Genomic Regions Involved in Differences in Eating and Cooking Quality Other than Wx and Alk Genes between indica and japonica Rice Cultivars

Abstract

Background In temperate rice cultivation regions, japonica rice cultivars are grown preferentially because consumers deem them to have good eating quality, whereas indica rice cultivars have high grain yields and strong heat tolerance but are considered to have poor eating quality. To mitigate the effects of global warming on rice production, it is important to develop novel rice cultivars with both desirable eating quality and resilience to high temperatures. Eating quality and agronomic traits were evaluated in a reciprocal set of chromosome segment substitution lines derived from crosses between a japonica rice cultivar ‘Koshihikari’ and an indica rice cultivar ‘Takanari’. Results We detected 112 QTLs for amylose and protein contents, whiteness, stickiness, hardness and eating quality of cooked rice grains. Almost of ‘Koshihikari’ chromosome segments consistently improved eating quality. Among detected QTLs, six QTLs on chromosomes 1–5 and 11 were detected that increased whiteness and stickiness of cooked grains or decreased their hardness for 3 years. The QTLs on chromosomes 2–4 were not associated with differences in amylose or protein contents. QTLs on chromosomes 1–5 did not coincide with QTLs for agronomic traits such as heading date, culm length, panicle length, spikelet fertility and grain yield. Genetic effects of the detected QTLs were confirmed in substitution lines carrying chromosome segments from five other indica cultivars in the ‘Koshihikari’ genetic background. Conclusion The detected QTLs were associated with differences in eating quality between indica and japonica rice cultivars. These QTLs appear to be widely distributed among indica cultivars and to be novel genetic factors for eating quality traits because their chromosome regions differed from those of the GBSSI (Wx) and SSIIa (Alk) genes. The detected QTLs would be very useful for improvement of eating quality of indica rice cultivars in breeding programs.

Genetic Background Negates Improvements in Rice Flour Characteristics and Food Processing Properties Caused by a Mutant Allele of the PDIL1-1 Seed Storage Protein Gene

“…High-yield rice cultivars are needed to produce large amounts of food for a growing global population. At the same time, income growth and urbanization will lead to increased consumer demands for high eating quality in various cereal foods including rice (Ito et al 1989 ; Hori and Yano 2013 ; Hori 2018 ; Sharma et al 2018 ; Hori et al 2021b ). The wide prevalence of celiac disease and wheat allergies is also increasing the demand for gluten-free foods (Ashida et al 2009 ; Yano 2012 ; Montemurro et al 2021 ).…”

“…Whole genome genotyping of Koshihikari esp2 and Oonari esp2 was carried out using the Fluidigm SNP genotyping platform (Fluidigm, San Francisco, CA, USA) with a set of 198 SNPs to detect polymorphisms between Koshihikari and EM747 and between Koshihikari and Oonari. Gene-specific DNA markers of 17 yield-related genes identified by Hori et al ( 2021b ) were used to genotype Koshihikari esp2 and Oonari esp2 . Koshihikari is a cultivar with high eating and cooking quality, which has been the most widely grown type in Japan for over 40 years (Kobayashi et al 2018 ; Hori et al 2021a ) while Oonari is cultivar with high grain yield (Kobayashi et al 2016 ).…”

“…Total protein and amylose contents in matured grains were evaluated in each year from 2013 to 2018 using the methods of Hori et al ( 2021b ). Apparent amylose content was determined using an Auto Analyzer II (Bran + Luebbe, Norderstedt, Germany).…”

“…All of these components affect the cooking characteristics and eating quality (Champagne et al 1999 ; Fitzgerald et al 2009 ). As the main component of the grain, starch largely controls the cooking characteristics and eating quality, but the seed storage proteins have the second most important effect on these traits (Martin and Fitzgerald 2002 ; Hori 2018 ; Hori et al 2021b ). Wheat flour contains the seed storage protein glutenin, which is necessary for the swelling and rising of doughs in breads, noodles, and cakes.…”

FLOURY ENDOSPERM19 encoding a class I glutamine amidotransferase affects grain quality in rice

“…The base substitutions in ALK cause amino acid changes in SSSII-3 and result in the alteration of enzymatic activity, and thereafter alter the ne structure of crystalline lamellae of amylopectin, and are nally re ected in GT (Gao et al 2011). So far, most of the researches on CEQ have focused on the abundant Wx allelic variations and ALK gene (Zhang et al 2019;Zhang et al 2020b;Hori et al 2021;Zhou et al 2020), or the interaction between them (Yang et al 2018a). Protein content is also an important factor affecting CEQ.…”