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BMC Genetics

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https://www.readbyqxmd.com/read/28637429/effects-of-selection-for-fast-growth-on-survival-rate-during-grow-out-phase-in-giant-freshwater-prawn-macrobrachium-rosenbergii
#1
Nguyen Thanh Vu, Trinh Quoc Trong, Nguyen Hong Nguyen
BACKGROUND: 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 and estimate heritability for this character (survival rate) and its genetic associations with body traits in a GFP population selected over eight generations from 2008 to 2015. Statistical analyses were conducted on 106,696 data records, using threshold logistic mixed model...
June 21, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28637423/the-relation-between-dna-methylation-patterns-and-serum-cytokine-levels-in-community-dwelling-adults-a-preliminary-study
#2
Chris P Verschoor, Lisa M McEwen, Vikas Kohli, Christina Wolfson, Dawn Me Bowdish, Parminder Raina, Michael S Kobor, Cynthia Balion
BACKGROUND: 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 particularly sensitive to changes in the concentration of cytokines in their microenvironment, we hypothesized that serum levels of TNF, IL-6, IL-8 and IL-10 would correlate with genome-wide alterations in the DNA methylation levels of blood leukocytes. To test this, we evaluated community-dwelling adults (n = 14; 48-78 years old) recruited to a pilot study for the Canadian Longitudinal Study on Aging (CLSA), examining DNA methylation patterns in peripheral blood mononuclear cells using the Illumina HumanMethylation 450 K BeadChip...
June 21, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28606108/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
#3
Anke Hüls, Katja Ickstadt, Tamara Schikowski, Ursula Krämer
BACKGROUND: 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 reproducibility. One promising approach to overcome this problem might be the use of weighted genetic risk scores (GRS), which are defined as weighted sums of risk alleles of gene variants. The gold-standard is to use external weights from published meta-analyses. METHODS: In this study, we used internal weights from the marginal genetic effects of the SNPs estimated by a multivariate elastic net regression and thereby provided a method that can be used if there are no external weights available...
June 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28606097/genome-wide-identification-and-characterization-of-snrk2-gene-family-in-cotton-gossypium-hirsutum-l
#4
Zhao Liu, Xiaoyang Ge, Zuoren Yang, Chaojun Zhang, Ge Zhao, Eryong Chen, Ji Liu, Xueyan Zhang, Fuguang Li
BACKGROUND: 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 analysis of this protein family has been conducted previously in some plant species, but little is known about SnRK2 genes in upland cotton (Gossypium hirsutum L.). The recent release of the G. hirsutum genome sequence provides an opportunity to identify and characterize the SnRK2 kinase family in upland cotton...
June 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28578657/in-vivo-screening-reveals-interactions-between-drosophila-manf-and-genes-involved-in-the-mitochondria-and-the-ubiquinone-synthesis-pathway
#5
Riitta Lindström, Päivi Lindholm, Mari Palgi, Mart Saarma, Tapio I Heino
BACKGROUND: 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 only neurotrophic factors as yet identified in invertebrates with conserved amino acid sequence. Previous studies indicate that mammalian MANF and CDNF support and protect brain dopaminergic system in non-cell-autonomous manner. However, MANF has also been shown to function intracellularly in the endoplasmic reticulum...
June 2, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28577537/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
#6
Maéva Angélique Techer, Johanna Clémencet, Christophe Simiand, Sookar Preeaduth, Hamza Abdou Azali, Bernard Reynaud, Delatte Hélène
BACKGROUND: 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 Madagascar. It belongs to the African lineage, one of the four described evolutionary lineages in honey bees. Despite a long beekeeping tradition and several recorded European introductions, few studies have been carried out on the diversity and proportion of honey bee subspecies...
June 2, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28569139/genomic-prediction-in-early-selection-stages-using-multi-year-data-in-a-hybrid-rye-breeding-program
#7
Angela-Maria Bernal-Vasquez, Andres Gordillo, Malthe Schmidt, Hans-Peter Piepho
BACKGROUND: 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 less complex and computationally less demanding than multi-year GP models. In devising a suitable analysis strategy for multi-year data, we may exploit the fact that even if there is no replication of genotypes across years, there is plenty of replication at the level of marker loci...
May 31, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28549462/development-of-a-snp-panel-dedicated-to-parentage-assignment-in-french-sheep-populations
#8
F Tortereau, C R Moreno, G Tosser-Klopp, B Servin, J Raoul
BACKGROUND: 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 to identify the sires of lambs: animal insemination and natural matings with a single ram per group of ewes. Both methods have major drawbacks, notably time-consuming tasks for breeders, and are thus used at varying levels in breeding programs. As a consequence, the percentage of known sires can be very low in some breeds and results in less accurate estimated breeding values...
May 26, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525989/determination-of-genetic-effects-of-atf3-and-cdkn1a-genes-on-milk-yield-and-compositions-in-chinese-holstein-population
#9
REVIEW
Bo Han, Weijun Liang, Lin Liu, Yanhua Li, Dongxiao Sun
BACKGROUND: 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 and fat percentage so that both of them were considered as candidates for milk composition. Herein, we further verified whether these genes have genetic effects on milk production traits in a Chinese Holstein cow population. RESULTS: By re-sequencing the entire coding and regulatory regions, we identified four SNPs in 5'promoter region, two in exons, seven in 3' un-translated region (UTR), and six in 3'flanking region of ATF3 gene, and one SNP in exon 5, two in 3'UTR, and two in 3'flanking region of CDKN1A gene...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525987/genetic-correlation-of-the-plasma-lipidome-with-type-2-diabetes-prediabetes-and-insulin-resistance-in-mexican-american-families
#10
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, Joanne E Curran
BACKGROUND: 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 the genetic basis of T2D is unknown. Here, we investigated the potential overlap in the genetic basis of the plasma lipidome and T2D-related traits. RESULTS: We used plasma lipidomic data (1202 pedigreed individuals, 319 lipid species representing 23 lipid classes) from San Antonio Family Heart Study in Mexican Americans...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525980/the-distribution-of-mitochondrial-dna-haplogroup-h-in-southern-iberia-indicates-ancient-human-genetic-exchanges-along-the-western-edge-of-the-mediterranean
#11
Candela L Hernández, Jean M Dugoujon, Andrea Novelletto, Juan N Rodríguez, Pedro Cuesta, Rosario Calderón
BACKGROUND: 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 westernmost Mediterranean coasts, which were settled by individuals from two continents separated by a relatively narrow body of water, show the highest frequencies of mitochondrial haplogroup H. These characteristics permit the analysis of ancient migrations between both shores, which may have occurred via primitive sea crafts and early seafaring...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28525967/candidate-gene-based-association-mapping-in-fusarium-culmorum-for-field-quantitative-pathogenicity-and-mycotoxin-production-in-wheat
#12
Valheria Castiblanco, Jose J Marulanda, Tobias Würschum, Thomas Miedaner
BACKGROUND: 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 environments to assess their variation for two quantitative traits, aggressiveness and deoxynivalenol (DON) production on wheat plants grown in four different field environments (location-year combinations). Seventeen Fusarium graminearum pathogenicity candidate genes were assessed for their effect on the aggressiveness and DON production of F...
May 19, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28514941/effects-of-marker-density-and-population-structure-on-the-genomic-prediction-accuracy-for-growth-trait-in-pacific-white-shrimp-litopenaeus-vannamei
#13
Quanchao Wang, Yang Yu, Jianbo Yuan, Xiaojun Zhang, Hao Huang, Fuhua Li, Jianhai Xiang
BACKGROUND: 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 Litopenaeus vannamei (L. vannamei) showed that GS was feasible in penaeid shrimp. However, the applicability of GS might be influenced by many factors including heritability, marker density and population structure etc. Therefore it is necessary to evaluate the major factors affecting the prediction ability of GS in shrimp...
May 17, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28511641/network-based-regularization-for-high-dimensional-snp-data-in-the-case-control-study-of-type-2-diabetes
#14
Jie Ren, Tao He, Ye Li, Sai Liu, Yinhao Du, Yu Jiang, Cen Wu
BACKGROUND: 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 identified susceptibility loci can only account for a small portion of the T2D heritability. Some of the existing approaches proposed for the high dimensional genetic data from the T2D case-control study are limited by analyzing a few number of SNPs at a time from a large pool of SNPs, by ignoring the correlations among SNPs and by adopting inefficient selection techniques...
May 16, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28506298/fecx-bar-a-novel-bmp15-mutation-responsible-for-prolificacy-and-female-sterility-in-tunisian-barbarine-sheep
#15
Narjess Lassoued, Zohra Benkhlil, Florent Woloszyn, Ahmed Rejeb, Mohamed Aouina, Mourad Rekik, Stephane Fabre, Sonia Bedhiaf-Romdhani
BACKGROUND: 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. Observing the Tunisian Barbarine ewes of the "W" flock selected for improved prolificacy, we found prolific and infertile ewes with streaky ovaries. Blood genomic DNA was extracted from a subset of low-ovulating, prolific and infertile ewes of the "W" flock, and the entire coding sequences of GDF9 and BMP15 were sequenced...
May 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28506210/sucrose-non-ferment-1-related-protein-kinase-2-snrk2-genes-could-mediate-the-stress-responses-in-potato-solanum-tuberosum-l
#16
Jiangping Bai, Juan Mao, Hongyu Yang, Awais Khan, Aqi Fan, Siyan Liu, Junlian Zhang, Di Wang, Huijuan Gao, Jinlin Zhang
BACKGROUND: 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 stresses. To date, no genome-wide characterization of the sucrose non-ferment 1 related protein kinase 2 (SnRK2) subfamily has been conducted in potato (Solanum tuberosum L.). RESULTS: In this study, eight StSnRK2 genes (StSnRK2.1- StSnRK2.8) were identified in the genome of the potato (Solanum tuberosum L...
May 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28506208/a-strategy-to-apply-quantitative-epistasis-analysis-on-developmental-traits
#17
Marta K Labocha, Wang Yuan, Boanerges Aleman-Meza, Weiwei Zhong
BACKGROUND: 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 established for single cells. However, there is a substantial lack of such studies in multicellular organisms and their complex phenotypes such as development. Here we present a method to extend quantitative epistasis analysis to developmental traits. METHODS: In the nematode Caenorhabditis elegans, we applied RNA interference on mutants to inactivate two genes, used an imaging system to quantitatively measure phenotypes, and developed a set of statistical methods to extract genetic interactions from phenotypic measurement...
May 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28499390/high-content-behavioral-profiling-reveals-neuronal-genetic-network-modulating-drosophila-larval-locomotor-program
#18
Boanerges Aleman-Meza, Mario Loeza-Cabrera, Omar Peña-Ramos, Michael Stern, Weiwei Zhong
BACKGROUND: 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 Drosophila larval locomotor behaviors for over 100 genotypes. RESULTS: We studied 69 genes whose C. elegans orthologs were neuronal signalling genes with significant locomotor phenotypes, and conducted RNAi with ubiquitous, pan-neuronal, or motor-neuronal Gal4 drivers...
May 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28476152/a-novel-nonsense-mutation-in-the-tyrosinase-gene-is-related-to-the-albinism-in-a-capuchin-monkey-sapajus-apella
#19
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, Daniela Maria Oliveira Bonci
BACKGROUND: 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), which expresses the tyrosinase enzyme and has an important role in the synthesis of melanin pigment. The aim of this study was to identify the genetic mutation responsible for the albinism in a captive capuchin monkey, and to describe the TYR gene of normal phenotype individuals...
May 5, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28464792/detection-and-comparison-of-micrornas-in-the-caprine-mammary-gland-tissues-of-colostrum-and-common-milk-stages
#20
Jinxing Hou, Xiaopeng An, Yuxuan Song, Binyun Cao, Heping Yang, Zhou Zhang, Wenzheng Shen, Yunpu Li
BACKGROUND: 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 periods (common milk lactation and dry period), but little is known about differentially expressed miRNAs in the caprine mammary gland of colostrum and peak lactation periods. RESULT: This study identified 131 differentially expressed miRNAs (P < 0...
May 2, 2017: BMC Genetics
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