Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps

Randy C. Shoemaker, David Grant, Terry Olson, Wesley C. Warren, Rod A Wing, Yeisoo Yu, Hyeran Kim, Perry Cregan, Bindu Joseph, Montona Futrell-Griggs, Will Nelson, Jon Davito, Jason Walker, John Wallis, Colin Kremitski, Debbie Scheer, Sandra W. Clifton, Tina Graves, Henry Nguyen, Xiaolei Wu & 8 others Mingcheng Luo, Jan Dvorak, Rex Nelson, Steven Cannon, Jeff Tomkins, Jeremy Schmutz, Gary Stacey, Scott Jackson

Research output: Contribution to journalArticle

39 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)294-302
Number of pages9
JournalGenome
Volume51
Issue number4
DOIs
StatePublished - Apr 2008

Fingerprint

Soybeans
Microsatellite Repeats
chromosome mapping
microsatellite repeats
soybeans
physical chromosome mapping
Genome
Dinucleotide Repeats
genetic polymorphism
Population
genome
Clone Cells
Glycine max
clones

Keywords

  • Assembly
  • Genome sequence
  • Molecular marker
  • Physical map
  • SSR

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biotechnology
  • Genetics
  • Genetics(clinical)

Cite this

Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. / Shoemaker, Randy C.; Grant, David; Olson, Terry; Warren, Wesley C.; Wing, Rod A; Yu, Yeisoo; Kim, Hyeran; Cregan, Perry; Joseph, Bindu; Futrell-Griggs, Montona; Nelson, Will; Davito, Jon; Walker, Jason; Wallis, John; Kremitski, Colin; Scheer, Debbie; Clifton, Sandra W.; Graves, Tina; Nguyen, Henry; Wu, Xiaolei; Luo, Mingcheng; Dvorak, Jan; Nelson, Rex; Cannon, Steven; Tomkins, Jeff; Schmutz, Jeremy; Stacey, Gary; Jackson, Scott.

In: Genome, Vol. 51, No. 4, 04.2008, p. 294-302.

Research output: Contribution to journalArticle

Shoemaker, RC, Grant, D, Olson, T, Warren, WC, Wing, RA, Yu, Y, Kim, H, Cregan, P, Joseph, B, Futrell-Griggs, M, Nelson, W, Davito, J, Walker, J, Wallis, J, Kremitski, C, Scheer, D, Clifton, SW, Graves, T, Nguyen, H, Wu, X, Luo, M, Dvorak, J, Nelson, R, Cannon, S, Tomkins, J, Schmutz, J, Stacey, G & Jackson, S 2008, 'Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps', Genome, vol. 51, no. 4, pp. 294-302. https://doi.org/10.1139/G08-010
Shoemaker, Randy C. ; Grant, David ; Olson, Terry ; Warren, Wesley C. ; Wing, Rod A ; Yu, Yeisoo ; Kim, Hyeran ; Cregan, Perry ; Joseph, Bindu ; Futrell-Griggs, Montona ; Nelson, Will ; Davito, Jon ; Walker, Jason ; Wallis, John ; Kremitski, Colin ; Scheer, Debbie ; Clifton, Sandra W. ; Graves, Tina ; Nguyen, Henry ; Wu, Xiaolei ; Luo, Mingcheng ; Dvorak, Jan ; Nelson, Rex ; Cannon, Steven ; Tomkins, Jeff ; Schmutz, Jeremy ; Stacey, Gary ; Jackson, Scott. / Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps. In: Genome. 2008 ; Vol. 51, No. 4. pp. 294-302.
@article{ba28fa3453be4cfe937d76570a00c4db,
title = "Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps",
abstract = "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.",
keywords = "Assembly, Genome sequence, Molecular marker, Physical map, SSR",
author = "Shoemaker, {Randy C.} and David Grant and Terry Olson and Warren, {Wesley C.} and Wing, {Rod A} and Yeisoo Yu and Hyeran Kim and Perry Cregan and Bindu Joseph and Montona Futrell-Griggs and Will Nelson and Jon Davito and Jason Walker and John Wallis and Colin Kremitski and Debbie Scheer and Clifton, {Sandra W.} and Tina Graves and Henry Nguyen and Xiaolei Wu and Mingcheng Luo and Jan Dvorak and Rex Nelson and Steven Cannon and Jeff Tomkins and Jeremy Schmutz and Gary Stacey and Scott Jackson",
year = "2008",
month = "4",
doi = "10.1139/G08-010",
language = "English (US)",
volume = "51",
pages = "294--302",
journal = "Genome / National Research Council Canada = Genome / Conseil national de recherches Canada",
issn = "0831-2796",
publisher = "National Research Council of Canada",
number = "4",

}

TY - JOUR

T1 - Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps

AU - Shoemaker, Randy C.

AU - Grant, David

AU - Olson, Terry

AU - Warren, Wesley C.

AU - Wing, Rod A

AU - Yu, Yeisoo

AU - Kim, Hyeran

AU - Cregan, Perry

AU - Joseph, Bindu

AU - Futrell-Griggs, Montona

AU - Nelson, Will

AU - Davito, Jon

AU - Walker, Jason

AU - Wallis, John

AU - Kremitski, Colin

AU - Scheer, Debbie

AU - Clifton, Sandra W.

AU - Graves, Tina

AU - Nguyen, Henry

AU - Wu, Xiaolei

AU - Luo, Mingcheng

AU - Dvorak, Jan

AU - Nelson, Rex

AU - Cannon, Steven

AU - Tomkins, Jeff

AU - Schmutz, Jeremy

AU - Stacey, Gary

AU - Jackson, Scott

PY - 2008/4

Y1 - 2008/4

N2 - 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.

AB - 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.

KW - Assembly

KW - Genome sequence

KW - Molecular marker

KW - Physical map

KW - SSR

UR - http://www.scopus.com/inward/record.url?scp=43549118881&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=43549118881&partnerID=8YFLogxK

U2 - 10.1139/G08-010

DO - 10.1139/G08-010

M3 - Article

VL - 51

SP - 294

EP - 302

JO - Genome / National Research Council Canada = Genome / Conseil national de recherches Canada

JF - Genome / National Research Council Canada = Genome / Conseil national de recherches Canada

SN - 0831-2796

IS - 4

ER -