© CSIRO 2003 10.1071/AR02177 0004-9409/03/111173 www.publish.csiro.au/journals/ajar Australian Journal of Agricultural Research, 2003, 54, 1173–1185 CSIRO PUBLISHING A consensus map of barley integrating SSR, RFLP, and AFLP markers A. Karakousis A , J. P. Gustafson B , K. J. Chalmers A , A. R. Barr A , and P. Langridge A,C,D A Cooperative Research Centre for Plant Molecular Breeding, University of Adelaide, Glen Osmond, SA 5064, Australia. B USDA-ARS, Plant Genetics Research Unit and Plant Science Unit, University of Missouri, Columbia, MO 65211, USA. C Australian Centre for Plant Functional Genomics, University of Adelaide, Glen Osmond, SA 5064, Australia. D Corresponding author; email: peter.langridge@adelaide.edu.au Abstract. A consensus map of barley combining simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) markers has been developed by combining 5 Australian barley linkage maps, Galleon × Haruna Nijo, Chebec × Harrington, Clipper × Sahara, Alexis × Sloop, and Amaji Nijo × WI2585, using the software package JOINMAP 2.0. The new consensus map consists of 700 markers, with 136 being SSRs, and has a total genetic distance of 933 cM. The consensus map order appears to be in good agreement with the Australian barley linkage maps, with the exception of a small inversion located close to the centromere of chromosome 5H. Similarly, the SSR map orders are in good agreement with SSR markers integrated into the doubled haploid linkage map of Lina × Hordeum spontaneum, Canada Park. The new consensus map provides a framework to cross examine and align partial and complete barley linkage maps using markers common to many barley maps. This map will allow researchers to rapidly and accurately select SSR markers for chromosome regions of interest for barley genetic and plant breeding studies. AR0217 A.Karakousis etal. Aconsensus maps of barl ey Additional keywords: linkage map. Introduction Microsatellite markers, also known as simple sequence repeats (SSRs), are known to be very useful for plant breeding and genetic diversity studies for several reasons. They require small amounts of sample DNA, are easy to detect by polymerase chain reaction (PCR), are amenable to high-throughput analysis, co-dominantly inherited, multi-allelic, highly informative, and abundant in plant genomes (Powell et al. 1996). These markers use primers designed from sequences flanking short repeat blocks made of di-, tri-, or tetra-nucleotides. Approximately 700 microsatellite markers have been developed for barley (Hordeum vulgare L.) (Sagahi-Maroof et al. 1994; Becker and Heun 1995; Liu et al. 1996; Struss and Plieske 1998; Pillen et al. 2000; Ramsay et al. 2000) and ~300 have been integrated into several partial and complete linkage maps comprised mainly restriction fragment length polymorphism (RFLP), and amplified fragment length polymorphism (AFLP) markers. Most have been developed by Ramsay et al. (2000) and integrated into a linkage map of the doubled haploid mapping population ‘Lina’ × Hordeum spontaneum, Canada Park, comprised mainly of SSR markers. Fewer numbers of SSRs have also been included into the linkage maps of Steptoe × Morex (22 SSRs) and Igri × Franka (4 SSRs) (Ramsay et al. 2000). More recently, 173 SSR markers were mapped into 5 Australian mapping populations, Galleon × Haruna Nijo (40 SSRs), Chebec × Harrington (39 SSRs), Clipper × Sahara (33 SSRs), Alexis × Sloop (52 SSRs) and Amaji Nijo × WI2585 (9 SSRs), well covered with RFLP and AFLP markers (this issue: Barr et al. 2003a, 2003b; Karakousis et al. 2003a, 2003b; Pallotta et al. 2003) In the past, barley consensus maps based on RFLP markers have been used to assist in the identification of RFLP markers closely linked to traits of interest (Langridge et al. 1995; Qi et al. 1996). A similar strategy has been difficult to achieve with SSR markers due to the difficulty in aligning barley maps integrating SSR markers (http://wheat.usda.gov). The development of a consensus map combining RFLP, AFLP, and SSR markers would provide a framework for the alignment of SSR markers within the barley genome and a rapid and accurate means of locating SSR markers for chromosome segments of interest. In this paper, we develop