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

Abstract

BackgroundDirect-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.ResultsQuantitative 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.ConclusionVariation 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-017-0173-2) contains supplementary material, which is available to authorized users.

Mesocotyl elongation, an essential trait for dry-seeded rice (Oryza sativa L.): a review of physiological and genetic basis

“…2 (Lee et al 2012b). Using the same population Lee et al (2017) found a QTL on chromosome 3 in both replication 1 (R 2 = 37.56%) and 2 (R 2 = 26.97%), and a QTL on chromosome 6 (R 2 = 8.28%) in replication 2 only.…”

“…Generally, different emergence rate and mesocotyl length were observed among the varied sowing depths and mesocotyl length increased with the increase of sowing depth. In detail, the specific performance of mesocotyl length was 24.9 mm, 33.7 mm, and 36.5 mm at the sowing depth of 5 cm, 7 cm, and 10 cm, respectively (Lee et al 2017). Furthermore, the genotypes with long mesocotyl usually had stronger germination ability (Zhang et al 2005).…”

“…Deep sowing is a common practice in dry-seeded rice. Since shallow seeding usually leads to the incidences of bird damage, drought stress, and lodging after heading (Wang et al 2004;Lee et al 2017). However, seedling growth was adversely affected when seeds were sown deeper than the optimum seeding depth of 2-3 cm (Lee et al 2002).…”

An Improved Mesocotyl Elongation Assay for the Rapid Identification and Characterization of Strigolactone-Related Rice Mutants

“…Mesocotyl is a specialized organ located between the coleoptilar node and the basal part of the seminal root. Mesocotyl elongation is an important adaptive trait especially in the context of deep sowing tolerance or in the direct-seeding condition [17]. According to previous studies, this trait is regulated by the complex interaction of phytohormones [15,[18][19][20][21].…”

Dynamic Genome-Wide Association Analysis and Identification of Candidate Genes Involved in Anaerobic Germination Tolerance in Rice

“…Septiningsih et al (2013) used 118 simple sequence repeat (SSR) molecular markers and an F 2:3 population constructed from IR42 and Ma-Zhan Red to detect 6 QTLs related to seed germination and ooding tolerance under 10 cm ooding stress, and the BC 2 F 3 generation was used to verify the major effect locus qAG7.1 on chromosome 7 and estimate its contribution rate at 31.7%. Lee et al (2017) used backcross inbred lines (BILs) of Kasalath and Nipponbare to evaluate deep sowing (5 cm sowing depth) performance. With coleoptile length (CL) as an indicator, a QTL location assay identi ed sites that affected coleoptile elongation on chromosomes 3 and 5, and these sites explained phenotypic variations of 11.8% and 12.0%, respectively (Lee et al 2017).…”