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BMC Genetics

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https://www.readbyqxmd.com/read/29448946/correction-to-high-density-marker-panels-snps-prioritizing-and-accuracy-of-genomic-selection
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/29334890/characterization-of-the-late-embryogenesis-abundant-lea-proteins-family-and-their-role-in-drought-stress-tolerance-in-upland-cotton
#9
Richard Odongo Magwanga, Pu Lu, Joy Nyangasi Kirungu, Hejun Lu, Xingxing Wang, Xiaoyan Cai, Zhongli Zhou, Zhenmei Zhang, Haron Salih, Kunbo Wang, Fang Liu
BACKGROUND: Late embryogenesis abundant (LEA) proteins are large groups of hydrophilic proteins with major role in drought and other abiotic stresses tolerance in plants. In-depth study and characterization of LEA protein families have been carried out in other plants, but not in upland cotton. The main aim of this research work was to characterize the late embryogenesis abundant (LEA) protein families and to carry out gene expression analysis to determine their potential role in drought stress tolerance in upland cotton...
January 15, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29304753/high-density-marker-panels-snps-prioritizing-and-accuracy-of-genomic-selection
#10
Ling-Yun Chang, Sajjad Toghiani, Ashley Ling, Sammy E Aggrey, Romdhane Rekaya
BACKGROUND: The availability of high-density (HD) marker panels, genome wide variants and sequence data creates an unprecedented opportunity to dissect the genetic basis of complex traits, enhance genomic selection (GS) and identify causal variants of disease. The disproportional increase in the number of parameters in the genetic association model compared to the number of phenotypes has led to further deterioration in statistical power and an increase in co-linearity and false positive rates...
January 5, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29298667/genome-wide-association-study-of-seedling-stage-salinity-tolerance-in-temperate-japonica-rice-germplasm
#11
Dariga Batayeva, Benedick Labaco, Changrong Ye, Xiaolin Li, Bakdaulet Usenbekov, Aiman Rysbekova, Gulzhamal Dyuskalieva, Georgina Vergara, Russell Reinke, Hei Leung
BACKGROUND: Salinity has a significant impact on rice production in coastal, arid and semi-arid areas in many countries, including countries growing temperate rice, such as Kazakhstan. Recently, the complete genomes of 3000 rice accessions were sequenced through the 3 K rice genome project, and this set included 203 temperate japonica rice accessions. To identify salinity-tolerant germplasm and related genes for developing new salinity-tolerant breeding lines for the temperate japonica rice growing regions, we evaluated the seedling stage salinity tolerance of these sequenced temperate japonica rice accessions, and conducted genome-wide association studies (GWAS) for a series of salinity tolerance related traits...
January 3, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29298661/de-novo-transcriptome-sequencing-and-analysis-of-male-and-female-swimming-crab-portunus-trituberculatus-reproductive-systems-during-mating-embrace-stage-ii
#12
Zhengfei Wang, Linxia Sun, Weibing Guan, Chunlin Zhou, Boping Tang, Yongxu Cheng, Jintian Huang, Fujun Xuan
BACKGROUND: The swimming crab Portunus trituberculatus is one of the most commonly farmed crustaceans in China. As one of the most widely known and high-value edible crabs, it crab supports large crab fishery and aquaculture in China. Only large and sexually mature crabs can provide the greatest economic benefits, suggesting the considerable effect of reproductive system development on fishery. Studies are rarely conducted on the molecular regulatory mechanism underlying the development of the reproductive system during the mating embrace stage in this species...
January 3, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29295702/high-resolution-melting-curve-analysis-targeting-the-hbb-gene-mutational-hot-spot-offers-a-reliable-screening-approach-for-all-common-as-well-as-most-of-the-rare-beta-globin-gene-mutations-in-bangladesh
#13
Md Tarikul Islam, Suprovath Kumar Sarkar, Nusrat Sultana, Mst Noorjahan Begum, Golam Sarower Bhuyan, Shezote Talukder, A K M Muraduzzaman, Md Alauddin, Mohammad Sazzadul Islam, Pritha Promita Biswas, Aparna Biswas, Syeda Kashfi Qadri, Tahmina Shirin, Bilquis Banu, Salma Sadya, Manzoor Hussain, Golam Sarwardi, Waqar Ahmed Khan, Mohammad Abdul Mannan, Hossain Uddin Shekhar, Emran Kabir Chowdhury, Abu Ashfaqur Sajib, Sharif Akhteruzzaman, Syed Saleheen Qadri, Firdausi Qadri, Kaiissar Mannoor
BACKGROUND: Bangladesh lies in the global thalassemia belt, which has a defined mutational hot-spot in the beta-globin gene. The high carrier frequencies of beta-thalassemia trait and hemoglobin E-trait in Bangladesh necessitate a reliable DNA-based carrier screening approach that could supplement the use of hematological and electrophoretic indices to overcome the barriers of carrier screening. With this view in mind, the study aimed to establish a high resolution melting (HRM) curve-based rapid and reliable mutation screening method targeting the mutational hot-spot of South Asian and Southeast Asian countries that encompasses exon-1 (c...
January 2, 2018: BMC Genetics
https://www.readbyqxmd.com/read/29297395/between-lake-baikal-and-the-baltic-sea-genomic-history-of-the-gateway-to-europe
#14
Petr Triska, Nikolay Chekanov, Vadim Stepanov, Elza K Khusnutdinova, Ganesh Prasad Arun Kumar, Vita Akhmetova, Konstantin Babalyan, Eugenia Boulygina, Vladimir Kharkov, Marina Gubina, Irina Khidiyatova, Irina Khitrinskaya, Ekaterina E Khrameeva, Rita Khusainova, Natalia Konovalova, Sergey Litvinov, Andrey Marusin, Alexandr M Mazur, Valery Puzyrev, Dinara Ivanoshchuk, Maria Spiridonova, Anton Teslyuk, Svetlana Tsygankova, Martin Triska, Natalya Trofimova, Edward Vajda, Oleg Balanovsky, Ancha Baranova, Konstantin Skryabin, Tatiana V Tatarinova, Egor Prokhortchouk
BACKGROUND: The history of human populations occupying the plains and mountain ridges separating Europe from Asia has been eventful, as these natural obstacles were crossed westward by multiple waves of Turkic and Uralic-speaking migrants as well as eastward by Europeans. Unfortunately, the material records of history of this region are not dense enough to reconstruct details of population history. These considerations stimulate growing interest to obtain a genetic picture of the demographic history of migrations and admixture in Northern Eurasia...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29297384/upregulation-of-neto2-gene-in-colorectal-cancer
#15
Maria S Fedorova, Anastasiya V Snezhkina, Elena A Pudova, Ivan S Abramov, Anastasiya V Lipatova, Sergey L Kharitonov, Asiya F Sadritdinova, Kirill M Nyushko, Kseniya M Klimina, Mikhail M Belyakov, Elena N Slavnova, Nataliya V Melnikova, Maria A Chernichenko, Dmitry V Sidorov, Marina V Kiseleva, Andrey D Kaprin, Boris Y Alekseev, Alexey A Dmitriev, Anna V Kudryavtseva
BACKGROUND: Neuropilin and tolloid-like 2 (NETO2) is a single-pass transmembrane protein that has been shown primarily implicated in neuron-specific processes. Upregulation of NETO2 gene was also detected in several cancer types. In colorectal cancer (CRC), it was associated with tumor progression, invasion, and metastasis, and seems to be involved in epithelial-mesenchymal transition (EMT). However, the mechanism of NETO2 action is still poorly understood. RESULTS: We have revealed significant increase in the expression of NETO2 gene and deregulation of eight EMT-related genes in CRC...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29297313/a-compendium-and-functional-characterization-of-mammalian-genes-involved-in-adaptation-to-arctic-or-antarctic-environments
#16
Nikolay S Yudin, Denis M Larkin, Elena V Ignatieva
BACKGROUND: Many mammals are well adapted to surviving in extremely cold environments. These species have likely accumulated genetic changes that help them efficiently cope with low temperatures. It is not known whether the same genes related to cold adaptation in one species would be under selection in another species. The aims of this study therefore were: to create a compendium of mammalian genes related to adaptations to a low temperature environment; to identify genes related to cold tolerance that have been subjected to independent positive selection in several species; to determine promising candidate genes/pathways/organs for further empirical research on cold adaptation in mammals...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29297312/generation-of-megabase-scale-deletions-inversions-and-duplications-involving-the-contactin-6-gene-in-mice-by-crispr-cas9-technology
#17
Alexei N Korablev, Irina A Serova, Oleg L Serov
BACKGROUND: Copy Number Variation (CNV) of the human CNTN6 gene (encoding the contactin-6 protein), caused by deletions or duplications, is responsible for severe neurodevelopmental impairments, often in combination with facial dysmorphias. Conversely, deleterious point mutations of this gene do not show any clinical phenotypes. The aim of this study is to generate mice carrying large deletions, duplications and inversions involving the Cntn6 gene as a new experimental model to study CNV of the human CNTN6 locus...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29297311/application-of-geographic-population-structure-gps-algorithm-for-biogeographical-analyses-of-populations-with-complex-ancestries-a-case-study-of-south-asians-from-1000-genomes-project
#18
Ranajit Das, Priyanka Upadhyai
BACKGROUND: The utilization of biological data to infer the geographic origins of human populations has been a long standing quest for biologists and anthropologists. Several biogeographical analysis tools have been developed to infer the geographical origins of human populations utilizing genetic data. However due to the inherent complexity of genetic information these approaches are prone to misinterpretations. The Geographic Population Structure (GPS) algorithm is an admixture based tool for biogeographical analyses and has been employed for the geo-localization of various populations worldwide...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29297308/dep1-gene-in-wheat-species-with-normal-compactoid-and-compact-spikes
#19
Valeriya Vavilova, Irina Konopatskaia, Anastasia E Kuznetsova, Alexandr Blinov, Nikolay P Goncharov
BACKGROUND: In rice, a variant of DEP1 gene results in erect panicle architecture, well-developed vascular bundles, an increase in the number of grains per panicle and a consequent increase in the grain yield. Interestingly, DEP1 homologs are present in the other cereals including species of wheat and barley (Hordeum vulgare), even though they do not produce panicles but spikes. In barley, HvDEP1 alleles do not differ between strains of various ear types and geographic origins, while in at least three OsDEP1 variants have been described...
December 28, 2017: BMC Genetics
https://www.readbyqxmd.com/read/29297300/genetics-at-belyaev-conference-2017-introductory-note
#20
Yuriy L Orlov, Ancha V Baranova, Tatiana V Tatarinova, Nikolay A Kolchanov
No abstract text is available yet for this article.
December 28, 2017: BMC Genetics
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