Comparing Genotyping-by-Sequencing and Single Nucleotide Polymorphism Chip Genotyping for Quantitative Trait Loci Mapping in Wheat

Crop Science ◽  
2016 ◽  
Vol 56 (1) ◽  
pp. 232-248 ◽  
Author(s):  
Prabin Bajgain ◽  
Matthew N. Rouse ◽  
James A. Anderson
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Quantitative Trait Loci ◽  
Quantitative Trait ◽  
Genotyping By Sequencing ◽  
Quantitative Trait Loci Mapping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Single Nucleotide Polymorphism Chip ◽  
Trait Loci

The TG5 thyroglobulin gene test for a marbling quantitative trait loci evaluated in feedlot cattle

2004 ◽  
Vol 44 (7) ◽  
pp. 669 ◽  
Author(s):  
W. Barendse ◽  
R. Bunch ◽  
M. Thomas ◽  
S. Armitage ◽  
S. Baud ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Quantitative Trait Loci ◽  
Dna Sequence ◽  
Dna Markers ◽  
Quantitative Trait ◽  
Allelic Association ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Trait Loci ◽  
Thyroglobulin Gene

The TG5 (thyroglobulin 5′ leader sequence) single nucleotide polymorphism has been associated with marbling in cattle fed for periods longer than 250 days. To test whether the association could be detected in diverse cattle, fed for less than 250 days, and to measure the size of the effect, we sampled 1750 cattle from the AMH Toowoomba feedlot. These cattle were sampled on 28 separate days, over 9 months. Their marbling scores covered the complete range. We found that the TG5 single nucleotide polymorphism was associated with marbling scores (P<0.05) and estimated that TG5 genotypes explained 6.5% of the residual deviance for the marbling phenotype. We also found that the '3' allele was more frequent in animals with higher marbling scores. The consistency of the allelic association between studies and, in particular, the association found in diverse cattle, indicate that the TG5 polymorphism can be used as a breeding tool and possibly a feedlot entry tool. To estimate the size of the genetic region in which the marbling quantitative trait loci are located, we tested the nearby DNA markers CSSM66 and BMS1747. These do not show allelic associations to marbling. The consistency of the allelic association between studies, the lack of association to nearby DNA markers and the complementary information on gene action of genes near Thyroglobulin suggest that DNA sequence variations, in or near the Thyroglobulin gene sequence, are the likely causes for the marbling quantitative trait loci. Further studies of single nucleotide polymorphism in and near the Thyroglobulin DNA sequence should allow causal mutations for the effect to be identified.

scholarly journals Mapping quantitative trait loci associated with leaf rust resistance in five spring wheat populations using single nucleotide polymorphism markers

PLoS ONE ◽  
2020 ◽  
Vol 15 (4) ◽  
pp. e0230855
Author(s):  
Firdissa E Bokore ◽  
Ron E. Knox ◽  
Richard D. Cuthbert ◽  
Curtis J. Pozniak ◽  
Brent D. McCallum ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Quantitative Trait Loci ◽  
Leaf Rust ◽  
Spring Wheat ◽  
Quantitative Trait ◽  
Rust Resistance ◽  
Leaf Rust Resistance ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Trait Loci
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