The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean

Jeffry L. Shultz, Samreen Kazi, Rabia Bashir, Jawaad A. Afzal, David A. Lightfoot

Research output: Contribution to journalArticle

Abstract

The composite map of soybean shared among Soybase, LIS and SoyGD (March 2006) contained 3,073 DNA markers in the "Locus" class. Among the markers were 1,019 class I microsatellite markers with 2-3 bp simple sequence repeats (SSRs) of >10 iterations (BARC-SSR markers). However, there were few class II SSRs (2-5 bp repeats with <10 iterations; mostly SIUC-Satt markers). The aims here were to increase the number of classes I and II SSR markers and to integrate bacterial artificial chromosome (BAC) clones onto the soybean physical map using the markers. Used was 10 Mb of BAC-end sequence (BES) derived from 13,473 reads from 7,050 clones constituting minimum tile path 2 of the soybean physical map ( http://www.soybeangenome.siu.edu ; SoyGD). Identified were 1,053 1-6 bp motif, repeat sequences, 333 from class I (>10 repeats) and 720 from class II (<10 repeats). Potential markers were shown on the MTP_SSR track at Gbrowse. Primers were designed as 20-24 bp oligomers that had Tm of 55 ± 1 C that would generate 100-500 bp amplicons. About 853 useful primer pairs were established. Motifs were not randomly distributed with biases toward AT rich motifs. Strong biases against the GC motif and all tetra-nucleotide repeats were found. The markers discovered were useful. Among the first 135 targeted for use in genetic map improvement about 60% of class II markers and 75% of class I markers were polymorphic among on the parents of four recombinant inbred line (RIL) populations. Many of the BES-based SSRs were located on the soybean genetic map in regions with few BARC-SSR markers. Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited.

Original languageEnglish (US)
Pages (from-to)1081-1090
Number of pages10
JournalTheoretical and Applied Genetics
Volume114
Issue number6
DOIs
StatePublished - Apr 1 2007

Fingerprint

Soybeans
Microsatellite Repeats
microsatellite repeats
soybeans
Genetic Markers
Population
inbred lines
Nucleotides
loci
genetic markers

Keywords

  • Legume
  • Microsatellite
  • Motif
  • Physical map
  • Repeat
  • Soybean

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Genetics

Cite this

The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. / Shultz, Jeffry L.; Kazi, Samreen; Bashir, Rabia; Afzal, Jawaad A.; Lightfoot, David A.

In: Theoretical and Applied Genetics, Vol. 114, No. 6, 01.04.2007, p. 1081-1090.

Research output: Contribution to journalArticle

Shultz, Jeffry L. ; Kazi, Samreen ; Bashir, Rabia ; Afzal, Jawaad A. ; Lightfoot, David A. / The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean. In: Theoretical and Applied Genetics. 2007 ; Vol. 114, No. 6. pp. 1081-1090.
@article{1ab493cbf71247bb852a75dbb3aa8745,
title = "The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean",
abstract = "The composite map of soybean shared among Soybase, LIS and SoyGD (March 2006) contained 3,073 DNA markers in the {"}Locus{"} class. Among the markers were 1,019 class I microsatellite markers with 2-3 bp simple sequence repeats (SSRs) of >10 iterations (BARC-SSR markers). However, there were few class II SSRs (2-5 bp repeats with <10 iterations; mostly SIUC-Satt markers). The aims here were to increase the number of classes I and II SSR markers and to integrate bacterial artificial chromosome (BAC) clones onto the soybean physical map using the markers. Used was 10 Mb of BAC-end sequence (BES) derived from 13,473 reads from 7,050 clones constituting minimum tile path 2 of the soybean physical map ( http://www.soybeangenome.siu.edu ; SoyGD). Identified were 1,053 1-6 bp motif, repeat sequences, 333 from class I (>10 repeats) and 720 from class II (<10 repeats). Potential markers were shown on the MTP_SSR track at Gbrowse. Primers were designed as 20-24 bp oligomers that had Tm of 55 ± 1 C that would generate 100-500 bp amplicons. About 853 useful primer pairs were established. Motifs were not randomly distributed with biases toward AT rich motifs. Strong biases against the GC motif and all tetra-nucleotide repeats were found. The markers discovered were useful. Among the first 135 targeted for use in genetic map improvement about 60{\%} of class II markers and 75{\%} of class I markers were polymorphic among on the parents of four recombinant inbred line (RIL) populations. Many of the BES-based SSRs were located on the soybean genetic map in regions with few BARC-SSR markers. Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited.",
keywords = "Legume, Microsatellite, Motif, Physical map, Repeat, Soybean",
author = "Shultz, {Jeffry L.} and Samreen Kazi and Rabia Bashir and Afzal, {Jawaad A.} and Lightfoot, {David A.}",
year = "2007",
month = "4",
day = "1",
doi = "10.1007/s00122-007-0501-9",
language = "English (US)",
volume = "114",
pages = "1081--1090",
journal = "Theoretical And Applied Genetics",
issn = "0040-5752",
publisher = "Springer Verlag",
number = "6",

}

TY - JOUR

T1 - The development of BAC-end sequence-based microsatellite markers and placement in the physical and genetic maps of soybean

AU - Shultz, Jeffry L.

AU - Kazi, Samreen

AU - Bashir, Rabia

AU - Afzal, Jawaad A.

AU - Lightfoot, David A.

PY - 2007/4/1

Y1 - 2007/4/1

N2 - The composite map of soybean shared among Soybase, LIS and SoyGD (March 2006) contained 3,073 DNA markers in the "Locus" class. Among the markers were 1,019 class I microsatellite markers with 2-3 bp simple sequence repeats (SSRs) of >10 iterations (BARC-SSR markers). However, there were few class II SSRs (2-5 bp repeats with <10 iterations; mostly SIUC-Satt markers). The aims here were to increase the number of classes I and II SSR markers and to integrate bacterial artificial chromosome (BAC) clones onto the soybean physical map using the markers. Used was 10 Mb of BAC-end sequence (BES) derived from 13,473 reads from 7,050 clones constituting minimum tile path 2 of the soybean physical map ( http://www.soybeangenome.siu.edu ; SoyGD). Identified were 1,053 1-6 bp motif, repeat sequences, 333 from class I (>10 repeats) and 720 from class II (<10 repeats). Potential markers were shown on the MTP_SSR track at Gbrowse. Primers were designed as 20-24 bp oligomers that had Tm of 55 ± 1 C that would generate 100-500 bp amplicons. About 853 useful primer pairs were established. Motifs were not randomly distributed with biases toward AT rich motifs. Strong biases against the GC motif and all tetra-nucleotide repeats were found. The markers discovered were useful. Among the first 135 targeted for use in genetic map improvement about 60% of class II markers and 75% of class I markers were polymorphic among on the parents of four recombinant inbred line (RIL) populations. Many of the BES-based SSRs were located on the soybean genetic map in regions with few BARC-SSR markers. Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited.

AB - The composite map of soybean shared among Soybase, LIS and SoyGD (March 2006) contained 3,073 DNA markers in the "Locus" class. Among the markers were 1,019 class I microsatellite markers with 2-3 bp simple sequence repeats (SSRs) of >10 iterations (BARC-SSR markers). However, there were few class II SSRs (2-5 bp repeats with <10 iterations; mostly SIUC-Satt markers). The aims here were to increase the number of classes I and II SSR markers and to integrate bacterial artificial chromosome (BAC) clones onto the soybean physical map using the markers. Used was 10 Mb of BAC-end sequence (BES) derived from 13,473 reads from 7,050 clones constituting minimum tile path 2 of the soybean physical map ( http://www.soybeangenome.siu.edu ; SoyGD). Identified were 1,053 1-6 bp motif, repeat sequences, 333 from class I (>10 repeats) and 720 from class II (<10 repeats). Potential markers were shown on the MTP_SSR track at Gbrowse. Primers were designed as 20-24 bp oligomers that had Tm of 55 ± 1 C that would generate 100-500 bp amplicons. About 853 useful primer pairs were established. Motifs were not randomly distributed with biases toward AT rich motifs. Strong biases against the GC motif and all tetra-nucleotide repeats were found. The markers discovered were useful. Among the first 135 targeted for use in genetic map improvement about 60% of class II markers and 75% of class I markers were polymorphic among on the parents of four recombinant inbred line (RIL) populations. Many of the BES-based SSRs were located on the soybean genetic map in regions with few BARC-SSR markers. Therefore, BES-based SSRs represent useful tools for genetic map development in soybean. New members of a consortium to map the markers in additional populations are invited.

KW - Legume

KW - Microsatellite

KW - Motif

KW - Physical map

KW - Repeat

KW - Soybean

UR - http://www.scopus.com/inward/record.url?scp=34047140358&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=34047140358&partnerID=8YFLogxK

U2 - 10.1007/s00122-007-0501-9

DO - 10.1007/s00122-007-0501-9

M3 - Article

C2 - 17287974

AN - SCOPUS:34047140358

VL - 114

SP - 1081

EP - 1090

JO - Theoretical And Applied Genetics

JF - Theoretical And Applied Genetics

SN - 0040-5752

IS - 6

ER -