domestification and selection of productive traits

dna evidence for dual cattle domestication

• dna evidence

genetic drift

changes in allele frequency in a population due to random sampling

genetic bottleneck

• size of population reduced drastically

• surviviros may have diff allel frequencies from original

use of genetics to faciliate artificial selection

• how can we do this

• what can we detect

• what can it reveal

• transfer info from well annotated genomes to map poor species

• detect candidate disease and important trait genes

• reveal features that could not be detected within one species eg conserved regulatory element

type of genome comparisons

• between species- identify candidate genes and regulatory sequences

• within species (populations)- identify differences (polymorphisms), detect polymorphusms associated with important traits, use this info to perform marker assisted selection

3 methods of comparison

interspecies dna to dna hybridisation

• flurorescent in situ hybirisation, but probes will be hybridiesed with DNA from different species (zoo FISH)

map to map comparisons between species

• must contain orthologous genetic markers that are present in at least 2 genomes

sequence to sequence comparisions between/within species

• large scale sequence to sequence alignment algorithms are used

what will hybridisation reveal

chromosomes containing similar sequences

zoo fish

• what does it allow

• what is not needed

• 3 disadvantages

• allows for comparison of any pair of genomes with a reasonable level of conservation of chromosomes.

• no mapping info needed

• comparison is rough, missed many details

• no info on chromosomal coordinates of compared segments

• cannot be used to transfer gene info

comparativve mapping

• what does it allow

• what can it be integrated with

• what can it be used for

• allows for comparision of gene orders in two or more genomes

• a comparative map can be integrated with genetic or sequence maps

• it can be used to trsnsfer information between species

applications of itnerspecies genome comparisons

• transfer infor from well annotated genomes to map poor species

• reveal features that could not be detected within one species

• understand evolutionary similarities/ differences between species

mammalian gene orthology

• majority of genes are 1 to 1 orthologs

• some genes are duplicated in differnt species

• some genes are deleted in different species

• some genes are lineage specific or very diverged

positional cloning of candidate genes

• methods

• what does it detect

• map trait to linkage map

• build a comparative map of the critical region

• detect corresponding regions in thye human and mouse genomes

• detect the best candidate genes in the human and mouse genome regions

• detect polymorphisms and check their association with the trait of interest

bovine chondrodysplastic dwarfism

• shortness of long bones of limbs- deformity of the epiphysis of long boens

• insuffieicney of endochondral ossification

• irregularly arranged chondrocytes

cattle dwarfism

• map trait to 2 cM interval on Chr6

• build a comparative map

• conservation with human chr4p16

• detection of unknown human gene (expressed in long bones in human, mouse, cattle)

• sequencing cattle gene

• detection of two frame shift mutations= trait variation

trait chromosome association in cattle

• what are traits associated with more than one gene/ chromosome called?

• what are their loci called?

• what is important

Traits associated with more than one gene/chromosome location are called “quantitative traits”.

Their loci are quantitative trait loci (QTL).

❑Often, no single gene/mutation highly influences such traits. A combination of mutations is importan

milk yield/ composition qtl

• what can you build

• what is the segment conserved with what enzyme

• what does knockoutof this enzyme inhibit

• what gene to isolate

• which chromosome is it

Map trait to 3 cM interval of Chr14

❑Build a comparative map with human/mouse genomes

❑Segment conserved with mouse Dgat1

❑Mouse Dgat1 knockout inhibits lactation

❑Isolate bovine gene

❑Bovine DGAT1 mutations = trait variation

measured traits

Polygenic – controlled by many (100s, 1000s) genes

❑Phenotype is measured, commonly numerical

❑Traits affected by environment (all non-genetic influences) as well as genes

❑Examples – milk yield, parasite resistance, litter size ….. actually most things we observe on a population (within breed) of animals

how to measure the genotype

• estimation

• Phenotype = Genotype + Environment + ‘error’ or

• Genotype = Phenotype – Environment – ‘error’

• So we:

• ✓ Measure phenotype

• ✓ Remove effects of known environmental factors

• ✓ What’s left is the genotype

marker assisted sslection

Use of causative mutations to increase efficiency of selection within a breed. ❑Some commercially available tests in sheep & cattle:

❑Cattle (mendelian traits): coat colours, polling

❑Sheep (mendelian traits): scrapie resistance.

❑Cattle (quantitative traits): feed efficiency, meat yield, milk production, marbling.

❑Sheep (quantitative traits): WormStar, MyoMax, LionMax, cold tolerance.