QTL Mapping of Mesocotyl Elongation and Confirmation of a QTL in Dongxiang Common Wild Rice in China

Abstract

Direct-seeded rice (DSR) cultivation is an effective and important way to resolve agricultural labor scarcity, water scarcity and high production cost issues. Mesocotyl elongation (ME) is the main driver of the rapid emergence of rice seedlings from the soil and is an important indicator of the suitability of rice varieties for direct seeding. Hence, discovering ME-related genes is particularly important for breeding rice varieties suitable for direct seeding. In this study, a chromosome segment substitution line (CSSL) population generated from a cross between Dongxiang common wild rice and Nipponbare (Nip) was used to map quantitative trait loci (QTLs) for ME. Two QTLs for mesocotyl length were identified on chromosomes 3 and 6 with logarithm of odds (LOD) scores ranging from 5.47 to 6.04 and explaining 15.95–16.79% of the phenotypic variance. Among these QTLs, qML6 accounted for the highest phenotypic variance (16.79%). Then, to confirm the strongest QTL, we generated an F2 segregating population via the CSL127 line harboring the qML6 locus and the recurrent parent Nip. The QTL qML6-1 associated with ME was mapped to a location between markers DX-C6-2 and DX-C6-4, which is consistent with the location of the previously mapped QTL qML6. qML6-1 had an LOD score of 8.45 and explained 30.56% of the phenotypic variance. The QTLs detected in this study provide promising targets for further genetic characterization and for use in marker-assisted selection to develop varieties with improved ME for the cultivation of DSR.