Mapping and characterization of quantitative trait loci for mesocotyl elongation in rice (Oryza sativa L.)

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.

Ethylene-Inhibited Jasmonic Acid Biosynthesis Promotes Mesocotyl/Coleoptile Elongation of Etiolated Rice Seedlings

“…Previously, five quantitative trait loci (QTL) for mesocotyl elongation were detected from backcross inbred lines developed from Kasalath and Nipponbare (Lee et al, 2012). The present GY1 locus overlapped with one of them.…”

“…Introducing a wild-type GY1 376G into the Kasalath accession, which harbors the GY1 376T and has a long mesocotyl and coleoptile phenotype, increases the JA content and largely inhibits mesocotyl and coleoptile growth, indicating that GY1 may be the major factor regulating mesocotyl and coleoptile growth. Indeed, GY1 is located within a major QTL for mesocotyl regulation, which was identified from backcross inbred lines developed from Kasalath and Nipponbare (Lee et al, 2012). From these analyses, we identified an elite natural variation of GY1 376T , which promotes mesocotyl elongation and has no yield penalty.…”

“…In addition, many loci have been identified that may regulate mesocotyl growth. Using a population of backcross inbred lines, five QTL have been found to control mesocotyl length in rice (Lee et al, 2012). GY1 overlaps with one of these QTL.…”

Attenuation of low-temperature stress in rice seedlings

“…For GA 3 , there is a preference for shoot growth over the root system, in both cultivars. This is because GA 3 acts on mesocotyl elongation, mainly in Indica subspecies cultivars, showing a 10 mm difference between seedlings treated with GA 3 and control seedlings, due to increased cell wall plasticity and sugar hydrolysis, reducing water potential in the cell, resulting in water ingress and seedling elongation, especially in the mesocotyl (Lee et al 2012 (Tavares et al 2007, Lauxen et al 2010, Almeida et al 2011), but the reasons that lead to this stimulus have yet to be elucidated. In the field, this effect was attributed to greater water and nutrient absorption (Tavares et al 2007).…”

“…For example, gibberellic acid (GA 3 ) can act as a buffer to maintain good germination along with healthy stand establishment for rice (Lee et al 2012).…”