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Euphytica

, Volume 152, Issue 2, pp 141–148 | Cite as

QTLs and candidate genes for chlorate resistance in rice (Oryzasativa L.)

  • Sheng Teng
  • Chaoguang Tian
  • Mingsheng Chen
  • Dali Zeng
  • Longbiao Guo
  • Lihuang Zhu
  • Bin Han
  • Qian Qian
Original Paper

Abstract

Chlorate resistance is one of the reliable characters in Indica/Japonica classification. To understand the genetic basis of chlorate resistance is very important for revealing the evolutionary mechanism of Indica/Japonica differentiation. In this study, a doubled haploid (DH) population derived from anther culture of ZYQ8/JX17, a typical Indica and Japonica hybrid, was used as the genetic material to investigate chlorate sensitivity of the parents and DH lines. The quantitative trait loci (QTLs) of chlorate resistance were analyzed based on the molecular linkage map of this population. Total of 3 QTLs (qCHR-2, qCHR-8 and qCHR-10) for chlorate resistance were detected on chromosomes 2, 8 and 10, respectively. A QTL × QTL epistatic interaction was detected between qCHR-2 and qCHR-10. Genes involved in nitrogen assimilation, such as nitrate reduction, molybdenum cofactor biosynthesis and nitrate transport were strong candidates of QTLs for chlorate resistance. A putative nitrate reductase gene (8611.t00011), and two putative nitrate reductase genes (9319.t00010 and 9319.t00012) were in the genomic region of qCHR-2, and qCHR-8, respectively, and a putative nitrate transporter gene (756.t00011) was in the region of qCHR-10. The expression of 8611.t00011, 9319.t00010 and 756.t00011 were confirmed by the corresponding cDNAs, and 2 in/del and 12 SNPs in the coding regions of these three genes were found between Indica (cv. 9311) and Japonica (cv. Nipponbare) in silico. These results indicated that these three genes were candidates of the chlorate resistance QTLs. An in/del in the coding region of 8611.t00011 was used to develop a new PCR marker. A polymorphism was detected between JX17/Nipponbare and ZYQ8/9311. This polymorphism corresponds to the chlorate sensitivity of Nipponbare and 9311. This marker was located between Y8007R and RM250 on chromosome 2 in the DH population, where qCHR-2 was also located.

Keywords

Rice Chlorate resistance QTL analysis Nitrate reductase Nitrate transporter 

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Notes

Acknowledgements

This study is supported by the grants from the National “863” Project of China (2002AA2Z1003) and the National Natural Science Foundation of China (30425034).

References

  1. Aberg B (1947) On the mechanism of the toxic action of chlorates and some related substances upon young wheat plants. Ann R Agr Coll Sweden 15:37–107Google Scholar
  2. Barlaan EA, Ichii M (1996) Genotypic variation in nitrate and nitrite reductase activities in rice (Oryza sativa L). Breed Sci 46:125–131Google Scholar
  3. Chen X, Temnykh S, Xu Y, Cho YG, McCouch SR (1997) Development of a microsatellite framework map providing genome-wide coverage in rice (Oryza sativa L.). Theor Appl Genet 95:553–567CrossRefGoogle Scholar
  4. Crawford NM (1992) Study of chlorate resistant mutant of Arabidopsis: insights into nitrate assimilation and ion metabolism of plant. In: Setlow JK, Hollander A (Eds) Genetic engineering principles and methods. Plenum Press, New York, pp 89–98Google Scholar
  5. 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 gelatinization temperature of rice. Sci China Ser C) 46:661–668CrossRefGoogle Scholar
  6. Guerrero MG, Vega JM, Losada M (1981) The assimilatory nitrate-reducing system and its regulation. Ann Rev Plant Physiol 32:169–204CrossRefGoogle Scholar
  7. Hasegawa H, Yatou O, Ichii M (1995) A chlorate-hypersensitive, high chlorate uptake mutant in rice (Oryza sativa L.). Breed Sci 45:229–233Google Scholar
  8. Hasegawa H, Katagiri T, Ida S, Yatou O, Ichii M (1992) Characterization of a rice (Oryza sativa L.) mutant deficient in the heme domain of nitrate reductase. Theor Appl Genet 84:6–9CrossRefGoogle Scholar
  9. Huang NW (1989) Brief report in classification of indica—japonica using potassium chlorate. Crop Variation Germplasm 3:23–24Google Scholar
  10. Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage map. Genetics 121:185–199PubMedGoogle Scholar
  11. Lin SY, Nagamura Y, Kurata N, Yano M, Minobe Y, Sasaki T (1994) DNA markers tightly linked to genes, Ph, alk and Rc. Rice Genet Newsl 11:108–109Google Scholar
  12. Lincoln SE, Daly MJ, Lander ES (2004) Mapping genes controlling quantitative traits using Mapmaker/QTL version 1.1: a tutorial and reference manual 2nd edn. Whitehead Institute for Biometrical Research Cambridge, MassGoogle Scholar
  13. Lu C, Shen L, Tan Z, Xu Y, He P, Chen Y, Zhu L (1996) Comparative mapping of QTLs for agronomic traits of rice across environments using a doubled haploid population. Theor Appl Genet 93:1211–1217CrossRefGoogle Scholar
  14. McCouch SR, Cho YG, Yano M, Paul E, Blinstrub M (2004) Report on QTL nomenclature. Rice Genet Newsl 14:11–13Google Scholar
  15. Morishima H, Oka HI (1981) Phylogenetic differentiation of cultivated rice, XXII. Numerical evaluation of the Indica—Japonica differentiation. Japan J Breed 31:402–413Google Scholar
  16. Oka HI (1988) Origin of cultivated rice. Japan Scientific Societies Press, TokyoGoogle Scholar
  17. Panaud O, Chen X, McCouch SR (1996) Development of microsatellite markers and characterization of simple sequence length polymorphism (SSLP) in rice (Oryza sativa L.). Mol Gen Genet 252:597–607PubMedGoogle Scholar
  18. Qian Q, He P, Zheng XW, Chen Y, Zhu LH (2000) Genetic analysis of morphological index and its related taxonomic traits for classification of indica/japonica rice. Sci China Ser C 43:113–119CrossRefGoogle Scholar
  19. Sato YI, Chitrakon S, Morishima H (1986) The Indica—Japonica differentiation of rice cultivars in Thailand and its neighboring countries. In: Napompath B, Subhadravandha S (eds) New frontiers in breeding researches. Kasetsart Univ, Bangkok, pp 185–193Google Scholar
  20. Sato H, Ichii M (1998) New locus cnx 3 involved in molybdenum cofactor biosynthesis in rice (Oryza sativa L.). Breed Sci 48:123–128Google Scholar
  21. Sato H, Imiya Y, Ida S, Ichii M (1996) Characterization of four molybdenum cofactor mutants of rice, Oryza sativa L. Plant Sci 119:39–47CrossRefGoogle Scholar
  22. Teng S, Qian Q, Zeng DL, Kunihiro Y, Fujimoto K, Huang DN, Zhu LH (2002) Analysis of gene loci and epistasis for drought tolerance in seedling stage of rice (Oryza sativa L.). Yi Chuan Xue Bao 29:235–240PubMedGoogle Scholar
  23. Tsay YF, Schroeder JI, Feldmann KA, Crawford NM (1993) The herbicide sensitivity gene CHL1 of Arabidopsis encodes a nitrate-inducible nitrate transporter. Cell 72:705–713PubMedCrossRefGoogle Scholar
  24. Vanooijen JW (1992) Accuracy of mapping quantitative trait loci in autogamous species. Theor Appl Genet 84:803–811Google Scholar
  25. Wang YR (1995) Physiological breeding in rice. Beijing Science and Technology Literature Publishing Company BeijingGoogle Scholar
  26. Wilkinson JQ, Crawford NM (1991) Identification of the Arabidopsis CHL3 gene as the nitrate reductase structural gene NIA2. Plant Cell 3:461–471PubMedCrossRefGoogle Scholar
  27. Xu YB, Shen LS, McCouch SR, Zhu LH (1998) Extension of the rice DH population genetic map with microsatellite markers. Chin Sci Bull 43:149–153Google Scholar
  28. Yamaya T, Obara M, Nakajima H, Sasaki S, Hayakawa T, Sato T (2002) Genetic manipulation and quantitative-trait loci mapping for nitrogen recycling in rice. J Exp Bot 53:917–925PubMedCrossRefGoogle Scholar
  29. Zhao CM, Hasegawa H, Ichii M (2004) A chlorate resistant mutant of rice (Oryza sativa L.) with normal nitrate uptake and nitrate reductase activity. Breed Sci 50:9–16Google Scholar
  30. Zhu LH, Chen Y, Xu YB, Xu JC, Cai HW, Ling ZZ (1993) Construction of a molecular map of rice and gene mapping using a double haploid population of a cross between Indica and Japonica varieties. Rice Genet Newsl 10:132–134Google Scholar

Copyright information

© Springer Science+Business Media B.V. 2006

Authors and Affiliations

  • Sheng Teng
    • 1
  • Chaoguang Tian
    • 2
  • Mingsheng Chen
    • 2
  • Dali Zeng
    • 1
  • Longbiao Guo
    • 1
  • Lihuang Zhu
    • 2
  • Bin Han
    • 3
  • Qian Qian
    • 1
  1. 1.State Key Lab for Rice BiologyChina National Rice Research InstituteHangzhouChina
  2. 2.Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijingChina
  3. 3.National Center for Gene ResearchChinese Academy of SciencesShanghaiChina

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