Theoretical and Applied Genetics

, Volume 122, Issue 1, pp 63–76 | Cite as

Genetic analysis of starch paste viscosity parameters in glutinous rice (Oryza sativa L.)

  • Chang-Jie Yan
  • Zhi-Xi Tian
  • Yu-Wei Fang
  • Ya-Chun Yang
  • Jian Li
  • Sheng-Yuan Zeng
  • Shi-Liang Gu
  • Chen-Wu Xu
  • Shu-Zhu Tang
  • Ming-Hong Gu
Original Paper

Abstract

Starch paste viscosity plays an important role in estimating the cooking, eating, and processing quality of rice. The inheritance of starch paste viscosity in glutinous rice remains undefined. In the present study, 118 glutinous rice accessions were collected, and the genotypes of 17 starch synthesis-related genes (SSRG) were analyzed by using 43 gene-specific molecular markers. Association analysis indicated that 10 of 17 SSRGs were involved in controlling the rapid visco analyzer (RVA) profile parameters. Among these, the PUL gene was identified to play an important role in control of peak viscosity (PKV), hot paste viscosity (HPV), cool paste viscosity (CPV), breakdown viscosity (BDV), peak time (PeT), and paste temperature (PaT) in glutinous rice. Other SSRGs involved only a few RVA profile parameters. Furthermore, interactions between SSRGs were found being responsible for PeT, PaT, and BDV. Some of the RVA parameters, including PKV, HPV, CPV, CSV, and PaT, were mainly governed by single SSRG, whereas other parameters, such as BDV, SBV, and PeT, were controlled by a few SSRGs, functioning cooperatively. Further, three near-isogenic lines (NIL) of a japonica glutinous cv. Suyunuo as genetic background, with PUL, SSIII-1, and SSIII-2 alleles replaced with those of indica cv. Guichao 2, were employed to verify the genetic effects of the various genes, and the results were consistent with those obtained from the association analysis. These findings indicated that starch paste viscosity in glutinous rice had a complex genetic system, and the PUL gene played an important role in determining the RVA profile parameters in glutinous rice. These results provide important information for potentially improving the quality of glutinous rice.

Keywords

Glutinous rice Association analysis Starch synthesis related genes RVA profile parameters 

Notes

Acknowledgments

We are grateful to Mr. Xie Yulin (Taihu Institute of Agricultural Science, Jiangsu, China) for providing some materials. This study was financially supported by the Ministry of Science and Technology (Grant No. 2005CB120804 and 2006AA10Z118), the National Natural Science Foundation (Grant Nos. 30530470, 30771323 and 30871501), Fok Ying Tung Education Foundation (101030) and the Jiangsu Province Government (Grant No. 08KJA210002) of China.

References

  1. Abdurakhmonov IY, Abdukarimov A (2008) Application of association mapping to understanding the genetic diversity of plant germplasm resources. Int J Plant Genomics. doi:10.1155/2008/574927
  2. Aluko G, Martinez C, Tohme J, Castano C, Bergman C, Oard JH (2004) QTL mapping of grain quality traits from the interspecific cross Oryza sativa × O. glaberrima. Theor Appl Genet 109:630–639CrossRefPubMedGoogle Scholar
  3. American Association of Cereal Chemists (2000) Approved methods for the AACC, 10th edn. Method 61–01 (amylograph method for milled rice) and Method 61–02 (determination of the pasting properties of rice with rapid visco analyzer). The Association, St. PaulGoogle Scholar
  4. Aranzana MJ, Kim S, Zhao K, Bakker E, Horton M, Jakob K, Lister C, Molitor J, Shindo C, Tang C, Toomajian C, Traw B, Zheng H, Bergelson J, Marjoram P, Dean, Nordborg M (2005) Genome-wide association mapping in Arabidopsis identifies previously known flowering time and pathogen resistance genes. PLoS Genet 1(5):e60CrossRefPubMedGoogle Scholar
  5. Bao JS, Xia YW (1999) Genetic control of paste viscosity characteristics in indica rice (Oryza sativa L.). Theor Appl Genet 98:1120–1124CrossRefGoogle Scholar
  6. Bao JS, He P, Li SG, Xia YW, Chen Y, Zhu LH (2000a) Comparative mapping quantitative trait loci controlling the cooking and eating quality of rice. Sci Agric Sin 33:8–13 (in Chinese with English abstract)Google Scholar
  7. Bao JS, Zheng XW, Xia YW, He P, Shu QY, Lu X, Chen Y, Zhu LH (2000b) QTL mapping for the paste viscosity characteristics in rice (Oryza sativa L.). Theor Appl Genet 100:280–284CrossRefGoogle Scholar
  8. Bao JS, Wu YR, Hu B, Wu P, Cui HR, Shu QY (2002) QTL for rice grain quality based on a DH population derived from parents with similar apparent amylose content. Euphytica 128:317–324CrossRefGoogle Scholar
  9. Bao JS, Corke H, Sun M (2006) Microsatellites, single nucleotide polymorphisms and a sequence tagged site in starch-synthesizing genes in relation to starch physicochemical properties in nonwaxy rice (Oryza sativa L.). Theor Appl Genet 113:1185–1196CrossRefPubMedGoogle Scholar
  10. Cagampang GB, Perez CM, Juliano BO (1973) A gel consistency test for eating quality in rice. J Sci Food Agric 24:1589–1594CrossRefPubMedGoogle Scholar
  11. Cockram J, White J, Leigh FJ, Lea FJ, Chiapparino E, Laurie DA, Mackay IJ, Powell W, O’Sullivan DM (2008) Association mapping of partitioning loci in barley. BMC Genet 9:16. doi:10.1186/1471-2156-9-16 CrossRefPubMedGoogle Scholar
  12. Fan CC, Yu XQ, Xing YZ, Xu CG, Luo LJ, Zhang QF (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 110:1445–1452CrossRefPubMedGoogle Scholar
  13. Fujita N, Yoshida M, Kondo T, Saito K, Utsumi Y, Tokunaga T, Nishi A, Satoh H, Park JH, Jane JL, Miyao A, Hirochika H, Nakamura Y (2007) Characterization of SSIIIa-deficient mutants of rice: the function of SSIIIa and pleiotropic effects by SSIIIa deficiency in the rice endosperm. Plant Physiol 144:2009–2023CrossRefPubMedGoogle Scholar
  14. Fujita N, Toyosawa Y, Utsumi Y, Higuchi T, Hanashiro I, Ikegami A, Akuzawa S, Yoshida M, Mori A, Inomata K, Itoh R, Miyao A, Hirochika H, Satoh H, Nakamura Y (2009) Characterization of pullulanase (PUL)-deficient mutants of rice (Oryza sativa L.) and the function of PUL on starch biosynthesis in the developing rice endosperm. J Exp Bot 60(3):1009–1023CrossRefPubMedGoogle Scholar
  15. Gao ZY, Zeng DL, Cui X, Zhou YH, Yan M, Huang D, Li JY, Qian Q (2003) Map-based cloning of the ALK gene, which controls the GT of rice. Sci China (Ser C) 46:661–668CrossRefGoogle Scholar
  16. Ge XJ, Xing 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 124:121–126CrossRefGoogle Scholar
  17. Gravois KA, Webb BD (1997) Inheritance of long grain rice amylograph viscosity characteristics. Euphytica 97:25–29CrossRefGoogle Scholar
  18. Han YP, Xu ML, Liu XY, Yan CJ, Korban SS, Chen XL, Gu MH (2004) Genes coding for starch branching enzymes are major contributors to starch viscosity characteristics in waxy rice (Oryza sativa L.). Plant Sci 166:357–364CrossRefGoogle Scholar
  19. Hardy OJ, Vekemans X (2002) SPAGeDi: a versatile computer program to analyze spatial genetic structure at the individual or population levels. Mol Ecol Notes 2:618–620CrossRefGoogle Scholar
  20. He P, Li SG, Qian Q, Ma YQ, Li JZ, Wang WM, Chen Y, Zhu LH (1999) Genetic analysis of grain quality. Theor Appl Genet 98:502–508CrossRefGoogle Scholar
  21. He Y, Han YP, Jiang L, Xu CW, Lu JF, Xu ML (2006) Functional analysis of starch-synthesis genes in determining rice eating and cooking qualities. Mol Breed 18:277–290CrossRefGoogle Scholar
  22. Juliano BO (1985) Criteria and test for rice grain quality. In: Juliano BO (ed) Rice chemistry and technology. American Association of Cereal Chemists Inc., St. Paul, pp 443–513Google Scholar
  23. Juliano BO (1996) Rice quality screening with the Rapid Visco Analyser. In: Walker CE, Hazelton JL (eds) Applications of the rapid visco analyser. Newport Scientific, Sydney, pp 19–24Google Scholar
  24. Kubo A, Fujita N, Harada K, Matsuda T, Satoh H, Nakamura Y (1999) The starch debraching enzymes isoamylase and pullulanase are both involved in amylopectin biosynthesis in rice endosperm. Plant Physiol 121:399–409CrossRefPubMedGoogle Scholar
  25. Lanceras JC, Huang ZL, Naivikul O, Vanavichit A, Ruanjaichon V, Tragoonrung S (2000) Mapping of genes for cooking and eating qualities in Thai jasmine rice (KDML105). DNA Res 7:93–101CrossRefPubMedGoogle Scholar
  26. Little RR, Hilder GB, Dawson EH (1958) Differential effect of dilute alkali on 25 varieties of milled white rice. Cereal Chem 35:111–126Google Scholar
  27. Liu XY, Gu MH, Han YP, Ji Q, Lu JF, Gu SL, Zhang R, Li X, Chen JM, Korban SS, Xu ML (2004) Developing gene-tagged molecular markers for functional analysis of starch-synthesizing genes in rice (Oryza sativa L.). Euphytica 135:345–353CrossRefGoogle Scholar
  28. 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 116:979–989CrossRefPubMedGoogle Scholar
  29. Myers AM, Morell MK, James MG, Ball SG (2000) Recent progress toward understanding biosynthesis of the amylopectin crystal. Plant Physiol 122:989–997CrossRefPubMedGoogle Scholar
  30. Nakamura Y (2002) Towards a better understanding of the metabolic system for amylopectin biosynthesis in plants: rice endosperm as a model tissue. Plant Cell Physiol 43(7):718–725CrossRefPubMedGoogle Scholar
  31. Nakamura Y, Francisco PB Jr, 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 58:213–227CrossRefPubMedGoogle Scholar
  32. Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155(2):945–959PubMedGoogle Scholar
  33. Remington DL, Thornsberry JM, Matsuoka Y, Wilson LM, Whitt SR, Doebley J, Kresovich S, Goodman MM, Buckler ES (2001) Structure of linkage disequilibrium and phenotypic associations in the maize genome. Proc Natl Acad Sci USA 98:11479–11484CrossRefPubMedGoogle Scholar
  34. Roder W, Keoboulapha B, Vannalath K, Phouaravanh B (1996) Glutinous rice and its importance for hill farmers in Laos. Econ Bot 50:401–408CrossRefGoogle Scholar
  35. Septiningsih EM, Trijatmiko KR, Moeljopawiro S, McCouch SR (2003) Identification of quantitative trait loci for grain quality in an advanced backcross population derived from the Oryza sativa variety IR64 and the wild relative O. rufipogon. Theor Appl Genet 107:1433–1441CrossRefPubMedGoogle Scholar
  36. Shu QY, Wu DX, Xia YW, Gao MW, McClung A (1998) Relationship between RVA profile character and eating quality in Oryza sativa L. Sci Agric Sin 31:25–29Google Scholar
  37. Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang QF (1999) The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor Appl Genet 99:642–648CrossRefGoogle Scholar
  38. Tian R, Jiang GH, Shen LH, Wang LQ, He YQ (2005) Mapping quantitative trait loci underlying the cooking and eating quality of rice using a DH population. Mol Breed 15:117–124CrossRefGoogle Scholar
  39. 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 diversity in rice starch biosynthesis pathway leads to a diverse array of rice eating and cooking qualities. Proc Natl Acad Sci USA 106:21760–21765CrossRefPubMedGoogle Scholar
  40. Tian ZX, Yan CJ, Qian Q, Yan S, Xie HL, Wang F, Xu JF, Liu GF, Wang YH, Liu QQ, Tang SZ, Li JY, Gu MH (2010) Development of gene-tagged molecular markers for starch synthesis related genes in rice. Chinese Sci Bull (in press)Google Scholar
  41. Umemoto T, Aoki N (2005) Single-nucleotide polymorphisms in rice starch synthase IIa that alter starch gelatinization and starch association of the enzyme. Funct Plant Biol 32:763–768CrossRefGoogle Scholar
  42. Umemoto T, Yano M, Satoh H, Shomura A, Nakamura Y (2002) Mapping of a gene responsible for the difference in amylopectin structure between japonica-type and indica-type rice varieties. Theor Appl Genet 104:1–8CrossRefPubMedGoogle Scholar
  43. 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 165:1193–1199CrossRefGoogle Scholar
  44. Wang LQ, Liu WJ, Xu Y, He YQ, Luo LJ, Xing YZ, Xu CG, Zhang QF (2007) Genetic basis of 17 traits and viscosity parameters characterizing the eating and cooking quality of rice grain. Theor Appl Genet 115:463–476CrossRefPubMedGoogle Scholar
  45. Whitt SR, Wilson LM, Tenaillon MI, Gaut BS, Buckler ES (2002) Genetic diversity and selection in the maize starch pathway. Proc Natl Acad Sci USA 99:12959–12962CrossRefPubMedGoogle Scholar
  46. Wilson LM, Whitt R, Iba′nez AM, Rocheford TR, Goodman MM, Buckler ES (2004) Dissection of maize kernel composition and starch production by candidate gene association. Plant Cell 16:2719–2733CrossRefPubMedGoogle Scholar
  47. Wu HK, Liang GH, Gu YJ, Shan LL, Wang F, Han YP, Gu MH (2006) The effect of the starch-synthesizing genes on RVA profile characteristics in rice (Oryza sativa L.). Acta Agro Sin 32(11):1597–1603 (in Chinese with English abstract)Google Scholar
  48. Yu J, Buckler ES (2006) Genetic association mapping and genome organization of maize. Curr Opin Biotechnol 17:155–160PubMedGoogle Scholar
  49. Yu JM, Pressoir G, Briggs WH, Bi IV, Yamasaki M, Doebley JF, McMullen MD, Gaut BS, Nielsen DM, Holland JB, Kresovich S, Buckler ES (2005) An unified mixed-model method for association mapping that accounts for multiple levels of relatedness. Nat Genet 38:203–208CrossRefPubMedGoogle Scholar

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Chang-Jie Yan
    • 1
  • Zhi-Xi Tian
    • 2
  • Yu-Wei Fang
    • 1
  • Ya-Chun Yang
    • 1
  • Jian Li
    • 1
  • Sheng-Yuan Zeng
    • 1
  • Shi-Liang Gu
    • 1
  • Chen-Wu Xu
    • 1
  • Shu-Zhu Tang
    • 1
  • Ming-Hong Gu
    • 1
  1. 1.Jiangsu Key Laboratory of Crop Genetics and Physiology, Key Laboratory of Plant Functional Genomics, Ministry of Education of ChinaAgricultural College of Yangzhou UniversityJiangsuPeople’s Republic of China
  2. 2.Institute of Genetics and Developmental BiologyChinese Academy of ScienceBeijingChina

Personalised recommendations