Abstract:
:Genomic breed composition (GBC) of an individual animal refers to the partition of its genome according to the inheritance from its ancestors or ancestral breeds. For crossbred or composite animals, knowing their GBC is useful to estimate heterosis, to characterize their actual inheritance from foundation breeds, and to make management decisions for crossbreeding programs. Various statistical approaches have been proposed to estimate GBC in animals, but the interpretations of estimates have varied with these methods. In the present study, we proposed a causality interpretation of GBC based on path analysis. We applied this method to estimating GBC in two composite breeds of beef cattle, namely Brangus and Beefmaster. Three SNP panels were used to estimate GBC: a 10K SNP panel consisting of 10,226 common SNPs across three GeneSeek Genomic Profiler (GGP) bovine SNP arrays (GGP 30K, GGP 40K, and GGP 50K), and two subsets (1K and 5K) of uniformly distributed SNPs. The path analysis decomposed the relationships between the ancestors and the composite animals into direct and indirect path effects, and GBC was measured by the relative ratio of the coefficients of direct (D-GBC) and combined (C-GBC) effects from each ancestral breed to the progeny, respectively. Estimated GBC varied only slightly between different genotyping platforms and between the three SNP panels. In the Brangus cattle, because the two ancestral breeds had a very distant relationship, the estimated D-GBC and C-GBC were comparable to each other in the path analysis, and they corresponded roughly to the estimated GBC from the linear regression and the admixture model. In the Beefmaster, however, the strong relationship in allelic frequencies between Hereford and Shorthorn imposed a challenge for the linear regression and the admixture model to estimated GBC reliably. Instead, D-GBC by the path analysis included only direct ancestral effects, and it was robust to bias due to high genomic correlations between reference (ancestral) breeds.
journal_name
Front Genetjournal_title
Frontiers in geneticsauthors
Wu XL,Li Z,Wang Y,He J,Rosa GJM,Ferretti R,Genho J,Tait RG Jr,Parham J,Schultz T,Bauck Sdoi
10.3389/fgene.2020.546052subject
Has Abstractpub_date
2020-10-30 00:00:00pages
546052issn
1664-8021journal_volume
11pub_type
杂志文章abstract::The adaptation of the yeast Saccharomyces cerevisiae to man-made environments for the fermentation of foodstuffs and beverages illustrates the scientific, social, and economic relevance of microbe domestication. Here we address a yet unexplored aspect of S. cerevisiae domestication, that of the emergence of lineages h...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00449
更新日期:2019-05-29 00:00:00
abstract::Autism spectrum disorder (ASD) is mainly reflected in the communication and language barriers, difficulties in social communication, and it is a kind of neurological developmental disorder. Most researches have used the machine learning method to classify patients and normal controls, among which support vector machin...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00018
更新日期:2018-02-06 00:00:00
abstract::From a biological perspective aging (senescence) appears to be a form of complex disease syndrome, though this is not the traditional view. This essay aims to foster a realistic understanding of aging by scrutinizing ideas old and new. The conceptual division between aging-related diseases and an underlying, non-patho...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2015.00212
更新日期:2015-06-16 00:00:00
abstract:Background:Myopia is a common eye disorder that is approaching epidemic proportions worldwide. A genome-wide association study identified AREG (rs12511037), GABRR1 (rs13215566), and PDE10A (rs12206610) as being associated with refractive error in Asian populations. The present study investigated the associations betwee...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00276
更新日期:2020-03-25 00:00:00
abstract::A within-breed genome-wide association study (GWAS) is useful when identifying the QTL that segregates in a breed. However, an across-breed meta-analysis can be used to increase the power of identification and precise localization of QTL that segregate in multiple breeds. Precise localization will allow including QTL ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2018.00522
更新日期:2018-11-06 00:00:00
abstract::Commensal gut bacteria in many species including flies are integral part of their host, and are known to influence its development and homeostasis within generation. Here we report an unexpected impact of host-microbe interactions, which mediates multi-generational, non-Mendelian inheritance of a stress-induced phenot...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2014.00027
更新日期:2014-02-25 00:00:00
abstract::Mesopelagic fish are largely abundant poorly studied fish that are still intact, but which, due to their potentially great added value, will be imminently exploited by humans. Therefore, studies that provide information to anticipate the anthropogenic impact on this important resource are urgently needed. In particula...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2017.00195
更新日期:2017-11-28 00:00:00
abstract:Background:Lung disease phenotype varies widely even in the F508del (homozygous) genotype. Leukocyte-driven inflammation is important for pulmonary disease pathogenesis in cystic fibrosis (CF). Blood cytokines correlate negatively with pulmonary function in F508del homozygous patients, and gap junction proteins (GJA) m...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.570403
更新日期:2020-10-28 00:00:00
abstract::There are associations between DNA methylation and the expression of long non-coding RNA (lncRNA), also known as lncRNA expression quantitative trait methylations (lnc-eQTMs). Lnc-eQTMs may induce a wide range of carcinogenesis pathways. However, lnc-eQTMs have not been globally identified and studied, and their roles...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.602035
更新日期:2020-12-09 00:00:00
abstract::Cardiovascular diseases such as atherosclerosis are one of the leading causes of morbidity and mortality worldwide. The clinical manifestations of atherosclerosis, which include heart attack and stroke, occur several decades after initiation of the disease and become more severe with age. Inflammation of blood vessels...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2014.00422
更新日期:2014-12-10 00:00:00
abstract::Previous efforts to characterize conservation between the human and mouse genomes focused largely on sequence comparisons. These studies are inherently limited because they don't account for gene structure differences, which may exist despite genomic sequence conservation. Recent high-throughput transcriptome studies ...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2013.00183
更新日期:2013-09-26 00:00:00
abstract::Familial hemophagocytic lymphohistiocytosis Type 2 (FHL2) associated central nervous system (CNS) involvement is less understood in children, especially when considering neurologic manifestations as part of the initial presentation. We conducted a retrospective review of the clinical manifestations and genetic abnorma...
journal_title:Frontiers in genetics
pub_type:
doi:10.3389/fgene.2020.00126
更新日期:2020-03-04 00:00:00
abstract::Long non-coding RNAs (lncRNAs) are recognized as an important class of regulatory molecules involved in a variety of biological functions. However, the regulatory mechanisms of long non-coding genes expression are still poorly understood. The characterization of the genomic features of lncRNAs is crucial to get insigh...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00488
更新日期:2020-05-15 00:00:00
abstract::RNA is a unique bio-macromolecule that can both record genetic information and perform biological functions in a variety of molecular processes, including transcription, splicing, translation, and even regulating protein function. RNAs adopt specific three-dimensional conformations to enable their functions. Experimen...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.574485
更新日期:2020-10-26 00:00:00
abstract::Poultry feed constitutes the largest cost in poultry production, estimated to be up to 70% of the total cost. Moreover, there is pressure on the poultry industry to increase production to meet the protein demand of humans and simultaneously reduce emissions to protect the environment. Therefore, improving feed efficie...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00243
更新日期:2020-04-03 00:00:00
abstract::Mosquito-borne diseases cause more than 700 million people infected and one million people die (Caraballo and King, 2014). With the limitations of progress toward elimination imposed by insecticide- and drug-resistance, combined with the lack of vaccines, innovative strategies to fight mosquito-borne disease are urgen...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2020.00196
更新日期:2020-03-10 00:00:00
abstract::[This corrects the article on p. 23 in vol. 9, PMID: 29456554.]. ...
journal_title:Frontiers in genetics
pub_type: 杂志文章,已发布勘误
doi:10.3389/fgene.2018.00109
更新日期:2018-04-04 00:00:00
abstract::Filet quality traits determine consumer satisfaction and affect profitability of the aquaculture industry. Soft flesh is a criterion for fish filet downgrades, resulting in loss of value. Filet firmness is influenced by many factors, including rate of protein turnover. A 50K transcribed gene SNP chip was used to genot...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00386
更新日期:2019-05-03 00:00:00
abstract::MicroRNAs (miRNAs) are known to be important post-transcriptional regulators that are involved in the etiology of complex psychiatric traits. The present study aimed to incorporate miRNAs information into pathway analysis using a genome-wide association dataset to identify relevant biological pathways for bipolar diso...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2012.00293
更新日期:2012-12-18 00:00:00
abstract::MicroRNAs (miRNAs) crucial roles in translation repression and post-transcriptional adjustments contribute to regulate intestinal lipid metabolism. Even though their actions in different metabolic tissues have been elucidated, their intestinal activity is yet unclear. We aimed to investigate intestinal miRNA-regulated...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00707
更新日期:2020-07-10 00:00:00
abstract::Identification of non-protein-coding RNAs (ncRNAs) in genomes is a crucial task for not only molecular cell biology but also bioinformatics. Secondary structures of ncRNAs are employed as a key feature of ncRNA analysis since biological functions of ncRNAs are deeply related to their secondary structures. Although the...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2011.00054
更新日期:2011-08-31 00:00:00
abstract::Few studies have been conducted to explore the influence of the catechol-o-methyltransferase (COMT) genotype on the severity of and treatment efficacy on auditory verbal hallucination (AVH) symptoms in healthy individuals with AVHs (Hi-AVHs). We hypothesized that the efficacy of dopamine antagonist treatment on AVHs i...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00092
更新日期:2019-03-06 00:00:00
abstract::Cotton (Gossypium spp.) is the most important natural fiber crop in the world. The R2R3-MYB gene family is a large gene family involved in many plant functions including cotton fiber development. Although previous studies have reported its phylogenetic relationships, gene structures, and expression patterns in tetrapl...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00741
更新日期:2019-08-15 00:00:00
abstract::Atherosclerosis and its comorbidities are the major contributors to the global burden of death worldwide. Lower extremities arterial disease (LEAD) is a common manifestation of atherosclerotic disease of arteries of lower extremities. MicroRNAs belong to epigenetic factors that regulate gene expression and have not ye...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.01200
更新日期:2019-11-22 00:00:00
abstract::Abundant genomic heterozygosity can be found in wild strains of the budding yeast Saccharomyces cerevisiae isolated from industrial and clinical environments. The extent to which heterozygosity influences the phenotypes of these isolates is not fully understood. One such case is the PE-2/JAY270 strain, a natural hybri...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2019.00782
更新日期:2019-09-11 00:00:00
abstract::Identifying driver genes that contribute to cancer progression from numerous passenger genes, although a central goal, is a major challenge. The protein-protein interaction network provides convenient and reasonable assistance for driver gene discovery. Random walk-based methods have been widely used to prioritize nod...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00377
更新日期:2020-04-28 00:00:00
abstract::RNA-binding proteins (RBPs) are a kind of gene regulatory factor that presents a significant biological effect in the initiation and development of various tumors, including bladder cancer (BLCA). However, the RBP-based prognosis signature for BLCA has not been investigated. In this study, we attempted to develop an R...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00992
更新日期:2020-08-28 00:00:00
abstract::While efforts to control malaria with available tools have stagnated, and arbovirus outbreaks persist around the globe, the advent of clustered regularly interspaced short palindromic repeat (CRISPR)-based gene editing has provided exciting new opportunities for genetics-based strategies to control these diseases. In ...
journal_title:Frontiers in genetics
pub_type: 杂志文章,评审
doi:10.3389/fgene.2019.01072
更新日期:2019-10-30 00:00:00
abstract::Systemic sclerosis-associated with pulmonary arterial hypertension (SSc-PAH) is still a major cause of SSc related deaths. Early diagnosis and prompt treatment are crucial to reduce the mortality of patients with SSc-PAH. To screen the candidate biomarkers and potential therapeutic targets for SSc-PAH, we analyzed the...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.00816
更新日期:2020-07-24 00:00:00
abstract::Hepatocellular carcinoma (HCC) is the second leading cause of cancer-related death worldwide despite the availability of diverse treatment strategies. Much research progress has been made regarding immunotherapy but the effects remain unsatisfactory, highlighting the urgent need for novel immune-related therapy target...
journal_title:Frontiers in genetics
pub_type: 杂志文章
doi:10.3389/fgene.2020.575776
更新日期:2020-10-14 00:00:00