RNA-Seq identifies SNP markers for growth traits in rainbow trout.

PloS One
Mohamed SalemJianbo Yao

Abstract

Fast growth is an important and highly desired trait, which affects the profitability of food animal production, with feed costs accounting for the largest proportion of production costs. Traditional phenotype-based selection is typically used to select for growth traits; however, genetic improvement is slow over generations. Single nucleotide polymorphisms (SNPs) explain 90% of the genetic differences between individuals; therefore, they are most suitable for genetic evaluation and strategies that employ molecular genetics for selective breeding. SNPs found within or near a coding sequence are of particular interest because they are more likely to alter the biological function of a protein. We aimed to use SNPs to identify markers and genes associated with genetic variation in growth. RNA-Seq whole-transcriptome analysis of pooled cDNA samples from a population of rainbow trout selected for improved growth versus unselected genetic cohorts (10 fish from 1 full-sib family each) identified SNP markers associated with growth-rate. The allelic imbalances (the ratio between the allele frequencies of the fast growing sample and that of the slow growing sample) were considered at scores >5.0 as an amplification and <0.2 as loss of he...Continue Reading

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Citations

Apr 22, 2014·Comparative Biochemistry and Physiology. Part D, Genomics & Proteomics·Jun CuiXiuli Wang
Dec 5, 2013·Physiological Reports·Mohamed SalemJianbo Yao
Jan 2, 2014·Omics : a Journal of Integrative Biology·Xi QianGuofang Zhong
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Oct 31, 2013·BMC Genomics·Mariangela BonizzoniAnthony A James

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Methods Mentioned

BETA
genotyping
RNA-Seq
Assay

Software Mentioned

Alpheus detection pipeline
package ( GWAF )
MTDFREML
Alpheus
SAS
GWAF )
PLINK
STEPWISE
SOLAR
PEDCHECK

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