Abstract:
:Multilocus genome-wide association studies (GWAS) have become the state-of-the-art procedure to identify quantitative trait nucleotides (QTNs) associated with complex traits. However, implementation of multilocus model in GWAS is still difficult. In this study, we integrated least angle regression with empirical Bayes to perform multilocus GWAS under polygenic background control. We used an algorithm of model transformation that whitened the covariance matrix of the polygenic matrix K and environmental noise. Markers on one chromosome were included simultaneously in a multilocus model and least angle regression was used to select the most potentially associated single-nucleotide polymorphisms (SNPs), whereas the markers on the other chromosomes were used to calculate kinship matrix as polygenic background control. The selected SNPs in multilocus model were further detected for their association with the trait by empirical Bayes and likelihood ratio test. We herein refer to this method as the pLARmEB (polygenic-background-control-based least angle regression plus empirical Bayes). Results from simulation studies showed that pLARmEB was more powerful in QTN detection and more accurate in QTN effect estimation, had less false positive rate and required less computing time than Bayesian hierarchical generalized linear model, efficient mixed model association (EMMA) and least angle regression plus empirical Bayes. pLARmEB, multilocus random-SNP-effect mixed linear model and fast multilocus random-SNP-effect EMMA methods had almost equal power of QTN detection in simulation experiments. However, only pLARmEB identified 48 previously reported genes for 7 flowering time-related traits in Arabidopsis thaliana.
journal_name
Heredity (Edinb)journal_title
Heredityauthors
Zhang J,Feng JY,Ni YL,Wen YJ,Niu Y,Tamba CL,Yue C,Song Q,Zhang YMdoi
10.1038/hdy.2017.8subject
Has Abstractpub_date
2017-06-01 00:00:00pages
517-524issue
6eissn
0018-067Xissn
1365-2540pii
hdy20178journal_volume
118pub_type
杂志文章相关文献
HEREDITY文献大全abstract::Chromosome polymorphism in Drosophila buzzatii is under selection but the genes responsible for the effect of the inversions of fitness are unknown. On the other hand, there is evidence for selection on several allozyme loci but the presence of paracentric inversions on the second chromosome, where most of the polymor...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.1995.27
更新日期:1995-02-01 00:00:00
abstract::Mitochondrial DNA diversity of seven Silurus glanis populations (six from Greece and one from the Danube Delta) and three populations of the endemic Greek Silurus aristotelis was investigated. RFLP analysis of four regions of mitochondrial DNA (cytochrome b, D-loop, ND-5/6) amplified by PCR was used. Ten and nine hapl...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/sj.hdy.6885140
更新日期:1999-05-01 00:00:00
abstract::Recent evidence suggests the frequent occurrence of a simple non-Darwinian (but non-Lamarckian) model for the evolution of adaptive phenotypic traits, here entitled the plasticity-relaxation-mutation (PRM) mechanism. This mechanism involves ancestral phenotypic plasticity followed by specialization in one alternative ...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2011.97
更新日期:2012-04-01 00:00:00
abstract::Genomic resources developed for domesticated species provide powerful tools for studying the evolutionary history of their wild relatives. Here we use 61K single-nucleotide polymorphisms (SNPs) evenly spaced throughout the canine nuclear genome to analyse evolutionary relationships among the three largest European pop...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2013.122
更新日期:2014-04-01 00:00:00
abstract::We have studied in Drosophila melanogaster the effects of allozyme variation at the alpha Gpdh and Adh loci on the following fitness components: female fecundity, egg hatchability, egg-to-adult survival under near-optimal and competitive conditions, rate of development under near-optimal and competitive conditions, an...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.1989.108
更新日期:1989-12-01 00:00:00
abstract::Despite the evidence that the Pleistocene climatic fluctuations have seriously affected the distribution of intraspecific diversity, less is known on its impact on interspecific divergence. In this study, we aimed to test the hypothesis that the divergence of two desert poplar species Populus euphratica Oliv. and P. p...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2013.87
更新日期:2014-02-01 00:00:00
abstract::Equilibrium sex ratios have been determined analytically under Wright's island model in order to determine the effect of population structure with limited dispersal. When mating occurs before dispersal, the dispersal rate has little or no effect, and the equilibrium sex ratio remains the same as under complete dispers...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.1986.10
更新日期:1986-02-01 00:00:00
abstract::Disease-associated variants in the human genome are continually being identified using DNA sequencing technologies that are especially effective for Mendelian disorders. Here we sequenced whole genome to high coverage (>30×) of 6 members of a 7-generation family with dwarfism from a consanguineous tribe in Pakistan to...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/s41437-017-0021-6
更新日期:2018-01-01 00:00:00
abstract::This corrects the article DOI: 10.1038/hdy.2015.89. ...
journal_title:Heredity
pub_type: 杂志文章,已发布勘误
doi:10.1038/hdy.2017.38
更新日期:2017-11-01 00:00:00
abstract::How life-history strategies influence the evolution of populations is not well understood. Most existing models stem from the Wright-Fisher model which considers discrete generations and a fixed population size, thus not taking into account any potential consequences of overlapping generations and demographic stochast...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/s41437-018-0118-6
更新日期:2018-10-01 00:00:00
abstract::North Africa is now recognized as a major area for the emergence and dispersal of anatomically modern humans from at least 315 kya. The Mediterranean Basin is thus particularly suited to study the role of climate versus human-mediated changes on the evolutionary history of species. The Algerian mouse (Mus spretus Lata...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/s41437-018-0089-7
更新日期:2019-02-01 00:00:00
abstract::Insect cuticle melanism is linked to a number of life-history traits, and a positive relationship is hypothesized between melanism and the strength of immune defense. In this study, the phenotypic and genetic relationships between cuticular melanization, innate immune defense, individual development time and body size...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2013.20
更新日期:2013-08-01 00:00:00
abstract::The ubiquity of satellite DNA (satDNA) sequences has raised much controversy over the abundance of divergent monomer variants and the long-time nucleotide sequence stability observed for many satDNA families. In this work, we describe the satDNA BIV160, characterized in nine species of the three main bivalve clades (P...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2009.141
更新日期:2010-06-01 00:00:00
abstract::For morphological traits that are negatively correlated, the genetic correlation (rg) between them might strongly influence patterns of morphological divergence and shape. Here, the pattern of divergence between two sibling species of cactophilic Drosophila, D. buzzatii and D. koepferae, is examined for two traits tha...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1046/j.1365-2540.2000.00735.x
更新日期:2000-08-01 00:00:00
abstract::We present a study of fine-scale spatial genetic structure (SGS) and assess the impact of seed and pollen dispersal on the pattern of genetic diversity in the predominantly selfing Hordeum spontaneum. The study included (1) direct measurement of dispersal in a controlled environment, and (2) analyses of SGS and estima...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2009.168
更新日期:2010-10-01 00:00:00
abstract::A population resulting from the diallel cross of a set of elite inbred lines was selected under two strategies: (i) inbred strategy (IS) under brother-sister mating; and (ii) random strategy (RIS) under random mating. The final lines in both cases were completely inbred. RIS populations clearly responded better than I...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1046/j.1365-2540.1999.00520.x
更新日期:1999-06-01 00:00:00
abstract::The prevalence of Haldane's rule suggests that sex chromosomes commonly have a key role in reproductive barriers and speciation. However, the majority of research on Haldane's rule has been conducted in species with conventional sex determination systems (XY and ZW) and exceptions to the rule have been understudied. H...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2016.127
更新日期:2017-06-01 00:00:00
abstract::Growth rate of 12 groups of common carp was measured at five experimental environments. Three of the 12 tested groups were strains of the domesticated European race of the common carp, one group was a representative of the Big-Belly Chinese race, and the remaining eight groups were F1 crossbreds among the European str...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.1975.42
更新日期:1975-06-01 00:00:00
abstract::Two hundred and thirty-six mitochondrial DNA nucleotide sequences were used in combination with polymorphism at four nuclear microsatellite loci to assess the amount and distribution of genetic variation within and between African savannah elephants. They were sampled from 11 localities in eastern, western and souther...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/sj.hdy.6800110
更新日期:2002-08-01 00:00:00
abstract::Investigations into the genetic basis of reproductive barriers among recognized and putative varieties in Phacelia dubia have provided evidence that even among closely related taxa, multiple pathways can lead to reproductive isolation. A nuclear-based reproductive barrier, expressed as partial hybrid sterility of both...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.1991.97
更新日期:1991-12-01 00:00:00
abstract::Invasive species are believed to spread through a process of stratified dispersal consisting of short-distance diffusive spread around established foci and human mediated long-distance jumps. Brazilian peppertree (Schinus terebinthifolius), native to South America, was introduced twice as an ornamental plant into Flor...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/sj.hdy.6800936
更新日期:2007-05-01 00:00:00
abstract::Evolve and resequence (E&R) is a new approach to investigate the genomic responses to selection during experimental evolution. By using whole genome sequencing of pools of individuals (Pool-Seq), this method can identify selected variants in controlled and replicable experimental settings. Reviewing the current state ...
journal_title:Heredity
pub_type: 杂志文章,评审
doi:10.1038/hdy.2014.86
更新日期:2015-05-01 00:00:00
abstract::The a priori probability of noticeable linkage among all conceivable experiments of the size reported by Mendel cannot reasonably be taken as greater than 24-36 per cent; and therefore, the frequently heard opinion that his chances of encountering linkage were high, approaching 99-4 per cent, appears to be mistaken. ...
journal_title:Heredity
pub_type: 传,历史文章,杂志文章
doi:10.1038/hdy.1977.30
更新日期:1977-04-01 00:00:00
abstract::Many Odonata species exhibit female-limited polymorphisms, where one morph is similar to the conspecific male in body color and other traits (andromorph), whereas one or more other morphs differ from the male (gynomorphs). Here we investigated the differentially expressed transcripts (DETs) among males and two female ...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/s41437-018-0076-z
更新日期:2019-01-01 00:00:00
abstract::As important as the events that influence selection for specific chromosome types in the derivation of novel karyotypes, are the events that initiate the changes in chromosome number and structure between species, and likewise polymorphisms, variants and disease states within species. Although once thought of as trans...
journal_title:Heredity
pub_type: 杂志文章,评审
doi:10.1038/hdy.2011.104
更新日期:2012-01-01 00:00:00
abstract::Gene flow via pollen movement affects genetic variation in plant populations and is an important consideration in plant domestication. Fontainea picrosperma is a subcanopy rainforest tree that is of commercial interest because it is the source of tigilanol tiglate, a natural product used for the treatment of solid tum...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/s41437-019-0231-1
更新日期:2019-10-01 00:00:00
abstract::Recent molecular evidence has shown that many MHC polymorphisms are not only shared between species but are in fact identical at the molecular level. Species that share these polymorphisms may be very distantly related and often diverged millions of generations ago. It is now known that this phenomenon is very unlikel...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.1992.39
更新日期:1992-03-01 00:00:00
abstract::The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded ...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2014.5
更新日期:2014-07-01 00:00:00
abstract::To address the multiple challenges to food security posed by global climate change, population growth and rising incomes, plant breeders are developing new crop varieties that can enhance both agricultural productivity and environmental sustainability. Current breeding practices, however, are unable to keep pace with ...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2015.113
更新日期:2016-04-01 00:00:00
abstract::Many lepidopteran insects exhibit body colour variations, where the high phenotypic diversity observed in the wings and bodies of adults provides opportunities for studying adaptive morphological evolution. In the silkworm Bombyx mori, two genes responsible for moth colour mutation, Bm and Ws, have been mapped to 0.0 ...
journal_title:Heredity
pub_type: 杂志文章
doi:10.1038/hdy.2015.69
更新日期:2016-01-01 00:00:00