scholarly journals Identification of genes for controlling swine adipose deposition by integrating transcriptome, whole-genome resequencing, and quantitative trait loci data

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Kai Xing ◽  
Feng Zhu ◽  
LiWei Zhai ◽  
ShaoKang Chen ◽  
Zhen Tan ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Trait Loci ◽  
Whole Genome Resequencing

Whole-genome resequencing identifies quantitative trait loci associated with mycorrhizal colonization of soybean

2019 ◽  
Vol 133 (2) ◽  
pp. 409-417 ◽  
Author(s):  
Michelle L. Pawlowski ◽  
Tri D. Vuong ◽  
Babu Valliyodan ◽  
Henry T. Nguyen ◽  
Glen L. Hartman
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Mycorrhizal Colonization ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Trait Loci ◽  
Whole Genome Resequencing

scholarly journals Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

2020 ◽  
Author(s):  
Alia Parveen ◽  
Christa D. Jackson ◽  
Shatovisha Dey ◽  
Katy Tarrant ◽  
Nicholas B Anthony ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Assembly ◽  
Quantitative Trait ◽  
Whole Genome ◽  
Chicken Chromosome ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Whole Genome Resequencing ◽  
Ascites Syndrome

Abstract Background Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

scholarly journals Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing.

2020 ◽  
Author(s):  
Alia Parveen ◽  
Christa Jackson ◽  
Shatovisha Dey ◽  
Katy Tarrant ◽  
Nicholas B Anthony ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Genome Assembly ◽  
Quantitative Trait ◽  
Whole Genome ◽  
Chicken Chromosome ◽  
Genome Resequencing ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Whole Genome Resequencing ◽  
Ascites Syndrome

Abstract Background Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. Results The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. Conclusions The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.

scholarly journals QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

2013 ◽  
Vol 74 (1) ◽  
pp. 174-183 ◽  
Author(s):  
Hiroki Takagi ◽  
Akira Abe ◽  
Kentaro Yoshida ◽  
Shunichi Kosugi ◽  
Satoshi Natsume ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Rapid Mapping ◽  
Trait Loci ◽  
Whole Genome Resequencing

A whole-genome scan for quantitative trait loci affecting teat number in pigs.

2001 ◽  
Vol 79 (9) ◽  
pp. 2320 ◽  
Author(s):  
H Hirooka ◽  
D J de Koning ◽  
B Harlizius ◽  
J A van Arendonk ◽  
A P Rattink ◽  
...  
Keyword(s):  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Genome Scan ◽  
Whole Genome ◽  
Trait Loci ◽  
Teat Number ◽  
Whole Genome Scan
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