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BMC Genetics

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https://www.readbyqxmd.com/read/29642872/karyotype-diversity-and-2c-dna-content-in-species-of-the-caesalpinia-group
#1
Polliana Silva Rodrigues, Margarete Magalhães Souza, Cláusio Antônio Ferreira Melo, Telma Nair Santana Pereira, Ronan Xavier Corrêa
BACKGROUND: The Leguminosae family is the third-largest family of angiosperms, and Caesalpinioideae is its second-largest subfamily. A great number of species (approximately 205) are found in the Caesalpinia group within this subfamily; together with these species' phenotypic plasticity and the similarities in their morphological descriptors, make this a complex group for taxonomic and phylogenetic studies. The objective of the present work was to evaluate the karyotypic diversity and the 2C DNA content variation in 10 species of the Caesalpinia group, representing six genera: Paubrasilia, Caesalpinia, Cenostigma, Poincianella, Erythrostemon and Libidibia...
April 11, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29636022/genomic-heritability-estimates-in-sweet-cherry-reveal-non-additive-genetic-variance-is-relevant-for-industry-prioritized-traits
#2
Julia Piaskowski, Craig Hardner, Lichun Cai, Yunyang Zhao, Amy Iezzoni, Cameron Peace
BACKGROUND: Sweet cherry is consumed widely across the world and provides substantial economic benefits in regions where it is grown. While cherry breeding has been conducted in the Pacific Northwest for over half a century, little is known about the genetic architecture of important traits. We used a genome-enabled mixed model to predict the genetic performance of 505 individuals for 32 phenological, disease response and fruit quality traits evaluated in the RosBREED sweet cherry crop data set...
April 10, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29636014/genetic-loci-for-resistance-to-podocyte-injury-caused-by-the-tensin2-gene-deficiency-in-mice
#3
Yuki Takahashi, Hayato Sasaki, Shiori Okawara, Nobuya Sasaki
BACKGROUND: Tensin2 is a focal adhesion-localized multidomain protein expressed in various tissues, and its dysfunction leads to alterations in podocytes. However, these podocyte-related manifestations are dependent on murine strain. Tensin2 dysfunction results in susceptible strains developing podocyte foot process effacement and massive albuminuria, whereas podocytes in resistant strains remain almost intact. In our previous studies, quantitative trait loci analysis and congenic analysis using resistant C57BL/6J and susceptible ICGN mice identified a modifier locus associated with podocyte injury caused by tensin2 dysfunction on chromosome 2...
April 10, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29614956/power-and-precision-of-qtl-mapping-in-simulated-multiple-porcine-f2-crosses-using-whole-genome-sequence-information
#4
Markus Schmid, Robin Wellmann, Jörn Bennewitz
BACKGROUND: During the last two decades, many QTL (quantitative trait locus) mapping experiments in pigs have been conducted using F2 crosses established from two outbred founder breeds. The founder breeds were frequently chosen from the Asian and European type breeds. A combination of next-generation sequencing, SNP (single nucleotide polymorphism) genotyping technology using SNP-chips, and genotype imputation techniques, can be used to infer the sequence information of all F2 individuals in a cost-effective way...
April 3, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29614950/genetic-insights-into-dispersal-distance-and-disperser-fitness-of-african-lions-panthera-leo-from-the-latitudinal-extremes-of-the-kruger-national-park-south-africa
#5
Pim van Hooft, Dewald F Keet, Diana K Brebner, Armanda D S Bastos
BACKGROUND: Female lions generally do not disperse far beyond their natal range, while males can disperse distances of over 200 km. However, in bush-like ecosystems dispersal distances less than 25 km are reported. Here, we investigate dispersal in lions sampled from the northern and southern extremes of Kruger National Park, a bush-like ecosystem in South Africa where bovine tuberculosis prevalence ranges from low to high across a north-south gradient. RESULTS: A total of 109 individuals sampled from 1998 to 2004 were typed using 11 microsatellite markers, and mitochondrial RS-3 gene sequences were generated for 28 of these individuals...
April 3, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29609562/including-gene-networks-to-predict-calving-difficulty-in-holstein-brown-swiss-and-jersey-cattle
#6
Francesco Tiezzi, Maria E Arceo, John B Cole, Christian Maltecca
BACKGROUND: Calving difficulty or dystocia has a great economic impact in the US dairy industry. Reported risk factors associated with calving difficulty are feto-pelvic disproportion, gestation length and conformation. Different dairy cattle breeds have different incidence of calving difficulty, with Holstein having the highest dystocia rates and Jersey the lowest. Genomic selection becomes important especially for complex traits with low heritability, where the accuracy of conventional selection is lower...
April 2, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29609543/rna-seq-analysis-of-lncrna-controlled-developmental-gene-expression-during-puberty-in-goat-rat
#7
Xiaoxiao Gao, Jing Ye, Chen Yang, Lei Luo, Ya Liu, Jianping Ding, Yunhai Zhang, Yinghui Ling, Weiping Huang, Xiaorong Zhang, Kaifa Zhang, Xiumei Li, Jie Zhou, Fugui Fang, Zubing Cao
BACKGROUND: Puberty is a pivotal stage in female animal development, and marks the onset of reproductive capability. However, little is known about the function of lncRNAs (long noncoding RNAs) in puberty. Therefore, RNA-seq analysis were performed between goats and rats to clarify the roles of lncRNAs and mRNAs in the onset of puberty. RESULTS: In the present study, the length of lncRNAs, the length of the open reading frame and the exon count were compared between the two species...
April 2, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29587653/efficient-anchoring-of-alien-chromosome-segments-introgressed-into-bread-wheat-by-new-leymus-racemosus-genome-based-markers
#8
Offiong Ukpong Edet, June-Sik Kim, Masanori Okamoto, Kousuke Hanada, Tomoyuki Takeda, Masahiro Kishii, Yasir Serag Alnor Gorafi, Hisashi Tsujimoto
BACKGROUND: The tertiary gene pool of bread wheat, to which Leymus racemosus belongs, has remained underutilized due to the current limited genomic resources of the species that constitute it. Continuous enrichment of public databases with useful information regarding these species is, therefore, needed to provide insights on their genome structures and aid successful utilization of their genes to develop improved wheat cultivars for effective management of environmental stresses. RESULTS: We generated de novo DNA and mRNA sequence information of L...
March 27, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29571286/refining-a-major-qtl-controlling-spotted-wilt-disease-resistance-in-cultivated-peanut-arachis-hypogaea-l-and-evaluating-its-contribution-to-the-resistance-variations-in-peanut-germplasm
#9
Zifan Zhao, Yu-Chien Tseng, Ze Peng, Yolanda Lopez, Charles Y Chen, Barry L Tillman, Phat Dang, Jianping Wang
BACKGROUND: Spotted wilt, caused by tomato spotted wilt virus (TSWV), has been one of major diseases in cultivated peanut grown in the southeastern United States (US) since 1990. Previously a major quantitative trait locus (QTL) controlling spotted wilt disease resistance was mapped to an interval of 2.55 cM genetic distance corresponding to a physical distance of 14.4 Mb on chromosome A01 of peanut by using a segregating F2 population. The current study focuses on refining this major QTL region and evaluating its contributions in the US peanut mini-core germplasm...
March 23, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29566674/a-genome-wide-association-study-identifies-candidate-loci-associated-to-syringomyelia-secondary-to-chiari-like-malformation-in-cavalier-king-charles-spaniels
#10
Frédéric Ancot, Philippe Lemay, Susan P Knowler, Karen Kennedy, Sandra Griffiths, Giunio Bruto Cherubini, Jane Sykes, Paul J J Mandigers, Guy A Rouleau, Clare Rusbridge, Zoha Kibar
BACKGROUND: Syringomyelia (SM) is a common condition affecting brachycephalic toy breed dogs and is characterized by the development of fluid-filled cavities within the spinal cord. It is often concurrent with a complex developmental malformation of the skull and craniocervical vertebrae called Chiari-like malformation (CM) characterized by a conformational change and overcrowding of the brain and cervical spinal cord particularly at the craniocervical junction. CM and SM have a polygenic mode of inheritance with variable penetrance...
March 22, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29548277/common-variants-in-the-herg-kcnh2-voltage-gated-potassium-channel-are-associated-with-altered-fasting-and-glucose-stimulated-plasma-incretin-and-glucagon-responses
#11
Line Engelbrechtsen, Yuvaraj Mahendran, Anna Jonsson, Anette Prior Gjesing, Peter E Weeke, Marit E Jørgensen, Kristine Færch, Daniel R Witte, Jens J Holst, Torben Jørgensen, Niels Grarup, Oluf Pedersen, Henrik Vestergaard, Signe Torekov, Jørgen K Kanters, Torben Hansen
BACKGROUND: Patients with long QT syndrome due to rare loss-of-function mutations in the human ether-á-go-go-related gene (hERG) have prolonged QT interval, risk of arrhythmias, increased secretion of insulin and incretins and impaired glucagon response to hypoglycemia. This is caused by a dysfunctional Kv11.1 voltage-gated potassium channel. Based on these findings in patients with rare variants in hERG, we hypothesized that common variants in hERG may also lead to alterations in glucose homeostasis...
March 16, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29486732/whole-genome-scan-reveals-significant-non-additive-effects-for-sire-conception-rate-in-holstein-cattle
#12
Paula Nicolini, Rocío Amorín, Yi Han, Francisco Peñagaricano
BACKGROUND: Service sire has a considerable impact on reproductive success in dairy cattle. Most gene mapping studies for bull fertility have focused on additive effects, while non-additive effects have been largely ignored. The main goal of this study was to assess the relevance of non-additive effects on Sire Conception Rate (SCR) in Holstein dairy cattle. The analysis included 7.5 k Holstein bulls with both SCR records and 57.8 k single nucleotide polymorphism (SNP) markers spanning the entire genome...
February 27, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29448946/correction-to-high-density-marker-panels-snps-prioritizing-and-accuracy-of-genomic-selection
#13
Ling-Yun Chang, Sajjad Toghiani, Ashley Ling, Sammy E Aggrey, Romdhane Rekaya
BMC GENETICS (2018) 19:4 DOI: 10.1186/S12863-017-0595-2: The original version of this article [1], published on 5 January 2018, contained 3 formatting errors. In this Correction the affected parts of the article are shown. The original article has been updated.
February 15, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29439656/genetic-diversity-and-ex-situ-conservation-of-loropetalum-subcordatum-an-endangered-species-endemic-to-china
#14
Bai-Jun Li, Jie-Yu Wang, Zhong-Jian Liu, Xue-Ying Zhuang, Jiu-Xiang Huang
BACKGROUND: Loropetalum subcordatum is an endangered species endemic to China that is characterized by narrow distribution, small population size, and delayed fertilization. However, the genetic diversity of the entire extant natural and ex situ populations has not been assessed to date. In this study, we evaluated the genetic diversity and structure of six natural populations and a single ex situ population (the only known ex situ population of L. subcordatum) using sequence-related amplified polymorphism data...
February 13, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29361905/diversity-of-plant-defense-elicitor-peptides-within-the-rosaceae
#15
Cristina Ruiz, Anna Nadal, Laura Foix, Laura Montesinos, Emilio Montesinos, Maria Pla
BACKGROUND: Plant elicitor peptides (Peps) are endogenous molecules that induce and amplify the first line of inducible plant defense, known as pattern-triggered immunity, contributing to protect plants against attack by bacteria, fungi and herbivores. Pep topic application and transgenic expression have been found to enhance disease resistance in a small number of model plant-pathogen systems. The action of Peps relies on perception by specific receptors, so displaying a family-specific activity...
January 23, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29357837/detecting-tf-mirna-gene-network-based-modules-for-5hmc-and-5mc-brain-samples-a-intra-and-inter-species-case-study-between-human-and-rhesus
#16
Ujjwal Maulik, Sagnik Sen, Saurav Mallik, Sanghamitra Bandyopadhyay
BACKGROUND: Study of epigenetics is currently a high-impact research topic. Multi stage methylation is also an area of high-dimensional prospect. In this article, we provide a new study (intra and inter-species study) on brain tissue between human and rhesus on two methylation cytosine variants based data-profiles (viz., 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC) samples) through TF-miRNA-gene network based module detection. RESULTS: First of all, we determine differentially 5hmC methylated genes for human as well as rhesus for intra-species analysis, and differentially multi-stage methylated genes for inter-species analysis...
January 22, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29357832/dart-snp-and-ssr-analyses-of-genetic-diversity-in-lolium-perenne-l-using-bulk-sampling
#17
Siyang Liu, Ulf Feuerstein, Wilbert Luesink, Sabine Schulze, Torben Asp, Bruno Studer, Heiko C Becker, Klaus J Dehmer
BACKGROUND: Lolium perenne L. is the most important forage grass species in temperate regions. It is also considered as a sustainable source of biomass for energy production. However, improvement in biomass yield has been limited by comparison with other major crops. More efficient utilisation of genetic resources and improved breeding schemes are required to advance L. perenne breeding. In an attempt to elucidate the extent of genetic diversity in L. perenne, 1384 DArT, 182 SNP and 48 SSR markers were applied to 297 accessions (Set I) contributed by three German breeding companies and the IPK Genebank...
January 22, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29338687/use-of-easy-measurable-phenotypic-traits-as-a-complementary-approach-to-evaluate-the-population-structure-and-diversity-in-a-high-heterozygous-panel-of-tetraploid-clones-and-cultivars
#18
Martin E Tagliotti, Sofia I Deperi, Maria C Bedogni, Ruofang Zhang, Norma C Manrique Carpintero, Joseph Coombs, David Douches, Marcelo A Huarte
BACKGROUND: Diversity in crops is fundamental for plant breeding efforts. An accurate assessment of genetic diversity, using molecular markers, such as single nucleotide polymorphism (SNP), must be able to reveal the structure of the population under study. A characterization of population structure using easy measurable phenotypic traits could be a preliminary and low-cost approach to elucidate the genetic structure of a population. A potato population of 183 genotypes was evaluated using 4859 high-quality SNPs and 19 phenotypic traits commonly recorded in potato breeding programs...
January 16, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29334899/association-between-sequence-variants-in-panicle-development-genes-and-the-number-of-spikelets-per-panicle-in-rice
#19
Su Jang, Yunjoo Lee, Gileung Lee, Jeonghwan Seo, Dongryung Lee, Yoye Yu, Joong Hyoun Chin, Hee-Jong Koh
BACKGROUND: Balancing panicle-related traits such as panicle length and the numbers of primary and secondary branches per panicle, is key to improving the number of spikelets per panicle in rice. Identifying genetic information contributes to a broader understanding of the roles of gene and provides candidate alleles for use as DNA markers. Discovering relations between panicle-related traits and sequence variants allows opportunity for molecular application in rice breeding to improve the number of spikelets per panicle...
January 15, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29334894/rare-variant-association-analysis-in-case-parents-studies-by-allowing-for-missing-parental-genotypes
#20
Yumei Li, Yang Xiang, Chao Xu, Hui Shen, Hongwen Deng
BACKGROUND: The development of next-generation sequencing technologies has facilitated the identification of rare variants. Family-based design is commonly used to effectively control for population admixture and substructure, which is more prominent for rare variants. Case-parents studies, as typical strategies in family-based design, are widely used in rare variant-disease association analysis. Current methods in case-parents studies are based on complete case-parents data; however, parental genotypes may be missing in case-parents trios, and removing these data may lead to a loss in statistical power...
January 15, 2018: BMC Genetics
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