Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps.
Whole-genome sequencing of the soybean (Glycine max (L.) Merr. 'Williams 82') has made it important to integrate its physical and genetic maps. To facilitate this integration of maps, we screened 3290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the 'Williams 82' physical map. SSRs were screened against 3 mapping populations. We found the AAT and ACT motifs produced the greatest frequency of length polymorphisms, ranging from 17.2% to 32.3% and from 11.8% to 33.3%, respectively. Other useful motifs include the dinucleotide repeats AG, AT, and AG, with frequency of length polymorphisms ranging from 11.2% to 18.4% (AT), 12.4% to 20.6% (AG), and 11.3% to 16.4% (GT). Repeat lengths less than 16 bp were generally less useful than repeat lengths of 40-60 bp. Two hundred and sixty-five SSRs were genetically mapped in at least one population. Of the 265 mapped SSRs, 60 came from BAC singletons not yet placed into contigs of the physical map. One hundred and ten originated in BACs located in contigs for which no genetic map location was previously known. Ninety-five SSRs came from BACs within contigs for which one or more other BACs had already been mapped. For these fingerprinted contigs (FPC) a high percentage of the mapped markers showed inconsistent map locations. A strategy is introduced by which physical and genetic map inconsistencies can be resolved using the preliminary 4x assembly of the whole genome sequence of soybean.
Shoemaker
Randy C
RC
USDA-ARS-CICGR Unit, Department of Agronomy, Ames, IA 50011-1010, USA. rcsshoe@iastate.edu
Grant
David
D
Olson
Terry
T
Warren
Wesley C
WC
Wing
Rod
R
Yu
Yeisoo
Y
Kim
HyeRan
H
Cregan
Perry
P
Joseph
Bindu
B
Futrell-Griggs
Montona
M
Nelson
Will
W
Davito
Jon
J
Walker
Jason
J
Wallis
John
J
Kremitski
Colin
C
Scheer
Debbie
D
Clifton
Sandra W
SW
Graves
Tina
T
Nguyen
Henry
H
Wu
Xiaolei
X
Luo
Mingcheng
M
Dvorak
Jan
J
Nelson
Rex
R
Cannon
Steven
S
Tomkins
Jeff
J
Schmutz
Jeremy
J
Stacey
Gary
G
Jackson
Scott
S
D002874:Chromosome Mapping / Q000592:standards; D022202:Chromosomes, Artificial, Bacterial / Q000737:chemistry; D023281:Genomics; D018895:Microsatellite Repeats; D020161:Physical Chromosome Mapping / Q000592:standards; D011110:Polymorphism, Genetic; D013025:Glycine max / Q000235:genetics*