Direct and correlated responses to selection. 1. EGR Primary correlated response to selection for fast growth to 42 days of age is still EGR 14 . Correlated response to selection for EGR 14 is still EGR 14/42 .

Primary correlated response to selection for fast growth to 42 days of age is still EGR 14 .

Correlated response to selection for EGR 14 is still EGR 14/42 .

Correlated responses to selection 2. Body Weight Direct response to selection for fast EGR 14 still makes a large, lean bird at 42 days of age. Divergence between 14H and 42H birds at 42 days of age is largely fat! 14L chicks largest at hatch, smallest at 14 days of age, but getting bigger by 42 days of age.

Direct response to selection for fast EGR 14 still makes a large, lean bird at 42 days of age.

Divergence between 14H and 42H birds at 42 days of age is largely fat!

14L chicks largest at hatch, smallest at 14 days of age, but getting bigger by 42 days of age.

14L and 14H Lines at 14 and 42 Days (S 14 ) 14L 14H 38 g 319 g 172 g 861 g

Life Cycle of Selection Lines

QTL Analysis F 2 segregating generations Substantial heterosis or dominance for early growth

QTL Analysis F 2 segregating generations Substantial additive variation for late growth

Types of Molecular Markers Restriction Fragment Length Polymorphisms RFLP Restriction enzyme in conjunction with probe. Randomly Amplified Polymorphic DNA RAPD PCR using random primer sequences Microsatellite DNA Short sequences of tandemly repeated DNA PCR with resultant different length cDNA

Restriction Fragment Length Polymorphisms

RFLP

Restriction enzyme in conjunction with probe.

Randomly Amplified Polymorphic DNA

RAPD

PCR using random primer sequences

Microsatellite DNA

Short sequences of tandemly repeated DNA

PCR with resultant different length cDNA

RFLP A a AA Aa aa Resulting gel

RAPD A a AA Aa aa Resulting gel No PCR product

Microsatellite A a AA Aa aa Resulting gel GCC GCC GCC GCC GCC GCC GCC GCC

Molecular marker loci properties Rafalski and Tingey, 1993

Molecular mechanism for crossing-over (Robin Holliday, 1960s): Homologous chromosomes “recognize” and align. Single strands of each DNA (one on each chromosome) break and anneal to the opposite chromosome forming Holliday intermediate. As chromosome ends pull apart, branch point migrations occur to create a 4-arm intermediate structure. 4-arm intermediate is cut by by endonucleases in one of 2 planes. DNA seals the gaps. Model predicts that physical exchange between two gene loci at the ends of the chromosomes should occur about 50% of the time. One pattern (intermediate cut in one plane) yields the parental arrangement, the other (cut in the other plane) is recombinant.

Homologous chromosomes “recognize” and align.

Single strands of each DNA (one on each chromosome) break and anneal to the opposite chromosome forming Holliday intermediate.

As chromosome ends pull apart, branch point migrations occur to create a 4-arm intermediate structure.

4-arm intermediate is cut by by endonucleases in one of 2 planes.

DNA seals the gaps.

Model predicts that physical exchange between two gene loci at the ends of the chromosomes should occur about 50% of the time. One pattern (intermediate cut in one plane) yields the parental arrangement, the other (cut in the other plane) is recombinant.

Holliday model of chromosome recombination

Experimental designs for QTL detection Inbred lines Back cross Test cross F 2 Recombinant Inbred Lines Segregating populations Full-sibs Half-sibs Grand-daughter Animal model

Inbred lines

Back cross

Test cross

F 2

Recombinant Inbred Lines

Segregating populations

Full-sibs

Half-sibs

Grand-daughter

Animal model

Backcross design Parental strains X X F 1 strains Backcross Progeny Non-recombinants Recombinants Frequency = 1 - r Frequency = r m q m q M Q M Q m q M Q M Q M Q m q M Q M Q M Q m Q M Q M q M Q

Bulked segregant analysis 14L 14H F 1 F 2 Bulk 1 Mostly qq ; enriched for m , depleted for M Bulk 2 Mostly QQ ; enriched for M , depleted for m m q m q M Q M Q M Q m q

Recombinant inbred lines (by selfing)

Recombinant inbred lines (by sibling mating)

Advantages of RI lines Each strain is an eternal resource. Only need to genotype once. Reduce individual variation by phenotyping multiple individuals from each strain. Study multiple phenotypes on the same genotype. Greater mapping precision. More dense breakpoints on the RI chromosomes.

Each strain is an eternal resource.

Only need to genotype once.

Reduce individual variation by phenotyping multiple individuals from each strain.

Study multiple phenotypes on the same genotype.

Greater mapping precision.

More dense breakpoints on the RI chromosomes.

Grand-daughter design X Grandsire & Grandam(s) X X Sons x random dams (genotyped) Son Son Grand-daughters M 1 Q 1 M 2 Q 2 M x Q x M x Q x M x Q x M x Q x M 1 Q 1 M x Q x M 2 Q 2 M x Q x M x Q x M x Q x M 1 Q 1 M x Q x M x Q x M x Q x M x Q x M x Q x M 2 Q 2 M x Q x

Determining the genome sequence Sequence assembly Partial digest Library of bacterial artificial chromosomes (BACs) with genomic fragments Alignment of BAC clones > contigs and anchoring On the molecular gene map Sequencing of overlapping BAC clone fragments “ Tiling path” > selection of BAC clones to be sequenced Annotation of genome sequence > prediction of genes

Genomes of human and mouse compared human: 22 chromosomes + X or Y mouse: 19 chromosomes + X or Y homologous segments are color-coded (total >300) human chromosomes correspond to segments of different mouse chromosomes e.g.. Segments of chr. 10, 11, 15, 16 and 19 correspond to mouse chromosome 7

Historical perspective: from genetic map to genome sequence

Chicken Chromosome 4 25 cM LEI122 * LEI76 LEI81 ** 270 cM SPP1 Murine SPP1 56.0 cM Chicken Chromosome 4 Murine Chromosome 5 (Late Growth QTL) (Cluster 1) (Cluster 2) Cluster 1 - Protein kinase II, glucokinase, VDR, galactosyltransferase, Ubiquitin C and FGF5 Cluster 2 - Acads, Phkg and Asl Cluster 3 - ZP3, Zonadhesin , Epo and Actin (Cluster 3)

Different markers corresonding to the same genes in prior slide.