Young Wha Lee - Revision history

Young Wha Lee: /* About */

2008-11-20T01:54:09Z

About

←Older revision		Revision as of 01:54, 20 November 2008
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	== About ==		== About ==
	[[Image:IRON_MT_026.jpg\|150px\|thumb\|right\|Iron Mountain OR]]		[[Image:IRON_MT_026.jpg\|150px\|thumb\|right\|Iron Mountain OR]]
-	I am a ~~7th year~~ graduate student in the University Program in Genetics and Genomics at Duke, advised by Dr. John Willis (Duke) and Dr. John Kelly (University of Kansas). I am interested in complex trait variation and evolution.	+	I am a graduate student in the University Program in Genetics and Genomics at Duke, advised by Dr. John Willis (Duke) and Dr. John Kelly (University of Kansas). I am interested in complex trait variation and evolution.

	*What is the the genetic basis of complex traits?		*What is the the genetic basis of complex traits?

Young Wha Lee: /* About */

2008-11-20T01:50:33Z

About

←Older revision		Revision as of 01:50, 20 November 2008
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	== About ==		== About ==
	[[Image:IRON_MT_026.jpg\|150px\|thumb\|right\|Iron Mountain OR]]		[[Image:IRON_MT_026.jpg\|150px\|thumb\|right\|Iron Mountain OR]]
-	I am a ~~6th~~ year graduate student in the University Program in Genetics and Genomics at Duke, advised by Dr. John Willis (Duke) and Dr. John Kelly (University of Kansas). I am interested in complex trait variation and evolution.	+	I am a 7th year graduate student in the University Program in Genetics and Genomics at Duke, advised by Dr. John Willis (Duke) and Dr. John Kelly (University of Kansas). I am interested in complex trait variation and evolution.

	*What is the the genetic basis of complex traits?		*What is the the genetic basis of complex traits?

Young Wha Lee: /* Genetic dissection */

2008-11-07T23:57:43Z

Genetic dissection

←Older revision		Revision as of 23:57, 7 November 2008
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	Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs) in a breeding design that combined phenotypic selection with backcrossing. Though a large undertaking, this NIL generation approach allowed us to relatively quickly and cheaply screen up to four alleles at each QTL locus for effect size and consistency in the cloning genetic background.		Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs) in a breeding design that combined phenotypic selection with backcrossing. Though a large undertaking, this NIL generation approach allowed us to relatively quickly and cheaply screen up to four alleles at each QTL locus for effect size and consistency in the cloning genetic background.

-	I have confirmed the effects of many of the same flower size QTLs mapped in the F2 genome scan in the NILs by phenotyping BC4F2s. By phenotyping BC4F3 progeny, I have successfully pegged 3 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 7x build of the Mimulus genome. Recombination rates are quite high in these QTL regions (50-100 kB per cM), facilitating cloning efforts. Current finemapping resolution ranges at ~~300~~-900 kb and recombinant progeny testing in additional BC4F4 and BC4F5 populations is projected to rapidly narrow the region down to a target of 50 kB, after which I will move to an LD mapping approach to define the alleles using an existing panel of 200 randomly extracted Iron Mountain inbred lines. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence variants to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.	+	I have confirmed the effects of many of the same flower size QTLs mapped in the F2 genome scan in the NILs by phenotyping BC4F2s. By phenotyping BC4F3 progeny, I have successfully pegged 3 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 7x build of the Mimulus genome. Recombination rates are quite high in these QTL regions (50-100 kB per cM), facilitating cloning efforts. Current finemapping resolution ranges at 200-900 kb depending on locus and recombinant progeny testing in additional BC4F4 and BC4F5 populations is projected to rapidly narrow the region down to a target of 50 kB, after which I will move to an LD mapping approach to define the alleles using an existing panel of 200 randomly extracted Iron Mountain inbred lines. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence variants to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.

	*'''Comparative QTL mapping''':		*'''Comparative QTL mapping''':

Young Wha Lee: /* Contact Info */

2008-11-07T23:52:36Z

Contact Info

←Older revision		Revision as of 23:52, 7 November 2008
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	here is a CV:		here is a CV:
-	*[[Media:YW_CV ~~6.30.08~~.doc\|CV]]	+	*[[Media:YW_CV.doc\|CV]]

Young Wha Lee: /* Genetic dissection */

2008-10-05T07:17:59Z

Genetic dissection

←Older revision		Revision as of 07:17, 5 October 2008
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	Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs) in a breeding design that combined phenotypic selection with backcrossing. Though a large undertaking, this NIL generation approach allowed us to relatively quickly and cheaply screen up to four alleles at each QTL locus for effect size and consistency in the cloning genetic background.		Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs) in a breeding design that combined phenotypic selection with backcrossing. Though a large undertaking, this NIL generation approach allowed us to relatively quickly and cheaply screen up to four alleles at each QTL locus for effect size and consistency in the cloning genetic background.

-	I have confirmed the effects of many of the same flower size QTLs mapped in the F2 genome scan in the NILs by phenotyping BC4F2s. By phenotyping BC4F3 progeny, I have successfully pegged 3 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 7x build of the Mimulus genome. Recombination rates are quite high in these QTL regions (50-100 kB per cM), facilitating cloning efforts. Current finemapping resolution ranges ~~from 600 to ~~~900 kb ~~(~10-15 cM)~~ and recombinant progeny testing in additional ~~BC4F3 and~~ BC4F4 populations is projected to rapidly narrow the region down to a target of 50 kB, after which I will move to an LD mapping approach to define the alleles using a panel of ~~~150-180~~ randomly extracted Iron Mountain inbred lines. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence variants to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.	+	I have confirmed the effects of many of the same flower size QTLs mapped in the F2 genome scan in the NILs by phenotyping BC4F2s. By phenotyping BC4F3 progeny, I have successfully pegged 3 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 7x build of the Mimulus genome. Recombination rates are quite high in these QTL regions (50-100 kB per cM), facilitating cloning efforts. Current finemapping resolution ranges at 300-900 kb and recombinant progeny testing in additional BC4F4 and BC4F5 populations is projected to rapidly narrow the region down to a target of 50 kB, after which I will move to an LD mapping approach to define the alleles using an existing panel of 200 randomly extracted Iron Mountain inbred lines. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence variants to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.

	*'''Comparative QTL mapping''':		*'''Comparative QTL mapping''':

Young Wha Lee: /* Genetic dissection */

2008-08-12T04:48:52Z

Genetic dissection

←Older revision		Revision as of 04:48, 12 August 2008
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	*'''Defining the alleles''':		*'''Defining the alleles''':
	[[Image:DSCN1522.JPG\|thumb\|right\|Growouts in Duke greenhouse]]		[[Image:DSCN1522.JPG\|thumb\|right\|Growouts in Duke greenhouse]]
-	Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs) in a breeding design that combined phenotypic selection with backcrossing. Though a large undertaking, this NIL generation approach allowed us to quickly screen up to four alleles at each QTL locus for effect size and consistency in the cloning genetic background.	+	Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs) in a breeding design that combined phenotypic selection with backcrossing. Though a large undertaking, this NIL generation approach allowed us to relatively quickly and cheaply screen up to four alleles at each QTL locus for effect size and consistency in the cloning genetic background.

	I have confirmed the effects of many of the same flower size QTLs mapped in the F2 genome scan in the NILs by phenotyping BC4F2s. By phenotyping BC4F3 progeny, I have successfully pegged 3 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 7x build of the Mimulus genome. Recombination rates are quite high in these QTL regions (50-100 kB per cM), facilitating cloning efforts. Current finemapping resolution ranges from 600 to ~900 kb (~10-15 cM) and recombinant progeny testing in additional BC4F3 and BC4F4 populations is projected to rapidly narrow the region down to a target of 50 kB, after which I will move to an LD mapping approach to define the alleles using a panel of ~150-180 randomly extracted Iron Mountain inbred lines. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence variants to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.		I have confirmed the effects of many of the same flower size QTLs mapped in the F2 genome scan in the NILs by phenotyping BC4F2s. By phenotyping BC4F3 progeny, I have successfully pegged 3 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 7x build of the Mimulus genome. Recombination rates are quite high in these QTL regions (50-100 kB per cM), facilitating cloning efforts. Current finemapping resolution ranges from 600 to ~900 kb (~10-15 cM) and recombinant progeny testing in additional BC4F3 and BC4F4 populations is projected to rapidly narrow the region down to a target of 50 kB, after which I will move to an LD mapping approach to define the alleles using a panel of ~150-180 randomly extracted Iron Mountain inbred lines. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence variants to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.

Young Wha Lee: /* Genetic dissection */

2008-08-12T04:48:19Z

Genetic dissection

←Older revision		Revision as of 04:48, 12 August 2008
Line 37:		Line 37:
	*'''Defining the alleles''':		*'''Defining the alleles''':
	[[Image:DSCN1522.JPG\|thumb\|right\|Growouts in Duke greenhouse]]		[[Image:DSCN1522.JPG\|thumb\|right\|Growouts in Duke greenhouse]]
-	Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs) in a breeding design that combined phenotypic selection with backcrossing. I have confirmed the effects of many of the same flower size QTLs mapped in the F2 ~~experiment~~ in the NILs by phenotyping BC4F2s. By phenotyping BC4F3 progeny, I have successfully pegged 3 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 7x build of the Mimulus genome. Recombination rates are quite high in these QTL regions (50-100 kB per cM), facilitating cloning efforts. Current finemapping resolution ranges from 600 to ~900 kb and recombinant progeny testing in ~~more~~ BC4F3 and BC4F4 populations is projected to rapidly narrow the region down to a target of 50 kB, after which I will ~~move then~~ move to an LD mapping approach to define the alleles using a panel of ~150-180 randomly extracted Iron Mountain inbred lines. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence variants to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.	+	Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs) in a breeding design that combined phenotypic selection with backcrossing. Though a large undertaking, this NIL generation approach allowed us to quickly screen up to four alleles at each QTL locus for effect size and consistency in the cloning genetic background.
		+
		+	I have confirmed the effects of many of the same flower size QTLs mapped in the F2 genome scan in the NILs by phenotyping BC4F2s. By phenotyping BC4F3 progeny, I have successfully pegged 3 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 7x build of the Mimulus genome. Recombination rates are quite high in these QTL regions (50-100 kB per cM), facilitating cloning efforts. Current finemapping resolution ranges from 600 to ~900 kb (~10-15 cM) and recombinant progeny testing in additional BC4F3 and BC4F4 populations is projected to rapidly narrow the region down to a target of 50 kB, after which I will move to an LD mapping approach to define the alleles using a panel of ~150-180 randomly extracted Iron Mountain inbred lines. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence variants to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.

	*'''Comparative QTL mapping''':		*'''Comparative QTL mapping''':

Young Wha Lee: /* Genetic dissection */

2008-08-12T04:42:46Z

Genetic dissection

←Older revision		Revision as of 04:42, 12 August 2008
Line 33:		Line 33:

	*'''Genetic architecture of flower size standing variation''':		*'''Genetic architecture of flower size standing variation''':
-	I have generated 3 independent F2 mapping populations of large flowered individuals from Iron Mountain crossed to small flowered individuals, sample size 400 each. I have completed linkage maps of 150-180 markers for each population and measured 11 traits: flower size and other floral morphology traits, flowering time, leaf width, and fertililty components such as seed set, pollen viability, and pollen number. The goal of this study is to describe the genetic architecture of flower size & floral morphology traits, compare the latter with that of fertility components, and show the degree to which morphological variation in floral traits is a pleiotropic consequence of unconditionally deleterious mutations affecting fertility.	+	I have generated 3 independent F2 mapping populations of large flowered individuals from Iron Mountain crossed to small flowered individuals, sample size 400 each. I have completed linkage maps of 150-180 markers for each population and measured 11 traits: flower size and other floral morphology traits, flowering time, leaf width, and fertililty components such as seed set, pollen viability, and pollen number. The goal of this study is to describe the genetic architecture of flower size & floral morphology traits, compare the latter with that of fertility components, and show the degree to which morphological variation in floral traits is a pleiotropic consequence of unconditionally deleterious mutations affecting fertility. Two papers are in prep from this work, one focusing on the genetic architecture of standing variation for floral and life history traits and another on the genetic architecture of inbreeding depression.

	*'''Defining the alleles''':		*'''Defining the alleles''':
	[[Image:DSCN1522.JPG\|thumb\|right\|Growouts in Duke greenhouse]]		[[Image:DSCN1522.JPG\|thumb\|right\|Growouts in Duke greenhouse]]
-	Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs). I have confirmed the effects of many of the same flower size QTLs mapped in the F2 experiment in the NILs. By phenotyping ~~BC4F2 and~~ BC4F3 progeny, I have successfully pegged 2 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 6x build of the Mimulus genome. Recombination rates are quite high in ~~many of the~~ QTL regions (50-100 kB per cM ~~in some cases~~), facilitating cloning efforts. ~~I aim~~ to ~~map~~ down to 50 kB ~~by recombination for several of the QTLs~~, then move to an LD mapping approach to define the alleles using a panel of ~150-180 randomly extracted Iron Mountain inbred lines ~~phenotyped for flower size and a number of related traits~~. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence ~~variation~~ to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.	+	Simultaneously I have introgressed the same F1 alleles into a common background (IM62, an Iron Mountain inbred line) and generated 4th generation near-isogenic lines (NILs) in a breeding design that combined phenotypic selection with backcrossing. I have confirmed the effects of many of the same flower size QTLs mapped in the F2 experiment in the NILs by phenotyping BC4F2s. By phenotyping BC4F3 progeny, I have successfully pegged 3 QTLs (mapped in both the F2 populations as well as the NILs) to scaffolds in the 7x build of the Mimulus genome. Recombination rates are quite high in these QTL regions (50-100 kB per cM), facilitating cloning efforts. Current finemapping resolution ranges from 600 to ~900 kb and recombinant progeny testing in more BC4F3 and BC4F4 populations is projected to rapidly narrow the region down to a target of 50 kB, after which I will move then move to an LD mapping approach to define the alleles using a panel of ~150-180 randomly extracted Iron Mountain inbred lines. Identification of the segregating units underlying flower size QTLs will enable us to connect sequence variants to the observed aspects of genetic architecture for this evolutionarily labile trait. It will also allow us to look directly at allele dynamics of flower size alleles in the source site as well as test for molecular signatures of selection.

	*'''Comparative QTL mapping''':		*'''Comparative QTL mapping''':

Young Wha Lee: /* The trait */

2008-08-12T04:34:47Z

The trait

←Older revision		Revision as of 04:34, 12 August 2008
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	Biometric tests (see Kelly and Willis 2001) have shown that much of the abundant standing variation for this trait in the Iron Mountain population is due to alleles at intermediate frequency. Flower size is genetically correlated with variation in pistil/anther and flower length (affecting mating strategy), flowering time (drought escape), water use efficiency (drought tolerance), as well as pollen number and seed set. Considering the heterogenous environment, a growing season demarcated by extremes in temperature and moisture, and extensive and variable pleiotropy, what maintains flower size variation at a given locus?		Biometric tests (see Kelly and Willis 2001) have shown that much of the abundant standing variation for this trait in the Iron Mountain population is due to alleles at intermediate frequency. Flower size is genetically correlated with variation in pistil/anther and flower length (affecting mating strategy), flowering time (drought escape), water use efficiency (drought tolerance), as well as pollen number and seed set. Considering the heterogenous environment, a growing season demarcated by extremes in temperature and moisture, and extensive and variable pleiotropy, what maintains flower size variation at a given locus?

-	There is also a lot of variation in the same traits among the members of the Mimulus species complex, often correlated with differences in mating system (pictured at right). ~~Thus the~~ system is ideal for an assessment of the relationship between standing variation and adaptive divergence.	+	There is also a lot of variation in the same traits among the members of the Mimulus species complex, often correlated with differences in mating system (pictured at right). The system is ideal for an assessment of the relationship between standing variation and adaptive divergence.

	==='''Genetic dissection===		==='''Genetic dissection===

Young Wha Lee: /* Contact Info */

2008-08-12T04:33:13Z

Contact Info

←Older revision		Revision as of 04:33, 12 August 2008
Line 61:		Line 61:

	here is a CV:		here is a CV:
-	*[[Media:~~YW CV~~.doc\|CV]]	+	*[[Media:YW_CV 6.30.08.doc\|CV]]