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I believe that all but maybe one of the SAM 288 lines have been sequenced based on emails exchanges in January which included Jennifer, Loren and Nicolas when I asked about the ISA abstract =E2=80=93 which describes the SAM pop as having 271 lines because = that was the number for which there was good data at the time the SAM 2013 paper was written. All of the SAMs have Ames numbers and are not tracked as their originating PI. 1. So everything is equal (since the INRA lines didn=E2= =80=99t have PI sources, they needed some number to be part of the distributions here). 2. Because as John said, there were additional selfings. It was Georgia who said that the SAMs and the PIs are not necessarily equal so I should not be distributing PIs as SAMs. It was far easier (for tracking, for setting up orders) and allowed us to keep the INRAs and the SAMs together, to give everything a new Ames number than to give the PI derived SAMs a different lot code. They do not have new PI numbers (yet) because Peter Bretting said I could not give them PI numbers. Does that answer your questions, Andries? Laura Laura Fredrick Marek, PhD Curator, Oil Seeds Crops North Central Regional Plant Introduction Station (NCRPIS) National Plant Germplasm System, ISU and USDA-ARS mail to: 1305 State Ave Ames, IA 50014 lmarek@iastate.edu 515-294-3519 (NCRPIS) 515-294-1903 (FAX) 515-451-7491 (cell) From: John M. Burke [mailto:jmburke@uga.edu] Sent: Thursday, February 11, 2016 2:19 PM To: Andries Temme ; Marek, Laura F [AGRON] Cc: Rishi Rajen Masalia ; Lisa Donovan Subject: Re: Origin of the SAM 288 (past, present, future) I think, but am not 100% sure, that Laura may have assigned new PI numbers to seed that's derived from the selling that we did hear at UGA since that could result in some divergence. That is, for lines that still exhibited substantial segregation, picking out one individual and self in it could result in a rather different genotype can constitution of the subsequent seeds (relative to the avg values for that original accession). I believe that Jen still referred to these all by their original PI designations in her paper, but they may have be pen renamed when the seed was seen back to Ames. That could account for the apparent discrepancies. I am cc'ing Laura to get her thoughts. You might also make some sense of this by spot heckling the records in GRIN,p. Thanks, John On Thursday, February 11, 2016, Andries Temme > wrote: Hi, I've gone through the PI numbers and line names from the Mandell 2011 and Mandell 2013 papers. If you could have a look at the attached file. - 220 of the current 288 SAM lines overlap in PI number with the 271 PI numbers from the Mandell 2013 paper - The column from Laura's sheet listing whether or not the line was in the Mandell 2011 paper "Core288" seems correct (I could find most of the PI numbers from Laura's sheet or the line name in the table from Mandell 2011. Name format issues makes comparisons difficult) - If the column is indeed correct, as I think it is, only 191 of the current SAM-288 are in the Mandell 2011 Core288 So, is this an issue? Is there sequence/marker/SNiP data for the current SAM-288 as in the table from Laura? 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}\htmlrtf {\htmlrtf0 = =0A=0D{\*\htmltag148 }\htmlrtf {\f4 \htmlrtf0 It is true tha= t there are only 191 of the SAM lines in the core 288 or, only 191 core 288= lines in SAM.=0A=0D{\*\htmltag84  }\htmlrtf \'a0\htmlrtf0 I believe = that all but maybe one of the SAM 288 lines=0A=0D{\*\htmltag4 \par }\htmlrt= f \htmlrtf0 =0A=0D{\*\htmltag4 }have been sequenced based on emails excha= nges in January which included Jennifer, Loren and Nicolas when I asked abo= ut the ISA abstract \'96 which describes the SAM pop as having 271 lines be= cause that was the number for which there was good data at the time=0A=0D{\= *\htmltag4 \par }\htmlrtf \htmlrtf0 =0A=0D{\*\htmltag4 }the SAM 2013 pape= r was written.=0A=0D{\*\htmltag244 }=0A=0D{\*\htmltag252 }=0A=0D= {\*\htmltag156 }\htmlrtf }\htmlrtf0 \htmlrtf\par}\htmlrtf0=0A=0D\htm= lrtf \par=0A=0D\htmlrtf0 =0A=0D{\*\htmltag72

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}\htmlrtf {\htmlrtf0 = =0A=0D{\*\htmltag148 }\htmlrtf {\f4 \htmlrtf0 All of the SAM= s have Ames numbers and are not tracked as their originating PI.=0A=0D{\*\h= tmltag84  }\htmlrtf \'a0\htmlrtf0 1.=0A=0D{\*\htmltag84  }\htmlr= tf \'a0\htmlrtf0 So everything is equal (since the INRA lines didn\'92t ha= ve PI sources, they=0A=0D{\*\htmltag4 \par }\htmlrtf \htmlrtf0 =0A=0D{\*\h= tmltag4 }needed some number to be part of the distributions here).=0A=0D{\= *\htmltag84  }\htmlrtf \'a0\htmlrtf0 2.=0A=0D{\*\htmltag84  }\ht= mlrtf \'a0\htmlrtf0 Because as John said, there were additional selfings.= =0A=0D{\*\htmltag84  }\htmlrtf \'a0\htmlrtf0 It was Georgia who said = that the SAMs and the PIs are not necessarily equal so I should not be dist= ributing PIs as SAMs.=0A=0D{\*\htmltag84  }\htmlrtf \'a0\htmlrtf0 It = was far easier=0A=0D{\*\htmltag4 \par }\htmlrtf \htmlrtf0 =0A=0D{\*\htmlta= g4 }(for tracking, for setting up orders) and allowed us to keep the INRAs= and the SAMs together, to give everything a new Ames number than to give t= he PI derived SAMs a different lot code.=0A=0D{\*\htmltag84  }\htmlrtf= \'a0\htmlrtf0 They do not have new PI numbers (yet) because Peter Brettin= g said I could=0A=0D{\*\htmltag4 \par }\htmlrtf \htmlrtf0 =0A=0D{\*\htmlta= g4 }not give them PI numbers.=0A=0D{\*\htmltag244 }=0A=0D{\*\htmltag2= 52 }=0A=0D{\*\htmltag156 }\htmlrtf }\htmlrtf0 \htmlrtf\par}\ht= mlrtf0=0A=0D\htmlrtf \par=0A=0D\htmlrtf0 =0A=0D{\*\htmltag72

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}\htm= lrtf {\htmlrtf0 =0A=0D{\*\htmltag148 }\htmlrtf {\f4 \htmlrtf= 0 Does that answer your questions, Andries?=0A=0D{\*\htmltag244 }=0A= =0D{\*\htmltag252 }=0A=0D{\*\htmltag156 }\htmlrtf }\htmlrtf0 \= htmlrtf\par}\htmlrtf0=0A=0D\htmlrtf \par=0A=0D\htmlrtf0 =0A=0D{\*\htmltag72=

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}\htmlrtf {\htmlrtf0 = =0A=0D{\*\htmltag148 }\htmlrtf {\f4 \htmlrtf0 Laura Fredrick= Marek, PhD=0A=0D{\*\htmltag244 }=0A=0D{\*\htmltag252 }=0A=0D{\*= \htmltag156 }\htmlrtf }\htmlrtf0 \htmlrtf\par}\htmlrtf0=0A=0D\htmlrt= f \par=0A=0D\htmlrtf0 =0A=0D{\*\htmltag72

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}\htmlrtf {\htmlrtf0 =0A=0D{\*\html= tag148 }\htmlrtf {\f4 \htmlrtf0 Curator, Oil Seeds Crops=0A= =0D{\*\htmltag244 }=0A=0D{\*\htmltag252 }=0A=0D{\*\htmltag156 }\htmlrtf }\htmlrtf0 \htmlrtf\par}\htmlrtf0=0A=0D\htmlrtf \par=0A=0D\h= tmlrtf0 =0A=0D{\*\htmltag72

}=0A=0D{\*\htmltag0 \par }=0A=0D{\*\htmltag= 64

}\htmlrtf {\htmlrtf0 =0A=0D{\*\htmltag148 }\htmlrtf {\f4 \htmlrtf0 North Central Regional Plant Introduction = Station (NCRPIS)=0A=0D{\*\htmltag244 }=0A=0D{\*\htmltag252 }=0A= =0D{\*\htmltag156 }\htmlrtf }\htmlrtf0 \htmlrtf\par}\htmlrtf0=0A=0D\= htmlrtf \par=0A=0D\htmlrtf0 =0A=0D{\*\htmltag72

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}\htmlrtf \line=0A= =0D\htmlrtf0 =0A=0D{\*\htmltag4 \par }=0A=0D{\*\htmltag84 }\htmlrtf {\b = \htmlrtf0 Sent:=0A=0D{\*\htmltag92 }\htmlrtf }\htmlrtf0 Thursday, Febr= uary 11, 2016 2:19 PM=0A=0D{\*\htmltag116
}\htmlrtf \line=0A=0D\htmlrtf= 0 =0A=0D{\*\htmltag4 \par }=0A=0D{\*\htmltag84 }\htmlrtf {\b \htmlrtf0 T= o:=0A=0D{\*\htmltag92 }\htmlrtf }\htmlrtf0 Andries Temme =0A=0D{\*\htm= ltag84 <}\htmlrtf <\htmlrtf0 atemme@uga.edu=0A=0D{\*\htmltag84 >}\htm= lrtf >\htmlrtf0 ; Marek, Laura F [AGRON] =0A=0D{\*\htmltag84 <}\htmlrtf = <\htmlrtf0 lmarek@iastate.edu=0A=0D{\*\htmltag84 >}\htmlrtf >\htmlrtf0 = =0A=0D{\*\htmltag116
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}\= htmlrtf \line=0A=0D\htmlrtf0 =0A=0D{\*\htmltag4 \par }=0A=0D{\*\htmltag84 <= b>}\htmlrtf {\b \htmlrtf0 Subject:=0A=0D{\*\htmltag92 }\htmlrtf }\htmlr= tf0 Re: Origin of the SAM 288 (past, present, future)=0A=0D{\*\htmltag244 = }=0A=0D{\*\htmltag252 }=0A=0D{\*\htmltag156 }\htmlrtf }\h= tmlrtf0 \htmlrtf\par}\htmlrtf0=0A=0D\htmlrtf \par=0A=0D\htmlrtf0 =0A=0D{\*\= htmltag72

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}\htmlrtf {\html= rtf0 I think, but am not 100% sure, that Laura may have assigned new PI num= bers to seed that's derived from the selling that we did hear at UGA since = that could result in some divergence. That is, for lines that still exhibit= ed=0A=0D{\*\htmltag84  }\htmlrtf \'a0\htmlrtf0 substantial segregation= ,=0A=0D{\*\htmltag4 \par }\htmlrtf \htmlrtf0 =0A=0D{\*\htmltag4 }picking = out one individual and self in it could result in a rather different genoty= pe can constitution of the subsequent seeds (relative to the avg values for= that original accession). I believe that Jen still referred to these all b= y their original PI designations=0A=0D{\*\htmltag4 \par }\htmlrtf \htmlrtf= 0 =0A=0D{\*\htmltag4 }in her paper, but they may have be pen renamed when = the seed was seen back to Ames. That could account for the apparent discrep= ancies. I am cc'ing Laura to get her thoughts. You might also make some sen= se of this by spot heckling the records in GRIN,p. Thanks,=0A=0D{\*\htmltag= 4 \par }\htmlrtf \htmlrtf0 =0A=0D{\*\htmltag4 }John=0A=0D{\*\htmltag244 <= o:p>}=0A=0D{\*\htmltag252 }\htmlrtf\par}\htmlrtf0=0A=0D\htmlrtf \par= =0A=0D\htmlrtf0 =0A=0D{\*\htmltag72

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}\htmlrtf {\htmlrtf0 =0A=0D{\*\htmltag116 }\htmlrtf \line=0A=0D\htmlrtf0 =0A=0D{\*\htmltag4 \par }On Thursday, Febru= ary 11, 2016, Andries Temme =0A=0D{\*\htmltag84 <}\htmlrtf <\htmlrtf0 = =0A=0D{\*\htmltag84 }\htmlrtf {\field{\*\= fldinst{HYPERLINK "mailto:atemme@uga.edu"}}{\fldrslt\cf1\ul \htmlrtf0 atemm= e@uga.edu\htmlrtf }\htmlrtf0 \htmlrtf }\htmlrtf0 =0A=0D{\*\htmltag92 }= =0A=0D{\*\htmltag84 >}\htmlrtf >\htmlrtf0 wrote:=0A=0D{\*\htmltag244 }=0A=0D{\*\htmltag252 }\htmlrtf\par}\htmlrtf0=0A=0D\htmlrtf \par= =0A=0D\htmlrtf0 =0A=0D{\*\htmltag72

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}\htmlrtf {\htmlrtf0 \li360 =0A= =0D{\*\htmltag148 }\htmlrtf {\f4 \htmlrtf0 I've gone through the PI numbers and= line names from the Mandell 2011 and Mandell 2013 papers. If you could hav= e a look at the attached file.=0A=0D{\*\htmltag244 }=0A=0D{\*\htmltag2= 52 }=0A=0D{\*\htmltag156 }\htmlrtf }\htmlrtf0 \htmlrtf\par}\ht= mlrtf0=0A=0D\htmlrtf \par=0A=0D\htmlrtf0 =0A=0D{\*\htmltag72

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}\htmlrtf {\htmlrtf0 \li360 =0A=0D{\*\htmltag148 }\htmlrtf {\f4 = \htmlrtf0 - The column from Laura's sheet listing whether or not the line w= as in the Mandell 2011 paper =0A=0D{\*\htmltag84 "}\htmlrtf "\htmlrtf0= Core288=0A=0D{\*\htmltag84 "}\htmlrtf "\htmlrtf0 seems correct (I co= uld find most of the PI numbers from Laura's sheet=0A=0D{\*\htmltag4 \par }= \htmlrtf \htmlrtf0 =0A=0D{\*\htmltag4 }or the line name in the table from= Mandell 2011. Name format issues makes comparisons difficult)=0A=0D{\*\htm= ltag244 }=0A=0D{\*\htmltag252 }=0A=0D{\*\htmltag156 }\htm= lrtf }\htmlrtf0 \htmlrtf\par}\htmlrtf0=0A=0D\htmlrtf \par=0A=0D\htmlrtf0 = =0A=0D{\*\htmltag72

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It is true that there are only 191 of= the SAM lines in the core 288 or, only 191 core 288 lines in SAM.  I = believe that all but maybe one of the SAM 288 lines have been sequenced based on emails exchanges in January which included Je= nnifer, Loren and Nicolas when I asked about the ISA abstract =E2=80=93 whi= ch describes the SAM pop as having 271 lines because that was the number fo= r which there was good data at the time the SAM 2013 paper was written.

 

All of the SAMs have Ames numbers and= are not tracked as their originating PI.  1.  So everything is e= qual (since the INRA lines didn=E2=80=99t have PI sources, they needed some number to be part of the distributions here).  2.  B= ecause as John said, there were additional selfings.  It was Georgia w= ho said that the SAMs and the PIs are not necessarily equal so I should not= be distributing PIs as SAMs.  It was far easier (for tracking, for setting up orders) and allowed us to keep the INRAs and= the SAMs together, to give everything a new Ames number than to give the P= I derived SAMs a different lot code.  They do not have new PI numbers = (yet) because Peter Bretting said I could not give them PI numbers.

 

Does that answer your questions, Andr= ies?

 

Laura

Laura Fredrick Marek, PhD<= /span>

Curator, Oil Seeds Crops

North Central Regional Plant Introduc= tion Station (NCRPIS)

National Plant Germplasm System, ISU = and USDA-ARS

mail to: 1305 State Ave

Ames, IA 50014

lmarek@iastate.edu

 

515-294-3519 (NCRPIS)

515-294-1903 (FAX)<= /p>

515-451-7491 (cell)

 

From: John M. Burke [mailto:jmburke@= uga.edu]
Sent: Thursday, February 11, 2016 2:19 PM
To: Andries Temme <atemme@uga.edu>; Marek, Laura F [AGRON] <= ;lmarek@iastate.edu>
Cc: Rishi Rajen Masalia <masalia@uga.edu>; Lisa Donovan <ld= onovan@uga.edu>
Subject: Re: Origin of the SAM 288 (past, present, future)

 

I think, but am not 100% sure, that Laura may have a= ssigned new PI numbers to seed that's derived from the selling that we did = hear at UGA since that could result in some divergence. That is, for lines = that still exhibited substantial segregation, picking out one individual and self in it could result in a rather differe= nt genotype can constitution of the subsequent seeds (relative to the avg v= alues for that original accession). I believe that Jen still referred to th= ese all by their original PI designations in her paper, but they may have be pen renamed when the seed was seen back= to Ames. That could account for the apparent discrepancies. I am cc'ing La= ura to get her thoughts. You might also make some sense of this by spot hec= kling the records in GRIN,p. Thanks, John


On Thursday, February 11, 2016, Andries Temme <atemme@uga.edu> wrote:

Hi,

 

I've gone through the PI numbers and line names f= rom the Mandell 2011 and Mandell 2013 papers. If you could have a look at t= he attached file.

 

- 220 of the current 288 SAM lines overlap i= n PI number with the 271 PI numbers from the Mandell 2013 paper

 

- The column from Laura's sheet listing whether o= r not the line was in the Mandell 2011 paper "Core288" seems corr= ect (I could find most of the PI numbers from Laura's sheet or the line name in the table from Mandell 2011. Name format issues makes = comparisons difficult)

 

- If the column is indeed correct, as I thin= k it is, only  191 of the current SAM-288 are in the Mandell= 2011 Core288

 

So, is this an issue? Is there sequence/marker/SN= iP data for the current SAM-288 as in the table from Laura?

 

Thanks, Andries



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