Portal de Periódicos da CAPES

Molecular advances in QTL discovery and application in pig breeding

2013; Elsevier BV; Volume: 29; Issue: 4 Linguagem: Inglês

10.1016/j.tig.2013.02.002

1362-4555

Catherine W. Ernst, Juan P. Steibel,

Wheat and Barley Genetics and Pathology

Thousands of quantitative trait loci (QTL) have been identified for a wide range of economically important phenotypes in pigs. Recently, QTL analyses have begun to use high-density single nucleotide polymorphism (SNP) panels and applications have extended beyond experimental intercrosses to outbred populations by exploiting long-range linkage disequilibrium that results in higher resolution QTL mapping. Relevant phenotypes generally fall under categories of growth and body composition, carcass and meat quality, reproduction, and disease resistance. A few expression QTL (eQTL) studies have been performed that integrate transcriptional profiles with genotype data by considering expression levels as response variables in QTL analyses for identifying genes controlling important trait phenotypes. Rapidly evolving genomics technologies, including RNAseq, provide tremendous opportunities for QTL and eQTL discovery. In this review, we discuss recent progress in pig QTL and eQTL discovery, including approaches for allele-specific expression, and implications of these discoveries for pig breeding and genetics. Thousands of quantitative trait loci (QTL) have been identified for a wide range of economically important phenotypes in pigs. Recently, QTL analyses have begun to use high-density single nucleotide polymorphism (SNP) panels and applications have extended beyond experimental intercrosses to outbred populations by exploiting long-range linkage disequilibrium that results in higher resolution QTL mapping. Relevant phenotypes generally fall under categories of growth and body composition, carcass and meat quality, reproduction, and disease resistance. A few expression QTL (eQTL) studies have been performed that integrate transcriptional profiles with genotype data by considering expression levels as response variables in QTL analyses for identifying genes controlling important trait phenotypes. Rapidly evolving genomics technologies, including RNAseq, provide tremendous opportunities for QTL and eQTL discovery. In this review, we discuss recent progress in pig QTL and eQTL discovery, including approaches for allele-specific expression, and implications of these discoveries for pig breeding and genetics. the differential expression of one of the two copies of a gene carried by a diploid organism as a result of differences in DNA sequence between the two alleles. gene identified based on its physiological function and/or its genomic position as potentially controlling a portion of the variation for a phenotype of interest. the probability that two alleles chosen at random originated from a common ancestral allele, computed conditionally on observed marker segregation information. DNA segments containing variants associated with the expression level of a transcript. eQTLs that map to the approximate location of their gene-of-origin are referred to as cis-acting, whereas eQTLs that map far from the location of their gene-of-origin, usually on different chromosomes, are referred to as trans-acting. in an experiment where multiple hypotheses are tested and at least one is rejected, the FDR is the expected proportion of incorrectly rejected null hypotheses among all rejected hypotheses. an allele for which all individuals in a population are homozygous, such that no other alleles at that locus are segregating in the population. the examination of many DNA variants in different individuals to test whether they are associated with a particular phenotype or set of phenotypes. a statistical model used to map QTL in outbred populations. A reduced number of common parents assumed to segregate the QTL alleles are mated to a random set of animals to originate a large number of progeny, where genotypes for a two-generation pedigree are used to infer QTL genotyped in the progeny. Within-parent QTL effects are then tested simultaneously using nested effects in a linear model to assess the significance of putative QTL. a statistical model used to map QTL in crosses of outbred lines (backcross or F2). It assumes that QTL alleles are fixed in parental lines and typically uses genotypes from a three-generation pedigree to infer QTL alleles inherited in 'terminal animals'. The putative QTL genotypes are used to test for mean differences in the quantitative trait of interest. a study that tracks inheritance of putative QTL in pedigrees with the goal of testing whether genomic regions cosegregate with phenotypic trait variation. the nonrandom association of alleles at two or more loci. Several measures of association have been proposed; for a pair of bi-allelic loci, the squared correlation coefficient (r2) is the most commonly used. repeating sequences of two to six base pairs also referred to as short tandem repeats (STR) or simple sequence repeats (SSR) occurring at thousands of loci throughout eukaryotic genomes, and resulting in high levels of polymorphism within populations due to variation in copy number of the repeat unit. DNA segments containing or linked to genes underlying variation in phenotypic trait(s). a range of values (interval) estimating a QTL position that indicates the reliability of the estimate. DNA sequence variation at a locus where more than one nucleotide is segregating among individuals in a population.