| Literature DB >> 25750652 |
Elisabeth Jonas1, Dirk-Jan de Koning1.
Abstract
Genomic selection is a promising development in agriculture, aiming improved production by exploiting molecular genetic markers to design novel breeding programs and to develop new markers-based models for genetic evaluation. It opens opportunities for research, as novel algorithms and lab methodologies are developed. Genomic selection can be applied in many breeds and species. Further research on the implementation of genomic selection (GS) in breeding programs is highly desirable not only for the common good, but also the private sector (breeding companies). It has been projected that this approach will improve selection routines, especially in species with long reproduction cycles, late or sex-limited or expensive trait recording and for complex traits. The task of integrating GS into existing breeding programs is, however, not straightforward. Despite successful integration into breeding programs for dairy cattle, it has yet to be shown how much emphasis can be given to the genomic information and how much additional phenotypic information is needed from new selection candidates. Genomic selection is already part of future planning in many breeding companies of pigs and beef cattle among others, but further research is needed to fully estimate how effective the use of genomic information will be for the prediction of the performance of future breeding stock. Genomic prediction of production in crossbreeding and across-breed schemes, costs and choice of individuals for genotyping are reasons for a reluctance to fully rely on genomic information for selection decisions. Breeding objectives are highly dependent on the industry and the additional gain when using genomic information has to be considered carefully. This review synthesizes some of the suggested approaches in selected livestock species including cattle, pig, chicken, and fish. It outlines tasks to help understanding possible consequences when applying genomic information in breeding scenarios.Entities:
Keywords: breeding; estimated breeding value; generation interval; marker-assisted selection; modeling; non-additive effects
Year: 2015 PMID: 25750652 PMCID: PMC4335173 DOI: 10.3389/fgene.2015.00049
Source DB: PubMed Journal: Front Genet ISSN: 1664-8021 Impact factor: 4.599
FIGURE 1Schematic overview of traditional breeding in dairy cattle: Selection candidates (bulls) are born and mated to multiple cows at around 12 months of age. In month 60 the first phenotypic recordings (milk yields) are available from the daughters of the selection candidate, as they had to reach puberty, be mated and finished a first lactation. Estimated breeding values are available after approximately 63 months and the bulls for further breeding are selected.
Overview of genome structure and genotyping platforms of the main livestock species.
| Cattle ( | Diploid (2n = 60) | ∼2870 | ∼26835 | 3000000 SNP identified | Highly variable extent of LD | Illumina: 54609 SNP, Affymetrix: 640000 SNP | Hereford cow (whole genome shotgun), her sire (hierarchical BAC clone; |
| Pig ( | Diploid (2n = 38) | ∼2596 | ∼21640 | 510000 SNP identified | Higher LD (than some Holstein cattle) | Illumina: 64232 SNP | Female domestic Duroc pig (Illumina whole-genome shotgun, BAC clone; |
| Chicken ( | Diploid (2n = 78) | ∼1000 | 20000–23000 | 1800000 SNP identified | Difference of LD between layer lines | Affymetrix: 580000 SNP | Single red jungle fowl female from inbred line; ∼6.6 × whole-genome, shotgun reads BAC-end read pairs ( |
| Atlantic salmon ( | Diploid (2n = 58) | ∼6000 | 33709 (identified in 2010) | Many chromosomal rearrangements | Moderate LD | iSelect Atlantic salmon 16,500 SNP | Female fish; aimed end of 2013 ( |
SNP, single nucleotide polymorphism; LD, linkage disequilibrium; BAC, bacterial artificial chromosome.
FIGURE 2Marker enhanced breeding using Genomic Selection in dairy cattle: Genome-wide marker panels are used to identify association or linkage with traits of interest using bulls with information on daughter lactation and genotypic data. Estimated effects of each marker are summarized into genomic estimated breeding values (GEBV), which can be used for selection. The figure assumes that GEBVs are available from an existing training population in month 0 and are being updated in month 63 with additional information. Only selected animals (based on GEBVs) are used for testing. Semen of superior bulls can be used earlier on commercial farms, allowing for higher genetic gain. Genomic selection allows a significant reduction of the generation interval from 6 to 1.5 years if applied as suggested in the figure.
FIGURE 3Numbers of animals in active genomic selection breeding programs adapted from (Thomasen, 2013). Shown is the total number of bulls in the reference panel (A) and recorded cows (B).