Abstract
Simple sequence repeat (SSR) markers provide a powerful tool for genetic linkage map construction that can be applied for identification of quantitative trait loci (QTL). In this study, a total of 640 new SSR markers were developed from an enriched genomic DNA library of the cassava variety ‘Huay Bong 60’ and 1,500 novel expressed sequence tag-simple sequence repeat (EST-SSR) loci were developed from the Genbank database. To construct a genetic linkage map of cassava, a 100 F1 line map** population was developed from the cross Huay Bong 60 by ‘Hanatee’. Polymorphism screening between the parental lines revealed that 199 SSRs and 168 EST-SSRs were identified as novel polymorphic markers. Combining with previously developed SSRs, we report a linkage map consisted of 510 markers encompassing 1,420.3 cM, distributed on 23 linkage groups with a mean distance between markers of 4.54 cM. Comparison analysis of the SSR order on the cassava linkage map and the cassava genome sequences allowed us to locate 284 scaffolds on the genetic map. Although the number of linkage groups reported here revealed that this F1 genetic linkage map is not yet a saturated map, it encompassed around 88% of the cassava genome indicating that the map was almost complete. Therefore, sufficient markers now exist to encompass most of the genomes and efficiently map traits in cassava.
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Acknowledgments
This research was supported by National Center for Genetic Engineering and Biotechnology (Thailand), Commission on Higher Education, Ministry of Education (Thailand), the Thailand Research Fund and Mahidol University. Supajit Sraphet and Athipong Boonchanawiwat were supported from Thailand Graduate Institute of Science and Technology (TGIST) for PhD and MS studies, respectively. The cassava genome sequence was downloaded from “Cassava Genome Project 2009 http://www.phytozome.net/cassava”.
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Communicated by A. Bervillé.
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Sraphet, S., Boonchanawiwat, A., Thanyasiriwat, T. et al. SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz). Theor Appl Genet 122, 1161–1170 (2011). https://doi.org/10.1007/s00122-010-1520-5
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DOI: https://doi.org/10.1007/s00122-010-1520-5