QTL Analysis for Plant and Grain Characters of Sake-brewing Rice Using a Doubled Haploid Population.

Abstract

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.

QTL-Based Analysis of Heterosis for Grain Shape Traits and Seedling Characteristics in an indica-japonica Hybrid in Rice (Oryza saliva L.)

“…3). QTLs similar to qWEI-4 and qWEI-5 were previously reported by Yoshida et al (2002). A QTL similar to qWEI-5 was also reported by Cui et al (2002aCui et al ( , 2002b.…”

“…QTLs similar to qWIJ-1 and qWIJ-5 were previously reported by Tan et al (2000). A QTL similar to qWIJ-5 was also reported by Yoshida et al (2002). A QTL similar to qWIJ-2 was reported by Yan et al (2003).…”

“…3). Yoshida et al (2002) reported a single QTL at a similar position for this trait. A QTL for grain thickness i.e., qTHJ-5 was found on chromosome 5.…”

Meiotic analysis and FISH with rDNA and rice BAC probes of the Thai KPS 01-01-25 sugarcane cultivar

“…Nipponbare (CUGI, Clemson University Genomics Institute, USA, http://www.genome.clemson.edu), see also: The International Rice Genome Sequencing Project, IRGSP (reviewed by Sasaki and Burr 2000;Cheng et al 2005). BACs with genetic markers near the genes for grain width (Wan et al 2008), grain weight of rice (Yoshida et al 2002), and root trait (Khowaja et al 2009) were chosen ( Table 1). The E. coli strains containing the selected rice BACs were transferred to 1 mL LB medium with 12.5 lg/ mL chloramphenicol and spread on a LB agar plate with 10 lL LB, and were left to grow overnight at 37°C.…”

“…We further performed FISH with the ubiquitous 5S and 45S rDNA repeats in order to determine ploidy level of this cultivar. Cross-species chromosome painting is used with rice chromosome 5 BACs that are known to contain economically important genes for grain width (Wan et al 2008), root trait (Khowaja et al 2009) and grain weight (Yoshida et al 2002). The rice probes were then hybridized on spread sugarcane chromosome slides under adapted stringency conditions.…”