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Lee, Hyun-Sook,Sasaki, Kazuhiro,Higashitani, Atsushi,Ahn, Sang-Nag,Sato, Tadashi Springer New York 2012 Rice Vol.5 No.-
<P>Mesocotyl elongation is an important trait for seedling emergence in direct-seeding cultivation in rice. In this study, a backcross inbred line (BIL) population from a cross between Kasalath and Nipponbare was employed to map quantitative trait loci (QTLs) for mesocotyl elongation. A total of 5 QTLs for mesocotyl length were identified on chromosomes 1, 3, 7, 9, and 12 in 2 independent experiments. At all QTL, the Kasalath alleles contributed to an increase in mesocotyl length. Two QTLs (<I>qMel-1</I> and <I>qMel-3</I>) on chromosomes 1 and 3 were consistently detected in both experiments. To fine map the QTLs, a cross was made between 2 chromosome segment substitution lines (CSSL-6 and CSSL-15), each harboring the Kasalath allele across the <I>qMel-1</I> and <I>qMel-3</I> regions, and an F<SUB>2:3</SUB> population was developed. A two-way ANOVA indicated that no epistatic interaction was detected between the 2 QTLs in the F<SUB>2</SUB> population (<I>P</I> = 0.31). Moreover, analysis of two F<SUB>3</SUB> near-isogenic lines (NILs) derived from the same cross, indicated that the 2 QTLs act additively in distinct or complementary pathways in controlling mesocotyl elongation. Substitution mapping indicated that the <I>qMel-1</I> QTL was located between the 2 SSR markers RM5448 and RM5310, which are 3,799-kb apart, and that the <I>qMel-3</I> QTL was located between the 2 SSR markers RM3513 and RM1238, which are 6,964-kb apart. To our knowledge, this is the first report to fine-map QTLs for mesocotyl elongation and to analyze their interaction.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/1939-8433-5-13) contains supplementary material, which is available to authorized users.</P>