population geneticsSNP ascertainment biaswhole genome sequencingWhole genome sequencing and SNP genotyping arrays can paint strikingly different pictures of demographic history and natural selection. This is be
We used eQTL mapping to identify cis- (within 1 megabase (Mb) of each gene on either side) and trans- (>1 Mb apart or on a different chromosome) regulatory variants (eVariants) that are associated with differences in gene expression. We leveraged approximately 2.7 million SNPs with ...
SNPs are single base-pair changes in the DNA sequence and may fall within the coding regions of genes, non-coding regions of genes, or in intergenic regions14. In this aspect, association researches can determine whether a genetic variant is connected with PBC or not. To date, the ...
For simplicity, we assume that the genetic markers are single nucleotide polymorphisms (SNPs). For a given sample (e.g. a mouse), a bi-allelic SNP can take on one of three possible genotypes. By default, we assume an additive genetic effect and encode these genotypes as 0, 1, or 2, ...
With a single genotype sequence, the probability of detecting SNPs will be limited by the fact that only two haploid genomes are represented in any one individual, even in cases where the read depth is high (whole genome sequence data usually have a minimum read depth of 10× coverage). ...
Accessions (Yugu 1, mainland China; JP 71626 & 71640, Japan; JP 222588 & 73913, Taiwan of China; JP 222569, the Philippines; JP 222981 & 222982, India; JP 222570, Myanmar; JP 222971, ex-Czechoslovakia; JP 223004, France) with indels and SNPs are indicated in parentheses (See details ...
Population genetics structure. (A–C) Principal component analysis of identified SNPs. (D) Linkage disequilibrium (LD) decay. (E) Genome-wide admixture analysis Full size image To further investigate the degree of selection of different goose breeds, we calculated LD values for each breed (Fig....
North temperate tree species such as white spruce (Picea glauca [Moench] Voss) have evolved strategies to protect themselves against abiotic and biotic str
number of genes represented in the set and the diversity when more than one SNP was selected for a gene. Three primers were then designed by Illumina for each SNP locus, using the Veracode Assay Designer software. Sequence and primer information for the 384 SNPs are listed in Additional ...
PCA applications, implemented in well-cited packages like EIGENSOFT and PLINK, are extensively used as the foremost analyses in population genetics and related fields (e.g., animal and plant or medical genetics). PCA outcomes are used to shape study design, identify, and characterize individuals ...