scholarly journals Genome-wide association analyses of multiple traits in Duroc pigs using low-coverage whole-genome sequencing strategy

2019 ◽  
Author(s):  
Ruifei Yang ◽  
Xiaoli Guo ◽  
Di Zhu ◽  
Cheng Bian ◽  
Yiqiang Zhao ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Association Analysis ◽  
Genome Sequencing ◽  
Association Studies ◽  
Genotype Imputation ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Genome Wide Association Analysis ◽  
Genome Wide ◽  
Low Coverage

AbstractHigh-density markers discovered in large size samples are essential for mapping complex traits at the gene-level resolution for agricultural livestock and crops. However, the unavailability of large reference panels and array designs for a target population of agricultural species limits the improvement of array-based genotype imputation. Recent studies showed very low coverage sequencing (LCS) of a large number of individuals is a cost-effective approach to discover variations in much greater detail in association studies. Here, we performed cohort-wide whole-genome sequencing at an average depth of 0.73× and identified more than 11.3 M SNPs. We also evaluated the data set and performed genome-wide association analysis (GWAS) in 2885 Duroc boars. We compared two different pipelines and selected a proper method (BaseVar/STITCH) for LCS analyses and determined that sequencing of 1000 individuals with 0.2× depth is enough for identifying SNPs with high accuracy in this population. Of the seven association signals derived from the genome-wide association analysis of the LCS variants, which were associated with four economic traits, we found two QTLs with narrow intervals were possibly responsible for the teat number and back fat thickness traits and identified 7 missense variants in a single sequencing step. This strategy (BaseVar/STITCH) is generally applicable to any populations and any species which have no suitable reference panels. These findings show that the LCS strategy is a proper approach for the construction of new genetic resources to facilitate genome-wide association studies, fine mapping of QTLs, and genomic selection, and implicate that it can be widely used for agricultural animal breeding in the future.

scholarly journals Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Gabriel Costa Monteiro Moreira ◽  
Clarissa Boschiero ◽  
Aline Silva Mello Cesar ◽  
James M. Reecy ◽  
Thaís Fernanda Godoy ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Association Studies ◽  
Fat Deposition ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Wide

scholarly journals Genome-Wide Association Study Using Whole-Genome Sequencing Identifies a Genomic Region on Chromosome 6 Associated With Comb Traits in Nandan-Yao Chicken

2021 ◽  
Vol 12 ◽  
Author(s):  
Zhuliang Yang ◽  
Leqin Zou ◽  
Tiantian Sun ◽  
Wenwen Xu ◽  
Linghu Zeng ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Improvement ◽  
Genome Wide Association Study ◽  
Association Studies ◽  
Genome Wide Association ◽  
Genome Wide Association Studies ◽  
Chromosome 6 ◽  
Whole Genome ◽  
Genome Wide

Comb traits have potential economic value in the breeding of indigenous chickens in China. Identifying and understanding relevant molecular markers for comb traits can be beneficial for genetic improvement. The purpose of this study was to utilize genome-wide association studies (GWAS) to detect promising loci and candidate genes related to comb traits, namely, comb thickness (CT), comb weight (CW), comb height, comb length (CL), and comb area. Genome-wide single-nucleotide polymorphisms (SNPs) and small insertions/deletions (INDELs) in 300 Nandan-Yao chickens were detected using whole-genome sequencing. In total, we identified 134 SNPs and 25 INDELs that were strongly associated with the five comb traits. A remarkable region spanning from 29.6 to 31.4 Mb on chromosome 6 was found to be significantly associated with comb traits in both SNP- and INDEL-based GWAS. In this region, two lead SNPs (6:30,354,876 for CW and CT and 6:30,264,318 for CL) and one lead INDEL (a deletion from 30,376,404 to 30,376,405 bp for CL and CT) were identified. Additionally, two genes were identified as potential candidates for comb development. The nearby gene fibroblast growth factor receptor 2 (FGFR2)—associated with epithelial cell migration and proliferation—and the gene cytochrome b5 reductase 2 (CYB5R2)—identified on chromosome 5 from INDEL-based GWAS—are significantly correlated with collagen maturation. The findings of this study could provide promising genes and biomarkers to accelerate genetic improvement of comb development based on molecular marker-assisted breeding in Nandan-Yao chickens.

scholarly journals Improved power and precision with whole genome sequencing data in genome-wide association studies of inflammatory biomarkers

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Julia Höglund ◽  
Nima Rafati ◽  
Mathias Rask-Andersen ◽  
Stefan Enroth ◽  
Torgny Karlsson ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Association Studies ◽  
Accurate Determination ◽  
Genome Wide Association ◽  
Inflammatory Biomarkers ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Genome Wide ◽  
Common Genetic Variants

AbstractGenome-wide association studies (GWAS) have identified associations between thousands of common genetic variants and human traits. However, common variants usually explain a limited fraction of the heritability of a trait. A powerful resource for identifying trait-associated variants is whole genome sequencing (WGS) data in cohorts comprised of families or individuals from a limited geographical area. To evaluate the power of WGS compared to imputations, we performed GWAS on WGS data for 72 inflammatory biomarkers, in a kinship-structured cohort. When using WGS data, we identified 18 novel associations that were not detected when analyzing the same biomarkers with genotyped or imputed SNPs. Five of the novel top variants were low frequency variants with a minor allele frequency (MAF) of <5%. Our results suggest that, even when applying a GWAS approach, we gain power and precision using WGS data, presumably due to more accurate determination of genotypes. The lack of a comparable dataset for replication of our results is a limitation in our study. However, this further highlights that there is a need for more genetic epidemiological studies based on WGS data.

scholarly journals Whole genome sequencing identifies common and rare structural variants contributing to hematologic traits in the NHLBI TOPMed program

2021 ◽  
Author(s):  
Marsha M. Wheeler ◽  
Adrienne M Stilp ◽  
Shuquan Rao ◽  
Bjarni V Halldorsson ◽  
Doruk V Beyter ◽  
...  
Keyword(s):  
Blood Cell ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Association Studies ◽  
Regulatory Elements ◽  
Chromatin Domain ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Structural Variants ◽  
Genome Wide

Genome-wide association studies (GWAS) have identified thousands of single nucleotide variants and small indels that contribute to the genetic architecture of hematologic traits. While structural variants (SVs) are known to cause rare blood or hematopoietic disorders, the genome-wide contribution of SVs to quantitative blood cell trait variation is unknown. Here we utilized SVs detected from whole genome sequencing (WGS) in ancestrally diverse participants of the NHLBI TOPMed program (N=50,675). Using single variant tests, we assessed the association of common and rare SVs with red cell-, white cell-, and platelet-related quantitative traits. The results show 33 independent SVs (23 common and 10 rare) reaching genome-wide significance. The majority of significant association signals (N=27) replicated in independent datasets from deCODE genetics and the UK BioBank. Moreover, most trait-associated SVs (N=24) are within 1Mb of previously-reported GWAS loci. SV analyses additionally discovered an association between a complex structural variant on 17p11.2 and white blood cell-related phenotypes. Based on functional annotation, the majority of significant SVs are located in non-coding regions (N=26) and predicted to impact regulatory elements and/or local chromatin domain boundaries in blood cells. We predict that several trait-associated SVs represent the causal variant. This is supported by genome-editing experiments which provide evidence that a deletion associated with lower monocyte counts leads to disruption of an S1PR3 monocyte enhancer and decreased S1PR3 expression.

scholarly journals Genome-wide association study and whole-genome sequencing identify a deletion in LRIT3 associated with canine congenital stationary night blindness

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Rueben G. Das ◽  
Doreen Becker ◽  
Vidhya Jagannathan ◽  
Orly Goldstein ◽  
Evelyn Santana ◽  
...  
Keyword(s):  
Association Study ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Night Blindness ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Whole Genome ◽  
Congenital Stationary Night Blindness ◽  
Genome Wide ◽  
A Genome

Abstract Congenital stationary night blindness (CSNB), in the complete form, is caused by dysfunctions in ON-bipolar cells (ON-BCs) which are secondary neurons of the retina. We describe the first disease causative variant associated with CSNB in the dog. A genome-wide association study using 12 cases and 11 controls from a research colony determined a 4.6 Mb locus on canine chromosome 32. Subsequent whole-genome sequencing identified a 1 bp deletion in LRIT3 segregating with CSNB. The canine mutant LRIT3 gives rise to a truncated protein with unaltered subcellular expression in vitro. Genetic variants in LRIT3 have been associated with CSNB in patients although there is limited evidence regarding its apparently critical function in the mGluR6 pathway in ON-BCs. We determine that in the canine CSNB retina, the mutant LRIT3 is correctly localized to the region correlating with the ON-BC dendritic tips, albeit with reduced immunolabelling. The LRIT3-CSNB canine model has direct translational potential enabling studies to help understand the CSNB pathogenesis as well as to develop new therapies targeting the secondary neurons of the retina.

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