated with a progressive loss of muscle mass, quality and strength. Age-related muscle loss (sarcopenia) is an important health problem associated with the aged population. RESULTS: We investigated the alteration of genome-wide transcription in mouse skeletal muscle tissue (rectus femoris muscle) during aging using a high-throughput sequencing technique. Analysis revealed significant transcriptional changes between skeletal muscles of mice at 3 (young group) and 24 (old group) months of age...
August 8, 2018: BMC Genetics
P Daca-Roszak, M Swierniak, R Jaksik, T Tyszkiewicz, M Oczko-Wojciechowska, J Zebracka-Gala, B Jarzab, M Witt, E Zietkiewicz
BACKGROUND: Numerous studies have demonstrated significant differences in the expression level across continental human populations. Most of published results were performed on B-cell lines materials examined under specific laboratory conditions, without further validation in a primary biological material. The goal of our study was to identify mRNA markers characterized by a significant and stable difference in the gene expression profile in Caucasian and Chinese populations, both in the commercially available B-lymphocyte cell lines and in the primary samples of the peripheral blood...
August 7, 2018: BMC Genetics
Judith Galeng-Lawilao, Arvind Kumar, Dirk De Waele
BACKGROUND: The root-knot nematode Meloidogyne graminicola is an obligate biotrophic pathogen considered to be the most damaging nematode species that causes significant yield losses to upland and rainfed lowland rice production in South and Southeast Asia. Mapping and identification of quantitative trait loci (QTL) for resistance to and tolerance for M. graminicola may offer a safe and economic management option to farmers. In this study, resistance to and tolerance for M. graminicola in Asian rice (Oryza sativa L...
August 6, 2018: BMC Genetics
Ruijuan Li, John E Erpelding, Salliana R Stetina
BACKGROUND: Reniform nematode (Rotylenchulus reniformis) has emerged as one of the most destructive root pathogens of upland cotton (Gossypium hirsutum) in the United States. Management of R. reniformis has been hindered by the lack of resistant G. hirsutum cultivars; however, resistance has been frequently identified in germplasm accessions from the G. arboreum collection. To determine the genetic basis of reniform nematode resistance, a genome-wide association study (GWAS) was performed using 246 G...
August 3, 2018: BMC Genetics
Miyassa Meriem Aci, Antonio Lupini, Antonio Mauceri, Abdelkader Morsli, Lakhdar Khelifi, Francesco Sunseri
BACKGROUND: The ability of maize populations/landraces to tolerate drastically extreme environments over the past four centuries in Algeria leads to characterize these genetic resources for germplasm management as well as the identification of the best landraces useful for genetic improvement. Thus, the aim of the present work was a fingerprinting of an Algerian maize collection (47 landraces) from Saharan oasis by using 24 agro-morphological traits and18 Simple Sequence Repeats to evaluate genetic diversity and population structure...
August 1, 2018: BMC Genetics
Mui-Keng Tan, Mustapha El-Bouhssini, Ossie Wildman, Wuletaw Tadesse, Grant Chambers, Shuming Luo, Livinus Emebiri
BACKGROUND: The Hessian fly response genes, Hfr-1 and Hfr-2, have been reported to be significantly induced in a Hessian fly attack. Nothing is known about the allelic variants of these two genes in susceptible (S) and resistant (R) wheat cultivars. RESULTS: Basic local alignment search tool (BLAST) analysis of Hessian fly response genes have identified three alleles of Hessian fly response gene 1 (Hfr-1) on chromosome 4AL and 7DS, and 10 alleles of Hessian fly response gene 2 (Hfr-2) on chromosome 2BS, 2DL, 4BS, 4BL, 5AL and 5BL...
July 31, 2018: BMC Genetics
Anouk Schurink, Vinicius H da Silva, Brandon D Velie, Bert W Dibbits, Richard P M A Crooijmans, Liesbeth Franҫois, Steven Janssens, Anneleen Stinckens, Sarah Blott, Nadine Buys, Gabriella Lindgren, Bart J Ducro
BACKGROUND: Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide...
July 30, 2018: BMC Genetics
Lijiao Gu, Hengling Wei, Hantao Wang, Junji Su, Shuxun Yu
BACKGROUND: WRKY transcription factors (TFs) participate in various physiological processes of plants. Although WRKY genes have been well studied in model plants, knowledge of the functional roles of these genes is still extremely limited in cotton. RESULTS: In this study, a group IId WRKY gene from cotton, GhWRKY42, was isolated and characterized. Our data showed that GhWRKY42 localized to the nucleus. A transactivation assay in yeast demonstrated that GhWRKY42 was not a transcriptional activator...
July 30, 2018: BMC Genetics
Bo Ram Yi, Hyun Jeong Kim, Hye Sook Park, Yoon Jeong Cho, Ju Young Kim, Jeong Yee, Jee Eun Chung, Joo Hee Kim, Kyung Eun Lee, Hye Sun Gwak
BACKGROUND: The present study aimed to investigate the association between MKRN3 and LIN28B gene polymorphisms and precocious puberty in Korean boys and girls. RESULTS: Children 7 to 9 years of age in 2011 to 2012 who were part of the Ewha Birth & Growth Cohort Study were recruited for this study. A total of 103 girls and 70 boys were included in the analyses. Seven girls and 26 boys were identified to have precocious puberty. Among four single nucleotide polymorphisms (SNPs) of MKRN3 and two SNPs of LIN28B examined, three SNPs (rs2239669, rs6576457, and rs12441827) showed significant associations with precocious puberty in additive models in boys but no significance was found in any SNPs in girls...
July 27, 2018: BMC Genetics
Jiaxuan He, Ya Gao, Gang Wu, Xiaoming Lei, Yong Zhang, Weikang Pan, Hui Yu
BACKGROUND: This study aimed to explore the molecular mechanism of estrogen-mediated neuroprotection in the relief of cerebral ischemic injury. The gene expression profiles were downloaded from Gene Expression Omnibus database, and differentially expressed genes (DEGs) were identified using limma package in R software. Further, DEGs were subjected to Gene Ontology (GO) cluster analysis using online Gene Ontology Enrichment Analysis Software Toolkit and to GO functional enrichment analysis using DAVID software...
July 20, 2018: BMC Genetics
Wenbin Liao, Shuxia Li, Cheng Lu, Ming Peng
BACKGROUND: Glutathione S-transferases (GSTs) have been reported to regulate the plant tolerance to environmental stresses. Many plant GSTs exhibited the roles on promoting tolerance to drought stress, oxidative stress and plant hormones. The biological function of GSTs has been well characterized in Arabidopsis thaliana in response to exogenous environmental stresses. However, their regulation function under exogenous environmental stresses regulating leaf abscission in cassava (Manihot esculenta Crantz) remained unknown...
July 13, 2018: BMC Genetics
Samer Omari, Yuri Kamenir, Jennifer I C Benichou, Sarah Pariente, Hanan Sela, Rafael Perl-Treves
Following publication of the original article [1], the authors reported the need for a more detailed acknowledgement of the source of the samples that were analyzed and their coordinates, which are discussed in the 'Methods' section of the article. This Correction provides an addition to the 'Methods' section, and a subsequently revised 'Acknowledgements' and 'Availability of data and materials' section.
July 12, 2018: BMC Genetics
Muhammad L Aslam, Roberta Carraro, Anastasia Bestin, Sophie Cariou, Anna K Sonesson, Jean-Sébastien Bruant, Pierrick Haffray, Luca Bargelloni, Theo H E Meuwissen
BACKGROUND: Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90-100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males)...
July 11, 2018: BMC Genetics
Geir Dahle, María Quintela, Torild Johansen, Jon-Ivar Westgaard, François Besnier, Asgeir Aglen, Knut E Jørstad, Kevin A Glover
BACKGROUND: Atlantic cod (Gadus morhua L.) has formed the basis of many economically significant fisheries in the North Atlantic, and is one of the best studied marine fishes, but a legacy of overexploitation has depleted populations and collapsed fisheries in several regions. Previous studies have identified considerable population genetic structure for Atlantic cod. However, within Norway, which is the country with the largest remaining catch in the Atlantic, the population genetic structure of coastal cod (NCC) along the entire coastline has not yet been investigated...
July 9, 2018: BMC Genetics
Justin C St John, Te-Sha Tsai
BACKGROUND: The mitochondrial genome (mtDNA) is an emerging determiner of phenotypic traits and disease. mtDNA is inherited in a strict maternal fashion from the population of mitochondria present in the egg at fertilisation. Individuals are assigned to mtDNA haplotypes and those with sequences that cluster closely have common origins and their migration patterns can be mapped. Previously, we identified five mtDNA haplotypes in the commercial breeding lines of Australian pigs, which defined their common origins, and showed how these mtDNA haplotypes influenced litter size and reproductive function in terms of egg and embryo quality and fertilisation efficiency...
July 6, 2018: BMC Genetics
Miriam Kessi, Jing Peng, Lifen Yang, Juan Xiong, Haolin Duan, Nan Pang, Fei Yin
BACKGROUND: Electrical status epilepticus during slow-wave sleep (ESESS) which is also known as continuous spike-wave of slow sleep (CSWSS) is type of electroencephalographic (EEG) pattern which is seen in ESESS/CSWSS/epilepsy aphasia spectrum. This EEG pattern can occur alone or with other syndromes. Its etiology is not clear, however, brain malformations, immune disorders, and genetic etiologies are suspected to contribute. We aimed to perform a systematic review of all genetic etiologies which have been reported to associate with ESESS/CSWSS/epilepsy-aphasia spectrum...
July 6, 2018: BMC Genetics
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