genomes

parts of a chrommosome

Telomeres – ends of chromosomes. Contain telomeric repetitive DNA sequences and not completely replicated in somatic cells (ageing)

❑p-arm – short arm of a chromosome.

❑q-arm – long arm of a chromosome.

❑Centromere – chromosome locus where kinetochore fibers bind to chromatids, allowing for the correct chromatid segregation in daughter cells (contains α-satellite DNA).

species karotype

• an individuals complete set of chromosomes

• defines its specific number, size and shape

c value paradox

• the c value is the amount of DNA in the haploid genome of an organism

• varies over a wide range with an increase in the c value with complexity of the organism

• paradox is that very similar organisms can show a large difference in c values,

• the amount of genomic DNA in complex eukaryotes is much greater than the amount needed to encode proteins

chromosom content

• genes

• repetitive dna (tandem, interspersed)

• regulatory DNA sequences

structure of genes

what do alternative splicing form

multiple isoforms

genes in mammals

around 90 percent of genes are present (have orthologs) in all mammals

human an dchimp share 99 percent genes

expansion of the beta defensin cluster in cattle

• what are beta defensins

• what are they characterised by

• what is extensive across mammals

• beta defensins are peptides with antimicrobial roles chatracterised by a conserved tertiary structure.

• copy number variation is extensive across mammals

telomer DNA

protects end of chromosomes

reproduced by telomerase in germ cells

interspersed DNA repeats

• what do they do and what do they not form

• what percent of the human and maize genome do they comprise

• what are they either

• what can they do

• no not form tandemly repeated blocks

• intermingle with other sequences

• together comprise around 45 percent of the human genome and more than 50 in maize

• either transposable elements or sequences derived from transposable elements

• can copy and move genes

regulatory DNA sequences

• 2 types

• functions

• cis is close and trans is on a diff chromosome

• by fucntions- enhancers, silenccers, insulators

• conserved or non

ultra conserved elements

• how many

• what species

481 elements that are conserved between human, fish, dog and mice

genetic marker

• a DNA sequence with a known location (physical or relative) on a chromosome. the marker itself may be a part of a gene or may have no known function

genetic linkage map

• what does it represent

• what are the distances expressed as

• requiremens

• what do they not connect

is a representation of markers on a chromsome in linear order with distances between them expressed as a percent of recombination (map units, centimorgans)

require special large mapping populations of more than 1000 individuals

do not directly connect markers to chromosomes. linkage groups

physical map

representation of physical position of markers in a chromosome

syntetic

genetic markers on the same chromosme

synteny

physical co localisation of genes of the saem chromosome in the same species

principles of genetic mapping

• what do we need to distinguish

• what must markers in a mapping population be

• what do we count

• what indicates independent assortment

To detect if markers are linked (syntenic) we should distinguish between maternal and paternal alleles of a genetic marker

. Markers must be polymorphic in a mapping population.

❑Counting number of offspring of different type and comparing to the numbers assuming independent assortment (chi square)

. ❑Recombination frequency between two markers of 50% indicates independent assortment

features of genetic maps

• what does distance between markers may not match

• what is it often impossible to do

• what is it useful for

• what is it not useful for

• distance between markers on a genetic map may not match physical distances on a chromosome

• it is often impossible to resolve order of closely located markers-no recombination

• useful for detection of association between markers and phenotypic traits within species

• not useful for comparative analysis between species

linkage maps for agricultural species

• what is used for

• are used to connect phenotypuc traits to markers

• plants- relaively easy to produce because construction of an appropriate mapping populations is not a problem

• animals- construction of mapping populations is diffuclt and expensie. untul very recently maker selection was complicatioed. Therefore animal linkage maps often contain very few markers (~300 genome-wide).

types of physical maps

• cytogenetic

• genome sequencs

cytogenetic maps

• what does it do

• what technique was first used to map genes in drosophila

• detection position of known DNA fragment on a chromosome by in situ hybridisation

• common used variation fluorescence in situ hybridisation

• FISH was first used to map genes in drosophila

genomic diversity

• gene point mutation

• ene duplication/deletion

• chromosome rearrangement

• transposable (mobile) element activity

gray causing mutation in horses

• phenotypic effects

• what type of mutation is it

• gradual loss of hair pigmentation

• dark skin pigmentation is maintained

• is a copy number variation

• ❑Linkage (genetic) mapping to a 352 kb interval, chr 25.

• ❑Genes: NR4A3, TXNDC4, INVS, STX17

• ❑PCR analysis detected a 4.6 kb insertion in intron no. 6 of STX17. ❑Duplication detected in all Gray horses and in none of non-Gray. ❑Regulatory mutation that affects expression of NR4A3 and STX17

white coat colour in dog

❑Linkage mapping to a region containing MITF gene (transcription factor).

❑Two mutations were found.

❑Short Interspersed Repeat (SINE)

. ❑Variation in MITF promoter.

❑Different combinations of the alleles lead to different phenotypes.

sulfites in wine

SO2 keeps wine fresh, prevents oxidation ❑Longer shelf life ❑Wines without sulfites must be stored at perfect conditions

Enhanced expression of SSU1 gene enables wine yeast strains carrying the translocation to resist higher sulfite concentrations.

what is evolution of a species dependent on

Genes are passed from one generation to another according to Mendelian principles. All offspring produced through sexual reproduction posses both differences and similarities to their parents. ❑Genetic changes that occur in populations and within species over time are the basis of evolution. Unlike individuals, populations continue over time.

❑Evolution of a species is dependent on changes in gene frequencies within or between populations over time.