QTL Analysis and Map-Based Cloning of Salt Tolerance Gene in Rice

Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
Methods in molecular biology (Clifton, N.J.) (Impact Factor: 1.29). 01/2013; 956:69-82. DOI: 10.1007/978-1-62703-194-3_6
Source: PubMed

ABSTRACT Most agronomic traits are governed by quantitative trait loci (QTLs) and exhibit continuous distribution in a segregating population. The hereditary characteristics of these traits are more complicated than those of monogenic traits. Detection and isolation of these QTLs can greatly improve crop production throughout the world. In recent times, significant progress has been made toward understanding the molecular basis underlying quantitative traits. Herein, we describe a QTL-mapping protocol for detecting and cloning a major QTL regulating rice shoot K(+) concentration under salt stress conditions. This QTL-mapping approach combined with the marker-assisted selection technique can be applied for the elucidation of complex traits in rice and other cereal crops.

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    ABSTRACT: Next-generation sequencing technologies provide opportunities to understand the genetic basis of phenotypic differences, such as abiotic stress response, even in the closely related cultivars via identification of large number of DNA polymorphisms. We performed whole-genome resequencing of three rice cultivars with contrasting responses to drought and salinity stress (sensitive IR64, drought-tolerant Nagina 22 and salinity-tolerant Pokkali). More than 356 million 90-bp paired-end reads were generated, which provided about 85% coverage of the rice genome. Applying stringent parameters, we identified a total of 1 784 583 nonredundant single-nucleotide polymorphisms (SNPs) and 154 275 InDels between reference (Nipponbare) and the three resequenced cultivars. We detected 401 683 and 662 509 SNPs between IR64 and Pokkali, and IR64 and N22 cultivars, respectively. The distribution of DNA polymorphisms was found to be uneven across and within the rice chromosomes. One-fourth of the SNPs and InDels were detected in genic regions, and about 3.5% of the total SNPs resulted in nonsynonymous changes. Large-effect SNPs and InDels, which affect the integrity of the encoded protein, were also identified. Further, we identified DNA polymorphisms present in the differentially expressed genes within the known quantitative trait loci. Among these, a total of 548 SNPs in 232 genes, located in the conserved functional domains, were identified. The data presented in this study provide functional markers and promising target genes for salinity and drought tolerance and present a valuable resource for high-throughput genotyping and molecular breeding for abiotic stress traits in rice.
    Plant Biotechnology Journal 10/2013; DOI:10.1111/pbi.12133 · 5.68 Impact Factor
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