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Mesocotyl Elongation Is Essential for Seedling Emergence Under Deep-Seeding Condition in Rice

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Mesocotyl Elongation Is Essential for Seedling Emergence Under Deep-Seeding Condition in Rice

Hyun-Sook Lee et al. Rice (N Y).

Abstract

Background: Direct-seeding cultivation by deep-seeding of seeds (drill seeding) is becoming popular due to the scarcity of land and labor. However, poor emergence and inadequate seedling establishment can lead to yield loss in direct-seeding cultivation by deep-sowing. In rice, mesocotyl and coleoptile are primarily responsible for seedling emergence from deeper levels of soil.

Results: Quantitative trait loci (QTLs) for mesocotyl and coleoptile length at 5-cm seeding depth were detected using 98 backcross inbred lines from a cross between Kasalath and Nipponbare. Three QTLs qMel-1, qMel-3, and qMel-6 for mesocotyl length were identified on chromosomes 1, 3, and 6, respectively, in two independent replicates. At two QTLs, qMel-1 and qMel-3, the Kasalath alleles increased mesocotyl length, whereas Nipponbare allele increased at qMel-6. The Nipponbare alleles at two QTLs (qCol-3 and qCol-5) increased the coleoptile length. Further, seeds of 54 chromosome segment substitution lines (CSSLs) from the cross between Kasalath and Nipponbare sown at 5 cm soil depth showed a significant positive correlation between seedling emergence and mesocotyl elongation (r > 0.6, P < 0.0001), but not with coleoptile elongation (r = 0.05, P = 0.7). Seedling emergence of Nipponbare, Kasalath, and the 3 of the 54 CSSLs rapidly decreased with increasing sowing depth. Seedling emergence at seeding depths of 7 and 10 cm was faster in Kasalath and CSSL-5 that harbored the Kasalath alleles across the qMel-1 and qMel-3 regions than in the other two CSSLs that contained a single QTL and Nipponbare alleles. CSSL-5 showed the longest mesocotyl among the 3 CSSLs, but no difference in coleoptile length was observed among the 3 CSSLs at seeding depths of 7 and 10 cm.

Conclusion: Variation of mesocotyl elongation was found to be associated with seedling emergence at the seeding depth of 5 cm. To our knowledge, this is the first study performed using CSSLs to detect QTLs for mesocotyl or coleoptile elongation and to determine the effect of mesocotyl elongation on seedling emergence in rice. Our findings provides a foundation for developing rice cultivars that show higher seedling emergence after direct seeding by introgressing QTLs for mesocotyl elongation in rice breeding.

Keywords: CSSLs (chromosome segment substitution lines); Coleoptile; Mesocotyl; QTL; Rice; Seedling emergence.

Conflict of interest statement

Competing interests

The authors declare that they have no competing interests.

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Figures

Fig. 1
Fig. 1
Phenotypic variation of mesocotyl and coleoptile elongation at varying soil depths. a Mesocotyl and b coleoptile length of Nipponbare and Kasalath under different burial depth in soil; 12 Seeds of Nipponbare and Kasalath were sown at 3 cm, 5 cm, 7 cm, and 10 cm soil depth and incubated at alternate temperatures of 30 °C and 26 °C (14 h/10 h). At 14 days after sowing, the seedling were excavated and length were measured. Bars represent mean of length with SD (n = 3). Comparisons of the varieties were made with the ANOVA test. * P < 0.05, *** P < 0.001
Fig. 2
Fig. 2
Mesocotyl and coleoptile length for 57 accessions of RDRS (a), Comparison of mesocotyl and coleoptile length in 4 rice variety groups (b) Japonica (Ja), Tropical Japonica (TJa), Indica-I (In-I), and Indica-II (In-II); Seeds were sown at 5 cm soil depth and incubated at alternate temperatures of 30 °C and 26 °C (14 h/10 h). At 14 days after sowing, the seedling were excavated and length were measured. b Means with different letters in the same row indicate significant differences according to the Duncan multiple range test (P < 0.001). Bars represent mean of length with SE
Fig. 3
Fig. 3
Frequency distribution of the mesocotyl length (a) and coleoptile length (b) in 98 backcross inbred lines (BILs) derived from Nipponbare/Kasalath at 5 cm soil depth; Arrowheads indicate mean values for Nipponbare and Kasalath. 12 seeds of 98 BILs, Nipponbare and Kasalath were sown at 5 cm soil depth and incubated at alternate temperatures of 30 °C and 26 °C (14 h/10 h). At 14 days after sowing, length were measured
Fig. 4
Fig. 4
Seedling emergence percentage at 6 days after sowing (a), mesocotyl (b) and coleoptile length (c) of 54 CSSLs (SL); 12 seeds of 54 CSSLs, Nipponbare and Kasalath were sown at 5 cm soil depth and incubated and the numbers of emerged seedling from the soil surface were counted. At 14 days after sowing, the length were measured. Each column represents emergence percentage or mean of length ± SE * P < 0.05 and **P < 0.01 versus Nipponbare (Dunnett’s multiple comparison test, two replicates)
Fig. 5
Fig. 5
Time course of seedling emergence (a) and mesocotyl and coleoptile length (b) of 3 CSSLs, Nipponbare and Kasalath in four soil burial depth; (a) Lines and bars represent the mean with SE of 5 lines, Nipponbare(Ni), Kasalath (Ka), CSSL-6 (SL6), CSSL-15 (SL15), and CSSL-5 (SL5). Seeds were sown at 3 cm, 5 cm, 7 cm, and 10 cm soil depth and the number of emerged seedling form soil surface were counted daily up to 14 days after sowing. b At 14 days after sowing, length of mesocotyl and coleoptile were measured. Means of length ± SE (n = 3) with different letters in the same row indicate significant differences according to the Duncan multiple range test (P < 0.05)

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