1,843 results match your criteria BMC Genetics [Journal]


Genetic dissection and fine mapping of a novel dt gene associated with determinate growth habit in sesame.

BMC Genet 2018 Jun 14;19(1):38. Epub 2018 Jun 14.

Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China.

Background: As an important oil crop, growth habit of sesame (Sesamum indicum L.) is naturally indeterminate, which brings about asynchronous maturity of capsules and causes loss of yield.

Results: The genetic basis of determinate growth habit in sesame was investigated by classical genetic analysis through multiple populations, results revealed that it was controlled by an unique recessive gene. Read More

View Article

Genome sequencing and protein domain annotations of Korean Hanwoo cattle identify Hanwoo-specific immunity-related and other novel genes.

BMC Genet 2018 May 29;19(1):37. Epub 2018 May 29.

Animal Genomics & Bioinformatics Division, National Institute of Animal Science, RDA, 77 Chuksan-gil, Kwonsun-gu, Suwon, 441-706, Republic of Korea.

Background: Identification of genetic mechanisms and idiosyncrasies at the breed-level can provide valuable information for potential use in evolutionary studies, medical applications, and breeding of selective traits. Here, we analyzed genomic data collected from 136 Korean Native cattle, known as Hanwoo, using advanced statistical methods.

Results: Results revealed Hanwoo-specific protein domains which were largely characterized by immunoglobulin function. Read More

View Article

Identification of genes regulating traits targeted for domestication of field cress (Lepidium campestre) as a biennial and perennial oilseed crop.

BMC Genet 2018 May 29;19(1):36. Epub 2018 May 29.

Department of Plant Breeding, Swedish University of Agricultural Sciences, Box 101, SE-23053, Alnarp, Sweden.

Background: The changing climate and the desire to use renewable oil sources necessitate the development of new oilseed crops. Field cress (Lepidium campestre) is a species in the Brassicaceae family that has been targeted for domestication not only as an oilseed crop that produces seeds with a desirable industrial oil quality but also as a cover/catch crop that provides valuable ecosystem services. Lepidium is closely related to Arabidopsis and display significant proportions of syntenic regions in their genomes. Read More

View Article
May 2018
1 Read

Genomic prediction of crown rust resistance in Lolium perenne.

BMC Genet 2018 May 29;19(1):35. Epub 2018 May 29.

Teagasc, Crop Science Department, Oak Park, Carlow, R93 XE12, Ireland.

Background: Genomic selection (GS) can accelerate genetic gains in breeding programmes by reducing the time it takes to complete a cycle of selection. Puccinia coronata f. sp lolli (crown rust) is one of the most widespread diseases of perennial ryegrass and can lead to reductions in yield, persistency and nutritional value. Read More

View Article

Landraces of snake melon, an ancient Middle Eastern crop, reveal extensive morphological and DNA diversity for potential genetic improvement.

BMC Genet 2018 May 23;19(1):34. Epub 2018 May 23.

Mina and Everard Goodman Faculty of Life Sciences, Bar Ilan University, 5290002, Ramat Gan, Israel.

Background: Snake melon (Cucumis melo var. flexuosus, "Faqqous") is a traditional and ancient vegetable in the Mediterranean area. A collection of landraces from 42 grower fields in Israel and Palestinian territories was grown and characterized in a "Common Garden" rain-fed experiment, at the morphological-horticultural and molecular level using seq-DArT markers. Read More

View Article

Genetic diversity of BoLA-DRB3 in South American Zebu cattle populations.

BMC Genet 2018 May 22;19(1):33. Epub 2018 May 22.

Nanomedical Engineering Laboratory, RIKEN Cluster for Pioneering Research, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan.

Background: Bovine leukocyte antigens (BoLAs) are used extensively as markers of disease and immunological traits in cattle. However, until now, characterization of BoLA gene polymorphisms in Zebu breeds using high resolution typing methods has been poor. Here, we used a polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence exon 2 of the BoLA class II DRB3 gene from 421 cattle (116 Bolivian Nellore, 110 Bolivian Gir, and 195 Peruvian Nellore-Brahman). Read More

View Article

TelNet - a database for human and yeast genes involved in telomere maintenance.

BMC Genet 2018 May 18;19(1):32. Epub 2018 May 18.

Division of Chromatin Networks, German Cancer Research Center (DKFZ) & Bioquant, 69120, Heidelberg, Germany.

Background: The ends of linear chromosomes, the telomeres, comprise repetitive DNA sequences in complex with proteins that protects them from being processed by the DNA repair machinery. Cancer cells need to counteract the shortening of telomere repeats during replication for their unlimited proliferation by reactivating the reverse transcriptase telomerase or by using the alternative lengthening of telomeres (ALT) pathway. The different telomere maintenance (TM) mechanisms appear to involve hundreds of proteins but their telomere repeat length related activities are only partly understood. Read More

View Article

Genome-wide detection of selection signatures in Chinese indigenous Laiwu pigs revealed candidate genes regulating fat deposition in muscle.

BMC Genet 2018 May 18;19(1):31. Epub 2018 May 18.

Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.

Background: Currently, genome-wide scans for positive selection signatures in commercial breed have been investigated. However, few studies have focused on selection footprints of indigenous breeds. Laiwu pig is an invaluable Chinese indigenous pig breed with extremely high proportion of intramuscular fat (IMF), and an excellent model to detect footprint as the result of natural and artificial selection for fat deposition in muscle. Read More

View Article
May 2018
2 Reads

Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle.

BMC Genet 2018 May 11;19(1):30. Epub 2018 May 11.

Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830, Tjele, Denmark.

Background: Genome-wide association studies (GWAS) have been successfully implemented in cattle research and breeding. However, moving from the associations to identifying the causal variants and revealing underlying mechanisms have proven complicated. In dairy cattle populations, we face a challenge due to long-range linkage disequilibrium (LD) arising from close familial relationships in the studied individuals. Read More

View Article

Hidden MHC genetic diversity in the Iberian ibex (Capra pyrenaica).

BMC Genet 2018 May 8;19(1):28. Epub 2018 May 8.

Espacio Natural Sierra Nevada, Carretera Antigua de Sierra Nevada, Km 7, E-18071, Pinos Genil, Granada, Spain.

Background: Defining hidden genetic diversity within species is of great significance when attempting to maintain the evolutionary potential of natural populations and conduct appropriate management. Our hypothesis is that isolated (and eventually small) wild animal populations hide unexpected genetic diversity due to their maintenance of ancient polymorphisms or introgressions.

Results: We tested this hypothesis using the Iberian ibex (Capra pyrenaica) as an example. Read More

View Article
May 2018
3 Reads

A deeper view into the significance of simple sequence repeats in pre-miRNAs provides clues for its possible roles in determining the function of microRNAs.

BMC Genet 2018 May 9;19(1):29. Epub 2018 May 9.

Plant Disease Biology and Biotechnology, Rajiv Gandhi Center for Biotechnology, Poojappura, Thiruvananthapuram, Kerala, 695014, India.

Background: The central tenet of 'genome content' has been that the 'non-coding' parts are highly enriched with 'microsatellites' or 'Simple Sequence Repeats' (SSRs). We presume that the presence and change in number of repeat unit (n) of SSRs in different genomic locations may or may not become beneficial, depending on the position of SSRs in a gene. Very few studies have looked into the existence of SSRs in the hair-pin precursors of miRNAs (pre-miRNAs). Read More

View Article

Can metamorphosis survival during larval development in spiny lobster Sagmariasus verreauxi be improved through quantitative genetic inheritance?

BMC Genet 2018 May 4;19(1):27. Epub 2018 May 4.

GeneCology Research Center, The University of the Sunshine Coast, Maroochydore DC, QLD, 4558, Australia.

Background: One of the major impediments to spiny lobster aquaculture is the high cost of hatchery production due to the long and complex larval cycle and poor survival during the many moult stages, especially at metamorphosis. We examined if the key trait of larval survival can be improved through selection by determining if genetic variance exists for this trait. Specifically, we report, for the first time, genetic parameters (heritability and correlations) for early survival rates recorded at five larval phases; early-phyllosoma stages (instars 1-6; S1), mid-phyllosoma stages (instars; 7-12; S2), late-phyllosoma stages (instars 13-17; S3), metamorphosis (S4) and puerulus stage (S5) in hatchery-reared spiny lobster Sagmariasus verreauxi. Read More

View Article

Identification and characterization of karyotype in Passiflora hybrids using FISH and GISH.

BMC Genet 2018 Apr 27;19(1):26. Epub 2018 Apr 27.

Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, SP, Brazil.

Background: A great interest exists in the production of hybrid plants of the genus Passiflora given the beauty and exotic features of its flowers which have ornamental value. Hybrid paternity confirmation is therefore important for assuring germplasm origin, and is typically carried out by molecular marker segregation. The aim of this study was to karyotypically characterize the chromosome heritance patterns of the progeny resultant from a cross of P. Read More

View Article

Karyotype diversity and 2C DNA content in species of the Caesalpinia group.

BMC Genet 2018 Apr 11;19(1):25. Epub 2018 Apr 11.

Departamento de Ciências Biológicas, Centro de Biotecnologia e Genética, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado, km 16, CEP, Ilhéus, BA, 45662-900, Brazil.

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. Read More

View Article
April 2018
4 Reads

Genomic heritability estimates in sweet cherry reveal non-additive genetic variance is relevant for industry-prioritized traits.

BMC Genet 2018 Apr 10;19(1):23. Epub 2018 Apr 10.

Department of Horticulture, Washington State University, Pullman, WA, 99164-6414, USA.

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. Read More

View Article
April 2018
1 Read

Genetic loci for resistance to podocyte injury caused by the tensin2 gene deficiency in mice.

BMC Genet 2018 Apr 10;19(1):24. Epub 2018 Apr 10.

Laboratory of Laboratory Animal Science and Medicine, School of Veterinary Medicine, Kitasato University, 35-1, Higashi-23, Towada, Aomori, 034-8628, Japan.

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. Read More

View Article
April 2018
1 Read

Power and precision of QTL mapping in simulated multiple porcine F2 crosses using whole-genome sequence information.

BMC Genet 2018 Apr 3;19(1):22. Epub 2018 Apr 3.

Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany.

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. Read More

View Article
April 2018
1 Read

Genetic insights into dispersal distance and disperser fitness of African lions (Panthera leo) from the latitudinal extremes of the Kruger National Park, South Africa.

BMC Genet 2018 Apr 3;19(1):21. Epub 2018 Apr 3.

Department of Zoology & Entomology, Mammal Research Institute,, University of Pretoria, Hatfield, South Africa.

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. Read More

View Article
April 2018
2 Reads

Including gene networks to predict calving difficulty in Holstein, Brown Swiss and Jersey cattle.

BMC Genet 2018 Apr 2;19(1):20. Epub 2018 Apr 2.

Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA.

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. Read More

View Article
April 2018
1 Read

RNA-seq analysis of lncRNA-controlled developmental gene expression during puberty in goat & rat.

BMC Genet 2018 Apr 2;19(1):19. Epub 2018 Apr 2.

Anhui Provincial Laboratory of Animal Genetic Resources Protection and Breeding, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, 230036, Anhui, China.

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. Read More

View Article
April 2018
2 Reads

Efficient anchoring of alien chromosome segments introgressed into bread wheat by new Leymus racemosus genome-based markers.

BMC Genet 2018 Mar 27;19(1):18. Epub 2018 Mar 27.

Arid Land Research Center, Tottori University, Tottori, Japan.

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. Read More

View Article
March 2018
2 Reads

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.

BMC Genet 2018 Mar 23;19(1):17. Epub 2018 Mar 23.

Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.

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. Read More

View Article
March 2018
6 Reads

A genome-wide association study identifies candidate loci associated to syringomyelia secondary to Chiari-like malformation in Cavalier King Charles Spaniels.

BMC Genet 2018 Mar 22;19(1):16. Epub 2018 Mar 22.

Department of Neurosciences, CHU Sainte Justine Research Center, University of Montréal, 3175 Cote-Sainte-Catherine, Room 3.17.006, Montreal, QC, H3T 1C5, Canada.

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. Read More

View Article
March 2018
6 Reads

Common variants in the hERG (KCNH2) voltage-gated potassium channel are associated with altered fasting and glucose-stimulated plasma incretin and glucagon responses.

BMC Genet 2018 Mar 16;19(1):15. Epub 2018 Mar 16.

Novo Nordisk Foundation Center for Basic Metabolic Research, Section of Metabolic Genetics, University of Copenhagen, Faculty of Health and Medical Sciences, Blegdamsvej 3B, Maersk Tower 8. floor, -2200, Copenhagen, DK, Denmark.

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. Read More

View Article
March 2018
2 Reads

Whole-genome scan reveals significant non-additive effects for sire conception rate in Holstein cattle.

BMC Genet 2018 Feb 27;19(1):14. Epub 2018 Feb 27.

Department of Animal Sciences, University of Florida, 2250 Shealy Drive, Gainesville, FL, 32611, USA.

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. Read More

View Article
February 2018
2 Reads

Correction to: High density marker panels, SNPs prioritizing and accuracy of genomic selection.

BMC Genet 2018 Feb 15;19(1):13. Epub 2018 Feb 15.

Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA.

Correction To: 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. Read More

View Article
February 2018
1 Read

Genetic diversity and ex situ conservation of Loropetalum subcordatum, an endangered species endemic to China.

BMC Genet 2018 Feb 13;19(1):12. Epub 2018 Feb 13.

South China Limestone Plants Research Center, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.

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. Read More

View Article
February 2018
2 Reads

Diversity of plant defense elicitor peptides within the Rosaceae.

BMC Genet 2018 Jan 23;19(1):11. Epub 2018 Jan 23.

Institute for Food and Agricultural Technology (INTEA), University of Girona, Campus Montilivi (EPS-1), 17003, Girona, Spain.

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. Read More

View Article
January 2018
1 Read

Detecting TF-miRNA-gene network based modules for 5hmC and 5mC brain samples: a intra- and inter-species case-study between human and rhesus.

BMC Genet 2018 Jan 22;19(1). Epub 2018 Jan 22.

Machine Intelligence Unit, Indian Statistical Institute, 203 B.T. Road, Kolkata, 700108, India.

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. Read More

View Article
January 2018
1 Read

DArT, SNP, and SSR analyses of genetic diversity in Lolium perenne L. using bulk sampling.

BMC Genet 2018 Jan 22;19(1):10. Epub 2018 Jan 22.

Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Gatersleben, Germany.

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. Read More

View Article
January 2018
3 Reads

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.

BMC Genet 2018 Jan 16;19(1). Epub 2018 Jan 16.

Potato Research Group, Estación Experimental Agropecuaria Balcarce, Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta 226 km 73.5, Balcarce, Buenos Aires, Argentina.

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. Read More

View Article
January 2018
2 Reads

Association between sequence variants in panicle development genes and the number of spikelets per panicle in rice.

BMC Genet 2018 Jan 15;19(1). Epub 2018 Jan 15.

Department of Plant Science, Plant Genomics and Breeding Institute, Research Institute for Agriculture and Life Sciences, Seoul National University, Seoul, 08826, South Korea.

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. Read More

View Article
January 2018
2 Reads

Rare variant association analysis in case-parents studies by allowing for missing parental genotypes.

BMC Genet 2018 Jan 15;19(1). Epub 2018 Jan 15.

Center for Bioinformatics and Genomics, Department of Global Biostatistics and Data Science, Tulane University, New Orleans, LA, 70112, USA.

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. Read More

View Article
January 2018
2 Reads

Characterization of the late embryogenesis abundant (LEA) proteins family and their role in drought stress tolerance in upland cotton.

BMC Genet 2018 Jan 15;19(1). Epub 2018 Jan 15.

Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR, CAAS)/State Key Laboratory of Cotton Biology, Anyang, 455000, China.

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. Read More

View Article
January 2018
4 Reads
1 PubMed Central Citation(source)
2.40 Impact Factor

High density marker panels, SNPs prioritizing and accuracy of genomic selection.

BMC Genet 2018 Jan 5;19(1). Epub 2018 Jan 5.

Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA.

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. At best, HD panels do not significantly improve GS accuracy and, at worst, reduce accuracy. Read More

View Article
January 2018
3 Reads

Genome-wide association study of seedling stage salinity tolerance in temperate japonica rice germplasm.

BMC Genet 2018 Jan 3;19(1). Epub 2018 Jan 3.

International Rice Research Institute, Laguna, 4031, Philippines.

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. Read More

View Article
January 2018
9 Reads

De novo transcriptome sequencing and analysis of male and female swimming crab (Portunus trituberculatus) reproductive systems during mating embrace (stage II).

BMC Genet 2018 Jan 3;19(1). Epub 2018 Jan 3.

Jiangsu Key Laboratory for Bioresources of Saline Soils, Jiangsu Synthetic Innovation Center for Coastal Bio-agriculture, Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, School of Ocean and Biological Engineering, Yancheng Teachers University, Yancheng, 224001, Jiangsu Province, People's Republic of China.

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. Read More

View Article
January 2018
3 Reads

Between Lake Baikal and the Baltic Sea: genomic history of the gateway to Europe.

BMC Genet 2017 Dec 28;18(Suppl 1):110. Epub 2017 Dec 28.

Federal State Institution "Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences", Moscow, Russia.

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. Read More

View Article
December 2017
6 Reads

Upregulation of NETO2 gene in colorectal cancer.

BMC Genet 2017 Dec 28;18(Suppl 1):117. Epub 2017 Dec 28.

Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.

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). Read More

View Article
December 2017
6 Reads

A compendium and functional characterization of mammalian genes involved in adaptation to Arctic or Antarctic environments.

BMC Genet 2017 Dec 28;18(Suppl 1):111. Epub 2017 Dec 28.

The Federal Research Center Institute of Cytology and Genetics, The Siberian Branch of the Russian Academy of Sciences, 630090, Novosibirsk, Russia.

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. Read More

View Article
December 2017
4 Reads

Generation of megabase-scale deletions, inversions and duplications involving the Contactin-6 gene in mice by CRISPR/Cas9 technology.

BMC Genet 2017 Dec 28;18(Suppl 1):112. Epub 2017 Dec 28.

Department of Molecular Mechanisms of Development, Institute of Cytology and Genetics, Russia Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia.

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. Read More

View Article
December 2017
6 Reads

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.

BMC Genet 2017 Dec 28;18(Suppl 1):109. Epub 2017 Dec 28.

Department of Medical Genetics, Kasturba Medical College, Manipal Academy of Higher Education, Manipal, Karnataka, India.

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. Read More

View Article
December 2017
5 Reads

DEP1 gene in wheat species with normal, compactoid and compact spikes.

BMC Genet 2017 Dec 28;18(Suppl 1):106. Epub 2017 Dec 28.

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.

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. Read More

View Article
December 2017
8 Reads

Genetics at Belyaev Conference - 2017: introductory note.

BMC Genet 2017 Dec 28;18(Suppl 1):116. Epub 2017 Dec 28.

Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia.

View Article
December 2017
4 Reads

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.

BMC Genet 2018 Jan 2;19(1). Epub 2018 Jan 2.

Laboratory of Genetics and Genomics, Institute for Developing Science and Health Initiatives, Mohakhali, Dhaka, Bangladesh.

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. Read More

View Article
January 2018
9 Reads

Novel methods for genotype imputation to whole-genome sequence and a simple linear model to predict imputation accuracy.

BMC Genet 2017 Dec 27;18(1):120. Epub 2017 Dec 27.

Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.

Background: Accurate imputation plays a major role in genomic studies of livestock industries, where the number of genotyped or sequenced animals is limited by costs. This study explored methods to create an ideal reference population for imputation to Next Generation Sequencing data in cattle.

Methods: Methods for clustering of animals for imputation were explored, using 1000 Bull Genomes Project sequence data on 1146 animals from a variety of beef and dairy breeds. Read More

View Article
December 2017
2 Reads

An integrated and comparative approach towards identification, characterization and functional annotation of candidate genes for drought tolerance in sorghum (Sorghum bicolor (L.) Moench).

BMC Genet 2017 Dec 22;18(1):119. Epub 2017 Dec 22.

South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Private Bag X17, Belleville, 7535, South Africa.

Background: Drought is the most disastrous abiotic stress that severely affects agricultural productivity worldwide. Understanding the biological basis of drought-regulated traits, requires identification and an in-depth characterization of genetic determinants using model organisms and high-throughput technologies. However, studies on drought tolerance have generally been limited to traditional candidate gene approach that targets only a single gene in a pathway that is related to a trait. Read More

View Article
December 2017
3 Reads

Evolutionary history of the NAM-B1 gene in wild and domesticated tetraploid wheat.

BMC Genet 2017 Dec 20;18(1):118. Epub 2017 Dec 20.

Linköping University, IFM Biology, SE-581 83, Linköping, Sweden.

Background: The NAM-B1 gene in wheat has for almost three decades been extensively studied and utilized in breeding programs because of its significant impact on grain protein and mineral content and pleiotropic effects on senescence rate and grain size. First detected in wild emmer wheat, the wild-type allele of the gene has been introgressed into durum and bread wheat. Later studies have, however, also found the presence of the wild-type allele in some domesticated subspecies. Read More

View Article
December 2017
4 Reads

Comparison of weighting approaches for genetic risk scores in gene-environment interaction studies.

BMC Genet 2017 Dec 16;18(1):115. Epub 2017 Dec 16.

Mathematical Institute, Heinrich Heine University, Düsseldorf, Germany.

Background: Weighted genetic risk scores (GRS), defined as weighted sums of risk alleles of single nucleotide polymorphisms (SNPs), are statistically powerful for detection gene-environment (GxE) interactions. To assign weights, the gold standard is to use external weights from an independent study. However, appropriate external weights are not always available. Read More

View Article
December 2017
2 Reads

Correction to: Mapping of leptin and its syntenic genes to chicken chromosome 1p.

BMC Genet 2017 12 15;18(1):113. Epub 2017 Dec 15.

Department of Animal Science, Agricultural Research Organization, Volcani Center, P.O. Box 15159, 7528809, Rishon LeTsiyon, Israel.

Correction: After the publication of this work [1] an error was noticed in one of the author surnames. The author name Leif Anderson should be spelt as Leif Andersson. Read More

View Article
December 2017
3 Reads