Genetic factors responsible for eating and cooking qualities of rice grains in a recombinant inbred population of an inter-subspecific cross

Abstract

The eating and cooking qualities of rice grains are the major determinants of consumer preference and, consequently, the economic value of a specific rice variety. These two qualities are largely determined by the physicochemical properties of the starch, i.e. the starch composition, of the rice grain. In our study, we determined the genetic factors responsible for the physicochemical properties of starch in recombinant inbred lines (RILs) of japonica cv. Tainung 78 × indica cv. Taichung Sen 17 (TCS 17) cultivated over two crop seasons by examining palatability characteristics and several Rapid Viscosity Analyzer (RVA) parameters. Thirty-four quantitative trait loci (QTLs), each explaining between 1.2 and 78.1 % phenotypic variation, were mapped in clusters on eight chromosomes in 190 RILs genotyped with 139 markers. Ten pairs of QTLs were detected in the two environments, of which seven were in agreement with previous findings, suggesting that these QTLs may express stable experimental populations across various environments. Waxy (Wx), which controls amylose synthesis, was determined to be a primary gene regulating the physicochemical properties of cooked rice grains, as indicated by the presence of a major QTL cluster on chromosome 6 and by marker regression analysis. Six starch synthesis-related genes (SSRGs) which were located in the QTL intervals significantly differed in terms of gene expression between the two parents during grain-filling and were important genetic factors affecting physicochemical properties. The expression of four genes, PUL, ISA2, GBSSI, and SSII-3, was significantly upregulated in TCS 17, and this expression was positively correlated with six traits. The effects of the six SSRGs and gene interaction depended on genetic background and environment; grain quality may be fine tuned by selecting for SBE4 for japonica and PUL for indica. We provide valuable information for application in the breeding of new rice varieties as daily staple food and for use in industrial manufacturing by marker-assisted selection.Electronic supplementary materialThe online version of this article (doi:10.1007/s11032-014-0065-8) contains supplementary material, which is available to authorized users.

Relationship of Rice Grain Amylose, Gelatinization Temperature and Pasting Properties for Breeding Better Eating and Cooking Quality of Rice Varieties

“…For instance, in the present study, no significant correlation between PT and SBV was observed in both IG (-0.07) and HG (-0.05), which was consistent with the findings of Xu et al [18] where r was 0.10. Although a significant positive correlation between PT and SBV was observed in the studies by Wang et al [17] and Hsu et al [15], r was very small at only 0.18 and 0.23, respectively. The weak correlation between PT and SBV indicates that maybe no apparent physicochemical relationship exists between them, so that the correlation coefficient between them was inconsistent across different studies.…”

Genomic characterization of African cultivated and wild Oryza species

“…This analysis shows that majority of the candidate genes that have previously been reported to be involved in amylose synthesis do not seem to be associated with amylose synthesis in the system under study. This finding is consistent with results of many studies which have reported that the effect of various starch related genes and their interaction depends on genetic background as well as environmental factors (Hsu et al 2014). The only locus that has consistently been stable across genetic backgrounds is the waxy locus which encodes GBSS1, indicating that it is a major effect locus involved in amylose biosynthesis (Mikami et al 2008;Septiningsih et al 2003;Tan et al 1999;Zhou et al 2003).…”

Physicochemical Characterization of Selected Rice (Oryza Sativa L.) Genotypes Based on Gel Consistency and Alkali Digestion

“…Determination of the ECQ traits is imperative given that it influences the multiple uses of rice at both industrial and domestic scale [19]. Genetic background and environmental interactions cause a variation in ECQs of different germplasms [20].…”