Mapping of quantitative trait loci for plant height and heading date in two inter-subspecific crosses of rice and comparison across Oryza genus

Abstract

Two inter-subspecific segregating populations were constructed to map quantitative trait loci (QTLs) for plant height (PH) and heading date (HD) in rice. A total of 99 and 95 polymorphic SSR and STS markers were used to establish linkage maps in japonica TK8 x indica IR1545-339 and japonica Nipponbare x IR1545-339, respectively. By employing composite interval mapping verified by single point analysis, ten PH and seven HD QTLs were located on seven and six chromosomes, respectively; only Qph1.2 and Qhd3 were common in the two populations. The phenotypic variance explained (PVE) by major PH and HD QTLs was 22.07% (Qph6.1) and 12.98% (Qph6.2), and 35.74% (Qhd3) and 15.54% (Qhd3), for TK8/IR1545-339 and Nipponbare/IR1545-339, respectively. Comparative genetic analysis of QTL intervals on rice pseudomolecules showing the convergence of QTLs affecting PH and HD across the Oryza genus revealed all QTLs uncovered in the two populations possibly allelic to QTLs previously published. By comparative mapping and candidate gene approach, we specified three PH, Qph1.2, Qph4, and Qph6.1, and one HD QTL, Qhd10, without high-resolution mapping, and the reality of QTLs identified by interval mapping were discussed herein.