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The QTL controlling amino acid content in grains of rice (Oryza sativa) are co-localized with the regions involved in the amino acid metabolism pathway

Abstract

The improvement of grain quality, such as protein content (PC) and amino acid composition, has been a major concern of rice breeders. We constructed a population of 190 recombinant inbred lines (RILs) from a cross between Zhenshan 97 and Nanyangzhan to map the quantitative trait locus or loci (QTL) for amino acid content (AAC) as characterized by each of the AACs, total essential AAC, and all AAC. Using the data collected from milled rice in 2002 and 2004, we identified 18 chromosomal regions for 19 components of AAC. For 13 of all the loci, the Zhenshan 97 allele increased the trait values. Most QTL were co-localized, forming ten QTL clusters in 2002 and six in 2004. The QTL clusters varied in both effects and locations, and the mean values of variation explained by individual QTL in the clusters ranged from 4.3% to 28.82%. A relatively strong QTL cluster, consisting of up to 19 individual QTL, was found at the bottom of chromosome 1. The major QTL clusters identified for two different years were coincident. A wide coincidence was found between the QTL we detected and the loci involved in amino acid metabolism pathways, including N assimilation and transfer, and amino acid or protein biosynthesis. The results will be useful for candidate gene identification and marker-assisted favorable allele transfer in rice breeding programs.

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References

  1. 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 109:630–639

    PubMed  Article  CAS  Google Scholar 

  2. Basten CJ, Weir BS, Zeng ZB (1997) QTLCartographer: a reference manual and tutorial for QTL mapping. Department of Statistics, North Carolina State University, Raleigh

    Google Scholar 

  3. Cagampang GB, Cruz LJ, Juliano BO (1971) Free amino acids in the bleeding sap and developing grain of the rice plant. Cereal Chem 48:533–539

    CAS  Google Scholar 

  4. Charmet G, Robert N, Branlard G, Linossier L, Martre P, Triboï E (2005) Genetic analysis of dry matter and nitrogen accumulation and protein composition in wheat kernels. Theor Appl Genet 111:540–550

    PubMed  Article  CAS  Google Scholar 

  5. Duan MJ, Sun SSM (2005) Profiling the expression of genes controlling rice grain quality. Plant Mol Biol 59:165–178

    PubMed  Article  CAS  Google Scholar 

  6. 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 110:1445–1452

    PubMed  Article  CAS  Google Scholar 

  7. FAO (Food, Agriculture Organization of The United Nations) (1970) Amino acid content of foods and biological proteins. FAO, Roma

    Google Scholar 

  8. Gupta MP, Gupta PK, Singh IB, Singh P (1988) Genetic analysis for quality characters in rice. Genetika 20:141–146

    Google Scholar 

  9. 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 18:277–290

    Article  CAS  Google Scholar 

  10. Hu ZL, Li P, Zhou MQ, Zhang ZH, Wang LX, Zhu LH, Zhu LG (2004) Mapping of quantitative trait loci (QTLs) for rice protein and fat content using doubled haploid lines. Euphytica 135:47–54

    Article  CAS  Google Scholar 

  11. Jiang GH, He YQ, Xu CG, Li XH, Zhang Q (2004) The genetic basis of stay-green in rice analyzed in a population of doubled haploid lines from an indica by japonica cross. Theor Appl Genet 108:688–698

    PubMed  Article  CAS  Google Scholar 

  12. Juliano BO (1985) Rice chemistry and technology, 2nd edn. American Association of Cereal Chemists, Incorporated Saint Paul, Minnesota

    Google Scholar 

  13. Kambayshi M, Tsurumi I, Sasahara T (1984) Genetic studies on improvement of protein content in rice grain. Jpn J Breed 34:356–363

    Google Scholar 

  14. 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 7:93–101

    PubMed  Article  CAS  Google Scholar 

  15. Lian XM, Xing YZ, Yan H, Xu CG, Li XH, Zhang QF (2005) QTLs for low nitrogen tolerance at seedling stage identified using a recombinant inbred line population derived from an elite rice hybrid. Theor Appl Genet 112:85–96

    PubMed  Article  CAS  Google Scholar 

  16. Lin R, Luo Y, Liu D, Huang C (1993) Determination and analysis on principal qualitative characters of rice germplasm. In: Ying C (ed) Rice germplasm resources in China. Agricultural Science and Technology Publisher of China, Beijing, pp 83–93

    Google Scholar 

  17. Lincoln S, Daly M, Lander E (1992) Constructing genetics maps with MAPMAKER/EXP 3.0. Whitehead Institute Technical Report, Whitehead Institute, Cambridge, Massachusetts

  18. Lohaus G, Moellers C (2000) Phloem transport of amino acids in two Brassica napus L. genotypes and one B. carinata genotype in relation to their seed protein content. Planta 211:833–840

    PubMed  Article  CAS  Google Scholar 

  19. Lohaus G, Büker M, Hußmann M, Soave C, Heldt HW (1998) Transport of amino acids with special emphasis on the synthesis and transport of asparagine in the Illinois low protein and Illinois high protein strains of maize. Planta 205:181–188

    Article  CAS  Google Scholar 

  20. Martin M, Fitzgerald MA (2002) Proteins in rice grain influence cooking properties. J Cereal Sci 36:285–294

    Article  CAS  Google Scholar 

  21. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L (2002) Development and mapping of 2,240 new SSR markers for rice (Oryza sativa L.). DNA Res 9:199–207

    PubMed  Article  CAS  Google Scholar 

  22. Obara M, Sato T, Sasaki S, Kashiba K, Nagano A, Nakamura I, Ebitani T, Yano M, Yamaya T (2004) Identification and characterization of a QTL on chromosome 2 for cytosolic glutamine synthetase content and panicle number in rice. Theor Appl Genet 110:1–11

    PubMed  Article  CAS  Google Scholar 

  23. 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 107:1433–1441

    PubMed  Article  CAS  Google Scholar 

  24. Shenoy VV, Seshu DV, Sachan JKS (1991) Inheritance of protein per grain in rice. Indian J Genet 51:214–220

    Google Scholar 

  25. Simon-sarkadi L, Kocsy G, Várhegyi Á, Galiba G, De ronde JA (2006) Stress-induced changes in the free amino acid composition in transgenic soybean plants having increased proline content. Biol Plant 50:793–796

    Article  CAS  Google Scholar 

  26. Sood BC, Siddiq EA (1986) Genetic analysis of crude protein content in rice. Indian J Agric Sci 56:796–797

    CAS  Google Scholar 

  27. StatSoft (1991) Statistica. StatSoft, Tulsa, Oklahoma

  28. Takahashi M, Uematsu Y, Kashiwaba K, Yagasaki K, Hajika M, Matsunaga R, Komatsu K, Ishimoto M (2003) Accumulation of high levels of free amino acids in soybean seeds through integration of mutations conferring seed protein deficiency. Planta 217:577–586

    PubMed  Article  CAS  Google Scholar 

  29. 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 99:642–648

    Article  CAS  Google Scholar 

  30. Tan YF, Sun M, Xing YZ, Hua JP, Sun XL, Zhang QF, Corke H (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. Theor Appl Genet 103:1037–1045

    Article  CAS  Google Scholar 

  31. Temnykh S, Park WD, Ayres N, Cartihour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR (2000) Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet 100:697–712

    Article  CAS  Google Scholar 

  32. Temnykh S, Declerck G, Luashova A, Lipovich L, Cartinhour S, McCouch S (2001) Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res 11:1441–1452

    PubMed  Article  CAS  Google Scholar 

  33. 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 15:117–124

    Article  CAS  Google Scholar 

  34. Wang XL, Larkins BA (2001) Genetic analysis of amino acid accumulation in opaque-2 maize endosperm. Plant Physiol 125:1766–1777

    PubMed  Article  CAS  Google Scholar 

  35. Wang XL, Stumpf DK, Larkins BA (2001) Aspartate kinase 2. A candidate gene of a quantitative trait locus influencing free amino acid content in maize endosperm. Plant Physiol 125:1778–1787

    PubMed  Article  CAS  Google Scholar 

  36. Wang WM, Zhao Q, Yu JJ, Zhu DY, Ao GM (2005) Transfer of high lysine gene sb401 into rice and analysis for protein and amino acid content in transgenic rice seeds. Acta Agronomica Sinica 31:603–607

    CAS  Google Scholar 

  37. WHO (1973) Energy and protein requirements. WHO Tech. Rep. Ser. 522. World Health Organization, Geneva

  38. Yoshida S, Ikegami M, Kuze J, Sawada K, Hashimoto Z, Ishii T, Nakamura C, Kamijima O (2002) QTL analysis for plant and grain characters of sake-brewing rice using a doubled haploid population. Breed Sci 52:309–317

    Article  CAS  Google Scholar 

  39. Zeng ZB (1994) Precision mapping of quantitative trait loci. Genetics 136:1457–1468

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported in part by a grant from the National Program on the Development of Basic Research, the National Program of 863 High Technology Development, and a grant from the National Natural Science Foundation of China.

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Correspondence to Yuqing He.

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Wang, L., Zhong, M., Li, X. et al. The QTL controlling amino acid content in grains of rice (Oryza sativa) are co-localized with the regions involved in the amino acid metabolism pathway. Mol Breeding 21, 127–137 (2008). https://doi.org/10.1007/s11032-007-9141-7

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Keywords

  • Amino acid content
  • Grain quality
  • Lys content
  • QTL
  • Rice (Oryza sativa L.)