QTLs and candidate genes for chlorate resistance in rice (Oryzasativa L.)
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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.
KeywordsRice Chlorate resistance QTL analysis Nitrate reductase Nitrate transporter
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This study is supported by the grants from the National “863” Project of China (2002AA2Z1003) and the National Natural Science Foundation of China (30425034).
- 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
- Barlaan EA, Ichii M (1996) Genotypic variation in nitrate and nitrite reductase activities in rice (Oryza sativa L). Breed Sci 46:125–131Google Scholar
- 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
- 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
- Huang NW (1989) Brief report in classification of indica—japonica using potassium chlorate. Crop Variation Germplasm 3:23–24Google Scholar
- 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
- 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
- McCouch SR, Cho YG, Yano M, Paul E, Blinstrub M (2004) Report on QTL nomenclature. Rice Genet Newsl 14:11–13Google Scholar
- 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
- Oka HI (1988) Origin of cultivated rice. Japan Scientific Societies Press, TokyoGoogle Scholar
- 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
- 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
- Vanooijen JW (1992) Accuracy of mapping quantitative trait loci in autogamous species. Theor Appl Genet 84:803–811Google Scholar
- Wang YR (1995) Physiological breeding in rice. Beijing Science and Technology Literature Publishing Company BeijingGoogle Scholar
- 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
- 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
- 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