SNP-based QTL mapping for panicle traits in the japonica super rice cultivar Liaoxing 1

Abstract

Panicle traits directly associated with yield are a target of selection in rice breeding. Although abundant QTL for panicle traits have been identified, there is little information about the genetic basis of panicle traits in japonica super rice (JSR) cultivars. In this study, we identified QTL for panicle traits in three environments using a population of recombinant inbred lines (RILs) derived from the JSR cultivar Liaoxing 1. A total of 197 RILs were genotyped with 285 polymorphic SNP markers. Phenotypic data and best linear unbiased prediction (BLUP) value of primary branch number (BNP), secondary branch number (BNS), grain number on primary branch (GNP), grain number on secondary branch (GNS), grain number per panicle (GN), panicle length (PL) and grain density (GD) were used for QTL mapping. A total of 105 QTL for seven panicle traits were detected in single environments using their BLUP values. Individual QTL explained 0.51%–52.22% of the phenotypic variation. Of the 105, 49 were also detected by joint multi-environment analyses. Five stable QTL: qGD9, qPL9, qGNP9, qGN6, and qBNS6.2 were identified in multiple environments. qGD9, qGNP9, and qPL9, co-localizing on chromosome 9, likely correspond to the known gene DEP1. Importantly, qGN6 and qBNS6.2 in a co-localization region were identified as novel QTL, and their Liaoxing 1 alleles had a positive effect. Several RILs with the QTL allele combinations qGD9/qPL9/qGNP9 and qGN6/qBNS6.2 showed greater GN. Further investigation of the putative gene underlying qGN6/qBNS6.2 would shed light on the molecular mechanism of JSR.