Dissection of gene loci underlying pasting temperature in cassava

References

• Alves, A. A. C. 2002. Cassava botany and physiology. In Cassava: Biology, production and utilization, ed R. J. Hillocks, J. M. Thresh, and A. C. Bellotti. New York: CABI Publishing.
   Google Scholar
• Benbouza, H., J. M. Jacquemin, J. P. Baudoin, and M. Guy. 2006. Optimization of a reliable, fast, cheap and sensitive silver staining method to detect SSR markers in polyacrylamidegels. Biotechnology, Agronomy, Society and Environment 10:77–81.
   Google Scholar
• Cantarel, B. L., P. M. Coutinho, C. Rancurel, T. Bernard, V. Lombard, and B. Henrissat. 2009. The Carbohydrate-Active EnZymes database (CAZy): An expert resource for Glycogenomics. Nucleic Acids Research 37:233–38. doi:10.1093/nar/gkn663.
   PubMed Web of Science ®Google Scholar
• Collard, B. C. Y., M. Z. Z. Jahufer, J. B. Brouwer, and E. C. K. Pang. 2005. An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: The basic concepts. Euphytica 142:169–96. doi:10.1007/s10681-005-1681-5.
   Web of Science ®Google Scholar
• Craig, J., J. R. Lloyd, K. Tomlinson, L. Barber, A. Edwards, T. L. Wang, C. Martin, C. L. Hedley, and A. M. Smith. 1998. Mutations in the gene encoding starch synthase II profoundly alter amylopectin structure in pea embryos. The Plant Cell 10:413–26.
   PubMed Web of Science ®Google Scholar
• Davies, G., and B. Henrissat. 1995. Structures and mechanisms of glycosyl hydrolases. Structure 3:853–59. doi:10.1016/S0969-2126(01)00220-9.
   PubMed Web of Science ®Google Scholar
• Edwards, A., D. C. Fulton, C. M. Hylton, S. A. Jobling, M. Gidley, U. Rössner, C. Martin, and A. M. Smith. 1999. A combined reduction in activity of starch synthases II and III of potato has novel effects on the starch of tubers. The Plant Journal 17:251–61. doi:10.1046/j.1365-313X.1999.00371.x.
   Web of Science ®Google Scholar
• Erlander, S. R. 1998. Starch biosynthesis. 3: The Glycogen precursor mechanism using Phosphorylase in the production of the Precursor Glycogen. Starch/Stärke 50:319–30. doi:10.1002/(ISSN)1521-379X.
   Web of Science ®Google Scholar
• FAO, 2016. Cassava, production quantity (tons) – For all Countries. Accessed March 27, 2017. http://www.factfish.com/statistic/cassava%2C%20production%20quantity).
   Google Scholar
• Franco, O. L., and D. J. Rigden. 2003. Fold recognition analysis of glycosyltransferase families: Further members of structural superfamilies. Glycobiology 13:707–12. doi:10.1093/glycob/cwg098.
   PubMed Web of Science ®Google Scholar
• Fregene, M., F. Angel, R. Gomez, F. Rodriguez, P. Chavarriaga, W. Roca, J. Tohme, and M. Bonierbale. 1997. A molecular genetic map of cassava (Manihot esculenta Crantz). Theoretical and Applied Genetics 95 (3):431–441.
   Web of Science ®Google Scholar
• Fulton, T. M., J. Chunwongse, and S. D. Tanksley. 1995. Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Molecular Biolology Reporter 13 (3):207–09. doi:10.1007/BF02670897.
   Web of Science ®Google Scholar
• Gupta, P. K., H. S. Balyan, R. K. Varshney, and K. S. Gill. 2013. Development and use of molecular markers for crop improvement. Plant Breeding 132:431–32. doi:10.1111/pbr.2013.132.issue-5.
   Web of Science ®Google Scholar
• Gupta, P. K., and R. K. Varshney. 2000. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113:163–85. doi:10.1023/A:1003910819967.
   Web of Science ®Google Scholar
• Hayward, A. C., R. Tollenaere, J. Dalton-Morgan, and J. Batley. 2015. Molecular marker applications in plants. Methods Molecular Biology 1245:13–27.
   PubMedGoogle Scholar
• Kalia, R. K., M. K. Rai, S. Kalia, R. Singh, and A. K. Dhawan. 2011. Microsatellite markers: An overview of the recent progress in plants. Euphytica 177:309–34. doi:10.1007/s10681-010-0286-9.
   Web of Science ®Google Scholar
• Katayama, K., K. Komae, K. Kohyama, T. Kato, S. Tamiya, and K. Komaki. 2002. New sweet potato lines having low gelatinization temperature and altered starch structure. Starch/Stärke 54:51–57. doi:10.1002/1521-379X(200202)54:2<51::AID-STAR51>3.0.CO;2-6.
   Web of Science ®Google Scholar
• Katayama, K., S. Tamiya, T. Kuranouchi, K. Komaki, and M. Nakatani. 2006. New sweetpotato cultivar “quick sweet” having low gelatinization temperature and alterd starch structure. Acta Horticulture 703:55–62. doi:10.17660/ActaHortic.2006.703.5.
   Google Scholar
• Kosambi, D. D. 1943. The estimation estimation of map distance from recombination values. Annals of Eugenics 12:172–75. doi:10.1111/j.1469-1809.1943.tb02321.x.
   Google Scholar
• Larsson, C. T., P. Hofvander, J. Khoshnoodi, B. Ek, L. Rask, and H. Larsson. 1996. Three isoforms of starch synthase and two isoforms of branching enzyme are present in potato tuber starch. Plant Science 117:9–16. doi:10.1016/0168-9452(96)04408-1.
   Web of Science ®Google Scholar
• Lloyd, J. R., V. Landschütze, and J. Kossmann. 1999. Simultaneous antisense inhibition of two starch-synthase isoforms in potato tubers leads to accumulation of grossly modified amylopectin. Biochemical Journal 338:515–21. doi:10.1042/bj3380515.
   PubMed Web of Science ®Google Scholar
• Martins, W. S., D. C. Soares Lucas, K. F. de Souza Neves, and D. J. Bertioli. 2009. WebSat - A web software for microsatellite marker development. Bioinformation 3:282–83. doi:10.6026/97320630003282.
   PubMedGoogle Scholar
• Morell, M. K., B. Kosar-Hashemi, M. Cmiel, M. S. Samuel, P. Chandler, S. Rahman, A. Buleon, I. L. Batey, and Z. Li. 2003. Barley sex6 mutants lack starch synthase IIa activity and contain a starch with novel properties. The Plant Journal 34:173–85. doi:10.1046/j.1365-313X.2003.01712.x.
   PubMed Web of Science ®Google Scholar
• Nakamura, Y., P. B. Francisco Jr, Y. Hosaka, A. Sato, T. Sawada, A. Kubo, and N. Fujita. 2005. Essecential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Molecular Biology 58:213–27. doi:10.1007/s11103-005-6507-2.
   PubMed Web of Science ®Google Scholar
• Ragaee, S., and E. M. Abdel-Aal. 2006. Pasting properties of starch and protein in selected cereals and quality of their food products. Food Chemistry 95:9–18. doi:10.1016/j.foodchem.2004.12.012.
   Web of Science ®Google Scholar
• Satoh, H., K. Shibahara, T. Tokunaga, A. Nishi, M. Tasaki, S. K. Hwang, T. W. Okita, N. Kaneko, N. Fujita, M. Yoshida, Y. Hosaka, A. Sato, Y. Utsumi, T. Ohdan, and Y. Nakamura. 2008. Mutation of the plastidial alpha-glucan phosphorylase gene in rice affects the synthesis and structure of starch in the endosperm. Plant Cell 20:1833–49. doi:10.1105/tpc.107.054007.
   PubMed Web of Science ®Google Scholar
• Schupp, N., and P. Ziegler. 2004. The relation of starch phosphorylases to starch metabolism in wheat. Plant and Cell Physiology 45:1471–84. doi:10.1093/pcp/pch170.
   PubMed Web of Science ®Google Scholar
• Soto, J. C., J. F. Ortiz, L. Perlaza-Jiménez, A. X. Vásquez, L. A. B. Lopez-Lavalle, B. Mathew, J. Léon, A. Ballvora, and C. E. López. 2015. A genetic map of cassava (Manihot esculenta Crantz) with integrated physical mapping of immunity-related genes. BMC Genomics 16:190.
   PubMed Web of Science ®Google Scholar
• Sraphet, S., A. Boonchanawiwat, T. Thanyasiriwat, O. Boonseng, S. Tabata, S. Sasamoto, K. Shirasawa, S. Isobe, D. A. Lightfoot, S. Tangphatsornruang, and K. Triwitayakorn. 2011. SSR and EST-SSR-based genetic linkage map of cassava (Manihot esculenta Crantz). Theoretical and Applied Genetics 122:1161–70. doi:10.1007/s00122-010-1520-5.
   PubMed Web of Science ®Google Scholar
• Takahata, Y., M. Tanaka, M. Otani, K. Katayama, K. Kitahara, O. Nakayachi, H. Nakayama, and M. Yoshinaga. 2010. Inhibition of the expression of the starch synthase II gene leads to lower pasting temperature in sweetpotato starch. Plant Cell Reports 29:535–43. doi:10.1007/s00299-010-0842-8.
   PubMed Web of Science ®Google Scholar
• Thanyasiriwat, T., S. Sraphet, S. Whankaew, O. Boonseng, J. Bao, D. A. Lightfoot, S. Tangphatsornruang, and K. Triwitayakorn. 2014. Quantitative trait loci and candidate genes associated with starch pasting viscosity characteristics in cassava (Manihot esculenta Crantz). Plant Biology (Stuttgart) 16:197–207. doi:10.1111/plb.12022.
   PubMed Web of Science ®Google Scholar
• Umemoto, T., N. Aoki, H. Lin, Y. Nakamura, N. Inouchi, Y. Sato, M. Yano, H. Hirabayashi, and S. Maruyama. 2004. Natural variation in rice starch sybthase IIa affects enzyme and starch properties. Functional Plant Biology 31:671–84. doi:10.1071/FP04009.
   Web of Science ®Google Scholar
• Van Ooijen, J. W., M. P. Boer, R. C. Jansen, and C. Maliepaard. 2002. MapQTL 4.0, software for the calculation of QTL positions on genetic maps. Wageningen, The Netherlands: Plant Research International.
   Google Scholar
• Van Ooijen, J. W., and R. E. Voorrips. 2001. Joinmap 3.0: Software for the calculation of genetic linkage maps. Wageningen, The Netherlands: Plant Research International.
   Google Scholar
• Vuong, T. V., and D. B. Wilson. 2010. Glycoside hydrolases: Catalytic base/nucleophile diversity. Biotechnology and Bioengineering 107:195–205. doi:10.1002/bit.22838.
   PubMed Web of Science ®Google Scholar
• Yang, J., D. An, and P. Zhang. 2011. Expression profiling of cassava storage roots reveals an active process of glycolysis/gluconeogenesis. Journal of Integrative Plant Biology 53:193–211. doi:10.1111/j.1744-7909.2010.01018.x.
   PubMed Web of Science ®Google Scholar
• Yu, Y., H. H. Mu, B. P. Wasserman, and G. M. Carman. 2001. Identification of the maize amyloplast stromal 112-kD protein as a plastidic starch phosphorylase. Plant Physiology 125:351–59. doi:10.1104/pp.125.1.351.
   PubMed Web of Science ®Google Scholar
• Zhang, X., C. Colleoni, V. Ratushna, M. Sirghie-Colleoni, M. James, and A. Myers. 2004. Molecular characterization demonstrates that the Zea mays gene sugary2 codes for the starch synthase isoform SSIIa. Plant Molecular Biology 54:865–79. doi:10.1007/s11103-004-0312-1.
   PubMed Web of Science ®Google Scholar
• Zhuang, Y., and K. L. Adams. 2007. Extensive allelic variation in gene expression in populus F1 hybrids. Genetics 177:1987–96. doi:10.1534/genetics.107.080325.
   PubMed Web of Science ®Google Scholar