Mapping, Cloning And Functional Analysis Of SKC1, A QTL Related To Salt Tolerance Of Rice

It is necessary to understand the mechanism of rice salt tolerance forimproving new salt tolerant rice variety, because soil salinity is more and moreseriously threatening rice production. An F2 and an equivalent F3 populationderived from a cross between a high salt-tolerance indica variety, Nona Bokra,and a susceptible elite japonica variety, Koshihikari, were produced. Weperformed QTL mapping for physiological traits related to rice salt-tolerance,and several QTLs were detected. Of these QTLs, a major QTL mapped on theshort arm of chromosome 1 with the very large effect, SKC1 for shoot K+concentration, explained 40.1% of the total phenotypic variance. The backcrosspopulations (Koshihikari was as the recurrent parent) was developed. Using 192lines from BC2F2 backcross population and their equivalent progeny BC2F3,fine mapping of SKC1 was performed. SKC1 was mapped in the 3.2 cM regionbetween the STS makers K159 and K061-2, and it was closely linked to theCAPS maker K0625. 133 lines with recombination between K159 and K061-2were screened from BC2F2 or BC3F2 population containing 2973 plants.High-resolution linkage analysis performed by using 30 BC2F4 or BC3F4 linesselected from those 133 lines enabled us to define a genomic region of ~7.4 kbas a candidate for SKC1. Only one candidate gene is in the region, and thefull-length ORF of SKC1 was obtained from the cDNA library of Nona by usingPCR. Blast analysis revealed that SKC1 is a homolog of HKT1 in Wheat.Sequencing analysis revealed 3 exons and 2 introns in SKC1 gene, and fouramino acids difference between NSKC1 from Nona and KSKC1 fromKoshihikari. Genetic complementation analysis proved the function of thecandidate gene by using promoter-ORF from Nona. Analysis of SKC1promoter-β-glucuronidase transgenic rice plants revealed expression of SKC1 invascular bundles, and mainly in parenchyma cells at the xylem. Analysis ofSKC1 promoter-β-glucuronidase and RT-PCR revealed strong expression ofSKC1 in root. A nearly isogenic line (NIL) of the target QTL, NIL (SKC1), inwhich a 5 cM chromosomal segment of Nona including SKC1 was substitutedinto the genetic background of Koshihikari, was selected based onmaker-assisted selection for studying the function of SKC1. Under 140 mMNaCl condition, NIL (SKC1) shoot could maintain more K+ and less Na+ thanthat of Koshihikari shoot. There also was higher K+ and less Na+ in the xylemsap of NIL (SKC1) plants exposed to 25 mM NaCl. Moreover, the salt toleranceof NIL (SKC1) plants was more slightly enhanced than that of Koshihikari undersalt stress. These results suggest that SKC1 play an important role in theprogress controlling long-distance K+ and Na+ transport from root to shoot.