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Lecture

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Department
Human Biology
Course Code
HMB265H1
Professor
Stephen Wright

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LECTURE 16 March 10/2011
Tomato size is quantitative trait correlations are made
Marker loci and QTL associations found when different genotypes of the marker loci are
CORRELATED with different average phenotypes or different mean trait values
Thats when correlation seen
No association if different marker genotypes all have same average trait value
Rarely allows you to find gene of interest so narrowing down gene to specific
chromosomal interval, which is normally 10cMorgans in size still pretty large
Sometimes there are hundreds of genes within interval how know which gene
controls quantitative traits?
Other techniques are used todays lectures focus
Inbred lines are created of these two separate types
ThesE Inbred lines are isogenic SAME GENES OR ALLELE COMBINATIONS EXCEPT
FOR LOCI THAT CONTROL THE QUANTItative trait
This was done with tomato size
Circled is the markers
Gene responsible is one of the circled next slide identifies the gene responsible
Look and find more closely spaced markers
Different individuals for marker loci that are more closely spaced
To fine-map locus
Also create recombinant inbred lines called near-isogenic lines or NILs
Only dealing with one quantitative trait locus when create these lines
With recombinant inbred lines only focusing on one region that encompasses
one quantitative trait locus
So how are these lines generated?
oInbreed selected individuals down line
oCross individuals from F2
oCalled single-seed descent
oCreates ladder-like mosaic
oOccurs because of maternal and paternal allele combinations down length
of chromosome
oTry to decrease interval that this QTL is in by increasing number of
markers
Frary slide
Recombinant linbred LINES Were genotypes and their marker genotypes were
compared with each other
And therefore the area of interest was DECREASED
Distance in cMorgans have decreased
www.notesolution.com
6 candidate genes listed at top of slide
Each of these lines is identical except for a crossover which occurs at QTL of
interest
Crossover shown by the change in colour from red to yellow
Red from one parent; yellow from other parent
Correlating phenotype (Averg) with genotype of marker
Kin1 locus
oSeems to be gene responsible for quantitative trait
oAll lines that contain kin1 allele from red parent are around 180g in
weight
oAll lines that contain kin1 allele from yellow parent are around 170g in
weight
oSO see that can correlate mean trait value with different genotype
Correlation only seen with kin1 gene
SO FOUND CANDIDATE GENE QTL is kinase gene
Frary slide
So now look at expression patterns, examining using RT-PCR
QTL correlated with expression pattern and function/role in growth
Then genetic engineering
Transgenic line showed decrease in size not on par with small fruit size
Not complete because one of many loci affecting fruit size
Further corroborates that this is one of the genes responsible for QTL
This can be also done in humans
Use molecular markers to narrow down candidate gene
At specific molecular marker, G8 marker, was located in region of Huntington
disease locus
Then map it to region that is about 5-10 cMorgans in size
Finemap it use
Compare structure and expression btw. Diseased and normal individuals
To narrow down gene of interest
Where would these genes normally be expressed? Brain
oThen any other gene that doesnt show this expression pattern would be
eliminated from analysis
Also look at structure
oSee any differences that may contribute to the phenotype
oUse G8 marker to pinpoint the candidate gene locus
oG8 marker mapped to tip of chromosome 4
oThen further narrowed down
Thenwant to look at candidate genes in this area
Their expression, structure, sequence?
www.notesolution.com

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Description
LECTURE 16 March 102011 Tomato size is quantitative trait correlations are made Marker loci and QTL associations found when different genotypes of the marker loci are CORRELATED with different average phenotypes or different mean trait values Thats when correlation seen No association if different marker genotypes all have same average trait value Rarely allows you to find gene of interest so narrowing down gene to specific chromosomal interval, which is normally 10cMorgans in size still pretty large Sometimes there are hundreds of genes within interval how know which gene controls quantitative traits? Other techniques are used todays lectures focus Inbred lines are created of these two separate types ThesE Inbred lines are isogenic SAME GENES OR ALLELE COMBINATIONS EXCEPT FOR LOCI THAT CONTROL THE QUANTItative trait This was done with tomato size Circled is the markers Gene responsible is one of the circled next slide identifies the gene responsible Look and find more closely spaced markers Different individuals for marker loci that are more closely spaced To fine-map locus Also create recombinant inbred lines called near-isogenic lines or NILs Only dealing with one quantitative trait locus when create these lines With recombinant inbred lines only focusing on one region that encompasses one quantitative trait locus So how are these lines generated? o Inbreed selected individuals down line o Cross individuals from F2 o Called single-seed descent o Creates ladder-like mosaic o Occurs because of maternal and paternal allele combinations down length of chromosome o Try to decrease interval that this QTL is in by increasing number of markers Frary slide Recombinant linbred LINES Were genotypes and their marker genotypes were compared with each other And therefore the area of interest was DECREASED Distance in cMorgans have decreased www.notesolution.com
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