70
Views
0
CrossRef citations to date
0
Altmetric
Research Articles

Identification and expression of gene loci underlying the quantitative trait loci of starch content in cassava

, , , , , , & ORCID Icon show all
Pages 368-391 | Received 16 May 2023, Accepted 06 May 2024, Published online: 21 May 2024

References

  • Adhikari, B., J. Shrestha, B. Dhakal, B. Joshi, and N. Bhatta. 2018. “Agronomic Performance and Genotypic Diversity for Morphological Traits Among Early Maize Genotypes.” International Journal of Applied Biology 2 (2): 33–43. https://doi.org/10.20956/ijab.v2i2.5633.
  • Asins, M. J. 2002. “Present and Future of Quantitative Trait Locus Analysis in Plant Breeding.” Plant Breeding 121 (4): 281–291. https://doi.org/10.1046/j.1439-0523.2002.730285.x.
  • Asins, M. J., I. Villalta, M. M. Aly, R. OlíOlíAs, D. E. M. P. Alvarez, R. Huertas, J. Li, et al. 2013. “Two Closely Linked Tomato HKT Coding Genes Are Positional Candidates for the Major Tomato QTL Involved in Na+/K+ Homeostasis.” Plant, Cell & Environment 36 (6): 1171–1191. Epub 2013 Jan 8. https://doi.org/10.1111/pce.12051.
  • Awoleye, F., M. van Duren, J. Dolezel, and F. J. Novak. 1994. “Nuclear DNA Content and in Vitro Induced Somatic Polyploidization Cassava (Manihot esculenta Crantz) Breeding.” Euphytica 76 (3): 195–202. https://doi.org/10.1007/BF00022164.
  • Bainbridge, Z., K. Tomlins, K. Wellings, and A. Westby. 1996. “Methods for Assessing Quality Characteristics of Non-Grain Starch Staples (Part 3 Laboratory Methods).” edited by Z. Bainbridge, K. Tomlins, K. Wellings and A. Westby, Chatham, UK: Natural Resources Institute.
  • Balyejusa Kizito, E., A. C. Rönnberg-Wästljung, T. Egwang, U. Gullberg, M. Fregene, and A. Westerbergh. 2007. “Quantitative Trait Loci Controlling Cyanogenic Glucoside and Dry Matter Content in Cassava (Manihot Esculenta Crantz) Roots.” Hereditas 144 (4): 129–136. https://doi.org/10.1111/j.2007.0018-0661.01975.x.
  • Begna, T., H. Yesuf, M. Abdurezake, and G. Eshetu. 2021. “Genetic Mapping in Crop Plants.” Open Journal of Plant Science 6 (1): 019–026. https://doi.org/10.17352/ojps.000028.
  • Benesi, I. R. M., M. T. Labuschagne, A. G. O. Dixon, and N. M. Mahungu. 2004. “Stability of Native Starch Quality Parameters, Starch Extraction and Root Dry Matter of Cassava Genotypes in Different Environments.” Journal of the Science of Food and Agriculture 84 (11): 1381–1388. https://doi.org/10.1002/jsfa.1734.
  • Boonchanawiwat, A., S. Sraphet, O. Boonseng, D. A. Lightfoot, and K. Triwitayakorn. 2011. “QTL Underlying Plant and First Branch Height in Cassava (Manihot Esculenta Crantz).” Field Crops Research 121 (3): 343–349. https://doi.org/10.1016/j.fcr.2010.12.022.
  • Boonchanawiwat, A., S. Sraphet, S. Whankaew, O. Boonseng, D. R. Smith, and K. Triwitayakorn. 2016. “Mapping of Quantitative Trait Loci Underlying Resistance to Cassava Anthracnose Disease.” The Journal of Agricultural Science 154 (7): 1209–1217. https://doi.org/10.1017/S0021859615001057.
  • Cao, M., L. Zheng, J. Li, Y. Mao, R. Zhang, X. Niu, M. Geng, et al. 2022. “Transcriptomic Profiling Suggests Candidate Molecular Responses to Waterlogging in Cassava.” Public Library of Science ONE 17 (1): e0261086. https://doi.org/10.1371/journal.pone.0261086.
  • Chen, X., Y. Fu, Z. Xia, L. Jie, H. Wang, C. Lu, and W. Wang. 2012. “Analysis of QTL for Yield-Related Traits in Cassava Using an F1 Population from Non-Inbred Parents.” Euphytica 187 (2): 227–234. https://doi.org/10.1007/s10681-012-0662-8.
  • Chen, X., Z. Xia, Y. Fu, C. Lu, and W. Wang. 2010. “Constructing a Genetic Linkage Map Using an F1 Population of Non-Inbred Parents in Cassava (Manihot Esculenta Crantz).” Plant Molecular Biology Reporter 28 (4): 676–683. https://doi.org/10.1007/s11105-010-0198-9.
  • Chipeta, M. M., R. Melis, P. Shanahan, J. Sibiya, and I. R. Benesi. 2017. “Genotype X Environment Interaction and Stability Analysis of Cassava Genotypes at Different Harvest Times.” Journal of Animal and Plant Sciences 27 (3): 901–919.
  • Chipeta, M. M., P. Shanahan, R. Melis, J. Sibiya, and I. R. M. Benesi. 2016. “Farmers’ Knowledge of Cassava Brown Streak Disease and Its Management in Malawi.” International Journal of Pest Management 62 (3): 175–184. https://doi.org/10.1080/09670874.2016.1167268.
  • Collard, B. C., and D. J. Mackill. 2008. “Marker-Assisted Selection: An Approach for Precision Plant Breeding in the Twenty-First Century.” Philosophical Transactions of the Royal Society of London Series B, Biological Sciences 363 (1491): 557–572. https://doi.org/10.1098/rstb.2007.2170.
  • Darvasi, A., A. Weinreb, V. Minke, J. I. Weller, and M. Soller. 1993. “Detecting Marker-QTL Linkage and Estimating QTL Gene Effect and Map Location Using a Saturated Genetic Map.” Genetics 134 (3): 943–951. https://doi.org/10.1093/genetics/134.3.943.
  • deVicente, M. C., and S. D. Tanksley. 1993. “QTL Analysis of Transgressive Segregation in an Interspecific Tomato Cross.” Genetics 134 (2): 585–596. https://doi.org/10.1093/genetics/134.2.585.
  • Doyle, J. J., and J. L. Doyle. 1987. “A Rapid DNA Isolation Procedure for Small Quantities of Fresh Leaf Tissue.” Phytochemical Bulletin 19 (1): 11–15.
  • 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. https://doi.org/10.1007/s001220050580.
  • Goodstein, D. M., S. Shu, R. Howson, R. Neupane, R. D. Hayes, J. Fazo, T. Mitros, et al. 2012. “Phytozome: A Comparative Platform for Green Plant Genomics.” Nucleic Acids Research 40 (D1): D1178–D1186. https://doi.org/10.1093/nar/gkr944.
  • Govindarajan, R., J. Duraiyan, K. Kaliyappan, and M. Palanisamy. 2012. “Microarray and Its Applications.” Journal of Pharmacy & Bioallied Sciences 4 (Suppl 2): S310–312. https://doi.org/10.4103/0975-7406.100283.
  • Gupta, P. K., S. Rustgi, S. Sharma, R. Singh, N. Kumar, and H. S. Balyan. 2003. “Transferable EST-SSR Markers for the Study of Polymorphism and Genetic Diversity in Bread Wheat.” Molecular Genetics & Genomics 270 (4): 315–323. https://doi.org/10.1007/s00438-003-0921-4.
  • Hill, W. G., M. E. Goddard, and P. M. Visscher. 2008. “Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits.” PloS Genetics 4 (2): e1000008. https://doi.org/10.1371/journal.pgen.1000008.
  • Hmwe, N. H., S. Sraphet, N. Srisawad, D. R. Smith, and K. Triwitayakorn. 2022. “Identification of QTL Underlying Plant Height and First Branch Height of Cassava.” Philippine Journal of Science 151 (2): 683–693. https://doi.org/10.56899/151.02.11.
  • José Muñoz, F., M. Teresa Morán Zorzano, N. Alonso-Casajús, E. Baroja-Fernández, E. Etxeberria, and J. Pozueta-Romero. 2006. “New Enzymes, New Pathways and an Alternative View on Starch Biosynthesis in Both Photosynthetic and Heterotrophic Tissues of Plants.” Biocatalysis and Biotransformation 24 (1–2): 63–76. https://doi.org/10.1080/10242420500518839.
  • Koressaar, T., and M. Remm. 2007. “Enhancements and Modifications of Primer Design Program Primer3.” Bioinformatics 23 (10): 1289–1291. https://doi.org/10.1093/bioinformatics/btm091.
  • Kunkeaw, S., T. Yoocha, S. Sraphet, A. Boonchanawiwat, O. Boonseng, D. A. Lightfoot, K. Triwitayakorn, and S. Tangphatsornruang. 2011. “Construction of a Genetic Linkage Map Using Simple Sequence Repeat Markers from Expressed Sequence Tags for Cassava (Manihot Esculenta Crantz).” Molecular Breeding 27 (1): 67–75. https://doi.org/10.1007/s11032-010-9414-4.
  • Lilliefors, H. W. 1967. “On the Kolmogorov-Smirnov Test for Normality with Mean and Variance Unknown.” Journal of the American Statistical Association 62 (318): 399–402. https://doi.org/10.1080/01621459.1967.10482916.
  • Livak, K. J., and T. D. Schmittgen. 2001. “Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2(-Delta Delta C(T)) Method.” Methods 25 (4): 402–408. https://doi.org/10.1006/meth.2001.1262.
  • Li, Y.-Z., J.-Y. Zhao, S.-M. Wu, X.-W. Fan, X.-L. Luo, and B.-S. Chen. 2016. “Characters Related to Higher Starch Accumulation in Cassava Storage Roots.” Scientific Reports 6 (1): 19823. https://doi.org/10.1038/srep19823.
  • Lopez, C., B. Piégu, R. Cooke, M. Delseny, J. Tohme, and V. Verdier. 2005. “Using cDNA and Genomic Sequences As Tools to Develop SNP Strategies in Cassava (Manihot Esculenta Crantz).” Theoretical and Applied Genetics 110 (3): 425–431. https://doi.org/10.1007/s00122-004-1833-3.
  • Lovén, J., D. A. Orlando, A. A. Sigova, C. Y. Lin, P. B. Rahl, C. B. Burge, D. L. Levens, T. I. Lee, and R. A. Young. 2012. “Revisiting Global Gene Expression Analysis.” Cell 151 (3): 476–482. https://doi.org/10.1016/j.cell.2012.10.012.
  • Marmey, P., J. R. Beeching, S. Hamon, and A. Charrier. 1993. “Evaluation of Cassava (Manihot Esculenta Crantz) Germplasm Collections Using RAPD Markers.” Euphytica 74 (3): 203–209. https://doi.org/10.1007/BF00040402.
  • Mba, R. E. C., P. Stephenson, K. Edwards, S. Melzer, J. Nkumbira, U. Gullberg, K. Apel, M. Gale, J. Tohme, and M. Fregene. 2001. “Simple Sequence Repeat (SSR) Markers Survey of the Cassava (Manihot Esculenta Crantz) Genome: Towards an SSR-Based Molecular Genetic Map of Cassava.” Theoretical and Applied Genetics 102 (1): 21–31. https://doi.org/10.1007/s001220051614.
  • Morgante, M., and A. M. Olivieri. 1993. “PCR-Amplified Microsatellites As Markers in Plant Genetics.” The Plant Journal: For Cell and Molecular Biology 3 (1): 175–182. https://doi.org/10.1046/j.1365313X.1993.t01-9-00999.x.
  • Nassar, N. 2000. “Wild Cassava, Manihot Spp.: Biology and Potentialities for Genetic Improvement.” Genetics and Molecular Biology 23 (1): 201–212. https://doi.org/10.1590/S1415-47572000000100035.
  • Obata, T., P. A. W. Klemens, L. Rosado-Souza, A. Schlereth, A. Gisel, L. Stavolone, W. Zierer, et al. 2020. “Metabolic Profiles of Six African Cultivars of Cassava (Manihot Esculenta Crantz) Highlight Bottlenecks of Root Yield.” The Plant Journal: For Cell and Molecular Biology 102 (6): 1202–1219. https://doi.org/10.1111/tpj.14693.
  • Okogbenin, E., J. Marín, and M. Fregene. 2008. “QTL Analysis for Early Yield in a Pseudo F2 Population of Cassava.” African Journal of Biotechnology 7 (2): 131–138.
  • Olsen, K., and B. Schaal. 2001. “Microsatellite Variation in Cassava (Manihot esculenta, Euphorbiaceae) and Its Wild Relatives: Further Evidence for a Southern Amazonian Origin of Domestication.” American Journal of Botany 88 (1): 131–142. https://doi.org/10.2307/2657133.
  • Paterson, A. H., E. S. Lander, J. D. Hewitt, S. Peterson, S. E. Lincoln, and S. D. Tanksley. 1988. “Resolution of Quantitative Traits into Mendelian Factors by Using a Complete Linkage Map of Restriction Fragment Length Polymorphisms.” Nature 335 (6192): 721–726. https://doi.org/10.1038/335721a0.
  • Pluskota, W. E., J. Szablińska, R. L. Obendorf, R. J. Górecki, and L. B. Lahuta. 2015. “Osmotic Stress Induces Genes, Enzymes and Accumulation of Galactinol, Raffinose and Stachyose in Seedlings of Pea (Pisum Sativum L.).” Acta Physiologiae Plantarum 37 (8): 156. https://doi.org/10.1007/s11738-015-1905-9.
  • Pushpalatha, R., and B. Gangadharan. 2020. “Is Cassava (Manihot Esculenta Crantz) a Climate “Smart” Crop? A Review in the Context of Bridging Future Food Demand Gap.” Tropical Plant Biology 13 (3): 201–211. https://doi.org/10.1007/s12042-020-09255-2.
  • Rabbi, I. Y., H. P. Kulembeka, E. Masumba, P. R. Marri, and M. Ferguson. 2012. “An EST-Derived SNP and SSR Genetic Linkage Map of Cassava (Manihot Esculenta Crantz).” Theoretical and Applied Genetics 125 (2): 329–342. https://doi.org/10.1007/s00122-012-1836-4.
  • Singh, B., and A. K. Singh. 2015. “Mapping of Quantitative Trait Loci.” In Marker-Assisted Plant Breeding: Principles and Practices, edited by B. D. Singh and A. K. Singh, 185-216. New Delhi: Springer India.
  • Song, X., Y. Han, W. Teng, G. Sun, and W. Li. 2010. “Identification of QTL Underlying Somatic Embryogenesis Capacity of Immature Embryos in Soybean (Glycine Max (L.) Merr.).” Plant cell reports 29 (2): 125–131. https://doi.org/10.1007/s00299-009-0804-1.
  • Sraphet, S., A. Boonchanawiwat, T. Thanyasiriwat, O. Boonseng, S. Tabata, S. Sasamoto, K. Shirasawa, et al. 2011. “SSR and EST-SSR-based Genetic Linkage Map of Cassava (Manihot Esculenta Crantz).” Theoretical and Applied Genetics 122 (6): 1161–1170. https://doi.org/10.1007/s00122-010-1520-5.
  • Sraphet, S., A. Boonchanawiwat, T. Thanyasiriwat, R. Thaikert, S. Whankaew, D. R. Smith, O. Boonseng, D. A. Lightfoot, and K. Triwitayakorn. 2017. “Quantitative Trait Loci Underlying Root Yield and Starch Content in an F1 Derived Cassava Population (Manihot Esculenta Crantz).” The Journal of Agricultural Science 155 (4): 569–581. https://doi.org/10.1017/S0021859616000678.
  • Sriroth, K., K. Piyachomkwan, S. Wanlapatit, and C. G. Oates. 2000. “Cassava Starch Technology: The Thai Experience.” Starch – Stärke 52 (12): 439–449. https://doi.org/10.1002/1521-379X(200012)52:12<439::AID-STAR439>3.0.CO;2-E.
  • Srisawad, N., S. Sraphet, N. Suksee, R. Boontung, D. R. Smith, and K. Triwitayakorn. 2023. “Use of Diversity Arrays Technology (DArT) for Detection of QTL Underlying Plant Architecture and Yield-Related Traits in Cassava.” Journal of Crop Improvement 37 (1): 99–118. https://doi.org/10.1080/15427528.2022.2058668.
  • Stein, L. 2001. “Genome Annotation: From Sequence to Biology.” Nature Reviews Genetics 2 (7): 493–503. https://doi.org/10.1038/35080529.
  • Tan, Y. F., M. Sun, Y. Z. Xing, J. P. Hua, X. L. Sun, Q. F. Zhang, and H. Corke. 2001. “Mapping Quantitative Trait Loci for Milling Quality, Protein Content and Color Characteristics of Rice Using a Recombinant Inbred Line Population Derived from an Elite Rice Hybrid.” Theoretical and Applied Genetics 103 (6): 1037–1045. https://doi.org/10.1007/s001220100665.
  • Tappiban, P., D. R. Smith, K. Triwitayakorn, and J. Bao. 2019. “Recent Understanding of Starch Biosynthesis in Cassava for Quality Improvement: A Review.” Trends in Food Science & Technology 83:167–180. https://doi.org/10.1016/j.tifs.2018.11.019.
  • Tappiban, P., S. Sraphet, N. Srisawad, D. R. Smith, and K. Triwitayakorn. 2018. “Identification and Expression of Genes in Response to Cassava Bacterial Blight Infection.” Journal of Applied Genetics 59 (4): 391–403. https://doi.org/10.1007/s13353-018-0457-2.
  • 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 16 (1): 197–207. https://doi.org/10.1111/plb.12022.
  • 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.
  • 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.
  • Voorrips, R. E. 2002. “MapChart: Software for the Graphical Presentation of Linkage Maps and QTLs.” The Journal of Heredity 93 (1): 77–78. https://doi.org/10.1093/jhered/93.1.77.
  • Wang, Z., W. Li, J. Qi, P. Shi, and Y. Yin. 2014. “Starch Accumulation, Activities of Key Enzyme and Gene Expression in Starch Synthesis of Wheat Endosperm with Different Starch Contents.” Journal of Food Science and Technology 51 (3): 419–429. https://doi.org/10.1007/s13197-011-0520-z.
  • Whankaew, S., S. Poopear, S. Kanjanawattanawong, S. Tangphatsornruang, O. Boonseng, D. A. Lightfoot, and K. Triwitayakorn. 2011. “A Genome Scan for Quantitative Trait Loci Affecting Cyanogenic Potential of Cassava Root in an Outbred Population.” BMC Genomics 12 (1): 266. https://doi.org/10.1186/1471-2164-12-266.
  • Whankaew, S., S. Sraphet, R. Thaikert, O. Boonseng, D. Smith, and K. Triwitayakorn. 2015. “Validation of a Reference Gene for Transcript Analysis in Cassava (Manihot Esculenta Crantz) and Its Application in Analysis of Linamarase and -Hydroxynitrile Lyase Expression at Different Growth Stages.” African Journal of Biotechnology 14 (9): 745–751. https://doi.org/10.5897/AJB2014.14316.
  • Youn, J. H., and T. W. Kim. 2015. “Functional Insights of Plant GSK3-Like Kinases: Multi-Taskers in Diverse Cellular Signal Transduction Pathways.” Molecular Plant 8 (4): 552–565. https://doi.org/10.1016/j.molp.2014.12.006.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.