QTLs and candidate genes for chlorate resistance
in rice (Oryzasativa L.) |
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| Authors: | Sheng Teng Chaoguang Tian Mingsheng Chen Dali Zeng Longbiao Guo Lihuang Zhu Bin Han Qian Qian |
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| Institution: | (1) State Key Lab for Rice Biology, China National Rice Research Institute, Hangzhou, 310006, China;(2) Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China;(3) National Center for Gene Research, Chinese Academy of Sciences, Shanghai, 200233, China |
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| 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. |
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| Keywords: | Rice Chlorate resistance QTL analysis Nitrate reductase Nitrate transporter |
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