Abstract
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 (qMel-1 and qMel-3) 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 qMel-1 and qMel-3 regions, and an F2:3 population was developed. A two-way ANOVA indicated that no epistatic interaction was detected between the 2 QTLs in the F2 population (P = 0.31). Moreover, analysis of two F3 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 qMel-1 QTL was located between the 2 SSR markers RM5448 and RM5310, which are 3,799-kb apart, and that the qMel-3 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1939-8433-5-13) contains supplementary material, which is available to authorized users.
Highlights
In rice, direct-seeding cultivation is becoming popular in Korea and Japan, because it requires less labor relative to transplanting one
The aims of this study were 1) to identify Quantitative trait locus (QTL) controlling mesocotyl elongation using backcross inbred lines (BILs) derived from a cross between Nipponbare and Kasalath, 2) to confirm and fine-map the QTLs detected in the BILs by using Chromosome segment substitution line (CSSL) and their progeny, and 3) to analyze the interaction of QTLs in controlling mesocotyl elongation
The BILs from a cross whereas that of Nipponbare was less than 2.6 mm
Summary
Direct-seeding cultivation is becoming popular in Korea and Japan, because it requires less labor relative to transplanting one. The mesocotyl is an embryonic structure between the scutellar node and coleoptilar node and is directly related to rice seedling emergence, since it elongates during germination to push the shoot tip above the soil surface. Poor emergence and inadequate stand establishment of seedlings caused by short mesocotyls can lead to yield loss in direct seeding cultivation. Mesocotyl elongation displays a large variation among rice germplasm. Dilday et al (1990) found that mesocotyl elongation could be inherited stably from generation to generation in semi-dwarf rice cultivars. Mgonja et al (1994) reported the partial dominance and preponderance of additive gene effects for mesocotyl elongation using diallel crosses among 6 rice cultivars. Lin et al (2006) showed that mesocotyl elongation in rice was mainly controlled by 2 recessive genes
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