Identification of Quantitative Trait Loci for Lipid Metabolism in Rice Seeds

Abstract

Plant seed oil is important for human dietary consumption and industrial application. The oil trait is controlled by quantitative trait loci (QTLs), but no QTLs for fatty acid composition are known in rice, the monocot model plant. QTL analysis was performed using F(2) and F(2:3) progeny from a cross of an indica variety and a japonica variety. Gas chromatography-mass spectrometry (GC-MS) analysis revealed significant differences between parental lines in fatty acid composition of brown rice oil, and 29 associated QTLs in F(2) and/or F(2:3) populations were identified throughout the rice genome, except chromosomes 9 and 10. Eight QTLs were repeatedly identified in both populations across different environments. Five loci pleiotropically controlled different traits, contributing to complex interactions of oil with fatty acids and between fatty acids. Nine rice orthologs of Arabidopsis genes encoding key enzymes in lipid metabolism co-localized with 11 mapped QTLs. A strong QTL for oleic (18:1) and linoleic (18:2) acid were associated with a rice ortholog of a gene encoding acyl-CoA:diacylglycerol acyltransferase (DGAT), and another for palmitic acid (16:0) mapped similarly to the acyl-ACP thioesterase (FatB) gene ortholog. Our approach rapidly and efficiently identified candidate genes for mapped QTLs controlling fatty acid composition and oil concentration, providing information for improving rice grain quality by marker assisted selection.

Quantitative trait loci (QTLs) analysis of palm oil fatty acid composition in an interspecific pseudo-backcross from Elaeis oleifera (H.B.K.) Cortés and oil palm (Elaeis guineensis Jacq.)

“…These correlations are congruent with those of the study by Singh et al (2009) in an Elaeis interspecific cross and also with other correlations in E. guineensis (Noh et al 2002). The positive correlation between C14:0 and C16:0 or C16:1 is in accordance with reports in rice by Ying et al (2012) and in oil palm by Singh et al (2009). The negative correlation between C16:0 and C18:1 has been reported in oil palm by several authors (Meunier 1975;Wuidart and Gascon 1975;Noh et al 2002;Singh et al 2009).…”

Natural variation of plant metabolism: genetic mechanisms, interpretive caveats, evolutionary and mechanistic insights.

“…Across Arabidopsis, rice, and maize, each locus explained on average 15% to 25% of metabolite variation ( Fig. 2; Rowe et al, 2008;Ying et al, 2012;Gong et al, 2013;Chen et al, 2014;Dong et al, 2015;Matsuda et al, 2015). These averages, however, hide a wide range of individual locus variation.…”

“…These averages, however, hide a wide range of individual locus variation. For example, individual rice loci have been found to explain 35% or more of an individual metabolite's variation up to nearly 90% (Ying et al, 2012;Chen et al, 2014;Dong et al, 2015;Matsuda et al, 2015). In intraspecific studies, a single locus explained at most over 90% of metabolite variation in Arabidopsis (Rowe et al, 2008) and in rice (Gong et al, 2013) but at most only 62% in maize (Riedelsheimer et al, 2012;Fig.…”

“…All maize and Arabidopsis comparisons are intraspecific. The rice comparisons are intraspecific (Ying et al, 2012;Gong et al, 2013;Dong et al, 2015) and across subspecies .…”

“…In rice, analysis of an indica 3 japonica cross indicated that only eight out of 29 QTLs associated with fatty acid abundance were consistently identified across two generations in two field trials (Ying et al, 2012). In maize GWA studies, only 17% of the metabolite-locus associations were consistently detectable across at least two of three concurrent field trials (Wen et al, 2014).…”