Quantitative trait loci for whiteness of cooked rice detected in improved rice cultivars in Hokkaido

Abstract

Improving the eating quality of cooked rice has been one of the most important objectives in rice breeding programs. Eating quality of cooked rice is a complex trait including several components, such as external appearance, taste, aroma, and texture. Therefore, dissection of these components followed by marker-assisted selection of detected QTL(s) may be a useful approach for achieving desirable eating quality in rice breeding. Whiteness of cooked rice (WCR) is an important factor related to the external appearance of cooked rice. WCR is known to be associated with the amylose and protein contents of the endosperm. However, the genetic basis of WCR remains unclear. In this study, we evaluated phenotypic variation in WCR among recently developed rice cultivars from Hokkaido, Japan. Then, we developed doubled haploid lines (DHLs) derived from a cross between two cultivars from Hokkaido, Joiku No. 462 (high WCR) and Jokei06214 (low WCR). Using the DHLs, we detected two QTLs for WCR, qWCR3 and qWCR11, on chromosomes 3 and 11, respectively. We also examined the dosage effect of the two QTLs based on both the categorized segregants in the DHLs and the relationship between the WCR phenotype and inheritance around the QTL regions in cultivars from Hokkaido.

Development of genome-wide PCR-based markers from insertion, deletion and single nucleotide polymorphisms for closely related Japanese rice cultivars and identification of QTLs for the appearance of cooked rice and polished rice

“…After rice production was improved so that Japan was almost completely self-sufficient, the main breeding objective was changed from high yield to good eating quality ( Horie et al 2005 ). Preferences for eating quality of cooked rice vary depending on end-use, culture, and climate of each local region ( Shinada et al 2015 ). Consumers in Japan currently demand new rice cultivars with high eating quality, including rice that appears glossy and white, with good flavor and a soft and sticky consistency.…”

Quantitative trait loci for rice blast resistance detected in a local rice breeding population by genome-wide association mapping

“…The first consisted of 88 doubled haploid lines (DHLs), A 3 , derived from a cross between ‘Joiku No. 462’ (blast resistant) and ‘Jokei06214’ (blast susceptible) developed by Shinada et al 2015 . The second was 120 recombinant inbred lines (RILs), F 4 , derived from a cross between ‘Kuiku No.…”

“…This left 545 selected SNPs. All experimental procedures for SNP typing were performed as described by Shinada et al (2015) .…”

“…A linkage map of DHLs constructed in Shinada et al ( 2015) was used for QTL analysis. The detection of QTLs was conducted by composite interval mapping with QTL Cartographer 2.5 ( http://statgen.nesu.edu/qtlcart/WQTLcart.htem ).…”

“…Recent advances in molecular genetics technology, such as genome-wide single nucleotide polymorphism (SNP) typing, has allowed the elucidation of detailed information on genetic polymorphisms even in genetically close rice populations ( Nagasaki et al 2010 ). The advent of high-density SNP typing has allowed the successful identification of a number of QTLs in such populations by bi-parental QTL mapping ( Shinada et al 2015 , Shirasawa et al 2012 ). Furthermore, these advances have enabled the detection of QTLs in rice populations with genetic variations in a genome-wide association mapping study (GWAS) ( Brachi et al 2011 ).…”