Fine Mapping and Cloning of a Major QTL qph12 , Which Simultaneously Affects the Plant Height, Panicle Length, Spikelet Number and Yield in Rice ( Oryza sativa L.)

Plant height is one of the most important agronomical traits in rice ( L.). Introducing the rice in the 1960s significantly enhanced the rice yield potential in Asia. Implementing near-isogenic lines (NILs) is the most powerful tool for the identification and fine mapping of quantitative trait loci (QTLs). In this study, 176 NILs were produced from the crossing and back-crossing of two rice cultivars. Specifically, the rice cultivar Jiafuzhan served as a recipient, and the restorer cultivar Hui1586 served as a donor. Using the 176 NILs, we identified a novel major QTL for reduced plant height in the NIL36 line. The QTL was mapped to a 31 kb genomic region between the indel markers and . The rice genome annotation indicated the presence of three candidate genes in this genomic region. Through gene prediction and cDNA sequencing, we confirmed that ( ) is the target gene in the NIL36 line. Further analysis showed that the QTL is caused by a 1 bp deletion in the first exon that resulted in premature termination of the . Knockout experiments showed that the QTL is responsible for the reduced plant height phenotype of the NIL36 line. Although the gene from the NIL36 line showed a shorter panicle length, fewer spikelets per panicle and a lower plant grain yield, the plant also exhibited a lower plant height. Taken together, our results revealed that the have good specific application prospects in future rice breeding.