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BMC Genetics

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https://www.readbyqxmd.com/read/29037145/generalized-disequilibrium-test-for-association-in-qualitative-traits-incorporating-imprinting-effects-based-on-extended-pedigrees
#1
Jian-Long Li, Peng Wang, Wing Kam Fung, Ji-Yuan Zhou
BACKGROUND: 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 phenomenon and currently, there has been increasing interest of incorporating imprinting to improve the test power of association analysis. However, GDT-ME does not take imprinting effects into account, and it has not been investigated whether it can be used for association analysis when the effects indeed exist...
October 16, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29025415/genetic-evidence-of-multiple-invasions-and-a-small-number-of-founders-of-asian-palmyra-palm-borassus-flabellifer-in-thailand
#2
Kwanjai Pipatchartlearnwong, Akarapong Swatdipong, Supachai Vuttipongchaikij, Somsak Apisitwanich
BACKGROUND: 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 historical evidence indicated the presence of this species in Southeast Asia dating back at least 1500 years. B. flabellifer is believed to be originated in Africa, spread to South Asia and introduced into Southeast Asia through commercial routes and dissemination of cultures, however, the nature of its invasion and settlement in Thailand is unclear...
October 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29025391/identification-of-putative-markers-linked-to-grain-plumpness-in-rice-oryza-sativa-l-via-association-mapping
#3
Erbao Liu, Siyuan Zeng, Xiangong Chen, Xiaojing Dang, Lijun Liang, Hui Wang, Zhiyao Dong, Yang Liu, Delin Hong
BACKGROUND: Poor grain plumpness (GP) is one of the main constraints to reaching the yield potential of hybrid rice. RESULTS: In this study, the GP of 177 rice varieties was investigated in three locations across 2 years. By combining the genotype data of 261 simple sequence repeat (SSR) markers, association mapping was conducted to identify the marker-GP association loci. Among 31 marker-GP association loci detected in two or more environments and determined using general linear model (GLM) analyses, seven association loci were also detected using mixed linear model (MLM) analyses...
October 12, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29020941/fine-mapping-of-a-qtl-affecting-levels-of-skatole-on-pig-chromosome-7
#4
Maren van Son, Matthew P Kent, Harald Grove, Rahul Agarwal, Hanne Hamland, Sigbjørn Lien, Eli Grindflek
BACKGROUND: 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, which gives an undesirable smell and taste to the pig meat when heated. Surgical castration of boars is a common practice to reduce the risk of boar taint, however, a selection for boars genetically predisposed for low levels of taint would help eliminating the need for castration and be advantageous for both economic and welfare reasons...
October 11, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29020918/hox-genes-reveal-genomic-dna-variation-in-tetraploid-hybrids-derived-from-carassius-auratus-red-var-female-%C3%A3-megalobrama-amblycephala-male
#5
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, S J Liu
BACKGROUND: 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 been reported that Hox gene clusters are highly conserved among plants and vertebrates. In this study, we investigated the genomic organization of Hox gene clusters in the allotetraploid F1 hybrids and their parents to investigate the polyploidization process. RESULTS: There were three copies of Hox genes in the 4nF1 hybrids, two copies in RCC and one copy in BSB...
October 11, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29017444/quantitative-trait-loci-associated-with-different-polar-metabolites-in-perennial-ryegrass-providing-scope-for-breeding-towards-increasing-certain-polar-metabolites
#6
Alexandre Foito, Christine Anne Hackett, Derek Stewart, Janaki Velmurugan, Dan Milbourne, Stephen L Byrne, Susanne Barth
BACKGROUND: 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, organic acids and amino acids have been largely understudied despite their influence on the ruminal microbiome. RESULTS: In this study, we used a targeted gas-chromatography mass spectrometry (GC-MS) approach to profile the levels of 25 polar metabolites from different classes (sugars, amino acids, phenolic acids, organic acids and other nitrogen-containing compounds) present in a L...
October 10, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28877673/lait-a-local-ancestry-inference-toolkit
#7
Daniel Hui, Zhou Fang, Jerome Lin, Qing Duan, Yun Li, Ming Hu, Wei Chen
BACKGROUND: 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 available for inferring local ancestry in admixed individuals. However, most of these existing software packages require specific formatted input files and generate output files in various types, yielding practical inconvenience. RESULTS: We developed a tool set, Local Ancestry Inference Toolkit (LAIT), which can convert standardized files into software-specific input file formats as well as standardize and summarize inference results for four popular local ancestry inference software: HAPMIX, LAMP, LAMP-LD, and ELAI...
September 6, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28859608/refining-the-south-asian-origin-of-the-romani-people
#8
Bela I Melegh, Zsolt Banfai, Kinga Hadzsiev, Attila Miseta, Bela Melegh
BACKGROUND:  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 likely from the Northwest region of India. METHODS: In this study, based also on genome-wide SNP data, we attempted to refine these findings using significantly larger number of European Roma samples, an extended dataset of Indian groups and involving Pakistani groups into the analyses...
August 31, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28851268/the-satellite-dna-aflasat-1-in-the-a-and-b-chromosomes-of-the-grasshopper-abracris-flavolineata
#9
Diogo Milani, Érica Ramos, Vilma Loreto, Dardo Andrea Martí, Adauto Lima Cardoso, Karen Cristiane Martinez de Moraes, Cesar Martins, Diogo Cavalcanti Cabral-de-Mello
BACKGROUND: 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 concerted evolution model, and homogenization of repeats is observed at the intragenomic level. Satellite DNAs are the primary component of heterochromatin, located primarily in centromeres and telomeres. Moreover, satDNA enrichment in specific chromosomes has been observed, such as in B chromosomes, that can provide clues about composition, origin and evolution of this chromosome...
August 29, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28836937/identifying-highly-informative-genetic-markers-for-quantification-of-ancestry-proportions-in-crossbred-sheep-populations-implications-for-choosing-optimum-levels-of-admixture
#10
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, Johann Sölkner
No abstract text is available yet for this article.
August 24, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28830338/a-major-qtl-on-chromosome-7hs-controls-the-response-of-barley-seedling-to-salt-stress-in-the-nure%C3%A2-%C3%A3-%C3%A2-tremois-population
#11
Wentao Xue, Jun Yan, Gang Zhao, Yan Jiang, Jianping Cheng, Luigi Cattivelli, Alessandro Tondelli
BACKGROUND: 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 and genetic bases of salt tolerance during seedling establishment have been poorly investigated. Here, a novel and accurate phenotyping protocol was applied to characterize the response of seedlings to salt stress in two barley cultivars (Nure and Tremois) and their double-haploid population...
August 22, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28810876/prenatal-caloric-restriction-alters-lipid-metabolism-but-not-hepatic-fasn-gene-expression-and-methylation-profiles-in-rats
#12
Joanna Nowacka-Woszuk, Zofia E Madeja, Agata Chmurzynska
BACKGROUND: 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. In this study, we have applied a calorie-restricted diet during gestation and examined its effect on hepatic Fasn mRNA and DNA methylation profiles in rats and their female progeny. The body composition and blood lipid profiles were also evaluated in both generations...
August 15, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28793859/investigating-knockdown-resistance-kdr-mechanism-against-pyrethroids-ddt-in-the-malaria-vector-anopheles-funestus-across-africa
#13
Helen Irving, Charles S Wondji
BACKGROUND: 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 currently known about the role of the knockdown resistance (kdr) mechanism. Here, we investigated the presence and contribution of knockdown resistance (kdr) to pyrethroids/DDT resistance observed in Anopheles funestus across Africa. RESULTS: Pyrosequencing genotyping and sequencing of the voltage gated sodium channel (VGSC) gene did not detect the common L1014F mutation in field collected An...
August 9, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28793857/mapping-of-leptin-and-its-syntenic-genes-to-chicken-chromosome-1p
#14
Eyal Seroussi, Frédérique Pitel, Sophie Leroux, Mireille Morisson, Susanne Bornelöv, Shoval Miyara, Sara Yosefi, Larry A Cogburn, David W Burt, Leif Anderson, Miriam Friedman-Einat
BACKGROUND: 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 was identified in the chicken genome but without indicating its genomic position. This suggests that such GC-rich sequences are difficult to sequence and therefore substantial regions are missing from the current chicken genome assembly. RESULTS: A radiation hybrid panel of chicken-hamster Wg3hCl2 cells was used to map the genome location of the chicken leptin gene...
August 9, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28789633/variations-in-5s-rdnas-in-diploid-and-tetraploid-offspring-of-red-crucian-carp-%C3%A3-common-carp
#15
Lihai Ye, Chun Zhang, Xiaojun Tang, Yiyi Chen, Shaojun Liu
BACKGROUND: 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 an excellent platform to investigate the effect of hybridization and polyploidization on the evolution of 5S rDNA. The 5S rDNAs of paternal common carp were made up of a coding sequence (CDS) and a non-transcribed spacer (NTS) unit, and while the 5S rDNAs of maternal red crucian carp contained a CDS and a NTS unit, they also contained a variable number of interposed regions (IPRs)...
August 8, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28768473/a-de-novo-missense-mutation-of-fgfr2-causes-facial-dysplasia-syndrome-in-holstein-cattle
#16
Jørgen S Agerholm, Fintan J McEvoy, Steffen Heegaard, Carole Charlier, Vidhya Jagannathan, Cord Drögemüller
BACKGROUND: 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 dominant inheritance with incomplete penetrance or a mosaic germline mutation was suspected as all recorded cases were progeny of the same sire. Detailed investigations were performed to characterize the syndrome and to reveal its cause. RESULTS: Seven malformed calves were submitted examination...
August 2, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28764663/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
#17
Anke Hüls, Katja Ickstadt, Tamara Schikowski, Ursula Krämer
No abstract text is available yet for this article.
August 1, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28764649/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
#18
Dagmawit Chombe, Endashaw Bekele, Tomas Bryngelsson, Abel Teshome, Mulatu Geleta
BACKGROUND: 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 the first steps in conserving and measuring their genetic potential. The present study is aimed at characterizing the population genetic structure and relationships between cultivated and wild korarima in the southwestern part of Ethiopia. RESULTS: We analyzed a total of 195 individuals representing seven wild and fourteen cultivated populations...
August 1, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28743254/association-between-serotonin-transporter-gene-polymorphisms-and-increased-suicidal-risk-among-hiv-positive-patients-in-uganda
#19
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, Eugene Kinyanda
BACKGROUND: 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 poor adherence with antiretroviral therapy. Clinical risk factors have low predictive value for suicide, hence the interest in potential neurobiological correlates and specific heritable markers of suicide vulnerability. The serotonin transporter gene has previously been implicated in the aetiology of increased suicidal risk in non-HIV infected study populations and its variations may provide a platform for identifying genetic risk for suicidality among PLWHA...
July 25, 2017: BMC Genetics
https://www.readbyqxmd.com/read/28738830/resampling-based-tests-for-lasso-in-genome-wide-association-studies
#20
Jaron Arbet, Matt McGue, Snigdhansu Chatterjee, Saonli Basu
BACKGROUND: 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 phenotype. Alternatively, Lasso penalized regression allows one to jointly model the relationship between all genetic variants and the phenotype. However, it is unclear how to best conduct inference on the individual Lasso coefficients, especially in high-dimensional settings...
July 24, 2017: BMC Genetics
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