Invited review: quantitative trait nucleotide determination in the era of genomic selection

Genome-wide association studies based on tens of thousands of single nucleotide polymorphisms have been completed for several dairy cattle populations. Methods have been proposed to directly incorporate genome scan data into breeding programs, chiefly by selection of young sires based on their genotypes for the genetic markers and pedigree without progeny test. Thus, the rate of genetic gain is increased by reduction of the mean generation interval. The methods developed so far for application of genomic selection do not require identification of the actual quantitative trait nucleotides (QTN) responsible for the observed variation of quantitative trait loci (QTL). To date, 2 QTN affecting milk production traits have been detected in dairy cattle: DGAT1 and ABCG2. This review will attempt to address the following questions based on the current state of bovine genomics and statistics. What are the pros and cons for QTN determination? How can data obtained from high-density, genome-wide scans be used most efficiently for QTN determination? Can the genome scan results already available and next-generation sequencing data be used to determine QTN? Should QTN be treated differently than markers at linkage disequilibrium with QTL in genetic evaluation programs? Data obtained by genome-wide association studies can be used to deduce QTL genotypes of sires via application of the a posteriori granddaughter design for concordance testing of putative QTN. This, together with next-generation sequencing technology, will dramatically reduce costs for QTN determination. By complete genome sequencing of 21 sires with many artificial insemination sons, it should be possible to determine concordance for all potential QTN, thus establishing the field of QTNomics.