Mapping data involving W22

Matt Evans mmevans at facstaff.wisc.edu
Mon Apr 5 14:55:25 EST 1999



I have been comparing SSR markers in W22 and W23 to B73 and Mo17 to
determine which ones are polymorphic between these lines.  Unfortunately, I
don't know absolute sizes, only relative sizes.  I have compared them by
running them out on 4% metaphor agarose gels, so there may be some small
differences that I missed.  I can tell that this happened with a couple of
markers between B73 and Mo17 in which there is a difference listed on
MaizeDB of a few base pairs that I could not resolve.  The W22 parent used
is a C; r-g: stadler; W22 line that we use for backcrossing in the Kermicle
lab.  I have gone through my gels and entered the data in an excell file
which I am attaching.  Some of the markers need to be run further than
others to see the polymorphism.  I plan to scan the polaroids into the
computer at some point and can then send those images to MaizeDB.  If you
have trouble figuring out what I wrote let me know.  I have compared B73,
W23, W22, and Mo17 to each other in adjacent lanes on the same gels.  I
have also compared W22 to W64A on separate gels, so in the table I have
also included how W64A relates to W22.  I should also mention that I have
only had a chance to check each of these markers once and have not gone
back to double check them.
Good luck,
Matt

------------------------------------------------------------------------

Polymorphisms of SSR's detectable on 4% metaphor agarose

known polymorphisms of 3nt or less between B73 and Mo17 were difficult or
impossible to detect and for these it was hard to tell which one W22 and
W23 were like;

 if W22 or W23 was the same as Mo17 or B73 it is listed in the column; if
they were different from both the relative size (greater or less than) is
mentioned

"for multiple bands L=lower, M=middle, U=upper"

SSR	map position	amplification	B73	W22	W64A	W23
	Mo17
	consensus 1998	w/touchdown

phi056	1;  9	good		mo17	w22	mo17	>b73
bnlg109	1;  34	high		mo17		mo17	>b73
phi001	1;  61	faint		<mo17	<w22	>b73	<b73
phi095	1;  64	none
bnlg182	1;  65	fair	2bands	2 bands	2 bands	1 band	1 band
				U=b73L	U>w22U	">mo17,<b73L"	<b73 L

				"L>w23, <b73L"	L=w22U

bnlg421	1;  96	faint	1 band	2 bands		1 band	2 bands
				L=w23		<b73	both>b73

				U=mo17L
phi055	1;  130	faint		b73?	w22	b73?	3nt<b73
bnlg100	1;  135	faint		2 bands		>b73	<b73?
				u=mo17
				L<mo17
bnlg504	1;  162	good		w23	w22	<b73
phi064	1;  169	faint		mo17	<w22	b73	<b73
	1;  177

bnlg1092	2; 13	faint		mo17	>w22	">b73,>mo17"
	>b73?
phi098	2;  25	faint		b73	w22	b73	b73
bnlg1017	2; 26	high		"<b73,<mo17"	>w22	"<b73,<w22"
	b73
bnlg125	2;  47	high			>w22	">b73, >mo17"	<b73
(close)
bnlg1537	2; 55	high		>b73	>w22	b73	<b73

phi083	2;  73	faint		b73		b73	b73
bnlg108	2;  79	good		">mo17, <w23"	<w22	">b73,w22,mo17"
	>b73
dupssr24	2;  111	faint		<mo17		>b73	<b73

bnlg1520	2; 128	high			>w22

	2; 160

bnlg1523	3; 27	high			w22

bnlg1325	3; 36	high		w23	w22	">b73,<mo17"
	">b73,>w23"
phi029	3;  40	good		b73	w22	b73	b73
bnlg602	3;  47	high		2 bands		2 bands	1 band
				u=w23L		both>b73	<b73?

				L=mo17
bnlg420	3;  56	high		b73	w22	mo17	>b73
phi073	3;  59	good		b73	>w22	b73	b73
bnlg1117	3; 59

bnlg2241	3; 60

bnlg1904	3; 62	high		>b73		<b73	b73

dupssr23	3;  64	fair		mo17		"<b73,>mo17"
	<b73
bnlg1601	3; 67	high	2 bands	2 bands		2 bands	2 bands

				w23		L=b73U	L<b73
						U>b73
bnlg1798	3; 75	fair		mo17	>w22	">b73,<mo17"
	">b73,>w23"
bnlg1047A	3; 76	fair		mo17	>w22	>mo17	>b73

bnlg1063A	3; 77	good		<b73		>b73	b73

bnlg1350	3; 78	good		b73		b73	>b73

bnlg1449	3; 79	good		">b73,>mo17,<w23"	>w22
	">b73,w22,mo17"	b73
bnlg197	3;  90	good		b73		mo17	<b73
bnlg1496	3; 113	high		b73	>w22	">b73,<mo17"
	">b73,>w23"
	3;  134

phi072	4;  16	good		b73	w22	b73	b73
bnlg372	4;  18				w22	b73
phi021	4;  44	good	1 band	2 bands	<w22	1 band	1 band
				L<mo17		mo17	<b73
				U>b73
phi074	4;  58	good		b73		>b73	b73
phi096	4;  61	fair		b73	>w22	b73	2 bands
							U>b73
							L=b73
nc005	4;  63	high		>mo17		mo17	>b73
bnlg490	4;  65	good		b73		mo17	>b73
dupssr28	4;  103	none

phi093	4;  109	high	all similar		w22

phi006	4;  142	fair to poor		">b73,<mo17"	w22

bnlg589	4;  153	high		b73	<w22	mo17	<b73
	4;  155

bnlg1006	5; 8	high		>b73		b73	<b73

phi024	5;  22	fair		b73		">b73,<mo17"	>b73

bnlg565	5;  44	fair		b73	<w22	"<b73,>mo17"	<b73

phi008	5;  50	faint	2 bands	1 band		2 bands	2 bands
				b73L		mo17	L=b73U
							U>b73
phi113	5;  57	fair		>b73	<w22	>w22	b73
bnlg1208	5; 70	good		b73		mo17	<b73

dupssr10	5;  73	good		"<b73, (>mo17?)"	>w22
	>b73	<b73
bnlg609	5; 92	fair					<b73
bnlg278	5;  95	good		<b73	>w22	b73	b73
phi085	5;  117	good		mo17		mo17	>b73
bnlg118	5;  128	fair		">b73,<mo17"	<w22	b73	">b73,>w22"

bnlg389	5; 146	faint		>mo17	<w22	">b73,<mo17"	>b73

	5;  146

phi077	6;  9	high		w23	<w22	„b73	<b73
bnlg238	6;  24	high		<mo17		>b73	<b73
phi075	6;  25	good to poor		<b73		(<b73?)	b73

nc010	6;  41	faint		b73	<w22	mo17	<b73
phi078	6;  58	fair		b73	>w22(close)	b73	>b73

bnlg345	6;  73	good		b73	w22	b73	>b73
phi070	6;  88	faint		mo17			>b73
dupssr15	6;  108	good	3 bands	3 bands		3 bands	3 bands

				U>mo17U		U=b73U	U>b73U
				M=b73U		M>b73M	M=b73M
				L<mo17L		L>b73L	L<b73L
	6;  113

bnlg2132	7; 13	good		b73	w22	>mo17	>b73

phi057	7;  36	good		b73	w22	b73	>b73(close)

dupssr9	7;  54	fair		w23	<w22	"<b73, >mo17"	"<b73,<w23"

bnlg339	7; 63	fair		mo17	>w22	<mo17	<b73(close)

bnlg1892	7; 78	faint		mo17	<w22	b73	>b73

bnlg2259	7; 83	good		mo17	w22	>mo17	>b73

dupssr13	7;  88	fair		w23	>w22(close)
	">b73,<mo17"	">b73,>w23"
phi082	7;  108	fair		b73	>w22	b73	b73
	7;  121

bnlg1073	8; 9	multiple bands	2 bands	1 band=mo17L		3
bands	2 bands
						U=mo17L	both>b73

						M>b73U
						"L<b73U,>b73L"

dupssr3	8;  25	fair		b73		b73	b73
phi115	8;  25	good		w23		<b73	b73
phi014	8;  30	good		b73	(>w22?(close))	mo17	>b73

bnlg240	8;  56	fair		b73	w22	b73	b73 (4nt<b73)

bnlg1828	8; 77	fair		b73	<w22	<b73	b73

dupssr14	8;  85	good		<mo17	>w22	b73	<b73

phi015	8; 100	good to poor		mo17	w22	(¾mo17)	<b73

	8;  101

bnlg2122	9; 11	good		<mo17	>w22	mo17	<b73

phi017	9;  17	faint		b73	b73	b73	b73
phi044	9;  22	good		b73	w22	b73	<b73(close)

dupssr6	9;  26	fair		w23	>w22	"<b73,<mo17"	b73

phi061	9;  42	good		b73	w22	mo17	>b73
bnlg127	9;  46	good		b73		>b73	b73 (2nt>b73)

phi065	9;  46	good		<b73	>w22	b73	b73(5nt<b73)

bnlg469a	9; 53	good		mo17	w22	<mo17	<b73(close)

phi016	9;  54	good		mo17	w22	mo17	<b73(close)

bnlg128	9;  72	good		<b73	>b73	mo17	>b73
bnlg1588	9; 79	good	none	w23	>w22	<mo17

bnlg279	9;  95	faint		<b73	>w22	mo17	>b73
	9;  96

phi041	10; 00	fair		mo17		mo17	<b73(close)

phi059	10; 35	fair		b73	w22	b73	>b73
bnlg210	10; 47	fair		b73	<w22	mo17	<b73
phi071	10; 53	fair		b73	w22	b73	>b73?
bnlg137	10; 62	none
bnlg1677	10; 81	fair to poor				<mo17
	<b73
	10; 94

dupssr28	unknown	faint		mo17		mo17	<b73



>We would be more than pleased to provide on MaizeDB,
>molecular-marker mapping data that specifically involve W22,
>if data are available.  If population data with W22 as one
>parent have been published, I am not aware of the source.
>This is a request for genome-wide data if possible, and for
>any localized mapping data.
>
>The point: For various good reasons, W22 inbred line is
>often used as a source for mutants and clones, or as a
>"standard" line against which mapping is done to localize a
>target.
>
>Actually, more precisely, the inbred line is the
>**Wisconsin-derived W22 R-scm2** in most studies, though
>probably other conversions or derivatives are being used.
>If the W22 parent is 90% or more W22 genome, data should be
>useful.  A number of Cooperators have asked for SSR
>screening data on this inbred, which prompts this net
>request.
>
>Please let me know, or post to the net, what data you may be
>able to provide that involve this line.  Ideally, users need
>the identity of the two parents, any side history on the
>pedigree of the W22 parent, size of the population, map
>scores (and band sizes) for any and all markers, and
>identity of person(s) to whom credit is due.
>
>If any lab has produced a set of RI lines with W22, you can
>rest assured that the community will be interested in that
>resource as well.
>
>You may be aware of possible data sources with colleagues
>who do not subscribe to the net, in which case please pass
>this request on.  Thanks much.
>
>Ed

Matthew Evans
Laboratory of Genetics
445 Henry Mall
University of Wisconsin-Madison
Madison, Wisconsin  53706
(608) 262-3286 (phone)
(608) 262-2976 (fax)



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