Inferring Quantitative Trait Pathways Associated with Bull Fertility from a Genome-Wide Association Study

Association analysis is an alternative to conventional, family-based methods for detecting the location of gene(s) or quantitative trait loci (QTLs), and provides relatively high resolution in terms of defining the genome position of a gene or QTL. Flavour is an essential quality characteristic of soymilk; however, soymilk contains volatile compounds unacceptable to consumers. One of main constituents in the volatiles of normal soymilk is 2-heptenal, which is thought to be a degradative oxidation product of polyunsaturated acids. In this study, a genome-wide association study using 24651 single-nucleotide polymorphisms (SNPs) was performed to identify quantitative trait nucleotides (QTNs) controlling 2-heptenal content in soybean (Glycine max (L.) Merr.) seed from a natural population of 110 soybean germplasm accessions. We detected 62 significant QTNs located on 18 different chromosomes that are significantly associated with 2-heptenal content in soybean seed. Among these, 17 QTNs co-localised with QTLs previously found to be related to protein, oil and/or fatty acid content in soybean seed. We also identified some candidate genes involved in lipid metabolism. These findings further our understanding of the genetic basis of 2-heptenal content in soybean seed and the improvement of marker-assisted breeding efficiency, which will be important for breeding soybean cultivars with low 2-heptenal content.

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A Genome-Wide Association Study Identifies Protein Quantitative Trait Loci (pQTLs)

PLoS Genetics ◽

10.1371/journal.pgen.1000072 ◽

2008 ◽

Vol 4 (5) ◽

pp. e1000072 ◽

Cited By ~ 294

Author(s):

David Melzer ◽

John R. B. Perry ◽

Dena Hernandez ◽

Anna-Maria Corsi ◽

Kara Stevens ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Association Study ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome ◽

Trait Loci

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Hippocampal Atrophy as a Quantitative Trait in a Genome-Wide Association Study Identifying Novel Susceptibility Genes for Alzheimer's Disease

PLoS ONE ◽

10.1371/journal.pone.0006501 ◽

2009 ◽

Vol 4 (8) ◽

pp. e6501 ◽

Cited By ~ 231

Author(s):

Steven G. Potkin ◽

Guia Guffanti ◽

Anita Lakatos ◽

Jessica A. Turner ◽

Frithjof Kruggel ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Association Study ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Susceptibility Genes ◽

Genome Wide Association ◽

Hippocampal Atrophy ◽

Genome Wide ◽

A Genome

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Identification of Quantitative Trait Loci for Leaf Rust and Stem Rust Seedling Resistance in Bread Wheat Using a Genome-Wide Association Study

Plants ◽

10.3390/plants11010074 ◽

2021 ◽

Vol 11 (1) ◽

pp. 74

Author(s):

Alibek Zatybekov ◽

Yuliya Genievskaya ◽

Aralbek Rsaliyev ◽

Akerke Maulenbay ◽

Gulbahar Yskakova ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Association Study ◽

Leaf Rust ◽

Bread Wheat ◽

Stem Rust ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Genome Wide ◽

A Genome

In recent years, leaf rust (LR) and stem rust (SR) have become a serious threat to bread wheat production in Kazakhstan. Most local cultivars are susceptible to these rusts, which has affected their yield and quality. The development of new cultivars with high productivity and LR and SR disease resistance, including using marker-assisted selection, is becoming an important priority in local breeding projects. Therefore, the search for key genetic factors controlling resistance in all plant stages, including the seedling stage, is of great significance. In this work, we applied a genome-wide association study (GWAS) approach using 212 local bread wheat accessions that were phenotyped for resistance to specific races of Puccinia triticina Eriks. (Pt) and Puccinia graminis f. sp. tritici (Pgt) at the seedling stages. The collection was genotyped using a 20 K Illumina iSelect SNP assay, and 11,150 polymorphic SNP markers were selected for the association mapping. Using a mixed linear model, we identified 11 quantitative trait loci (QTLs) for five out of six specific races of Pt and Pgt. The comparison of the results from this GWAS with those from previously published work showed that nine out of eleven QTLs for LR and SR resistance had been previously reported in a GWAS study at the adult plant stages of wheat growth. Therefore, it was assumed that these nine common identified QTLs were effective for all-stage resistance to LR and SR, and the two other QTLs appear to be novel QTLs. In addition, five out of these nine QTLs that had been identified earlier were found to be associated with yield components, suggesting that they may directly influence the field performance of bread wheat. The identified QTLs, including novel QTLs found in this study, may play an essential role in the breeding process for improving wheat resistance to LR and SR.

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Integration of genome-wide association study and expression quantitative trait locus mapping for identification of endometriosis-associated genes

Scientific Reports ◽

10.1038/s41598-020-79515-4 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Ya-Ching Chou ◽

Ming-Jer Chen ◽

Pi-Hua Chen ◽

Ching-Wen Chang ◽

Mu-Hsien Yu ◽

...

Keyword(s):

Association Study ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Chromosome 9 ◽

Genome Wide Association ◽

Chromosome 1 ◽

Eqtl Analysis ◽

Taiwanese Population ◽

Genome Wide ◽

A Genome

AbstractTo determine whether genetic predisposition to endometriosis varies depending on ethnicity and in association with expression quantitative trait loci (eQTL) in a Taiwanese population. We conducted a genome-wide association study (GWAS) and replicated it in 259 individuals with laparoscopy-confirmed stage III or IV endometriosis (cases) and 171 women without endometriosis (controls). Their genomic DNA was extracted from blood and evaluated by the GWAS of Taiwan Biobank Array. Novel genetic variants that predispose individuals to endometriosis were identified using GWAS and replication, including rs10739199 (P = 6.75 × 10−5) and rs2025392 (P = 8.01 × 10−5) at chromosome 9, rs1998998 (P = 6.5 × 10−6) at chromosome 14, and rs6576560 (P = 9.7 × 10−6) at chromosome 15. After imputation, strong signals were exhibited by rs10822312 (P = 1.80 × 10−7) at chromosome 10, rs58991632 (P = 1.92 × 10−6) and rs2273422 (P = 2.42 × 10−6) at chromosome 20, and rs12566078 (P = 2.5 × 10−6) at chromosome 1. We used the Genotype-Tissue Expression (GTEx) database to observe eQTL. Among these SNPs, the cis-eQTL rs13126673 of inturned planar cell polarity protein (INTU) showed significant association with INTU expression (P = 5.1 × 10–33). Moreover, the eQTL analysis was performed on endometriotic tissues from women with endometriosis. The expression of INTU in 78 endometriotic tissue of women with endometriosis is associated with rs13126673 genotype (P = 0.034). To our knowledge, this is the first GWAS to link endometriosis and eQTL in a Taiwanese population.

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A genome-wide association study for equine recurrent airway obstruction in European Warmblood horses reveals a suggestive new quantitative trait locus on chromosome 13

Animal Genetics ◽

10.1111/age.12583 ◽

2017 ◽

Vol 48 (6) ◽

pp. 691-693 ◽

Cited By ~ 7

Author(s):

D. Schnider ◽

S. Rieder ◽

T. Leeb ◽

V. Gerber ◽

M. Neuditschko

Keyword(s):

Quantitative Trait Locus ◽

Airway Obstruction ◽

Association Study ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Recurrent Airway Obstruction ◽

Genome Wide ◽

A Genome ◽

Trait Locus

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A genome-wide association study reveals a quantitative trait locus for age at first calving indelta/notch-like EGF repeat containingon chromosome 2 in Japanese Black cattle

Animal Genetics ◽

10.1111/age.12109 ◽

2013 ◽

Vol 45 (2) ◽

pp. 285-287 ◽

Cited By ~ 2

Author(s):

Shinji Sasaki ◽

Takayuki Ibi ◽

Shogo Ikeda ◽

Yoshikazu Sugimoto

Keyword(s):

Quantitative Trait Locus ◽

Association Study ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Chromosome 2 ◽

Japanese Black Cattle ◽

Genome Wide ◽

A Genome ◽

Trait Locus

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A Genome-Wide Association Study Identifies Quantitative Trait Loci Affecting Hematological Traits in Camelus bactrianus

Animals ◽

10.3390/ani10010096 ◽

2020 ◽

Vol 10 (1) ◽

pp. 96 ◽

Cited By ~ 2

Author(s):

Fucheng Guo ◽

Liang Ming ◽

Rendalai Si ◽

Li Yi ◽

Jing He ◽

...

Keyword(s):

Association Study ◽

Candidate Genes ◽

Quantitative Trait ◽

Genome Wide Association Study ◽

Genome Wide Association ◽

Gobi Desert ◽

Camelus Bactrianus ◽

Genome Wide ◽

A Genome ◽

Bactrian Camels

Bactrian camels (Camelus bactrianus) are one of the few large livestock species that can survive in the Gobi Desert. Animal immunity and disease resistance are related to hematological traits, which are also associated with tolerance observed in Bactrian camels. However, no genome-wide association studies have examined the genetic mechanism of the immune capability of Bactrian camels. In the present study, we used genotyping-by-sequencing data generated from 366 Bactrian camel accessions to perform a genome-wide association study for 17 hematological traits. Of the 256,616 single-nucleotide polymorphisms (SNPs) obtained, 1,635 trait–SNP associations were among the top quantitative trait locus candidates. Lastly, 664 candidate genes associated with 13 blood traits were identified. The most significant were ZNF772, MTX2, ESRRG, MEI4, IL11, FRMPD4, GABPA, NTF4, CRYBG3, ENPP5, COL16A1, and CD207. The results of our genome-wide association study provide a list of significant SNPs and candidate genes, which offer valuable information for further dissection of the molecular mechanisms that regulate the camel’s hematological traits to ultimately reveal their tolerance mechanisms.

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