Abstract
The gelatinization temperature of rice is an important factor in determining the eating and cooking quality, and it affects consumer preference. The alkali digestion value (ADV) is one of the main methods used to test the quality of rice and has a high correlation with the gelatinization temperature. For the development of high-quality rice, it is important to understand the genetic basis of palatability-related traits, and QTL analysis is a statistical method linking phenotypic data and genotype data and is an effective method to explain the genetic basis of variation in complex traits. QTL map** related to the ADV of brown and milled rice was performed using the 120 Cheongcheong/Nagdong double haploid (CNDH) line. As a result, 12 QTLs related to ADV were detected, and 20 candidate genes were selected from the RM588–RM1163 region of chromosome 6 through screening by gene function analysis. The comparison of the relative expression level of candidate genes showed that OsSS1q6 is highly expressed in CNDH lines with high ADV in both brown rice and milled rice. In addition, OsSS1q6 has high homology with the starch synthase 1 protein and interacts with various starch biosynthesis-related proteins, such as GBSSII, SBE, and APL. Therefore, we suggest that OsSS1q6 identified through QTL map** could be one of the various genes involved in the gelatinization temperature of rice by regulating starch biosynthesis. This study can be used as basic data for breeding high-quality rice and provides a new genetic resource that can increase the palatability of rice.
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References
Arikit S, Wanchana S, Khanthong S, Saensuk C, Thianthavon T, Vanavichit A, Too**da T (2019) QTL-seq identifies cooked grain elongation QTLs near soluble starch synthase and starch branching enzymes in rice (Oryza sativa L.). Sci Rep 9(1):8328. https://doi.org/10.1038/s41598-019-44856-2
Balindong JL, Ward RM, Liu L, Rose TJ, Pallas LA, Ovenden BW, Snell PJ, Waters DLE (2018) Rice grain protein composition influences instrumental measures of rice cooking and eating quality. J Cereal Sci 79:35–42. https://doi.org/10.1016/j.jcs.2017.09.008
Bao J-S, Corke H, ** HE, Li-Huang ZHU (2003) Analysis of quantitative trait loci for starch properties of rice based on an RIL population. J Integr Plant Biol 45(8):986. https://doi.org/10.1016/j.jcs.2004.01.004
Chemutai LR, Musyoki MA, Kioko WF, Mwenda NS, Muriira KG, Piero NM (2016) Genetic diversity studies on selected rice (Oryza sativa L.) genotypes based on gel consistency and alkali digestion. J Rice Res 4(3):1–6. https://doi.org/10.4172/2375-4338.1000172
Chen Y, Wang M, Ouwerkerk PBF (2012) Molecular and environmental factors determining grain quality in rice. Food Energy Secur 1(2):111–132. https://doi.org/10.1002/fes3.11
Chung H-J, Liu Q, Lee L, Wei D (2011) Relationship between the structure, physicochemical properties and in vitro digestibility of rice starches with different amylose contents. Food Hydrocoll 25(5):968–975. https://doi.org/10.1016/j.foodhyd.2010.09.011
Crevillén P, Ballicora MA, Mérida Á, Preiss J, Romero JM (2003) The different large subunit isoforms of Arabidopsis thaliana ADP-glucose pyrophosphorylase confer distinct kinetic and regulatory properties to the heterotetrameric enzyme. J Biol Chem 278(31):28508–28515. https://doi.org/10.1074/jbc.M304280200
Cui W, Cheng JJ (2015) Growing duckweed for biofuel production: a review. Plant Biol 17(s1):16–23. https://doi.org/10.1111/plb.12216
Delwiche SR (1996) Quality characteristics in rice by near-infrared reflectance analysis of whole-grain milled samples. Cereal Chem 73(2):257–263
Fan CC, Yu XQ, **ng YZ, Xu CG, Luo LJ, Zhang Q (2005) The main effects, epistatic effects and environmental interactions of QTLs on the cooking and eating quality of rice in a doubled-haploid line population. Theor Appl Genet 110(8):1445–1452. https://doi.org/10.1007/s00122-005-1975-y
Fredriksson H, Silverio J, Andersson R, Eliasson AC, Åman P (1998) The influence of amylose and amylopectin characteristics on gelatinization and retrogradation properties of different starches. Carbohydr Polym 35(3-4):119–134. https://doi.org/10.1016/S0144-8617(97)00247-6
Fujita N, Yoshida M, Asakura N, Ohdan T, Miyao A, Hirochika H, Nakamura Y (2006) Function and characterization of starch synthase I using mutants in rice. Plant Physiol 140(3):1070–1084. https://doi.org/10.1104/pp.105.071845
Gao Z, Zeng D, Cui X, Zhou Y, Yan M, Huang D, Li J, Qian Q (2003) Map-based cloning of the ALK gene, which controls the gelatinization temperature of rice. Sci China C Life Sci 46(6):661–668. https://doi.org/10.1360/03yc0099
Ge XJ, **ng YZ, Xu CG, He YQ (2005) QTL analysis of cooked rice grain elongation, volume expansion, and water absorption using a recombinant inbred population. Plant Breed 124(2):121–126. https://doi.org/10.1111/j.1439-0523.2004.01055.x
Griebel S, Webb MM, Campanella OH, Craig BA, Weil CF, Tuinstra MR (2019) The alkali spreading phenotype in Sorghum bicolor and its relationship to starch gelatinization. J Cereal Sci 86:41–47. https://doi.org/10.1016/j.jcs.2019.01.002
Hasjim J, Li E, Dhital S (2013) Milling of rice grains: effects of starch/flour structures on gelatinization and pasting properties. Carbohydr Polym 92(1):682–690. https://doi.org/10.1016/j.carbpol.2012.09.023
Hirose T, Terao T (2004) A comprehensive expression analysis of the starch synthase gene family in rice (Oryza sativa L.). Planta 220(1):9–16. https://doi.org/10.1007/s00425-004-1314-6
Igarashi H, Ito H, Shimada T, Kang D-J, Hamada S (2021) A novel rice dull gene, LowAC1, encodes an RNA recognition motif protein affecting Waxyb pre-mRNA splicing. Plant Physiol Biochem 162:100–109. https://doi.org/10.1016/j.plaphy.2021.02.035
James MG, Denyer K, Myers AM (2003) Starch synthesis in the cereal endosperm. Curr Opin Plant Biol 6(3):215–222. https://doi.org/10.1016/S1369-5266(03)00042-6
Juliano BO, Bautista GM, Lugay JC, Reyes AC (1964) Rice quality, studies on physicochemical properties of rice. J Agric Food Chem 12(2):131–138
Kim H, Imatong RVB, Tai TH (2020) Identification of rice mutants with altered grain alkali digestion trait. Plant Breed Biotechnol 8(1):19–27. https://doi.org/10.9787/PBB.2020.8.1.19
Li C, Gong B (2020) Insights into chain-length distributions of amylopectin and amylose molecules on the gelatinization property of rice starches. Int J Biol Macromol 155:721–729. https://doi.org/10.1016/j.ijbiomac.2020.04.006
Li Y, Li Y, Chen Z, Bu L, Shi F, Huang J (2021) High-temperature air fluidization improves cooking and eating quality and storage stability of brown rice. Innov Food Sci Emerg Technol 67:102536. https://doi.org/10.1016/j.ifset.2020.102536
Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2−ΔΔCT method. Methods 25(4):402–408. https://doi.org/10.1006/meth.2001.1262
Maddelein ML, Libessart N, Bellanger F, Delrue B, D'Hulst C, Van den Koornhuyse N, Fontaine T, Wieruszeski JM, Decq A, Ball S (1994) Toward an understanding of the biogenesis of the starch granule. Determination of granule-bound and soluble starch synthase functions in amylopectin synthesis. J Biol Chem 269(40):25150–25157. https://doi.org/10.1016/S0021-9258(17)31510-7
Mahanta CL, Bhattacharya KR (2010) Relationship of starch changes to puffing expansion of parboiled rice. J Food Sci Technol 47(2):182–187. https://doi.org/10.1007/s13197-010-0038-9
Mariotti M, Fongaro L, Catenacci F (2010) Alkali spreading value and image analysis. J Cereal Sci 52(2):227–235. https://doi.org/10.1016/j.jcs.2010.05.011
Maung TZ, Chu S-H, Park Y-J (2021) Functional haplotypes and evolutionary insight into the granule-bound starch synthase II (GBSSII) gene in Korean rice accessions (KRICE_CORE). Foods 10(10):2359. https://doi.org/10.3390/foods10102359
McCouch SR (2008) Gene nomenclature system for rice Rice 1(1):72–84. https://doi.org/10.1007/s12284-008-9004-9
Muroyama R, Ito H, Takahashi S, Kang D-J, Hamada S (2022) Biochemical analysis of a novel allele of the OsPPDKB gene associated with floury endosperm. J Cereal Sci 107:103529. https://doi.org/10.1016/j.jcs.2022.103529
Ohishi K, Kasai M, Shimada A, Hatae K (2007) Effects of acetic acid on the rice gelatinization and pasting properties of rice starch during cooking. Int Food Res J 40(2):224–231. https://doi.org/10.1016/j.foodres.2006.10.005
Parker R, Ring SG (2001) Aspects of the physical chemistry of starch. J Cereal Sci 34(1):1–17. https://doi.org/10.1006/jcrs.2000.0402
Punia Bangar S, Ashogbon AO, Singh A, Chaudhary V, Whiteside WS (2022) Enzymatic modification of starch: a green approach for starch applications. Carbohydr Polym 287:119265. https://doi.org/10.1016/j.carbpol.2022.119265
Rayee R, Xuan TD, Khanh TD, Tran H-D, Kakar K (2021) Efficacy of irrigation interval after anthesis on grain quality, alkali digestion, and gel consistency of rice. Agriculture 11(4):325. https://doi.org/10.3390/agriculture11040325
Sultana S, Faruque M, Islam MR (2022) Rice grain quality parameters and determination tools: a review on the current developments and future prospects. Int J Food Prop 25(1):1063–1078. https://doi.org/10.1080/10942912.2022.2071295
Takemoto-Kuno Y, Suzuki K, Nakamura S, Satoh H, Ohtsubo K (2006) Soluble starch synthase I effects differences in amylopectin structure between indica and japonica rice varieties. J Agric Food Chem 54(24):9234–9240. https://doi.org/10.1021/jf061200i
Tian R, Jiang G-H, Shen L-H, Wang L-Q, He Y-Q (2005) Map** quantitative trait loci underlying the cooking and eating quality of rice using a DH population. Mol Breed 15(2):117–124. https://doi.org/10.1007/s11032-004-3270-z
Ubwa S, Abah J, Asemave K, Shambe T (2012) Studies on the gelatinization temperature of some cereal starches. Int J Chem 4(6):22. https://doi.org/10.5539/ijc.v4n6p22
Umemoto T, Horibata T, Aoki N, Hiratsuka M, Yano M, Inouchi N (2008) Effects of variations in starch synthase on starch properties and eating quality of rice. Plant Prod Sci 11(4):472–480. https://doi.org/10.1626/pps.11.472
Unnevehr LJ (1986) Consumer demand for rice grain quality and returns to research for quality improvement in Southeast Asia. Am J Agric Econ 68(3):634–641. https://doi.org/10.2307/1241547
Varavinit S, Shobsngob S, Varanyanond W, Chinachoti P, Naivikul O (2003) Effect of amylose content on gelatinization, retrogradation and pasting properties of flours from different cultivars of Thai rice. Starke 55(9):410–415. https://doi.org/10.1002/star.200300185
Waters DLE, Henry RJ, Reinke RF, Fitzgerald MA (2006) Gelatinization temperature of rice explained by polymorphisms in starch synthase. Plant Biotechnol J 4(1):115–122. https://doi.org/10.1111/j.1467-7652.2005.00162.x
Yuan T, Huang W, Lei Z, Zhao Z, Zhang Z (2017) Effects of different alkalis on hydrolysis of swine manure during dry anaerobic digestion and resultant nutrients availability. Int Biodeter Biodegr 123:138–145. https://doi.org/10.1016/j.ibiod.2017.06.016
Zhang X, Wang L, Cheng M, Wang R, Luo X, Li Y, Chen Z (2015) Influence of ultrasonic enzyme treatment on the cooking and eating quality of brown rice. J Cereal Sci 63:140–146. https://doi.org/10.1016/j.jcs.2015.03.002
Zhang C, Hao W, Lu Y, Yang Y, Chen Z, Li Q, Fan X, Luo J, Liu Q (2022) A comparative evaluation of the effect of SSI and Wx allelic variation on rice grain quality and starch physicochemical properties. Food Chem 371:131205. https://doi.org/10.1016/j.foodchem.2021.131205
Zhao W-G, Chung J-W, Kwon S-W, Lee J-H, Ma K-H, Park Y-J (2013) Association analysis of physicochemical traits on eating quality in rice (Oryza sativa L.). Euphytica 191(1):9–21. https://doi.org/10.1007/s10681-012-0820-z
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This work was supported by a grant from the Low-Carbon Green Rice Production Technology Development Program (Project No. PJ01700602), Rural Development Administration, Republic of Korea.
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Y. -H. J., J. -R. P., and E. -G. K. conceptualized and wrote the manuscript. M. F. and D. D. Z. performed the experiments and collected the data. R. J., S. A., and K. -M. K revised the manuscript. K. -M. K. supervised this study. All authors read and approved the final manuscript.
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Jang, YH., Park, JR., Kim, EG. et al. Efficient identification of palatability-related genes using QTL map** in rice breeding. Mol Breeding 43, 39 (2023). https://doi.org/10.1007/s11032-023-01392-2
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DOI: https://doi.org/10.1007/s11032-023-01392-2