A high density barley microsatellite consensus map with 775 SSR loci

Varshney, R K and Marcel, T C and Ramsay, L and Russell, J and Roder, M S and Stein, N and Waugh, R and Langridge, P and Niks, R E and Graner, A (2007) A high density barley microsatellite consensus map with 775 SSR loci. TAG Theoretical and Applied Genetics, 114 (6). pp. 1091-1103. ISSN 1432-2242

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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.

Item Type: Article
Subjects: Others > Genetics and Genomics
Others > Agriculture-Farming, Production, Technology, Economics
Depositing User: Library ICRISAT
Date Deposited: 21 Oct 2011 12:36
Last Modified: 02 Jan 2012 07:49
URI: http://oar.icrisat.org/id/eprint/3000
Official URL: http://dx.doi.org/10.1007/s00122-007-0503-7
Funders: Grain Research and Development Corporation, Goverment of Germany -the Federal Ministry of Education and Research, Dutch Organization for Scientific Research
Acknowledgement: Thanks are due to the Grain Research and Development Corporation (GRDC), Australia (RKV, PL, AG), the Federal Ministry of Education and Research (BMBF), Germany (RKV, NS, MR, AG), the Federal Ministry of Socioeconomic Development and Corporation (RKV, AG), Germany, the Dutch Organization for Scientific Research (NWO), The Netherlands (TCM, REN), and the Scottish Executive and Rural Affairs Department (SEERAD), Scotland (LR, JR, RW) for the financial support.

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