QTL analysis for plant and grain characters of sake-brewing rice using a doubled haploid population

Rice (Oryza sativa L.) varieties used for brewing sake are commonly characterized by traits such as large grain size with white-core (an opaque structure inside the rice grain). A linkage map was constructed using doubled haploid lines derived from the cross of Reiho (a cooking variety) and Yamada-nishiki (a sake-brewing variety). Random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) marker systems were employed in QTL analysis. A total of 145 markers were identified and mapped on rice chromosomes. QTLs for plant and grain characters were detected by interval mapping and single point analysis. Several QTLs with a significant contribution were identified for important sake-brewing characters including grain size, grain shape, white-core grain rate and protein content. Several QTLs simultaneously affected the grain weight, width and thickness, while QTLs for the grain length independently affected the grain size. QTLs for the white-core grain rate did not affect the grain size, although one QTL for the white-belly grain rate simultaneously affected the grain weight, width and thickness. Several QTLs were detected for the protein content in both brown and polished rice. One QTL on chromosome 4 that was effective for the decrease of the protein content in polished rice showed a positive relation with the grain length. One QTL with the largest effect on the grain length on chromosome 11 did not contribute to the decrease of the protein content in polished rice. Therefore, it is suggested that the grain length QTL on chromosome 4 might control not only the grain shape but also the internal structure related to the milling efficiency and/or location of the storage protein.