Original Paper

Theoretical and Applied Genetics

, Volume 114, Issue 6, pp 1091-1103

First online:

A high density barley microsatellite consensus map with 775 SSR loci

  • R. K. VarshneyAffiliated withLeibniz-Institute of Plant Genetics and Crop Plant Research (IPK)Applied Genomics Laboratory, International Crops Research Centre for the Semi-Arid Tropics (ICRISAT) Email author 
  • , T. C. MarcelAffiliated withLaboratory of Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University
  • , L. RamsayAffiliated withGenetics, Scottish Crop Research Institute (SCRI)
  • , J. RussellAffiliated withGenetics, Scottish Crop Research Institute (SCRI)
  • , M. S. RöderAffiliated withLeibniz-Institute of Plant Genetics and Crop Plant Research (IPK)
  • , N. SteinAffiliated withLeibniz-Institute of Plant Genetics and Crop Plant Research (IPK)
  • , R. WaughAffiliated withGenetics, Scottish Crop Research Institute (SCRI)
  • , P. LangridgeAffiliated withAustralian Centre for Plant Functional Genomics (ACPFG), University of Adelaide
  • , R. E. NiksAffiliated withLaboratory of Plant Breeding, Graduate School for Experimental Plant Sciences, Wageningen University
    • , A. GranerAffiliated withLeibniz-Institute of Plant Genetics and Crop Plant Research (IPK)

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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 × Franka’, ‘Steptoe × Morex’, ‘OWBRec × OWBDom’, ‘Lina × Canada Park’, ‘L94 × Vada’ and ‘SusPtrit × 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.