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, 5 (1), 13

Mapping and Characterization of Quantitative Trait Loci for Mesocotyl Elongation in Rice (Oryza Sativa L.)

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Mapping and Characterization of Quantitative Trait Loci for Mesocotyl Elongation in Rice (Oryza Sativa L.)

Hyun-Sook Lee et al. Rice (N Y).

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.

Keywords: Chromosome segment substitution line (CSSL); Direct-seeding; Mesocotyl elongation; Quantitative trait locus (QTL); Rice (Oryza sativa L.).

Figures

Figure 1
Figure 1
Seedlings of parental plants, Kasalath (A) and Nipponbare (B), growing for 7days in darkness. Arrows indicate mesocotyl.
Figure 2
Figure 2
Frequency distribution of the mesocotyl length of BILs in the two experiments. Arrow indicates mean with SD for Nipponbare and Kasalath (Expt. 1: n = 30; Expt. 2: n = 36).
Figure 3
Figure 3
Chromosomal locations of QTLs for mesocotyl length of BILs in two experiments. Vertical boxes to the left of each chromosome represent the putative genomic regions harboring QTLs for mesocotyl length (P < 0.05). Arrowheads indicate the position with the highest LOD score for each QTL.
Figure 4
Figure 4
Frequency distribution of the mesocotyl length of 95 F2 plants derived from a cross between CSSL6 and CSSL15. Arrows indicate mean values with standard deviations (n = 11) for CSSL6 and CSSL15. White, black and gray bars indicate homozygous for Nipponbare and Kasalath alleles and heterozygous for the marker RM3602 on chromosome 1 (a) and RM8277 on chromosome 3 (b), respectively. The LOD score (LOD), proportion of the phenotypic variance (R2) and the additive effect of the Kasalath allele (a) are indicated in each figure (P < 0.05).
Figure 5
Figure 5
Comparison of mesocotyl length in 2 NILs and 2 parental lines, CSSL-6 and CSSL-15 with different genotypes at qMel-1 and qMel-3 . (a) Mean mesocotyl length with SE of 4 lines. (b) Graphical representation of the genotypes of 4 lines. Pair-wise comparison was conducted between each line based on the Duncan’s multiple range test. Means with the different letter are significantly different at P = 0.001.
Figure 6
Figure 6
Graphical genotypes of F3lines used in substitution mapping of qMel-1 and qMel-3. White portions of the graph indicate homozygous Nipponbare chromosome segments, black regions indicate homozygous Kasalath chromosomes, gray areas indicate heterozygous regions and slashed areas are regions where crossing-over occurred. The table to the right of the graphical genotypes indicates mean mesocotyl length for each of the three genotypes of F3 lines and two CSSLs. One line was genotyped with two markers, RM5475 and RM3513. The broken vertical lines define the interval containing the qMel-1 and qMel-3 loci. 1) Markers within the heterozygous regions were tested and the ones with the highest R2 scores are shown. 2) Numbers followed by the different letter in each row are significantly different at P = 0.05 based on the Duncan’s multiple range test. NN: Nipponbare homozygotes, NK: Nipponbare/Kasalath heterozygotes, KK: Kasalath homozygotes, 3) n: number of evaluated individuals in each line. * Number in () indicate the number of F3 plants in each genotype.

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