Summary OL2: genetic analysis of higher
organisms
Contents
1: epigenetics................................................................................................................................................ 3
1.1 epigenetic mechanisms – DNA methylation........................................................................................ 3
1.1.1 epigenetic mechanisms: methylation........................................................................................... 3
1.1.2 epigenetic mechanisms: histones................................................................................................. 3
1.2 reprogramming the embryo................................................................................................................ 4
1.3 long range control of gene expression................................................................................................ 4
1.3.1 Competition for enhancers or silencers........................................................................................ 4
1.3.2 X-inactivation in mammals........................................................................................................... 4
1.4 genomic imprinting............................................................................................................................ 4
1.4.1 definition and mechanisms.......................................................................................................... 5
1.4.2 importance of imprinting in animal production............................................................................6
1.4.3 transgenerational effects in humans............................................................................................ 6
2: chromosomal abberations – genetic etiology – gene markers.................................................................7
2.1 chromosomal abberations.................................................................................................................. 7
2.1.1 abnormal chromosome numbers................................................................................................. 7
2.1.2 abnormal chromosome structure................................................................................................. 7
2.2 evidence for genetic etiology.............................................................................................................. 7
2.2.1 general evidence for genetic ethiology......................................................................................... 7
2.2.2 4 types of simple mendelian einheritance....................................................................................7
2.2.3 pedigrees..................................................................................................................................... 7
2.3 gene markers: microsattelites & SNP’s................................................................................................ 7
2.3.1 gene mapping............................................................................................................................... 7
2.3.2 genetic markers............................................................................................................................ 7
3: population genetics.................................................................................................................................. 8
3.1 variation in populations...................................................................................................................... 8
3.1.1 genotype frequence & allele frequence.......................................................................................8
3.1.2 sources of genetic variation......................................................................................................... 8
3.2 HW-equilibrium................................................................................................................................... 8
3.2.1 fixation-index............................................................................................................................... 8
3.3 inbreeding & assortative mating......................................................................................................... 8
3.3.1 the inbreeding coefficient............................................................................................................ 8
3.3.2 the effective population size........................................................................................................ 8
, 3.3.3 ROH: runs of homozygocity.......................................................................................................... 8
4: GWAS........................................................................................................................................................ 9
4.1 introduction on linkage mapping........................................................................................................ 9
4.1.1 recombination & linkage.............................................................................................................. 9
4.1.2 genetic markers............................................................................................................................ 9
4.1.3 LOD score..................................................................................................................................... 9
4.1.4 Mapping traits.............................................................................................................................. 9
4.1.5 identity by descent....................................................................................................................... 9
4.2 Genome wide association studies....................................................................................................... 9
4.2.1 basic handling and analysis of GWAS SNP data............................................................................9
4.2.2 generate basic descriptive statistics............................................................................................. 9
4.2.3 perform quality control filtering................................................................................................... 9
4.2.4 check for stratification of your data............................................................................................. 9
4.2.5 perform the actual association analysis........................................................................................ 9
5: genomic breeding................................................................................................................................... 10
5.1 quantitative genetics......................................................................................................................... 10
5.1.1 quantitative traits....................................................................................................................... 10
5.1.2 reaction norm............................................................................................................................. 10
5.1.3 heritability.................................................................................................................................. 10
5.1.4 mapping QTL (quantitative trait locus).......................................................................................10
5.2 Genomic selection concept: genomic breeding.................................................................................10
organisms
Contents
1: epigenetics................................................................................................................................................ 3
1.1 epigenetic mechanisms – DNA methylation........................................................................................ 3
1.1.1 epigenetic mechanisms: methylation........................................................................................... 3
1.1.2 epigenetic mechanisms: histones................................................................................................. 3
1.2 reprogramming the embryo................................................................................................................ 4
1.3 long range control of gene expression................................................................................................ 4
1.3.1 Competition for enhancers or silencers........................................................................................ 4
1.3.2 X-inactivation in mammals........................................................................................................... 4
1.4 genomic imprinting............................................................................................................................ 4
1.4.1 definition and mechanisms.......................................................................................................... 5
1.4.2 importance of imprinting in animal production............................................................................6
1.4.3 transgenerational effects in humans............................................................................................ 6
2: chromosomal abberations – genetic etiology – gene markers.................................................................7
2.1 chromosomal abberations.................................................................................................................. 7
2.1.1 abnormal chromosome numbers................................................................................................. 7
2.1.2 abnormal chromosome structure................................................................................................. 7
2.2 evidence for genetic etiology.............................................................................................................. 7
2.2.1 general evidence for genetic ethiology......................................................................................... 7
2.2.2 4 types of simple mendelian einheritance....................................................................................7
2.2.3 pedigrees..................................................................................................................................... 7
2.3 gene markers: microsattelites & SNP’s................................................................................................ 7
2.3.1 gene mapping............................................................................................................................... 7
2.3.2 genetic markers............................................................................................................................ 7
3: population genetics.................................................................................................................................. 8
3.1 variation in populations...................................................................................................................... 8
3.1.1 genotype frequence & allele frequence.......................................................................................8
3.1.2 sources of genetic variation......................................................................................................... 8
3.2 HW-equilibrium................................................................................................................................... 8
3.2.1 fixation-index............................................................................................................................... 8
3.3 inbreeding & assortative mating......................................................................................................... 8
3.3.1 the inbreeding coefficient............................................................................................................ 8
3.3.2 the effective population size........................................................................................................ 8
, 3.3.3 ROH: runs of homozygocity.......................................................................................................... 8
4: GWAS........................................................................................................................................................ 9
4.1 introduction on linkage mapping........................................................................................................ 9
4.1.1 recombination & linkage.............................................................................................................. 9
4.1.2 genetic markers............................................................................................................................ 9
4.1.3 LOD score..................................................................................................................................... 9
4.1.4 Mapping traits.............................................................................................................................. 9
4.1.5 identity by descent....................................................................................................................... 9
4.2 Genome wide association studies....................................................................................................... 9
4.2.1 basic handling and analysis of GWAS SNP data............................................................................9
4.2.2 generate basic descriptive statistics............................................................................................. 9
4.2.3 perform quality control filtering................................................................................................... 9
4.2.4 check for stratification of your data............................................................................................. 9
4.2.5 perform the actual association analysis........................................................................................ 9
5: genomic breeding................................................................................................................................... 10
5.1 quantitative genetics......................................................................................................................... 10
5.1.1 quantitative traits....................................................................................................................... 10
5.1.2 reaction norm............................................................................................................................. 10
5.1.3 heritability.................................................................................................................................. 10
5.1.4 mapping QTL (quantitative trait locus).......................................................................................10
5.2 Genomic selection concept: genomic breeding.................................................................................10
