A high density barley microsatellite consensus map with 775 SSR loci

R. K. Varshney (Lead / Corresponding author), T. C. Marcel, L. Ramsay, J. Russell, M. S. Röder, N. Stein, R. Waugh, P. Langridge, R. E. Niks, A. Graner

Research output: Contribution to journalArticle

225 Citations (Scopus)

Abstract

A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWB Dom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap® 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.

Original languageEnglish
Pages (from-to)1091-1103
Number of pages13
JournalTheoretical and Applied Genetics
Volume114
Issue number6
DOIs
Publication statusPublished - 1 Apr 2007

Fingerprint

Hordeum
Microsatellite Repeats
barley
microsatellite repeats
loci
Software
DNA Shuffling
Linum
Flax
physical chromosome mapping
Expressed Sequence Tags
Consensus Sequence
plant breeding
linkage groups
Haplotypes
Population
Canada
linkage (genetics)
haplotypes
Chromosomes

Cite this

Varshney, R. K., Marcel, T. C., Ramsay, L., Russell, J., Röder, M. S., Stein, N., ... Graner, A. (2007). A high density barley microsatellite consensus map with 775 SSR loci. Theoretical and Applied Genetics, 114(6), 1091-1103. https://doi.org/10.1007/s00122-007-0503-7
Varshney, R. K. ; Marcel, T. C. ; Ramsay, L. ; Russell, J. ; Röder, M. S. ; Stein, N. ; Waugh, R. ; Langridge, P. ; Niks, R. E. ; Graner, A. / A high density barley microsatellite consensus map with 775 SSR loci. In: Theoretical and Applied Genetics. 2007 ; Vol. 114, No. 6. pp. 1091-1103.
@article{4a0248657a094e798b82f4330683f513,
title = "A high density barley microsatellite consensus map with 775 SSR loci",
abstract = "A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWB Dom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 {"}bridge markers{"} common to two or more individual maps with the help of the computer programme JoinMap{\circledR} 3.0. The final map was calculated by following a {"}neighbours{"} map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.",
author = "Varshney, {R. K.} and Marcel, {T. C.} and L. Ramsay and J. Russell and R{\"o}der, {M. S.} and N. Stein and R. Waugh and P. Langridge and Niks, {R. E.} and A. Graner",
year = "2007",
month = "4",
day = "1",
doi = "10.1007/s00122-007-0503-7",
language = "English",
volume = "114",
pages = "1091--1103",
journal = "Theoretical and Applied Genetics",
issn = "0040-5752",
publisher = "Springer Verlag",
number = "6",

}

Varshney, RK, Marcel, TC, Ramsay, L, Russell, J, Röder, MS, Stein, N, Waugh, R, Langridge, P, Niks, RE & Graner, A 2007, 'A high density barley microsatellite consensus map with 775 SSR loci', Theoretical and Applied Genetics, vol. 114, no. 6, pp. 1091-1103. https://doi.org/10.1007/s00122-007-0503-7

A high density barley microsatellite consensus map with 775 SSR loci. / Varshney, R. K. (Lead / Corresponding author); Marcel, T. C.; Ramsay, L.; Russell, J.; Röder, M. S.; Stein, N.; Waugh, R.; Langridge, P.; Niks, R. E.; Graner, A.

In: Theoretical and Applied Genetics, Vol. 114, No. 6, 01.04.2007, p. 1091-1103.

Research output: Contribution to journalArticle

TY - JOUR

T1 - A high density barley microsatellite consensus map with 775 SSR loci

AU - Varshney, R. K.

AU - Marcel, T. C.

AU - Ramsay, L.

AU - Russell, J.

AU - Röder, M. S.

AU - Stein, N.

AU - Waugh, R.

AU - Langridge, P.

AU - Niks, R. E.

AU - Graner, A.

PY - 2007/4/1

Y1 - 2007/4/1

N2 - A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWB Dom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap® 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.

AB - A microsatellite or simple sequence repeat (SSR) consensus map of barley was constructed by joining six independent genetic maps based on the mapping populations 'Igri x Franka', 'Steptoe x Morex', 'OWBRec x OWB Dom', 'Lina x Canada Park', 'L94 x Vada' and 'SusPtrit x Vada'. Segregation data for microsatellite markers from different research groups including SCRI (Bmac, Bmag, EBmac, EBmag, HVGeneName, scsssr), IPK (GBM, GBMS), WUR (GBM), Virginia Polytechnic Institute (HVM), and MPI for Plant Breeding (HVGeneName), generated in above mapping populations, were used in the computer program RECORD to order the markers of the individual linkage data sets. Subsequently, a framework map was constructed for each chromosome by integrating the 496 "bridge markers" common to two or more individual maps with the help of the computer programme JoinMap® 3.0. The final map was calculated by following a "neighbours" map approach. The integrated map contained 775 unique microsatellite loci, from 688 primer pairs, ranging from 93 (6H) to 132 (2H) and with an average of 111 markers per linkage group. The genomic DNA-derived SSR marker loci had a higher polymorphism information content value (average 0.61) as compared to the EST/gene-derived SSR loci (average 0.48). The consensus map spans 1,068 cM providing an average density of one SSR marker every 1.38 cM. Such a high-density consensus SSR map provides barley molecular breeding programmes with a better choice regarding the quality of markers and a higher probability of polymorphic markers in an important chromosomal interval. This map also offers the possibilities of thorough alignment for the (future) physical map and implementation in haplotype diversity studies of barley.

UR - http://www.scopus.com/inward/record.url?scp=34047186958&partnerID=8YFLogxK

U2 - 10.1007/s00122-007-0503-7

DO - 10.1007/s00122-007-0503-7

M3 - Article

C2 - 17345060

AN - SCOPUS:34047186958

VL - 114

SP - 1091

EP - 1103

JO - Theoretical and Applied Genetics

JF - Theoretical and Applied Genetics

SN - 0040-5752

IS - 6

ER -

Varshney RK, Marcel TC, Ramsay L, Russell J, Röder MS, Stein N et al. A high density barley microsatellite consensus map with 775 SSR loci. Theoretical and Applied Genetics. 2007 Apr 1;114(6):1091-1103. https://doi.org/10.1007/s00122-007-0503-7