Abstract
Rice eating and cooking quality (ECQ) is one of the most important qualities and it has attracted more and more interests of consumers and breeders. SSIIa and Wx are the major genes affecting rice ECQ, and several alleles of SSIIa and Wx have been identified. In this study, the effects of different allele combinations of SSIIa and Wx on rice ECQ were explored by analyzing amylose content (AC), gelatinization temperature (GT), and Rapid Viscosity Analyzer (RVA) profile properties of one natural population which is composed of 30 glutinous rice varieties and 342 non-glutinous varieties. Nine allele combinations of SSIIa and Wx were identified in all the non-glutinous varieties. The allele combination of SSIIac/Wxb harbored higher BDV, lower SBV, intermediate AC, and higher GT, which means better taste quality but more cooking time. For non-glutinous rice, stepwise regression analysis showed that RVA profile properties are mainly controlled by polymorphic loci of Wx-Int1(G/T) and Wx-EX10(C/T); AC, PV, BDV, and SBV are mainly controlled by Wx-Int1(G/T); HPV, CPV, and CSV are mainly controlled by Wx-EX10(C/T); GT is mainly controlled by SSIIa-EX8(GC/TT). Regression equation models also confirmed that SSIIac/Wxb had better ECQ compared to other allele combinations, indicating its potential to improve rice quality. Our results may provide useful clues for elite alleles of SSIIa and Wx for introgression to other rice varieties to improve rice ECQ.
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References
Bao J (2007) Accurate measurement of pasting temperature of rice flour by a rapid visco-analyser. Chin J Rice Sci 21(5):543–546. https://doi.org/10.16819/j.1001-7216.2007.05.017
Bao JS, Zheng XW, Xia YW, He P, Shu QY, Lu X, Chen Y, Zhu LH (2000) Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain. Theor Appl Genet 100:280–284. https://doi.org/10.1007/s001220050037
Bao JS, Corke H, Sun M (2006) Nucleotide diversity in starch synthase IIa and validation of single nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice (Oryza sativa L.). Theor Appl Genet 113(7):1171–1183. https://doi.org/10.1007/s00122-006-0355-6
Bao Jinsong HP, Yingwu X, Ying C, Lihuang Z (1999) Starch RVA profile parameters of rice are mainly controlled by Wx gene. Chin Sci Bull 44:2047–2051. https://doi.org/10.1007/bf02884919
Chen M-H, Bergman CJ, Pinson SRM, Fjellstrom RG (2008) Waxy gene haplotypes: associations with pasting properties in an international rice germplasm collection. J Cereal Sci 48(3):781–788. https://doi.org/10.1016/j.jcs.2008.05.004
Chen Z, Lu Y, Feng L, Hao W, Li C, Yang Y, Fan X, Li Q, Zhang C, Liu Q (2020a) Genetic dissection and functional differentiation of ALK(a) and ALK(b), two natural alleles of the ALK/SSIIa gene, responding to low gelatinization temperature in rice. Rice (N Y) 13(1):39. https://doi.org/10.1186/s12284-020-00393-5
Chen Z, Yang Y, Feng L, Sun Y, Zhang C, Fan X, Li Q, Liu Q (2020b) Effects of different combinations of Wx and ALK main alleles on rice grain quality. Chin J Rice Sci 34:228–236. https://doi.org/10.16819/j.1001-7216.2020.9140
Cozzolino D (2016) The use of the rapid visco analyser (RVA) in breeding and selection of cereals. J Cereal Sci 70:282–290. https://doi.org/10.1016/j.jcs.2016.07.003
Dobo M, Ayres N, Walker G, Park WD (2010) Polymorphism in the GBSS gene affects amylose content in US and European rice germplasm. J Cereal Sci 52(3):450–456. https://doi.org/10.1016/j.jcs.2010.07.010
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
Gao W, Chen S, Wang L, Chen L, Guo T, Wang H, Chen Z (2017) Association analysis of rice cooking quality traits with molecular markers. Sci Agric Sin 50(4):599–611. https://doi.org/10.3864/j.issn.0578-1752.2017.04.001
Hoai TT, Matsusaka H, Toyosawa Y, Suu TD, Satoh H, Kumamaru T (2014) Influence of single-nucleotide polymorphisms in the gene encoding granule-bound starch synthase I on amylose content in Vietnamese rice cultivars. Breed Sci 64(2):142–148. https://doi.org/10.1270/jsbbs.64.142
Hu P, Zhai H, Tang S, Wan J (2004) Rapid evaluation of rice cooking and palatability quality by RVA profile. Acta Agron Sin 30(06):519–524
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
Jia L, Ding X, Wang P, Deng X (2008) Rice RVA profile characteristics and correlation with the physical/chemical quality. Acta Agron Sin 34(05):790–794. https://doi.org/10.3724/SP.J.1006.2008.00790
Kharabian-Masouleh A, Waters DL, Reinke RF, Ward R, Henry RJ (2012) SNP in starch biosynthesis genes associated with nutritional and functional properties of rice. Sci Rep 2:557. https://doi.org/10.1038/srep00557
Lee CM, Park J, Kim B, Seo J, Lee G, Jang S, Koh HJ (2015) Influence of multi-gene allele combinations on grain size of rice and development of a regression equation model to predict grain parameters. Rice (N Y) 8(1):33. https://doi.org/10.1186/s12284-015-0066-1
Mikami I, Uwatoko N, Ikeda Y, Yamaguchi J, Hirano HY, Suzuki Y, Sano Y (2008) Allelic diversification at the wx locus in landraces of Asian rice. Theor Appl Genet 116(7):979–989. https://doi.org/10.1007/s00122-008-0729-z
Miura S, Crofts N, Saito Y, Hosaka Y, Oitome NF, Watanabe T, Kumamaru T, Fujita N (2018) Starch synthase IIa-deficient mutant rice line produces endosperm starch with lower gelatinization temperature than japonica rice cultivars. Front Plant Sci 9:645. https://doi.org/10.3389/fpls.2018.00645
Nakamura Y, Francisco PB, Hosaka Y, Sato A, Sawada T, Kubo A, Fujita N (2005) Essential amino acids of starch synthase IIa differentiate amylopectin structure and starch quality between japonica and indica rice varieties. Plant Mol Biol 58(2):213–227. https://doi.org/10.1007/s11103-005-6507-2
Sano Y (1984) Differential regulation of waxy gene expression in rice endosperm. Theor Appl Genet 68(5):467–473. https://doi.org/10.1007/BF00254822
Shu Q, Wu D, Xia Y, Gao M, McClung A (1998) Relationship between RVA profile character and eating quality in Oryza sativa L. Sci Agric Sin 31:25–29. https://doi.org/10.3321/j.issn:0578-1752.1998.03.005
Teng B, Zeng R, Wang Y, Liu Z, Zhang Z, Zhu H, Ding X, Li W, Zhang G (2011) Detection of allelic variation at the Wx locus with single-segment substitution lines in rice (Oryza sativa L). Mol Breeding 30(1):583–595. https://doi.org/10.1007/s11032-011-9647-x
Tian ZX, Qian Q, Liu QQ, Yan MX, Liu XF, Yan CJ, Liu GF, Gao ZY, Tang SZ, Zeng DL, Wang YH, Yu JM, Gu MH, Li JY (2009) Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106(51):21760–21765. https://doi.org/10.1073/pnas.0912396106
Tran NA, Daygon VD, Resurreccion AP, Cuevas RP, Corpuz HM, Fitzgerald MA (2011) A single nucleotide polymorphism in the waxy gene explains a significant component of gel consistency. Theor Appl Genet 123(4):519–525. https://doi.org/10.1007/s00122-011-1604-x
Wanchana S, Toojinda T, Tragoonrung S, Vanavichit A (2003) Duplicated coding sequence in the waxy allele of tropical glutinous rice (Oryza sativa L.). Plant Sci 165(6):1193–1199. https://doi.org/10.1016/S0168-9452(03)00326-1
Wang Z, Zheng F, Shen G, Gao J, Snustad DP, Li M, Zhang J, Hong M (1995) The amylose content in rice endosperm is related to the post-transcriptional regulation of the waxy gene. Plant J 7:613–622. https://doi.org/10.1046/j.1365-313X.1995.7040613.x
Wang X, Yin L, Shen G, Xu L, Liu Q (2010) Determination of amylose content and its relationship with RVA profile within genetically similar cultivars of rice (Oryza sativa L.ssp.japonica). Agric Sci China 9:1101–1107. https://doi.org/10.1016/S1671-2927(09)60196-6
Waters DL, 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
Xiang X, Kang C, Xu S, Yang B (2017) Combined effects of Wx and SSIIa haplotypes on rice starch physicochemical properties. J Sci Food Agric 97(4):1229–1234. https://doi.org/10.1002/jsfa.7854
Xuan Y, Yi Y, Liang H, Wei S, Chen N, Jiang L, Ali I, Ullah S, Wu X, Cao T, Zhao Q, Li T (2020) Amylose content and RVA profile characteristics of noodle rice under different conditions. Agron J 112(1):117–129. https://doi.org/10.1002/agj2.20079
Yan Y, Zhang L, Wan C, Cao L, Wu S (2016) Correlation analysis between taste value and RVA profile characteristics as well as physical/chemical indicator in rice. Plant Physiol J 52(12):1884–1890. https://doi.org/10.13592/j.cnki.ppj.2016.0289
Yang Y, Ni D, Song F, Li L, Lu X, Li Z, Yang J (2012) Identification of QTLs for rice starch RVA profile properties in different ecological sites. Acta Agron Sin 38(2):264–274. https://doi.org/10.1016/s1875-2780(11)60105-3
You H, Zhang O, Xu L, Liang C, Xiang X (2020) Effects of soluble starch synthase IIa allelic variation on rice grain quality with different waxy backgrounds. J Sci Food Agric 100(15):5344–5351. https://doi.org/10.1002/jsfa.10582
Zhang CQ, Chen SJ, Ren XY, Lu Y, Liu DR, Ca XL, Li QF, Gao JP, Liu QQ (2017) Molecular structure and physicochemical properties of starches from rice with different amylose contents resulting from modification of OsGBSSI activity. J Agric Food Chem 65(10):2222–2232. https://doi.org/10.1021/acs.jafc.6b05448
Zhang CQ, Zhu JH, Chen SJ, Fan XL, Li QF, Lu Y, Wang M, Yu HX, Yi CD, Tang SZ, Gu MH, Liu QQ (2019) Wx(lv), the ancestral allele of rice waxy gene. Mol Plant 12(8):1157–1166. https://doi.org/10.1016/j.molp.2019.05.011
Zhang CQ, Yang Y, Chen ZZ, Chen F, Pan LX, Lu Y, Li QF, Fan XL, Sun ZZ, Liu QQ (2020) Characteristics of grain physicochemical properties and the starch structure in rice carrying a mutated ALK/SSIIa gene. J Agric Food Chem 68(47):13950–13959. https://doi.org/10.1021/acs.jafc.0c01471
Zhang CQ, Yang Y, Chen SJ, Liu XJ, Zhu JH, Zhou LH, Lu Y, Li QF, Fan XL, Tang SZ, Gu MH, Liu QQ (2021) A rare Waxy allele coordinately improves rice eating and cooking quality and grain transparency. J Integr Plant Biol 63(5):889–901. https://doi.org/10.1111/jipb.13010
Zhang Y, Zhao J, Hu Y, Zhang Y, Ying Y, Xu F, Bao J (2022) Combined effects of different alleles of FLO2, Wx and SSIIa on the cooking and eating quality of rice. Plants (Basel) 11(17):2249. https://doi.org/10.3390/plants11172249
Zhao X, Zhou L, Ponce K, Ye G (2015) The usefulness of known genes/Qtls for grain quality traits in an indica population of diverse breeding lines tested using association analysis. Rice (N Y) 8(1):29. https://doi.org/10.1186/s12284-015-0064-3
Zhou L, Zhang C, Zhang Y, Wang C, Liu Q (2022) Genetic manipulation of endosperm amylose for designing superior quality rice to meet the demands in the 21st century. J Cereal Sci 105:103481. https://doi.org/10.1016/j.jcs.2022.103481
Zhu M, Liu Y, Jiao G, Yu J, Zhao R, Lu A, Zhou W, Cao N, Wu J, Hu S, Sheng Z, Wei X, Zhao F, Xie L, Ahmad S, Lin Y, Shao G, Tang S, Hu P (2024) The elite eating quality alleles Wx(b) and ALK(b) are regulated by OsDOF18 and coordinately improve head rice yield. Plant Biotechnol J. https://doi.org/10.1111/pbi.14288
Acknowledgements
Financial support for this research was supported by Research and Development Program in Key Areas of Guangdong Province (No. 2021B0707010010), Zhaoqing Science and Technology Plan Project (2021N027) and the "Unveiling and Leading" Project of Hainan Yazhou Bay Seed Laboratory and China National Seed Group (B23YQ1512, B23CQ15CP).
Funding
This work was funded by Research and Development Program in Key Areas of Guangdong Province (No. 2021B0707010010), Zhaoqing Science and Technology Plan Project (2021N027), and the "Unveiling and Leading" Project of Hainan Yazhou Bay Seed Laboratory and China National Seed Group (B23YQ1512, B23CQ15CP).
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HZ and GY designed the project and revised the manuscript. SZ performed all the experiments, analyzed the data and wrote the manuscript. AF, MG, JL, ZT and TG assisted in conducting experiments. All authors read and approved the final manuscript.
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Zhang, S., Fu, A., Guo, M. et al. Effect and identification of different allele combinations of SSIIa and Wx on rice eating and cooking quality. Euphytica 220, 63 (2024). https://doi.org/10.1007/s10681-024-03329-y
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DOI: https://doi.org/10.1007/s10681-024-03329-y