Identification and Analyses of Chromosome Segments Affecting Heterosis Using Chromosome‐Segment Substitution Lines in Rice

A high level of heterosis exists in intersubspecific crosses between indica and japonica rice ( Oryza sativa L.) cultivars, and the exploitation of heterosis has long been considered a promising method of increasing rice yield. To analyze the chromosome segments associated with heterosis for yield‐related traits and to dissect the major heterosis quantitative trait loci (QTL) for marker‐assisted selection in intersubspecific crosses to improve rice yield, we introduced a set of 37 chromosome‐segment substitution lines (CSSLs), each of which carried one or a few chromosome segments of the indica rice cultivar Habataki, in the genetic background of the japonica rice cultivar Sasanishiki. The CSSLs were individually crossed with ‘Changhui T025’ to generate a set of corresponding F 1 hybrids (chromosome‐segment substitution line hybrids, CSSLHs). These CSSLHs were field‐tested for nine yield‐related traits in two different environments, and 20 heterosis QTL were detected. These QTL were divided into two groups: the positive alleles of one group originated from the Habataki × Changhui T025 hybrid, whereas those of the other group originated from the Sasanishiki × Changhui T025 hybrid. This implied that many different genes that positively contribute to heterosis likely exist in indica and japonica cultivars. Four key heterosis QTL were identified in both environments: qHppp10 for panicle number per plant, qHph1‐1 for plant height, qHtgw4‐1 for 1000‐grain weight, and qHdsp1 for spikelet density per plant. The indica × indica segments at these QTL represent good candidates for marker‐assisted selection for the corresponding traits in intersubspecific crosses to improve yield. Moreover, the CSSLs harboring these QTL represent candidate parents of F 1 hybrids along with Changhui T025 or other indica lines.